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

[Mahendra B Thapa]

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 at 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 at 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 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.
> >
> >
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
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