[phenixbb] B-factor calculation

Wei Shi Wei.Shi.GR at dartmouth.edu
Thu Jan 24 15:19:10 PST 2013

Hi Nat,
Got it! Thank you so much!

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
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 <wei.shi118 at gmail.com> 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

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.

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