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Hi Elaine,
<div class=""><br class="">
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<div class="">Thanks again for the help! I am able to make my desired movie now. I’ll cite the corresponding chimera reference in our future publications.</div>
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<div>Have a good one,</div>
<div>Yifan</div>
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<blockquote type="cite" class="">
<div class="">On Jan 14, 2020, at 10:18 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hi
Yifan,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Those
quality-related settings all affect the size of the movie file and how nice the images look, but not their pixel size. You would set the pixel size with the “movie record” option “size”:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""><</span><a href="https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmovie.html%23record&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920901506&sdata=MaQhJrksbyIaTFvf1iSJtPppDgyEso%2BPT5wAIdZ%2FlAw%3D&reserved=0" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmovie.html%23record&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920901506&sdata=MaQhJrksbyIaTFvf1iSJtPppDgyEso%2BPT5wAIdZ%2FlAw%3D&reserved=0</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">For
example:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">movie
record supersample 3 size 1920,1080</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">I
hope this helps,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Elaine</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">-----</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Elaine
C. Meng, Ph.D. </span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">UCSF
Chimera(X) team</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Department
of Pharmaceutical Chemistry</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">University
of California, San Francisco</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
On Jan 13, 2020, at 4:56 PM, Yifan Wang <<a href="mailto:yifan.wang@utsa.edu" class="">yifan.wang@utsa.edu</a>> wrote:<br class="">
<br class="">
Dear Elaine,<br class="">
Sorry to bother your again. I have a question upon saving a movie with high resolution.<br class="">
I’d like to export a 1920 x 1080 pixels resolution movie. I have tried functions such as “quality”, “bitrate”, “qscale” etc, but it seems the only thing that really change the movie size is my window size. But I could not enlarge my window size of up to 1080P.
I am hoping there is a command line to specify the dimensions that I want to save. Could you please help me with this? Thank you!<br class="">
Yifan<br class="">
<br class="">
<blockquote type="cite" class="">On Jan 13, 2020, at 4:47 PM, Yifan Wang <<a href="mailto:yifan.wang@utsa.edu" class="">yifan.wang@utsa.edu</a>> wrote:<br class="">
<br class="">
Hi Elaine,<br class="">
<br class="">
Thank you very much for the kind reply and useful suggestions.<br class="">
I’ll look into these links and play with the program.<br class="">
<br class="">
Thanks,<br class="">
Yifan<br class="">
<br class="">
<blockquote type="cite" class="">On Jan 13, 2020, at 3:03 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
**EXTERNAL EMAIL**<br class="">
This email originated outside of The University of Texas at San Antonio.<br class="">
Please exercise caution when clicking on links or opening attachments.<br class="">
<br class="">
Hi Yifan,<br class="">
The ligand and ions will not be included in the morph trajectory model unless they are in both of the two input structures. However, you can display any of atoms from any of the input model(s) at the same time as the morph, as long as it is OK with you that
these atoms do not move. See in the Models panel on the lower right of your second screenshot that the checkboxes under the “eye” icon are turned off for your two input models. You can check the box to re-show either or both of those models. You would probably
want to hide the cartoon of that model, and most of its atoms except the ligand and ions.<br class="">
<br class="">
Here are the rules for which atoms from the input structures get included in the morph trajectory, in case you want to do anything fancier to get them included so that they move along with the protein parts. See “Atoms in Common”:<br class="">
<<a href="https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmorph.html%23pairing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=5PcHeBU4h4FeafNBrAMVkZoqqP7JmDKRp%2FCbX6jkdz4%3D&reserved=0" class="">https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmorph.html%23pairing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=5PcHeBU4h4FeafNBrAMVkZoqqP7JmDKRp%2FCbX6jkdz4%3D&reserved=0</a>><br class="">
<br class="">
Also you may not want to show the ligand and ions except when the morph is at or near the same conformation as that structure. This can be scripted with ChimeraX commands. The “coordset” command can play any part of the morph trajectory, and then you can
use “show" and “hide" between different coordset commands to turn ligand and ions on/off at the points where you wish.<br class="">
<<a href="https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoordset.html&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=PlqQVz8BcW3zczmY5gMvYkTHrGcKzmjtDjMBW11aIao%3D&reserved=0" class="">https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoordset.html&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=PlqQVz8BcW3zczmY5gMvYkTHrGcKzmjtDjMBW11aIao%3D&reserved=0</a>><br class="">
<br class="">
See for example the ChimeraX “feature highlight” with a morphing movie. It includes the command scripts that were used. You can do all kinds of things like put on fancy labels, rotate the structure, etc. as shown in the movie.<br class="">
<<a href="https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ffeatures.html%23morphing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=mig4bSqMCI0ttHFZjRhy4RnAlSK9qiKStxlEVKz%2BSHk%3D&reserved=0" class="">https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ffeatures.html%23morphing&data=02%7C01%7Cyifan.wang%40utsa.edu%7C545f040208ff409f790308d7990d583a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C0%7C637146154920911505&sdata=mig4bSqMCI0ttHFZjRhy4RnAlSK9qiKStxlEVKz%2BSHk%3D&reserved=0</a>><br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
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="">
<br class="">
<blockquote type="cite" class="">On Jan 13, 2020, at 12:16 PM, Yifan Wang <<a href="mailto:yifan.wang@utsa.edu" class="">yifan.wang@utsa.edu</a>> wrote:<br class="">
<br class="">
Dear chimeraX developer,<br class="">
<br class="">
I am a graduate student from university of Texas at San Antonio. I’m trying to make a movie to compare two of my structures (resting state and substrate bound) using the function “morph”. But there is a problem, I very appreciate if you can help me figure this
out.<br class="">
<br class="">
As show in Figure 1, I have two structures superposed. The resting state (nude) contains an active site metal ion coordinated by three residues and 3 water molecules. And the substrate bound (blue) also contains a metal coordinated by the same residues, a remaining
water molecule, and a new ligand as my substrate.<br class="">
<br class="">
After I entered command “morph #1,2 frames 60”, I got the result of Figure 2. However, the active site metal ion and the water and substrate are missing. I want to show the active site changes between model 1 and 2. Model #3.1 seems keep the metal coordination
bonds but I can’t make it present even with “show”. So my question is how to show the metal and the corresponding ligands in morph?<br class="">
<br class="">
<br class="">
Regards,<br class="">
Yifan Wang</blockquote>
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