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Hi Tom and Elaine,
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<div class="">Thank you for your help! These are all very helpful suggestions, and I appreciate you getting back to me so quickly.</div>
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<div class="">Regarding fitting atomic models to maps, what would you suggest as a starting point to globally fit? Is this something you'd suggest be done outside of ChimeraX? Is there perhaps a way to semi-automate the process where you can interactively
start from rough inspection — and then loop from there? Our group is hoping to do this for a few hundred models/maps, so manually doing this would be a bit time-consuming. However, we have fitted one model to a map, and it does seem to work very well when
done interactively.</div>
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<div class="">Many thanks,</div>
<div class="">Steven <br class="">
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<div class="">On Feb 19, 2021, at 3:00 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
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<div class="">Hi Steven,</div>
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Elaine pointed to the right place for the fitmap Python documentation. I've also added it under the Python Modules page under Volume data to make it easier to find. The open_pdb() and save_pdb() functions are here and have strangely not been documented.
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/pdb/src/pdb.py" class="">https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/pdb/src/pdb.py</a></div>
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<div class="">We will try to get those documented in the Programmer's manual.</div>
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<div class="">ChimeraX fitting of atomic models in maps is intended for interactive fitting. Keep that in mind if you are going to try to script it in Python. It doesn't have good capabilities for doing global searches and is really intended to locally optimize
a fit once you have atomic models close to their correct positions.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom<br class="">
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<div class="">On Feb 19, 2021, at 10:29 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrotey:</div>
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<div class="">Hi Steven,<br class="">
Maybe this page in the programmer documentation (and links therein) would help... it includes "fitmap," at least:<br class="">
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<<a href="https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.html</a>><br class="">
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I don't create the programmer documentation, but since the page says version 1.2 I'm hoping it's reasonably up-to-date.<br class="">
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The "save" link doesn't say much, however, so somebody else will have to give more information on writing files.<br class="">
Best,<br class="">
Elaine<br class="">
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Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
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<blockquote type="cite" class="">On Feb 19, 2021, at 10:05 AM, Steven Truong <<a href="mailto:sdt45@cam.ac.uk" class="">sdt45@cam.ac.uk</a>> wrote:<br class="">
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To whom it may concern,<br class="">
Hello! I was hoping to ask for some help in Python Scripting in ChimeraX. Specifically, I am trying to fit structure files (.PDB) to electron density maps (.MAP). Is there a way to do this in .PY scripts in ChimeraX? I can’t seem to find such a command
like “fitmap” in the documentation here (<a href="https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html</a>). Additionally, it seems like the “Read and Write PDB Files” page (<a href="https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/pdbio.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/pdbio.html</a>)
of the documentation page hasn’t been updated. Is there another place that outlines how to save structures?<br class="">
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