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<div><font size="2">Dear Elaine</font></div>
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<div><font size="2">Thank you - all those tips were useful.<br>
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<div><font size="2">With ChimeraX, am not able to lock the Cryo-EM density map and then use the crystal structure to fit into it.</font></div>
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<div><font size="2">Whereas Chimera allows me to do so - however am not able to move the crystal structure to superimpose on the CryoEM density to do the 'Fit in Map'</font></div>
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<div><font size="2">is it something am not doing right? I follow these instructions - <a href="https://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#fitmodel" id="LPlnk118503">https://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#fitmodel</a><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, March 11, 2020 5:22 PM<br>
<b>To:</b> Tirumalai, Madhan R <mrtirum2@Central.UH.EDU><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Making movies and fitting structures into cryoEM</font>
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<div class="PlainText">Dear Madhan,<br>
Although ChimeraX doesn't yet have a movie-making dialog (GUI), you can make movies with ChimeraX command scripts. In a command script (plain text file named ending in .cxc), the "movie" command does recording and creating a movie file, whereas other commands
(show/hide, color, turn, 2dlabel, etc.) can be used to control display, motions, and labeling... whatever you want to happen during the movie. Simply opening the .cxc file runs the commands.<br>
<br>
You can change volume thresholds with the "volume" command "level" option, for example:<br>
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volume #1 level 0.08<br>
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<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general">http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general</a>><br>
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To gradually change the threshold over multiple display frames, you can combine the "volume" command with the "perframe" command, for example:<br>
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perframe "volume #2 level $1" range 0.1,0.3 frames 120; wait 120<br>
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(those should be plain text quotation marks, although the e-mail display may change them to fancy quotation marks)
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<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html">http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html</a>><br>
<br>
See ChimeraX "making movies" page and links therein:<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/movies.html">http://rbvi.ucsf.edu/chimerax/docs/user/movies.html</a>><br>
<br>
...including movie-making tutorials:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html">http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html">http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html</a>><br>
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See also general information on ChimeraX command files:<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files">http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files</a>><br>
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For your other question, if you are asking how to fit an atomic structure into a map, see the "Fit in Map" tool and/or "fitmap" command:<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html">http://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html</a>><br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html">http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html</a>><br>
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Or to compare one atomic structure to another atomic structure, you can superimpose them with the "matchmaker" command:<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html">http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html</a>><br>
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Chimera has a Matchmaker GUI, but ChimeraX does not have the GUI yet, only the command.<br>
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I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
> <br>
>> Begin forwarded message:<br>
>> <br>
>> From: "Tirumalai, Madhan R" <br>
>> Subject: ChimeraX<br>
>> Date: March 11, 2020 at 1:10:41 PM PDT<br>
>> To: "goddard@cgl.ucsf.edu" <goddard@cgl.ucsf.edu><br>
>> <br>
>> Dear Dr. Goddard<br>
>> <br>
>> Warm Greetings!<br>
>> <br>
>> We have been using ChimeraX to look at mrc files.<br>
>> <br>
>> While I am able to use the "Spin movie" option, am not able to use the make movie option, which I could with the Chimera version.<br>
>> <br>
>> I would much appreciate if you could kindly let me know how: <br>
>> <br>
>> I can use the movie making option to make movies using different images with increasing/ decreasing thresholds (Volume Viewer)?<br>
>> <br>
>> Since am not familiar with docking programs, I would like to know how can one a related crystal structure into a new Cryo-EM structure to show the differences between the crystal structure and the Cryo-Em?<br>
>> <br>
>> Thanks<br>
>> Madhan<br>
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