[phenixbb] MR

[Randy Read]

Hi,

When running Phaser from the Phenix GUI, writing .sol files is suppressed, so you have to use the GUI pulldown (which gets information from Python pickle files instead).  

In any case, Pavel was asking about when you didn't get the partial model from a Phenix run.  In such a case, you can provide the model as an ensemble then, while you're still in the Ensembles tab in the GUI, check the box marked "Ensemble is fixed partial solution".  This tells Phaser to use this as a fixed component to which no rotation or translation should be applied.

Best wishes,

Randy

On 17 Jan 2014, at 16:09, "Oganesyan, Vaheh" <OganesyanV at MedImmune.com> wrote:

> I think in such cases you can use *.sol file generated during firs run. Would be interested to know if it not the case.
> 
> Regards,
> 
> Vaheh
> 8-5851
> 
> 
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
> Sent: Friday, January 17, 2014 11:04 AM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] MR
> 
> Hi Randy,
> 
> this reminded me I had a similar question... What if I have PDB file with a partial model (that is not a "partial solution form previous
> job") and I want to use Phaser to find the rest?
> 
> Thanks,
> Pavel
> 
> On 1/17/14, 5:11 AM, Randy Read wrote:
>> Dear Swastik
>> 
>> If you have a partial MR solution using the Phaser-MR GUI, then you can choose it with the "Use partial solution from previous job" pull-down, and set up a job to add more copies to it.
>> 
>> Best wishes,
>> 
>> Randy Read
>> 
>> On 17 Jan 2014, at 12:41, Swastik Phulera <swastik.phulera at gmail.com> wrote:
>> 
>>> Dear All,
>>> I am trying an MR, it looks like there would be 16 dimers in the asymmetric unit, Upon running Phaser once it could easily fit two copies.  I now wish to use this solution to perform further MR runs in order to locate the other dimers.
>>> I was just wondering what shall be the right way to go about it.
>>> Regards
>>> Swastik
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>> ------
>> Randy J. Read
>> Department of Haematology, University of Cambridge
>> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
>> Wellcome Trust/MRC 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
>> 
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> 
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC 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