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

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!) Best, Young-Jin ----- Original Message ----- From: "Pavel Afonine" To: "PHENIX user mailing list" 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 Pavel. 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