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
Subject: Re: [phenixbb] re-run jobs in GUI
To: PHENIX user mailing list
Message-ID: <529970F2-E319-4152-B4F1-E46184755554@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@lbl.gov
------------------------------
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: <4AF1BB45.20707@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
Subject: Re: [phenixbb] Elbow ligand building
To: PHENIX user mailing list
Message-ID: <4AF1C36B.3010500@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
Leo Sazanov