I think this script matches AJ's best relax flavor from SRC 2020 - #14

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I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
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smlewis/AJ_style_prep

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@smlewis

@smlewissmlewis commented Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)

@AJVincelli

AJVincelli commented Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.

@AJVincelli

AJVincelli commented Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.

@danielzaidman

danielzaidman commented Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli

@danielzaidman

danielzaidman commented Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.

@roccomoretti

roccomoretti commented Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.

@smlewis

smlewis commented Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.

@AJVincelli

AJVincelli commented Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?

@AJVincelli

AJVincelli commented Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).

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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?

@AJVincelli

AJVincelli commented Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...

@AJVincelli

AJVincelli commented Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?

@AJVincelli

AJVincelli commented Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)

@roccomoretti

roccomoretti commented Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503

@AJVincelli

AJVincelli commented Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...

@weitzner

weitzner commented Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?

@AJVincelli

AJVincelli commented Nov 29, 2021•
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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).

@weitzner

weitzner commented Dec 2, 2021

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Interesting! Thanks for passing the doc along!

@AJVincelli

AJVincelli commented Dec 2, 2021 via email

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@ajasja

ajasja commented Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...

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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja
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I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Conversation
@smlewis
@smlewissmlewis
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Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
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Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
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Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
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Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
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Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
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Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
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Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
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Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
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Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
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Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
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Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
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Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
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Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
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Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
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Nov 29, 2021•

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
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Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
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Dec 2, 2021
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@ajasja
ajasja
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Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

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Skip to content
I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Conversation
@smlewis
@smlewissmlewis
commented
Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
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Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
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Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
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Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
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Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
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Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
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Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
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Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
AJVincelli
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Jul 17, 2021
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@AJVincelliAJVincelli
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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
commented
Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
AJVincelli
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Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
commented
Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
roccomoretti
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Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
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Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
weitzner
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Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
commented
Nov 29, 2021•

edited

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
weitzner
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Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
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Dec 2, 2021
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@ajasja
ajasja
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Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

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(function(){
try {
var __m = "*";
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Skip to content
I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Conversation
@smlewis
@smlewissmlewis
commented
Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
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Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
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Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
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Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
commented
Sep 30, 2020

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MemberAuthor
It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
AJVincelli
reviewed
Jul 17, 2021
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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
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Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
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Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
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Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
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Nov 29, 2021•

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
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Interesting! Thanks for passing the doc along!
@AJVincelli
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@ajasja
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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
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smlewis/AJ_style_prep
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I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
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@smlewis
@smlewissmlewis
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Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
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Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
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Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
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Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
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Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
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Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
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Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
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Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
commented
Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
AJVincelli
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Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
commented
Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
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Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
commented
Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
weitzner
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Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
commented
Nov 29, 2021•

edited

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
weitzner
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Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
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Dec 2, 2021
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@ajasja
ajasja
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Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Conversation
@smlewis
@smlewissmlewis
commented
Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
commented
Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
danielzaidman
commented
Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
commented
Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
commented
Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
AJVincelli
reviewed
Jul 17, 2021
View reviewed changes
@AJVincelliAJVincelli
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edited

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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
commented
Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
AJVincelli
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Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
commented
Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
roccomoretti
commented
Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
commented
Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
weitzner
commented
Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
commented
Nov 29, 2021•

edited

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
weitzner
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Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
commented
Dec 2, 2021
via email 

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@ajasja
ajasja
commented
Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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6 participants

@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
I think this script matches AJ's best relax flavor from SRC 2020 - #14
Open
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
Conversation
@smlewis
@smlewissmlewis
commented
Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Member
Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
commented
Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
commented
Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
danielzaidman
commented
Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
commented
Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
commented
Sep 30, 2020

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MemberAuthor
It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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Member
Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
commented
Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
AJVincelli
reviewed
Jul 17, 2021
View reviewed changes
@AJVincelliAJVincelli
left a comment
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edited

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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
commented
Jul 18, 2021

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Member
Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
AJVincelli
commented
Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
commented
Jul 21, 2021

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Member
Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
roccomoretti
commented
Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
commented
Oct 19, 2021

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Member
Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
weitzner
commented
Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
commented
Nov 29, 2021•

edited

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
weitzner
commented
Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
commented
Dec 2, 2021
via email 

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Member
@ajasja
ajasja
commented
Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@AJVincelliAJVincelliAJVincelli left review comments
@roccomorettiroccomorettiAwaiting requested review from roccomoretti

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6 participants

@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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I think this script matches AJ's best relax flavor from SRC 2020 - #14
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smlewis wants to merge 2 commits into
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smlewis/AJ_style_prep
Open
I think this script matches AJ's best relax flavor from SRC 2020#14
smlewis wants to merge 2 commits into
mainfrom 
smlewis/AJ_style_prep
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@smlewis
@smlewissmlewis
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Aug 20, 2020

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Not going to merge without her explicit permission but I'll put it here for comment (it was discussed in slack yesterday)
@AJVincelli
AJVincelli
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Aug 28, 2020

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Thank you Steven! This would have taken me... a really long time... to write. I will test out this script and see if it performs similarly to the command-line version that I presented at SRC 2020, and report back. Give me... some time.
@AJVincelli
AJVincelli
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Aug 28, 2020

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Note that @danielzaidman recently reported that this script results in a slightly misaligned pose, which might affect RMSD. I will also look into this.
@danielzaidman
danielzaidman
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Sep 2, 2020

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I'm still not sure why (looking into it), but as it is at the moment, the result of this script is definitely different than "java", even after aligning the chains back. Java is much more conservative with the backbone. @smlewis@AJVincelli
@danielzaidman
danielzaidman
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Sep 3, 2020

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Hey @smlewis , @AJVincelli . I added a missing line, and now the output looks the same as "java". I think we can merge now.
@roccomoretti
roccomoretti
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Sep 30, 2020

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I think this is entirely @AJVincelli's call as to whether this script properly represents her best-practices settings. I don't see anything immediately at issue with it, but I don't have the full flag-set for Java with me at the moment, so I can't double check.
@smlewis
smlewis
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Sep 30, 2020

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It definitely shouldn't merge until closer to her paper.
@AJVincelli
AJVincelli
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Oct 1, 2020

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Well, the good news is that I'm working on Relax things... The bad news is that I haven't gotten to testing this script yet. I'm probably ~1 month away from testing and comparing with previous results. Even if the manuscript isn't mature and it won't be a good time to merge, I can still report back with a stamp of approval. Is that timeline acceptable?
@AJVincelli
AJVincelli
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Oct 1, 2020

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The main Java flags are -constrain_relax_to_start_coords-relax:ramp_constraints false-relax:script MonomerRelax2019 (I think Daniel's small fix added the MonomerRelax2019 equivalent?). And technically, Java uses -nstruct 5 (and -in:file:fullatom but I don't know if that actually does anything).
AJVincelli
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Jul 17, 2021
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In the scripts_to_parse.py file, is the / at the beginning of /scripts/public/preparation/constrained_relax.xml intentional?
@AJVincelli
AJVincelli
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Jul 18, 2021

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Hm, I'm getting an error when I include the commandline flag -out:mmCIF. I've asked Slack how I can specify a CIF file output using RosettaScripts. I'll post back when I have updates...
@AJVincelli
AJVincelli
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Jul 21, 2021

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It appears that the -out:mmCIF flag should work. Can anybody get this script to run with the -out:mmCIF flag?
@AJVincelli
AJVincelli
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Jul 21, 2021

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Rocco helped me debug the issue with -out:mmCIF. If I also add the flag -out::file::output_pose_cache_data false, it works! I will now test this script on my 500-structure dataset, and report back if it works as expected and reproduces my previous results. (Can you tell that I'm trying to get this before RosettaCON??)
@roccomoretti
roccomoretti
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Jul 22, 2021

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The issue with -out:mmCIF is RosettaCommons/main#5503
@AJVincelli
AJVincelli
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Oct 19, 2021

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Hi all, I've (finally!) tested this script with my benchmark dataset, and it works beautifully with Daniel's small fix and the -out::file::output_pose_cache_data false flag. I also removed the / at the beginning of the /scripts/public/preparation/constrained_relax.xml line (see above), I'm not sure if that matters. I'm hoping to write up the manuscript this autumn, so we're getting closer to merging...
@weitzner
weitzner
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Nov 29, 2021

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It seems interesting that there is not any cartesian space minimization used here. Was that tested as part of this work?
@AJVincelli
AJVincelli
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Nov 29, 2021•

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Hi @weitzner, yes! All of the juicy details are here: http://bit.ly/BestRelaxMethod I was surprised to find that Cartesian Relax didn’t improve the Quality Scores as much (such as the Latte flavor).
@weitzner
weitzner
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Dec 2, 2021

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Interesting! Thanks for passing the doc along!
@AJVincelli
AJVincelli
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Dec 2, 2021
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@ajasja
ajasja
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Mar 4, 2024

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@AJVincelli How are things going? Do you have plans to merge this? I guess it has to go into the new repo now...
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@smlewis@AJVincelli@danielzaidman@roccomoretti@weitzner@ajasja