Question about use of Chimera to view data from SALIGN program

Helllo: I used SALIGN to obtain alignment / superposition of peptides. On the SALIGN webpage there is a link for Launch Chimera. When I click this I get a download of a file named "show.chimerax". Then nothing happens. The file contents appear to be directing ChimeraX to the data on the web and are as follows: <?xml version="1.0"?> <ChimeraPuppet type="std_webdata"> <web_files> <file name="alignment.pir" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/str-str_out.a..." /> <file name="model1_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model1_fit.pd..." /> <file name="model2_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model2_fit.pd..." /> <file name="model3_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model3_fit.pd..." /> <file name="model4_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model4_fit.pd..." /> </web_files> <commands> <py_cmd>chimera.processNewMolecules(chimera.openModels.list(modelTypes=[chimera.Molecule]))</py_cmd> <py_cmd>import MultAlignViewer</py_cmd> <py_cmd>mols = chimera.openModels.list()</py_cmd> <py_cmd> m=chimera.extension.manager for i in m.instances: if isinstance(i, MultAlignViewer.MAViewer.MAViewer): mav = i </py_cmd> <py_cmd> for m in mols: if not m in mav.associations.keys(): mav.associate([m]) mav.match(mols[0], mols[1:], iterate=True)</py_cmd> </commands> </ChimeraPuppet> What am I supposed to do with this file. ChimeraX does not have a file extension .ChimeraX hence I do not know how to proceed next. Can anyone help? Thanks in advance.

On 10/26/22 11:48 AM, Edmund Marinelli via Chimera-users wrote:
I used SALIGN to obtain alignment / superposition of peptides. On the SALIGN webpage there is a link for Launch Chimera. When I click this I get a download of a file named "show.chimerax". Then nothing happens. Since you already asked me the same question directly, here's a summary of my previous answer to spare the Chimera folks some time:
Chimera and ChimeraX are two different programs. SALIGN outputs are for Chimera, not ChimeraX. If you have Chimera (not ChimeraX) installed, you can just open the showfile.chimerax file from within Chimera if it doesn't pop up automatically. Ben -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
participants (2)
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Ben Webb
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Edmund Marinelli