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<div class="moz-cite-prefix">Hi Anton,<br>
<br>
The molecular surface calculation (Actions / Surface / show)
fails much more often with 64-bit Windows Chimera. The 32-bit
Windows Chimera fails less often, and Linux and Mac versions fail
in even fewer cases. Maybe Chimera 1.5 worked for you because it
was 32-bit.<br>
<br>
Eric's trick of using the Multiscale dialog with resolution 0
computes the molecular surface for each chain separately. It
should give the same result as splitting the molecule into chains
with the "split" command and then surfacing.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] surface calculation<br>
From: Eric Pettersen <br>
To: Anton Vila Sanjurjo <br>
Date: 11/29/12 11:14 AM<br>
</div>
<blockquote
cite="mid:C7A752C0-DCBB-40E4-8ED8-92CAC1A73B9E@cgl.ucsf.edu"
type="cite">Hi Anton,
<div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm
not certain why you don't want to split the chains, but it is
possible to get Chimera to compute the per-chain surfaces
without splitting the model. The simplest way is to use the
Multiscale Models tool (in the Higher-Order Structure category).
With that dialog up, click its "Make models" button. Then in
the "Select chains" section at the top, click the "All" button.
Then in the "Resolution" entry field near the center of the
dialog type "0" (zero) and then click the "Resurface" button
near that field. You will get some complaints about
multiple-component surfaces failing, but since all the
single-component surfaces work the entire structure will be
surfaced.</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
</div>
<div>
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<div>
<div>On Nov 29, 2012, at 3:00 AM, Anton Vila Sanjurjo wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi,<br>
<br>
I have seen posts regarding this problem before. Here is the
log I got after attempting to render a surface
representation of the 50S ribosomal subunit (rcsb ID: 3CPW).
<br>
<br>
#0, chain 0: 23S ribosomal rna<br>
#0, chain 1: L35E<br>
#0, chain 2: 50S ribosomal protein L44E<br>
#0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3'<br>
#0, chain 9: 5S ribosomal rna<br>
#0, chain A: 50S ribosomal protein L2P<br>
#0, chain B: 50S ribosomal protein L3P<br>
#0, chain C: 50S ribosomal protein L4P<br>
#0, chain D: 50S ribosomal protein L5P<br>
#0, chain E: 50S ribosomal protein L6P<br>
#0, chain F: 50S ribosomal protein L7AE<br>
#0, chain G: HS6<br>
#0, chain H: 50S ribosomal protein L10E<br>
#0, chain I: 50S ribosomal protein L13P<br>
#0, chain J: HMAL13<br>
#0, chain K: 50S ribosomal protein L15P<br>
#0, chain L: 50S ribosomal protein L15E<br>
#0, chain M: 50S ribosomal protein LC12<br>
#0, chain N: 50S ribosomal protein L18E<br>
#0, chain O: 50S ribosomal protein L19E<br>
#0, chain P: 50S ribosomal protein L21E<br>
#0, chain Q: HL31<br>
#0, chain R: 50S ribosomal protein L23P<br>
#0, chain S: 50S ribosomal protein L24P<br>
#0, chain T: 50S ribosomal protein L24E<br>
#0, chain U: HL21/HL22<br>
#0, chain V: 50S ribosomal protein L30P<br>
#0, chain W: 50S ribosomal protein L31E<br>
#0, chain X: 50S ribosomal protein L32E<br>
#0, chain Y: HL5<br>
#0, chain Z: 50S ribosomal protein L37E<br>
C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000
2.000000 1<br>
MSMSLIB 1.3 started on Local PC<br>
Copyright M.F. Sanner (March 2000)<br>
Compilation flags <br>
C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000
2.000000 0<br>
MSMSLIB 1.3 started on Local PC<br>
Copyright M.F. Sanner (March 2000)<br>
Compilation flags <br>
Surface calculation failed, mscalc returned code 5.<br>
<br>
Surface calculation frequently fails for large, multi-chain
structures. The calculation may be successful if the chains
are treated individually, by using the "split" command
before generating a surface. If splitting is not desired or
the structure is already a single chain, changing molecular
surface parameters in the Selection Inspector or (before
surface creation) the New Surfaces category of Preferences
may allow the calculation to succeed.<br>
<br>
C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000
2.000000 1<br>
MSMSLIB 1.3 started on Local PC<br>
Copyright M.F. Sanner (March 2000)<br>
Compilation flags <br>
<br>
Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex
density 2<br>
1 connected surface components<br>
Total solvent excluded surface area = 989.35<br>
Total solvent accessible surface area = 1473.85<br>
<br>
In this case, I am not interested in splitting the file into
its individual chains. I have also unsuccessfully played
with the probe-radius and vertex parameters. I should
mention that I was able to get this to work with previous
versions of Chimera (1.5.something) and that small proteins
can be successfully rendered with the latest versions. <br>
<br>
best,<br>
<br>
Antón</blockquote>
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