Wei.Shi.GR at dartmouth.edu
Fri Nov 18 07:50:41 PST 2011
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.
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Morten Grøftehauge [mortengroftehauge at gmail.com]
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.
On 18/11/2011, Francois Berenger <berenger at riken.jp> wrote:
> 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).
> On 11/18/2011 05:07 AM, Wei Shi wrote:
>> Hi DrTerwilliger,
>> I see. Thank you so much!
>> *From:* phenixbb-bounces at phenix-online.org
>> [phenixbb-bounces at phenix-online.org] on behalf of Tom Terwilliger
>> [terwilliger at lanl.gov]
>> *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
>> 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
>>> 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 \
>>> use_all_plausible_sg=False \
>>> nproc=4 \
>>> 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:
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> Thomas C. Terwilliger
>> Mail Stop M888
>> Los Alamos National Laboratory
>> Los Alamos, NM 87545
>> Tel: 505-667-0072 email: terwilliger at LANL.gov
>> <mailto:terwilliger at LANL.gov>
>> 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:
>> 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
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