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

[Mahendra B Thapa]

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 at 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 at 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.
>
>
>
>
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