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 http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/keyword_tutorial.html. 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk