[Chimera-users] Question about use of Chimera to view data from SALIGN program

[Edmund Marinelli]

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.ali?passwd=lLzU3A8rBT"
/>
         <file  name="model1_fit.pdb" format="text"  loc="
https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model1_fit.pdb?passwd=lLzU3A8rBT"
/>
         <file  name="model2_fit.pdb" format="text"  loc="
https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model2_fit.pdb?passwd=lLzU3A8rBT"
/>
         <file  name="model3_fit.pdb" format="text"  loc="
https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model3_fit.pdb?passwd=lLzU3A8rBT"
/>
         <file  name="model4_fit.pdb" format="text"  loc="
https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model4_fit.pdb?passwd=lLzU3A8rBT"
/>
</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.
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