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

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.... 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 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