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

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 30 09:34:51 PDT 2012

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,

...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.

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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