[phenixbb] Phaser-MR output after each component placement

Randy Read rjr27 at cam.ac.uk
Tue Jul 28 01:02:06 PDT 2020

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 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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