Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log
Hi Wei, I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work. Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors. All the best, Tom T On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:
Hi all,
I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:
phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\
When I run the above script, it gives the following error message:
child process stderr output:
command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'
/bin/sh: qsub: not found
Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run.
My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much!
Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1
Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Hi Dr Terwilliger, I see. Thank you so much! Best, Wei ________________________________ From: [email protected] [[email protected]] on behalf of Tom Terwilliger [[email protected]] Sent: Thursday, November 17, 2011 2:57 PM To: PHENIX user mailing list Subject: Re: [phenixbb] MR_ROSETTA Hi Wei, I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work. Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors. All the best, Tom T On Nov 17, 2011, at 12:49 PM, Wei Shi wrote: Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected]mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
qsub is a Sun Grid Engine (SGE) command. It is used to send a job to a cluster (meaning submit to job queue I guess). Regards, F. On 11/18/2011 05:07 AM, Wei Shi wrote:
Hi DrTerwilliger, I see. Thank you so much!
Best, Wei ------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Tom Terwilliger [[email protected]] *Sent:* Thursday, November 17, 2011 2:57 PM *To:* PHENIX user mailing list *Subject:* Re: [phenixbb] MR_ROSETTA
Hi Wei,
I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work.
Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors.
All the best, Tom T
On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:
Hi all,
I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:
phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222\ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\
When I run the above script, it gives the following error message:
child process stderr output:
command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'
/bin/sh: qsub: not found
Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running.But, it takes forever to run.
My questions is: 1.Does anyone happen to know why it tells me “qsub: not found” when I include“group_run_command=qsub” in my script? 2.When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running.Butit just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much!
Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1
Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
4000 models, 500aa, 2 processors ~1.5Ghz. 30 days later my job is
still running. But it has done all 4000 models and the Phaser steps.
So patience may be in order for your job.
What's your sequence identity? If it's more than 30% you probably
don't have to do the pre_refine step which is gruelingly long.
Actually I would only use it if your run without pre_refine doesn't
produce a viable solution.
Cheers,
Morten Groftehauge
Pohl Group
Durham University
On 18/11/2011, Francois Berenger
qsub is a Sun Grid Engine (SGE) command. It is used to send a job to a cluster (meaning submit to job queue I guess).
Regards, F.
On 11/18/2011 05:07 AM, Wei Shi wrote:
Hi DrTerwilliger, I see. Thank you so much!
Best, Wei ------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Tom Terwilliger [[email protected]] *Sent:* Thursday, November 17, 2011 2:57 PM *To:* PHENIX user mailing list *Subject:* Re: [phenixbb] MR_ROSETTA
Hi Wei,
I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work.
Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors.
All the best, Tom T
On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:
Hi all,
I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:
phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222\ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\
When I run the above script, it gives the following error message:
child process stderr output:
command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'
/bin/sh: qsub: not found
Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running.But, it takes forever to run.
My questions is: 1.Does anyone happen to know why it tells me “qsub: not found” when I include“group_run_command=qsub” in my script? 2.When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running.Butit just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much!
Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1
Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thank you guys!
The sequence identity of the search model to my protein is 33%. I haven't tried mr_rosetta using this search model without pre-refinement. I only used this search model directly to do molecular replacement using phenix, and no viable solutions are generated.
Best,
Wei
________________________________________
From: [email protected] [[email protected]] on behalf of Morten Grøftehauge [[email protected]]
Sent: Friday, November 18, 2011 9:32 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] MR_ROSETTA
4000 models, 500aa, 2 processors ~1.5Ghz. 30 days later my job is
still running. But it has done all 4000 models and the Phaser steps.
So patience may be in order for your job.
What's your sequence identity? If it's more than 30% you probably
don't have to do the pre_refine step which is gruelingly long.
Actually I would only use it if your run without pre_refine doesn't
produce a viable solution.
Cheers,
Morten Groftehauge
Pohl Group
Durham University
On 18/11/2011, Francois Berenger
qsub is a Sun Grid Engine (SGE) command. It is used to send a job to a cluster (meaning submit to job queue I guess).
Regards, F.
On 11/18/2011 05:07 AM, Wei Shi wrote:
Hi DrTerwilliger, I see. Thank you so much!
Best, Wei ------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Tom Terwilliger [[email protected]] *Sent:* Thursday, November 17, 2011 2:57 PM *To:* PHENIX user mailing list *Subject:* Re: [phenixbb] MR_ROSETTA
Hi Wei,
I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work.
Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors.
All the best, Tom T
On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:
Hi all,
I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:
phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222\ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\
When I run the above script, it gives the following error message:
child process stderr output:
command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'
/bin/sh: qsub: not found
Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running.But, it takes forever to run.
My questions is: 1.Does anyone happen to know why it tells me “qsub: not found” when I include“group_run_command=qsub” in my script? 2.When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running.Butit just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much!
Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1
Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Fri, Nov 18, 2011 at 7:50 AM, Wei Shi
The sequence identity of the search model to my protein is 33%. I haven't tried mr_rosetta using this search model without pre-refinement. I only used this search model directly to do molecular replacement using phenix, and no viable solutions are generated.
It may also help to run the model through phenix.sculptor, which will modify it to more closely match the target protein (without doing anything to the conformation). Sometimes this is all that you need to make MR successful - although it's never guaranteed to work at 33% identity. -Nat
Thank you, Nat! I will try phenix.sculptor at the same time!
Best,
Wei
________________________________________
From: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]]
Sent: Friday, November 18, 2011 10:54 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] MR_ROSETTA
On Fri, Nov 18, 2011 at 7:50 AM, Wei Shi
The sequence identity of the search model to my protein is 33%. I haven't tried mr_rosetta using this search model without pre-refinement. I only used this search model directly to do molecular replacement using phenix, and no viable solutions are generated.
It may also help to run the model through phenix.sculptor, which will modify it to more closely match the target protein (without doing anything to the conformation). Sometimes this is all that you need to make MR successful - although it's never guaranteed to work at 33% identity. -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi All, Is it possible to define multiple twin domains in phenix refine ? I mean refmac like multiple twin domains as shown below. -------------------------------------------------------------------------------------------------- **** Twin operators with estimated twin fractions **** Twin operator: H, K, L: Fraction = 0.294 Twin operator: -H, -K, L: Fraction = 0.258 Twin operator: -K, H, L: Fraction = 0.284 Twin operator: K, -H, L: Fraction = 0.163 ------------------------------------------------------------------------------------------------- Many thanks Regards, -Kiran
participants (7)
-
Francois Berenger -
Kiran Kulkarni -
Morten Grøftehauge -
Nathaniel Echols -
Pavel Afonine -
Tom Terwilliger -
Wei Shi