[phenixbb] problem with B-factor plot within the Structure Comparison tool

Tim Gruene tg at shelx.uni-ac.gwdg.de
Sat Jun 6 04:48:26 PDT 2015

Dear Emily,

I don't recognise the problem, but you can easily generate such plots
yourself. You can extract the residue number and B-factor with grep,
cut, etc. and plot the graph with e.g. gnuplot (or a spreadsheet
program, or ...). The PDB format is a very nice format for such purposes.


On 06/06/2015 07:12 AM, Emilia C. Arturo (Emily) wrote:
> Hello All.
> I am trying to zoom in on a section of the B-factors v. residue plot that
> is generated using the Structure Comparison tool of the phenix GUI. I zoom
> in by selecting a narrow residue range. When I do so, the plot does not
> show all parts of each trace; they are broken up and/or residues are
> missing that are certainly in the pdb files that I supplied, and that
> showed up when I displayed a wider residue range.
> I am using phenix version 1.9-1692 on a Mac (OS X Yosemite). I'd input 21
> pdb files. I've done some typical refresher-type things like closed and
> reopened the project, and restarted phenix (with no rationale, really), but
> the display problem persists.
> Does anyone else recognize this problem?
> Regards,
> Emily.
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149


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