[Chimera-users] Distances in biological assembly

Elaine Meng meng at cgl.ucsf.edu
Wed May 27 09:48:25 PDT 2015

Dear Mahendra,
You can test the command on a smaller system to make sure it works the way you think.

Overlap -4, hbond 0 means it should find atoms with VDW surfaces up to 4 angstroms away from the VDW surface of the specified atom(s).  That is farther away than what I would consider a contact, but if you are trying to find nearby atoms, not just contacting, it could make sense. Those values work when I just choose some not-too-big protein PDB file and try them, e.g.

open 4hhb
findclash :110.b at ca overlap -4 hb 0 log true
(then look in Reply Log to see the log info)

Suggested defaults for contacts and clashes are described here:

Note also that by default, it will ignore contacts within the same residues and within 4 bonds of the specified atoms, unless you change those settings with the bondSeparation and intraRes options described in the link above.

I don’t know what is happening with your data, however.  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 27, 2015, at 8:59 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:

> Dear Chimera users
> The biological assembly of a virus in pdb format  consists of 60 models; each model with 3 chains :A, B and C. I am interested to find  atoms within  4 angstroms of  the atom, say CA atom of residue 2059 of chain B of model 2. The chimera crashed in graphical interface (it could be due to size of the pdb file.), so I used the following command [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-November/002069.html]:
> chimera --nogui file_test.cmd > data_rest.log
> where 'file_test.cmd' consists of
> open test.pdb
> findclash #2:2059.B at CA overlap -4 hbond 0
> The output file 'data_rest.log' consisted of 
> Opening test.pdb...
> 60 models opened
> Opened test.pdb containing 60 models, 677040 atoms, and 89700 residues
> No contacts
> No contacts
> I want to know whether I have used right chimera command /code. Any suggestion might help me.
> Thank you,
> Mahendra Thapa
> University of Cincinnati,OH

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