Dear Dr. Elaine, The last few lines of the file are as follows: ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 O TER ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 C TER ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 C TER I also tried with Ca instead of C in the last column , but no improvement. Thank you for help, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < thapamb@mail.uc.edu> wrote:
________________________________________ From: Elaine Meng Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America To: Thapa, Mahendra (thapamb) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] problem in visualising metal- atoms in simulated
Hi Mahendra, Probably the format is slightly wrong for the lines with the calcium ion coordinates. For example, the name CA for the calcium ion should *not* line up with the name CA in the protein alpha-carbon lines.
In the ATOM and HETATM lines of PDB files, < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coor...
...the ion name CA should be in columns 13-14, whereas the alpha-carbon name CA should be in columns 14-15.
Misalignment of ion names is a common problem with the output of many programs. < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#misa...
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 Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote:
Dear Chimera Users, I converted amber-12 generated rst-file in netCDF format [ test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the cpptraj command of amber 12. When I loaded it in chimera, the protein structure looks fine but two calcium atoms that the protein binds could not be visualised, although the pdb file-format looks good. Let me help in this respect.