[Chimera-users] precalculated void representation as surface

Wed Aug 3 06:32:40 PDT 2016

Hi Elaine,

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.

Thanks,
Karolina

From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Reply-To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Date: Tuesday, August 2, 2016 at 5:07 PM
To: "Michalska, Karolina M." <kmichalska at anl.gov<mailto:kmichalska at anl.gov>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] precalculated void representation as surface

Hi Karolina,
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.

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.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>

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.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

[cid:4CAA29BF-20BA-4535-B454-83FE044395DA at gateway.sonic.net]

[cid:1400A970-09CA-4B92-BB12-9ECA27B9A149 at gateway.sonic.net]

On Aug 2, 2016, at 2:35 PM, Michalska, Karolina M. <kmichalska at anl.gov<mailto:kmichalska at anl.gov>> wrote:

Hello,

I have one more question related to the subject. I have currently removed
all internal ³atoms² that describe my cavity, leaving only those on the
surface as I want to illustrate the interior with the clipping. However,
with that my surface has a certain thickness at the clipping plane. Is
there a way I could control it?

Thanks,
Karolina

On 7/27/16, 5:32 PM, "Elaine Meng" <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Karolina,
It is very difficult to answer questions like this without having the
input file or a more complete description of what you mean by ³cannot²
(looks bad?  error message?  if error message, what does it say??)  So I
can only make guesses.

Maybe it is hard to specify the atoms... at least in my attempt to
simulate the problem, even though the model was open as #1, command
³surface #1² didn¹t work and I had to use this command instead:

surface #1@*

(without any space between the model number and @*)

If that fails to give a surface, another possibility is simulating a
density map with ³molmap² and then adjusting the isosurface of that
density map, for example if you opened the fake PDB file as #3, a command
something like:

molmap #3@* 1.0

Then you will get the Volume Viewer dialog with a histogram and slider
you can drag to adjust the isosurface level.  The second number in the
example command is an adjustable parameter and I do not know what value
will work well with your file.  You should try different numbers and also
take a look at what other options are available with molmap.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska at anl.gov<mailto:kmichalska at anl.gov>>
wrote:

Hi,

I have a precalculated cavity represented as a grid  in the pdb format,
where ³atoms² are spaced by 0.3 A. What would be the option to visualize
this as a surface? I can easily show it as point or spheres, but I
cannot display it as surface.

I appreciate your help,
Karolina

_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160803/c381b783/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: slice1.png
Type: image/png
Size: 81487 bytes
Desc: slice1.png
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160803/c381b783/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: slice2.png
Type: image/png
Size: 24581 bytes
Desc: slice2.png
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160803/c381b783/attachment-0001.png>