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..

Rajesh

Date: Tue, 22 Nov 2011 10:50:53 -0500
From: [email protected]
To: [email protected]
Subject: [phenixbb] measuring angle

Hi,

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
ROTATE [INVERT] [MATRIX] values
CHAIN A
end
eof

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

Hena

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