[Chimera-users] Visualising PDB files from AMBER

Elaine Meng meng at cgl.ucsf.edu
Wed May 18 12:25:14 PDT 2011

Hi George,
I can see it, but it has supershort bonds: 0.035 and 0.045 angstroms!  Perhaps an example of the perils of averaging?  Anyway, I can display it without problem, but it just looks like a slightly misshapen little ball because the three atoms are so close together.  Open the file and try these commands:

show :wat
focus :wat

... see the "ball" which is actually compressed sticks.  To measure bond lengths, show as wire, zoom in, pause cursor over each bond:

rep wire
scale 50

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 18, 2011, at 10:37 AM, George Tzotzos wrote:

> Hi everybody,
> I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT).
> I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7
> Any ideas explaining this behaviour? I'm attaching the relevant file.
> Thank you in advance for your help
> Best regards
> George
> <aver.pdb>

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