[phenixbb] Omit map

Rajesh kumar ccp4_sc at hotmail.com
Tue Nov 22 19:35:20 PST 2011

Dear All,
I am new to Phenix. I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile.If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. This structure was solved by molecular replacement using a bacterial protein with 38% identity.I am wondering if there is an model bias? I have not identified particular region in model for bias.
My questions are: Am I right in thinking if there is model bias based on above info?I  added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before.I have couple of classical papers next to me but I need help.  I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB.
Happy Thanksgiving..

Date: Tue, 22 Nov 2011 10:50:53 -0500
From: hdutta10 at gmail.com
To: phenixbb at phenix-online.org
Subject: [phenixbb] measuring angle


Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? 
I have another question.

In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command

 in shell script to write a pdb file with a desired SEGID? As for example:-

pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log

This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate.

Thank you in advance and have a nice THANKS GIVING WEEKEND


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