[Chimera-users] Visualising PDB files from AMBER

[Elaine Meng]

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
-----
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>