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@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
Any suggestion might help me.