[phenixbb] Phaser

Randy Read rjr27 at cam.ac.uk
Fri Jul 13 05:27:36 PDT 2007

On Thursday 12 July 2007, john kryst wrote:
> Hi all !!!
>        Is it possible to fix one domain and search for the second one in
> phaser !!!  What are the keywords to use for that.
> I have a protein with two domains. It i give both the domains together it
> is not finding the solution. If i give only one domain it is giving the
> solution and the R and Rfee is 28 and 33. But it is not finding the second
> one.
> Thanks in advance for your suggestions..
> regards
> John

Hi John,

In the Phenix AutoMR wizard, we haven't yet implemented a way to search for 
one component of a structure in one job, then to fix it and search for 
another component in a subsequent job.  Most of the time, if you can solve 
such a structure with Phaser, it can be solved by looking for all components 
in the same job, so that's the approach that the wizard concentrates on.

I'm pretty sure this could be done by using the Tasks interfaces in Phenix, 
where there are Phaser tasks for individual steps in the pathway.  But at the 
moment, if you want to do something unusual, it's easier to do it either in 
shell scripts with the command-line interface or from the ccp4i GUI in CCP4.  
I think you've had suggestions on how to do that, from your similar query on 
the ccp4-bb.  There are also example scripts on our web page at 
These apply to version 1.3, but I don't think any of the minor changes in the 
syntax for version 2.0 and 2.1 will break them.

What is the relative size of the two domains?  The R and R-free values imply 
that the single domain explains the data pretty well on its own.  So I would 
guess that the second one must either be very small, or it's badly disordered 
in your crystal.  


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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