[phenixbb] phenixbb Digest, Vol 48, Issue 4

Leo Sazanov sazanov at mrc-mbu.cam.ac.uk
Wed Nov 4 12:40:30 PST 2009


Thanks, restore results works fine for what I need now.

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> Today's Topics:
>
>    1. Re: re-run jobs in GUI (Nathaniel Echols)
>    2. Elbow ligand building (Joe Krahn)
>    3. Re: Elbow ligand building (Nigel W Moriarty)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Nov 2009 08:34:24 -0800
> From: Nathaniel Echols <NEchols at lbl.gov>
> Subject: Re: [phenixbb] re-run jobs in GUI
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <529970F2-E319-4152-B4F1-E46184755554 at lbl.gov>
> Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes
>
> On Nov 4, 2009, at 8:08 AM, Leo Sazanov wrote:
>   
>> Hi, in a new GUI how can one re-run previous jobs (to make some
>> modifications to them)?
>>     
>
> Open the main GUI (the command 'phenix', or click the home button on  
> the toolbar of any other program), click the "job history" toolbar  
> button, select a job from the list, and click "restore results".  This  
> should restore both the results tab or window, and the configuration.   
> There is also a "restore last job [for the current project]" button on  
> the toolbar.  Any inconsistencies here are definitely a bug, but it  
> was working for most programs in 1.5-2.  (The main exception is the  
> reflection file editor, but that will also save/restore results in the  
> next available nightly build.)
>
>   
>> If I just try to open parameter (.eff) file from the main file menu in
>> Autobuild, the file does not show up, even though it exists.
>> Just adding it to the list of input files works, but the information  
>> is
>> not passed on into GUI?
>>     
>
>
> It's a little complicated right now.  If you want to apply the  
> contents of a parameter file, this is best done at startup - e.g. drag  
> and drop the file onto the launch icon, or use it as a command line  
> argument ('phenix.autobuild params.eff').  For phenix.refine, you can  
> also save default parameters (Preferences->Refinement, or project  
> settings, or from the utilities menu) and it will start with them pre- 
> loaded.  Once the program window is drawn, however, it's clumsier -  
> files *should* be passed down to the command-line module (if not, also  
> a bug), but they won't immediately be applied to the GUI, because of  
> the way it tracks parameters internally.
>
> I can't promise that every pre-existing configuration file will be  
> processed cleanly by the GUI - it's difficult to anticipate what users  
> will try to do.  If you encounter cases where the parameters are  
> misinterpreted, let me know.
>
> --------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 04 Nov 2009 12:35:01 -0500
> From: Joe Krahn <krahn at niehs.nih.gov>
> Subject: [phenixbb] Elbow ligand building
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <4AF1BB45.20707 at niehs.nih.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I am having some problems building ligand parameters with elbow.
>
> I have an accurate reference structure, but elbow seems to "regularize" 
> the coordinates in a way the distorts the structure. Is there a way to 
> disable this?
>
> With --opt, QM optimization should hopefully remove distortions, but it 
> is not doing a very good job for this molecule. So, I decided to 
> optimize using Gaussian, and a better basis set.
>
> It seems that the Gaussian interface is still fairly simple, and it 
> seems that you have to edit the Gaussian.csh template. So, I did that, 
> but got the "Gaussian does not seem to be installed" message. 
> Unfortunately, elbow runs the Gaussian script with output to /dev/null, 
> so there is no way to see any error messages. Maybe that should be done 
> only when the --quiet flag is given.
>
> I edited the Python source to let errors go to the tty, and found that 
> the problem is in the way the script is invoked using "csh -c %s.csh". 
> That only works if "." is in your $PATH, which is often the case. It 
> also invokes an extra instance of csh, because it is invoked as a system 
> command. The correct way to run a shell script is to leave out the '-c'. 
> Elbow makes the script executable, so an even better approach is to just 
> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the 
> script can be in sh/bash/etc. Maybe the was the intent of using '-c'?
>
> Thanks,
> Joe Krahn
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 04 Nov 2009 10:09:47 -0800
> From: Nigel W Moriarty <NWMoriarty at lbl.gov>
> Subject: Re: [phenixbb] Elbow ligand building
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <4AF1C36B.3010500 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Joe
>
> On 11/4/09 9:35 AM, Joe Krahn wrote:
>   
>> I have an accurate reference structure, but elbow seems to "regularize" 
>> the coordinates in a way the distorts the structure. Is there a way to 
>> disable this?
>>   
>>     
> eLBOW will always run a simple optimisation unless you specify the final 
> geometry you like using
>
> phenix.elbow --final-geometry accurate.pdb
>
> Naturally, you are smart to use a better input format thus
>
> phenix.elbow filename.sdf  --final-geometry accurate.pdb
>   
>> With --opt, QM optimization should hopefully remove distortions, but it 
>> is not doing a very good job for this molecule. So, I decided to 
>> optimize using Gaussian, and a better basis set.
>>   
>>     
> Good thinking.
>   
>> It seems that the Gaussian interface is still fairly simple, and it 
>> seems that you have to edit the Gaussian.csh template. So, I did that, 
>> but got the "Gaussian does not seem to be installed" message. 
>> Unfortunately, elbow runs the Gaussian script with output to /dev/null, 
>> so there is no way to see any error messages. Maybe that should be done 
>> only when the --quiet flag is given.
>>   
>>     
> Maybe I'll implement this with a --verbose flag.
>   
>> I edited the Python source to let errors go to the tty, and found that 
>> the problem is in the way the script is invoked using "csh -c %s.csh". 
>> That only works if "." is in your $PATH, which is often the case. It 
>> also invokes an extra instance of csh, because it is invoked as a system 
>> command. The correct way to run a shell script is to leave out the '-c'. 
>> Elbow makes the script executable, so an even better approach is to just 
>> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the 
>> script can be in sh/bash/etc. Maybe the was the intent of using '-c'?
>>     
> This is old code from before PHENIX had a smart module for running 
> commands.  I'll update to code.
>
> Nigel
>
>   


-- 
Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 0XY
WEB: www.mrc-mbu.cam.ac.uk
Tel: +44-1223-252910
Fax: +44-1223-252915




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