[Chimera-users] Saving ChimeraX log, saving protein sequence to file

[Elaine Meng]

Hi Prathvi,
These answers are both for ChimeraX so I CC'd the chimerax-users list.

(1) ChimeraX command "log save" saves it as HTML 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html>

(2) in ChimeraX, open the structure, show the sequence of the chain of interest (menu: Tools... Sequence... Show Sequence Viewer, choose chain if there is more than one chain preset).  Showing the sequence can also be done with the ChimeraX "sequence chain" command. 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain>

 Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). 
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context>

You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window.
<https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu>

In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

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 2, 2022, at 9:51 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks a lot Elaine. It helped enormously. I just have 2 more questions:
> 
> 1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error.
> 
> 2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets?
>