Hi Nat, Got it! Thank you so much! Best, Wei ________________________________________ From: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] Sent: Thursday, January 24, 2013 6:07 PM To: PHENIX user mailing list Subject: Re: [phenixbb] B-factor calculation On Thu, Jan 24, 2013 at 2:59 PM, Wei Shi wrote:

I am wondering how I can calculate average B-factor in phenix GUI. I read from an old post saying that, the following will give me complete statistics about B-factors, but in pdbtools in phenix GUI, I didn't find how to show adp statistics.

phenix.pbdtools your_model.pdb --show-adp-statistics

Besides, I am wondering how I can find the B-factor for each residue and plot the variation of B-factor by residue.

Several options: 1. In the validation GUI, the real-space correlation tab will have statistics for individual residues (you just need to lower the CC cutoff, and in the nightly builds there should be a button to dump the entire unfiltered table to a file). The multi-criterion plot will show the B-factor along with CC and map levels (and validation outliers). 2. In the main GUI, under "Other tools", "Display ADP statistics" will essentially do what that pdbtools command does. 3. In the same place, "Plot average B-factors in PDB file" will do exactly what it says. -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb