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Hi everyone,
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<div class="">I’ve been struggling with getting the structure surface of my molecule shown (actions surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g.
<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" class="">
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a> ), I can’t get all needed surfaces displayed.</div>
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<div class="">Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes.</div>
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<div class="">A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? </div>
<div class="">Or do the .pdb files have to be in a certain format?</div>
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<div class="">I usually get the following errors:</div>
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<div class="">"Surface calculation failed, mscalc returned code 2.</div>
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<div class="">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. More details are given at</div>
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<div class=""><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" class="">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a>”</div>
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<div class="">My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation).</div>
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<div class="">I'd appreciate any feedback or reply!</div>
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<div class="">Many thanks for your help,</div>
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<div class="">Sarah</div>
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Sarah Piper, PhD student</div>
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University of Queensland, St Lucia, 4072 QLD, Australia</div>
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Phone: +61 7 3346 2325<br class="">
Email: <a href="mailto:sarah.piper@uq.edu.au" class="">sarah.piper@uq.edu.au</a><br class="">
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