[Chimera-users] Saving changes made in PDB files

[Elaine Meng]

Hi Liam,
PDB files do not include information like residue highlighting and background color, they only include the locations of the atoms.

It is not possible to answer in more detail with the information you have given.  If you changed the structure, meaning you added or deleted or moved atoms, then yes, using File... Save PDB and choosing that structure should give the same thing that is in Chimera (same atoms in same locations).

However, if you want to save stuff like coloring and highlighting, you have to save a Chimera session file (File... Save Session) instead.

See "modifying and saving data"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>

Or, if you just want to save a picture, then menu: File... Save Image.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html>

However, if you want to be able to restore the same state of display in Chimera later, you should save a session.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 14, 2020, at 3:04 PM, Liam fletcher <lfletcher87 at hotmail.co.uk> wrote:
> 
> Good day,
> 
> I am hoping you may be able to help me with an enquire I have for current work I am performing using the Chimera software for my final year project.
> 
> I am attempting to save a PDB file separately following changes made e.g. Highlighted reside(s), change the background. I am having trouble in saving these files separately. More specifically, I am attempting to save different file versions where changes have been made to the protein for predicting the function.
> 
> Is there a way to save these PDB files as I have been following the instruction. But, I am confusion about which of these instructions is the right instructions to use.
> 
> I thank you in advance and hope to hear from you soon.
> 
> Kind regards,
> 
> Liam Fletcher