[Chimera-users] Unable to save file in pdb

[Neha Goel]

Dear Elaine,

If you will allow me, then I can share my .mrc file too.

Regards
Neha Goel

On Mon, May 10, 2021 at 11:22 PM Neha Goel <nehagoel24march at gmail.com>
wrote:

> 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
>> >
>> > _______________________________________________
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>> > Manage subscription:
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>>
>>
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