Re: [phenixbb] phenixbb Digest, Vol 48, Issue 4

Thanks, restore results works fine for what I need now. [email protected] wrote:

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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)

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Message: 1 Date: Wed, 4 Nov 2009 08:34:24 -0800 From: Nathaniel Echols Subject: Re: [phenixbb] re-run jobs in GUI To: PHENIX user mailing list Message-ID: <[email protected]> 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 [email protected]

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Message: 2 Date: Wed, 04 Nov 2009 12:35:01 -0500 From: Joe Krahn Subject: [phenixbb] Elbow ligand building To: PHENIX user mailing list Message-ID: <[email protected]> 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

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Message: 3 Date: Wed, 04 Nov 2009 10:09:47 -0800 From: Nigel W Moriarty Subject: Re: [phenixbb] Elbow ligand building To: PHENIX user mailing list Message-ID: <[email protected]> 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