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>