[Chimera-users] Distances in biological assembly

Mahendra B Thapa thapamb at mail.uc.edu
Wed May 27 08:59:48 PDT 2015

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 [
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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