[chimerax-users] How to view consurf result in chimerax

[Elaine Meng]

Hello,
Chimera and ChimeraX are two different programs. You cannot open that file in ChimeraX -- only Chimera knows how to open it.  I know it is really confusing because the file is named .chimerax, but we chose that filetype name long before we decided to name the new program ChimeraX. 

Actually you can open it Chimera, then export to another file that can be opened in ChimeraX, details below.

"chimerax" files that are really for Chimera:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html>

Example with image of how it looks in Chimera:
 <https://www.rbvi.ucsf.edu/chimera/consurf/consurf.html>
... that page includes a link to example .chimerax file:
<https://www.rbvi.ucsf.edu/chimera/consurf/pdb1rtt_isd.chimerax>

When you try to open the .chimerax file in Chimera you will get a warning dialog "some files contain code [etc.] would you like to open this file in Chimera?" and you need to click Yes.  Then it will show the structure and sequence alignment with color-coding, as in the image shown in the example page.

Then to export a file for ChimeraX, choose from the Chimera menu: File... Export Scene.  In the export dialog choose File type "ChimeraX [.py]" and specify file name and location.

Then you can open the new exported .py file in ChimeraX and you will get the color-coded structure and sequence alignment.  ChimeraX cannot yet show the phylogenetic tree to the left of the sequences, but all of the other stuff is exported.  It made my ChimeraX window really really wide, but I was able to resize the windows and panels manually and then it looked like the attached image:

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



> On Mar 2, 2022, at 7:41 PM, Shin, Yeonoh via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I ran MSA in Consurf website, however I can not open the color-coded pdb result in Chimera or ChimeraX.
> 
> When I click the link, attached error shows up.
> 
> When I tried to open the link in chimeraX command line, another error shows up (attached).
> 
> Could you tell me what I need to do to see the color-coded result in Chimera or X?
> 
> Thank you.
> Yeonoh
> <Screen Shot 2022-03-02 at 10.38.19 PM.png><Screen Shot 2022-03-02 at 10.38.33 PM.png>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220303/bdeec1cc/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2022-03-03 at 10.01.03 AM.png
Type: image/png
Size: 1278045 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220303/bdeec1cc/attachment-0001.png>