[Chimera-users] Unable to save file in pdb

[Neha Goel]

Dear Elaine,

I am sorry for this. I will explain in this email. The information and
images I  needed in ppt.
1. I have a .mrc file which I opened in chimera. then I tried to save
directly in pdb, it showed the needed molecular model.
2. I opened .mrc, .reference pdb which I opened in chimera.
3. I put it in the centre using the Active/focus option and Hide .map file
using volume viewer.
4. Then I clicked fit to map and save the file.pdb only reference was
saved.

I am heartily thankful to you.

Regards
Neha Goel



On Mon, May 10, 2021 at 11:13 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Neha,
> It is not possible to help you in detail unless you say exactly what steps
> you did in detail, and why you think it didn't work, any error messages,
> etc.  You didn't even say what command or tool you were trying to use!
> Also, sometimes it is necessary to provide your specific data.
>
> All of the Chimera commands and tools have help pages that you can read to
> learn how to use them yourself. There are at least two different ways of
> superimposing protein structures, as discussed in this page and links
> therein:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>
> Namely,
> (1) Probably the easier way, Matchmaker tool or command.  Either way you
> can tell it exactly which chain(s) to use, so it does not matter if the
> structures don't have the same numbers of chains.  Choose the Chain pairing
> method: Specific chain(s) in reference structure with specific chain(s) in
> match structure.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
>
> (2) "match" command.  Again you can tell it exactly which atoms to use for
> the fitting.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> ... how to specify atoms,residues,chains in command line:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic
> >
>
> I hope this helps,
> Elaine
>
> > On May 10, 2021, at 12:19 PM, Neha Goel <nehagoel24march at gmail.com>
> wrote:
> >
> > Dear Elaine,
> >
> > Thank you for your reply. When I am trying to fit model using reference
> pdb. I am not getting appropriate response. Because my reference pdb has
> only 11 chains while my protein has more than this. Kindly suggest some
> person who can help me with this. I will be heartily thankful to you
> >
> >
> > Regards
> > Neha Goel
> >
> > On Mon, 10 May 2021, 20:51 Elaine Meng, <meng at cgl.ucsf.edu> wrote:
> > Hi Neha,
> > An MRC file is a density map format.  You cannot save it as an atomic
> model, because it does not contain atomic coordinates.
> >
> > There is no tool in Chimera to create atomic structure instantly from a
> map.   Researchers use various programs to build atomic structures into a
> map or to build an atomic model separately and then fit it into a map, but
> it is generally an interactive process that takes many steps.  I am not an
> expert on this process, but you could read hundreds of research papers
> "Methods" sections to see descriptions of the ways in which it is done.
> >
> > Regards,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On May 10, 2021, at 10:24 AM, Neha Goel <nehagoel24march at gmail.com>
> wrote:
> > >
> > > Dear Chimera,
> > > I have a .mrc file. I reopened the file in chimera and would like to
> save it in pdb. I am unable to save it. It needed the molecular model pdb.
> Kindly guide me the way to save it.
> > > Regards
> > > Neha Goel
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210510/98ccb1f7/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: needed.ppt
Type: application/vnd.ms-powerpoint
Size: 11063296 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210510/98ccb1f7/attachment-0001.ppt>