Re: [ccp4bb] CCP4 GUI

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

Previous message:
Subject: Re: CCP4 GUI
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-05-11

Next message:
Subject: Re: Molecular Replacement issues with a WD-40 7-bladed beta propeller
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-11

Subject: Re: CCP4 GUI
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-05-11

On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
> The most useful aspect of the ccp4i GUI is its automatic generation of
> com files. However, I would prefer the GUI to output a .com file into my
> working directory (rather than the obscure location they are saved to
> now) every time I run a program so that I can then tinker with it and
> add any extra keywords I want to.

I often use the GUI to get a 'second opinion' about good default
values and options for a given CCP4 program - especially if the
documentation is a bit confusing. Kind of double-checking if I
understood the documentation correctly.

One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wants to
change things - which is nice, since it leads e.g. to a very short
SCALA comand-file. I'm not always convinced that the settings done by
the CCP4i interface (when keeping all edfaults) correspond to the
defaults as implemented in the program itself.

Maybe any parameter setting unchanged from the values in the
$CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
the 'default value' - resulting in them _not_ being written to the
com-file? This way any potential change in defaults inside the actual
program would have immediate effect, even if the CCP4i hasn't been
updated yet.

Cheers

Clemens

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

Previous message:
Subject: Re: CCP4 GUI
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-05-11

Next message:
Subject: Re: Molecular Replacement issues with a WD-40 7-bladed beta propeller
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-11