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

Elaine Meng meng at cgl.ucsf.edu
Sun Apr 3 08:18:41 PDT 2022

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 

(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. 

 Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). 

You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window.

In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file.

I hope this helps,
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?

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