<html>
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<p>Works for me :-)</p>
<p>I just tried the headless version of Chimera on CentOS 7.5. I
didn't use a script, but did the following commands:</p>
open 6c7m<br>
windowsize 512 512<br>
surf<br>
copy file test.png<br>
stop<br>
<br>
And it created the image file and exited without a problem.<br>
<br>
So it is unclear what the problem is. You'll need to run gdb to
find out where the segmentation fault occured. Create a debugging
version of the chimera program script, and change the 'exec $python'
at the end to 'gdb $python', run it, and then in gdb, 'run
$CHIMERA/share/__main__.py chimera_surface.py'. When chimera
segmentation faults, type 'bt' to get a backtrace and send it to me.<br>
<p>FYI, the headless version of Chimera comes with libOSMesa, so you
don't need to install it. But it shouldn't cause problems if you
did. The libOSMesa distributed with chimera is ancient, version
7.6.1. So, if the backtrace shows that the bug is in libOSMesa,
there's a good chance that if you replace chimera's libOSMesa.so
with the system version, it will work.</p>
<p> Good luck,</p>
<p> Greg<br>
</p>
<br>
<div class="moz-cite-prefix">On 08/01/2018 03:57 AM, Zhe Wang wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAPucnripan8qtrVvmW3HG6srS-HfuxTLcxzxs=vYNixA3deCBg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I am trying to using headless Chimera on RedHat linux
server 7.3 to produce some images. </div>
<div>But I end up with a segmentation fault. Does anyone have an
idea how it comes to this?</div>
<div>The headless chimera is from <a
href="https://www.cgl.ucsf.edu/chimera/download.html"
target="_blank" moz-do-not-send="true">https://www.cgl.ucsf.edu/chimera/download.html</a>
(64-bit daily build).</div>
<div>The test code was taken without changes from <a
href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html"
target="_blank" moz-do-not-send="true">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>.</div>
<div>Any ideas will be appreciated.</div>
<div><br>
</div>
<div>Best, </div>
<div>Zhe</div>
<div><br>
</div>
<div>PS: OSMesa 11.2.2 has been installed. </div>
<div><br>
</div>
<div><br>
</div>
<div>
<span></span>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Executing
chimera_surface.py...</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Processing
6c7m.pdb</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Opening
6c7m.pdb...</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">#0,
chain A: kemp eliminase KE07</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">6c7m.pdb
opened</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Center
of rotation: 0.867528 -1.77985 11.157</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 2.000000 1</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">MSMSLIB
1.3 started on <a href="http://ebi-cli-002.ebi.ac.uk"
target="_blank" moz-do-not-send="true">ebi-cli-002.ebi.ac.uk</a></span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span
class="m_-6911996100271192826gmail-Apple-converted-space"> </span></span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main, probe radius 1.4, vertex density
2</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>12 connected surface components</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent excluded surface area = 10612</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>component areas = 10035.4, 126.971, 97.9893,
90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681,
30.3253, 29.9037, 25.222</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent accessible surface area = 11324.6</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>component areas = 11265.5, 25.8506, 19.8737,
10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644,
0.177358, 0.178001, 0.00214196</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main has 12 components</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 10.000000 1</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">MSMSLIB
1.3 started on <a href="http://ebi-cli-002.ebi.ac.uk"
target="_blank" moz-do-not-send="true">ebi-cli-002.ebi.ac.uk</a></span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span
class="m_-6911996100271192826gmail-Apple-converted-space"> </span></span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">RESTART
FROM TRI: 1</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 5 goes from 1.880000 to 1.980000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 6 goes from 1.880000 to 1.980000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 1569 goes from 1.420000 to 1.520000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Partial
mode</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 10.000000 0</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">MSMSLIB
1.3 started on <a href="http://ebi-cli-002.ebi.ac.uk"
target="_blank" moz-do-not-send="true">ebi-cli-002.ebi.ac.uk</a></span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span
class="m_-6911996100271192826gmail-Apple-converted-space"> </span></span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">RESTART
FROM TRI: 1</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 5 goes from 1.880000 to 1.980000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 6 goes from 1.880000 to 1.980000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">radius
of atom 1569 goes from 1.420000 to 1.520000</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Partial
mode</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Calculation
of some surface components failed.</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">A
single component of the surface was calculated correctly -
the failure occurred for disconnected<span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>additional components such as inside bubbles.<span
class="m_-6911996100271192826gmail-Apple-converted-space"> </span>If
the desired surface is already shown, there is no need for
concern.<span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>However, if it is not shown, see below for possible
fixes.</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">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.<span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>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</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><a
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html"
target="_blank" moz-do-not-send="true">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a></span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main, probe radius 1.4, vertex density
10</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>1 connected surface components</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent excluded surface area = 10036.7</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><span
class="m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent accessible surface area = 11266.5</span></p>
<p class="m_-6911996100271192826gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9);min-height:17px"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main has 1 components</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Rendering
high resolution image...</span></p>
<p class="m_-6911996100271192826gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-family:Monaco;color:rgb(250,255,253);background-color:rgba(0,0,0,0.9)"><span
class="m_-6911996100271192826gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Segmentation
fault</span></p>
<br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
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