[Chimera-users] Problems detecting h-bonds

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 2 09:30:53 PDT 2015


Hi, 
It may be that the coordinates are weird somehow (strained, or multiple conformations of same atoms), or the structure input format was wrong.   Check the input carefully for format or other problems … it is not possible to tell specifically what is wrong without looking at your data.

Your setattr command doesn’t make sense because it doesn’t specify any type.  Maybe it erased all the types, which would certainly make everything worse!  A correct setattr command would be something like “setattr a idatmType C3 sel” to change the selected atom to type C3.  However, Chimera generally figures out the atom types itself and you would not need to change them (e.g. with setattr). Atom types:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

You could try “Help… Report a Bug” and attach the structure (or session) and describe exactly what to do to get that error in FindHBond.  Don’t change the atom types before sending us the data, since that is expected to really mess things up.
Best,
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 Oct 2, 2015, at 7:49 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi, 
> I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex?
> 
> Thanks in advance for your help.
> 
> Best regards,
> 
> Andrés Felipe Vásquez J., BSc, MSc.
> Profesional - Grupo de Fisiología Molecular
> Subdirección de Investigación Científica y Tecnológica
> Dirección de Investigación en Salud Pública
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> Bogotá, D.C., Colombia 




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