[Chimera-users] Unable to save file in pdb

[Tom Goddard]

Hi Neha,

  When you use Chimera menu entry File / Save PDB... you need to check the "Save relative to model" button and save relative to the MRC map in order to save the coordinates of the moved model.  Otherwise you just end up saving the unfitted original PDB coordinates.

	Tom

> On May 10, 2021, at 2:45 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Neha,
> I do not understand how you got an atomic structure from MRC.  As far as I knew, MRC files only contain the density map, no atom coordinates.  You can send the MRC to file to my individual e-mail address (see the "From" on this message) if you want to.
> Elaine
> 
>> On May 10, 2021, at 1:38 PM, Neha Goel <nehagoel24march at gmail.com> wrote:
>> 
>> 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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