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@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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> 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 ----- 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@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@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