[Chimera-users] problem in visualising metal- atoms in simulated

[Elaine Meng]

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
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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.