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<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>Elaine and Eric </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>Thanks very much for such a quick response.
</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>To Elaine, the version I was using should be pretty recent.
I downloaded about a month ago.</FONT></SPAN></DIV>
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color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>To Eric, you suggestion to split/surf worked out
beautifully. I haven't done anything with these surfaces yet, but I
will let you know if I encounter any new problems.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>Cheers!</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=032380901-06032009><FONT face=Arial
color=#0000ff size=2>Sean</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> Eric Pettersen [mailto:pett@cgl.ucsf.edu]
<BR><B>Sent:</B> Thursday, March 05, 2009 4:51 PM<BR><B>To:</B> Du,
Sean<BR><B>Cc:</B> chimera-users@cgl.ucsf.edu BB<BR><B>Subject:</B> Re:
[Chimera-users] (no subject)<BR></FONT><BR></DIV>
<DIV></DIV>Hi Sean,
<DIV><SPAN class=Apple-tab-span style="WHITE-SPACE: pre"></SPAN>I find that
these structures surface on my Mac, but do fail on the Windows machine I tried.
There is a workaround I recently found that isn't mentioned in the
messages Elaine listed and that is to split the model into separate models on a
per-chain basis and then surface those models. This works for both the
structures your mentioned, but of course might be awkward to work with depending
on what you intend to do after surfacing. Anyway, to do the
splitting/surfacing open the command line (Favorites->Command Line) and
type:</DIV>
<DIV><BR></DIV>
<DIV><SPAN class=Apple-tab-span style="WHITE-SPACE: pre"></SPAN>split</DIV>
<DIV><SPAN class=Apple-tab-span style="WHITE-SPACE: pre"></SPAN>surf</DIV>
<DIV><BR></DIV>
<DIV><SPAN class=Apple-tab-span style="WHITE-SPACE: pre"></SPAN>We intend to
replace our current surfacing library (MSMS) with our own custom library in our
next release, but that won't be until the middle of this year.</DIV>
<DIV><BR></DIV>
<DIV>--Eric<BR>
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size=5><SPAN class=Apple-converted-space>
<SPAN
class=Apple-converted-space> </SPAN></SPAN>Eric Pettersen</FONT></P>
<P style="MARGIN: 0px"><FONT style="FONT: 16px Helvetica" face=Helvetica
size=5><SPAN class=Apple-converted-space>
<SPAN
class=Apple-converted-space> </SPAN></SPAN>UCSF Computer Graphics
Lab</FONT></P>
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size=5><SPAN class=Apple-converted-space>
</SPAN><A
href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P><BR
class=Apple-interchange-newline></DIV></SPAN></DIV><BR>
<DIV>
<DIV>On Mar 5, 2009, at 4:34 PM, Elaine Meng wrote:</DIV><BR
class=Apple-interchange-newline>
<BLOCKQUOTE type="cite">
<DIV>Dear Sean,<BR>Unfortunately it is a very common problem relating to
numerical <BR>failure of the MSMS code on certain structures, and is
listed in our <BR>known bugs. We have been working on our own code
to replace MSMS, but <BR>it is not available yet. There are many
possible things to try to <BR>avoid the problem, but it is very
trial-and-error and different for <BR>each structure.<BR><BR>It is
helpful when reporting a problem to say what version of Chimera <BR>you
are using, since there have been some improvements throughout time
<BR>(although not eliminating the problem completely). It might
help to <BR>get a newer version of Chimera, or it might
not.<BR><BR>Please see these previous posts for more information and
workaround <BR>suggestions:<BR><BR><<A
href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html</A>
<BR>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE><<A
href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html</A>><BR><<A
href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/</A>
<BR>002954.html><BR><BR>I hope this helps,<BR>Elaine<BR>-----<BR>Elaine C.
Meng, Ph.D.
<A
href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</A><BR>UCSF Computer
Graphics Lab (Chimera team) and Babbitt Lab<BR>Department of Pharmaceutical
Chemistry<BR>University of California, San
Francisco<BR> <A
href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A><BR><BR><BR><BR>On
Mar 5, 2009, at 2:08 PM, Du, Sean wrote:<BR><BR>
<BLOCKQUOTE type="cite">Dear Chimera developers and sophisticated
users,<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">I have trouble to show the surfaces of serveral
crystal structures, <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">including 1rzk and 2b4c. Whenever I select:
Action/Surface/Show, I <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">would get pop-up error window and the following
message in my Reply <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Log:<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">C:\Program Files\Chimera\bin\mscalc.exe 1.400000
2.000000 0<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Surface calculation failed, mscalc returned code
5<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">C:\Program Files\Chimera\bin\mscalc.exe 1.400000
2.000000 0<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Surface calculation failed, mscalc returned code
5<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Since I don't have problem with other pdb files,
such as 3dnn, I <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">wonder if this problem is simply associated with
some particular pdb <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">files? If anyone out there knows a few tricks to
overcome this, I'd <BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">really appreciate it.<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Many thanks in advance,<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite">Sean<BR></BLOCKQUOTE>
<BLOCKQUOTE type="cite"><BR></BLOCKQUOTE>
<BLOCKQUOTE
type="cite"><BR></BLOCKQUOTE>_______________________________________________<BR>Chimera-users
mailing list<BR><A
href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A><BR>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<BR></DIV></BLOCKQUOTE></DIV><BR></DIV></DIV>
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