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Hi Natalie,<br>
<br>
It is unfortunately a bit tricky to show just the inner pocket
surface of a molecule in Chimera. Here's one way. Create the surface
then use the following command to make it possible to select the
separate connected pieces of the surface:<br>
<br>
ac Sc<br>
<br>
(This runs the keyboard shortcut "Sc" - split connected pieces of
selected surface.) Now select the outer surface with the mouse
(ctrl-click) and use a command to delete it:<br>
<br>
ac Ds<br>
<br>
(Keyboard shortcut "Ds" - delete selected surface pieces.)<br>
<br>
These steps that change the molecular confuse Chimera and the Actions
/ Surface menu then doesn't work on the inner piece. The problem is
that the molecular surface no longer matches the atomic coordinates in
the way Chimera expects. To get those menu entries to work delete the
atomic model and reload another copy. A drawback of all this is that
it will no longer color the surface to match the atoms.<br>
<br>
Tom<br>
<br>
-------- Original Message --------<br>
Subject: [Chimera-users] Thanks for the help, Is it possible to only
show the "inner surface"?<br>
From: Xarana<br>
To: chimera-users<br>
Date: 9/22/09 2:07 AM<br>
<blockquote cite="mid:FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4"
type="cite">
<pre wrap="">Hi Elaine,
Thank you very much for your quick help. That really helped a lot and the
differences are small. One last question:
Is there a possibility to only show this "inner surface" without the outer
one for more clarity? I have to compare in 10 different structures (NMR
solved) the extent of this cavities. And sadly SYBYL is not able to save as
any other file format.
Best wishes,
Natalie Bordag
PhD student
-----Ursprüngliche Nachricht-----
Von: Elaine Meng
Gesendet: Montag, 21. September 2009 22:28
An: Xarana
Cc: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or
visualisation of an inner surface (of a protein) in Chimera
Hi Natalie,
Chimera does not know the *.sld file type. Can SYBYL save this file
in a format Chimera knows, such as VRML?
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html"><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html></a>
If not, you could try opening the structure (PDB or Mol2 file) in
Chimera, instead of the surface file, and have Chimera calculate the
surface.
In Chimera, you can display the surface with "Actions... Surface...
show". The default in Chimera is also to use a 1.4 Angstrom probe.
That would generate both the inner and outer surfaces, which you could
see by slicing the structure in the Side View (under Favorites menu).
There will probably be differences in the surface due to the different
default atomic radii in Chimera and SYBYL, but I would not expect them
to be large.
I hope this helps,
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Sep 21, 2009, at 10:34 AM, Xarana wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
My interest is a 4 helix protein which has a cavity inside. A
colleague generated with a 1,4 Angström probe this “inner surface”
with Sybyl for me and exported the surface as .sld file. Can I
import this file into chimera somehow? Alternatively, can I generate
such a surface with chimera?
My knowledge of protein visualization is limited and I am very
thankful for any help
Thank you very much in advance.
Best Wishes
Natalie
</pre>
</blockquote>
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</pre>
</blockquote>
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