Dear Dr. Elaine, May I send my pdb file? I could not fix the problems; I tried my best as far as I can , with possible alternatives. Thanks, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:58 PM, Thapa, Mahendra (thapamb) < thapamb@mail.uc.edu> wrote:

________________________________________ From: Elaine Meng Sent: Monday, July 30, 2012 10:58:32 AM (UTC-06:00) Central America To: Thapa, Mahendra (thapamb) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] FW: problem in visualising metal- atoms in simulated

The atom names of the ions should not be lined up with the other names, and the last field should be CA not C. So there are at least two problems with these lines. Please see the format description in the link in my previous message.

Some additional problems are that the ion lines should probably be HETATM not ATOM, and the names CA not CO. So I would fix those things too. Best, Elaine

On Jul 30, 2012, at 9:46 AM, Mahendra B Thapa wrote:

...

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.

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