[phenixbb] Phaser-MR output after each component placement

Johannes Cramer johannes.cramer at gmail.com
Tue Jul 28 01:38:00 PDT 2020


thanks to the both of you. Looks like I will try again, once the new
version is out and in cases where I would like to examine the placements,
just run it via script.


Am Di., 28. Juli 2020 um 10:02 Uhr schrieb Randy Read <rjr27 at cam.ac.uk>:

> Hi Boaz,
> At the moment, that is indeed the only thing you can do with the partial
> solution information from the log file.  In the CCP4 environment, you can
> cut and paste lines from the log file to make a .sol file, and use that to
> run something like a refinement job to produce a PDB and MTZ for a partial
> solution, but the Phenix environment uses Python pickle files to store the
> transformations, so that option doesn’t apply.  (Unless you run Phaser from
> a script, in which case the Phenix and CCP4 versions work the same.)
> At one point, Phaser was writing out a PDB file for the top solution at
> every point in the process, but we felt that led to clutter and that it was
> confusing.
> There’s a major rewrite going on at the moment, and the new phasertng will
> primarily be run through the phaser.voyager pipeline.  One of the design
> criteria here was to be able to examine branches that weren’t taken or
> intermediate points in the ongoing search, and to be able to work with them
> while the overall job is still running.  So there will be a better option
> in the hopefully not too distant future!
> Best wishes,
> Randy
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research     Tel: +44 1223 336500
> The Keith Peters Building                               Fax: +44 1223
> 336827
> Hills Road                                                       E-mail:
> rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
> > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
> >
> > Hi,
> > The closest option that comes to mind to do what you're looking for is
> to take the Euler angles+translations for each of the monomers in the .sol
> file (or at the top of the final pdb file) and apply each of them to the
> initial model using any transformation program of your choice.
> > I am more familiar with running Phaser using the ccp4 gui but it
> shouldn't be very different under Phenix.
> > Phaser people may well suggest a more elegant option.
> > Stay safe,
> > Boaz
> >
> > Boaz Shaanan, Ph.D.
> > Department of Life Sciences
> > Ben Gurion University of the Negev
> > Beer Sheva
> > Israel
> >
> > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer at gmail.com>
> wrote:
> > Dear phenix board,
> >
> > does anyone of you know if there is an option in phaser-MR to output a
> pdb after each placed component?
> > For example: I suspect there to be 5 molecules in the AU. I start a
> replacement with 5 molecules and phaser places 1 (I would like to inspect
> that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so
> on...
> > Is that possible? I couldn't find the option in the gui or in the phenix
> documentation, but maybe in the CLI?
> > I know I can run one after the other, but that would potentially waste
> CPU time until I find time to inspect them.
> >
> > Cheers,
> > Johannes
> > _______________________________________________
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