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That is very nice - particularly is you can make the cap translucent (so you can see what the ligand might be interacting with.
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<div class="">M</div>
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<div class="">On Jul 27, 2020, at 3:15 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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Another thing users might not know is that one can also color the planar surface cap by the MLP, e.g. by saving the lipophilicity map and then using a separate command to recolor the surface including the cap. E.g. adding the following commands to my previous
example:
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<div class="">mlp map true<br class="">
color sample #1.1 map #2 palette lipophilicity range -20,20<br class="">
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This is not to say it would make a better figure... just giving options. :-)</div>
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<div class="">Best,</div>
<div class="">Elaine</div>
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<div class=""><span id="cid:01DEF852-05D4-4328-9014-A41AF413E729@gateway.sonic.net"><mlpclip.png></span><br class="">
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<blockquote type="cite" class="">On Jul 27, 2020, at 12:16 PM, Pufall, Miles A <<a href="mailto:miles-pufall@uiowa.edu" class="">miles-pufall@uiowa.edu</a>> wrote:<br class="">
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Thanks Elaine! I’ll save the full string of commands you sent.<br class="">
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Tom’s guidance helped a lot - the figure came out just how I wanted it.<br class="">
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Thanks again - <br class="">
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M<br class="">
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<blockquote type="cite" class="">On Jul 27, 2020, at 2:14 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
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Hi Miles,<br class="">
In case it's useful, here's a little example that works in the current daily build. This protein has oleic acid (residue name OLA) in a buried pocket. The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond
displays) but leaves it on for the molecular surface model #1.1.<br class="">
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open 1g74<br class="">
surface<br class="">
clip front 0 position :ola<br class="">
clip model #!1 false<br class="">
hide ~:ola target ar<br class="">
style :ola ball<br class="">
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Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only.<br class="">
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Elaine<br class="">
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<blockquote type="cite" class="">On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <<a href="mailto:miles-pufall@uiowa.edu" class="">miles-pufall@uiowa.edu</a>> wrote:<br class="">
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Cool - thanks! Downloading now - will let you know if all is well.<br class="">
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Miles<br class="">
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<blockquote type="cite" class="">On Jul 24, 2020, at 10:32 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class="">
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Hi Miles,<br class="">
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I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes:<br class="">
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clip model #!1 off<br class="">
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The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps<br class="">
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surface cap false<br class="">
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so that the hole left in the clipped surface is not covered by a cap.<br class="">
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Tom<br class="">
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<blockquote type="cite" class="">On Jul 24, 2020, at 11:35 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
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Hi Miles!<br class="">
I remember meeting you at UCSF years ago. I hope you are well.<br class="">
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This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).<br class="">
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I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket.<br class="">
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For now, you would still need to use Chimera for per-model clipping. Sorry about that,<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="">
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<blockquote type="cite" class="">On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <<a href="mailto:miles-pufall@uiowa.edu" class="">miles-pufall@uiowa.edu</a>> wrote:<br class="">
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Hi!<br class="">
I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the
ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that
shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand?<br class="">
Thanks!<br class="">
Miles<br class="">
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<DAC_binding_pocket.png><br class="">
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