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#coords>

...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#misalignment>

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.