[phenixbb] Follow up question: Re: B factor for DNA and Protein

Young-Jin Cho yjcho at brandeis.edu
Tue Apr 27 10:54:42 PDT 2010

Let me ask a similar but different question.
I have two molecules (A and B). I was trying to put A molecule with neighbor waters or inside A waters only while excluding B or B molecule neighbored waters: Let me simplify if we can make separate A and B pdb files while have waters only 5A near to A or B molecules?

I did from Pymol before, but wondering if phenix can do in simpler way.

Thanks in advance (especially today!)

----- Original Message -----
From: "Pavel Afonine" <PAfonine at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Tuesday, April 27, 2010 12:16:54 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] B factor for DNA and Protein

Yes, this trivial combination of two commands will do it:

phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb
phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb
phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb

then do --show-adp-statistics

phenix.pdbtools protein_only.pdb --show-adp-statistics
phenix.pdbtools rna_only.pdb --show-adp-statistics
phenix.pdbtools water_only.pdb --show-adp-statistics


On 4/27/10 9:08 AM, Raja Dey wrote:
> Hi,
>     I need the values of B factors for Protein and DNA part separately in a Protein-DNA complex to prepare Table 1. I am not sure if PHENIX is doing that calculation. Can anyone tell me how I can get those values?
> Thanks...     
> Raja 

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