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<div>Hi Elaine,</div>
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<div>I did not want to use a surface as with individual pockets ( I have three) I have more control how I want to clip them. I also find such figures less complicated. My mistake was that I removed internal fake atoms from my pocket file so the surface was
generated on both sides of the atoms. Consequently, without capping I¡¯m getting two skins. The reason for the removal of these atoms is their number (up to 43000 per pocket) which I thought was the reason for program hanging. But that was happening with the
surface command. With molmap it seems to be fine. </div>
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<div>Thanks,</div>
<div>Karolina</div>
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<span style="font-weight:bold">From: </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, August 2, 2016 at 5:07 PM<br>
<span style="font-weight:bold">To: </span>"Michalska, Karolina M." <<a href="mailto:kmichalska@anl.gov">kmichalska@anl.gov</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Chimera-users] precalculated void representation as surface<br>
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Hi Karolina,
<div>If I understand correctly, you just want to show the ¡°skin¡± of the pocket but then also what is on the inside. In that case, do you really need the void-volume atoms? Why not just show the surface of the protein and slice that surface with the clipping
plane? See first attached image.</div>
<div><br>
</div>
<div>However, if the protein is completely hidden and you just want the skin of the pocket, a second idea is to keep all the void-volume atoms for calculating the isosurface, but then also hide those fake atoms. When you slice the molmap isosurface, by default
it looks solid because there is a ¡°cap¡±. With Surface Capping (in menu under Tools¡¦ Depiction) you can just turn off the cap so that you just see the sliced skin of the pocket, and real atoms inside (if any). See second attached image.</div>
<div><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html</a>></div>
<div><br>
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<div>In both cases, if you use a per-model clipping plane instead of the main (global) clipping planes, you can slice at any angle and only the surface, so atoms can stick out beyond the clipping plane. Per-Model Clipping is in the menu under Tools¡¦ Depiction.</div>
<div><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html</a>></div>
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<div>I hope this helps,</div>
<div>Elaine<br>
<div>-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<img height="397" width="510" apple-width="yes" apple-height="yes" apple-inline="yes" id="9EC4A2D2-C385-4895-9275-0EC2CAC22013" src="cid:4CAA29BF-20BA-4535-B454-83FE044395DA@gateway.sonic.net"></div>
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<div><img height="397" width="510" apple-width="yes" apple-height="yes" apple-inline="yes" id="0D9F2EC4-45FC-47EE-B8F8-5FD78E5B088E" src="cid:1400A970-09CA-4B92-BB12-9ECA27B9A149@gateway.sonic.net"></div>
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On Aug 2, 2016, at 2:35 PM, Michalska, Karolina M. <<a href="mailto:kmichalska@anl.gov">kmichalska@anl.gov</a>> wrote:<br>
<br>
<blockquote type="cite">Hello,<br>
<br>
I have one more question related to the subject. I have currently removed<br>
all internal ©øatoms©÷ that describe my cavity, leaving only those on the<br>
surface as I want to illustrate the interior with the clipping. However,<br>
with that my surface has a certain thickness at the clipping plane. Is<br>
there a way I could control it?<br>
<br>
Thanks,<br>
Karolina<br>
<br>
<br>
<br>
On 7/27/16, 5:32 PM, "Elaine Meng" <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br>
<br>
<blockquote type="cite">Hi Karolina,<br>
It is very difficult to answer questions like this without having the<br>
input file or a more complete description of what you mean by ©øcannot©÷<br>
(looks bad? error message? if error message, what does it say??) So I<br>
can only make guesses.<br>
<br>
Maybe it is hard to specify the atoms... at least in my attempt to<br>
simulate the problem, even though the model was open as #1, command<br>
©øsurface #1©÷ didn©öt work and I had to use this command instead:<br>
<br>
surface #1@*<br>
<br>
(without any space between the model number and @*)<br>
<br>
If that fails to give a surface, another possibility is simulating a<br>
density map with ©ømolmap©÷ and then adjusting the isosurface of that<br>
density map, for example if you opened the fake PDB file as #3, a command<br>
something like:<br>
<br>
molmap #3@* 1.0<br>
<br>
Then you will get the Volume Viewer dialog with a histogram and slider<br>
you can drag to adjust the isosurface level. The second number in the<br>
example command is an adjustable parameter and I do not know what value<br>
will work well with your file. You should try different numbers and also<br>
take a look at what other options are available with molmap.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
On Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <<a href="mailto:kmichalska@anl.gov">kmichalska@anl.gov</a>><br>
wrote:<br>
<br>
<blockquote type="cite">Hi,<br>
<br>
I have a precalculated cavity represented as a grid in the pdb format,<br>
where ©øatoms©÷ are spaced by 0.3 A. What would be the option to visualize<br>
this as a surface? I can easily show it as point or spheres, but I<br>
cannot display it as surface.<br>
<br>
I appreciate your help,<br>
Karolina<br>
</blockquote>
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</blockquote>
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