<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Zhe,</div><div class=""><br class=""></div>This traceback shows the crash is in the OSMesa graphics rendering library. This is a big complex library that we did not develop and I do not know why it is failing. As Greg mentioned, Chimera includes a very old version of OSMesa and a newer version would have a good chance of fixing this. I don’t know how you could swap in a newer version although Greg might know. As to why “preset apply publication 1” leads to this crash I would bet it is because that preset enables silhouette edges and that the OSMesa bug is hit by the silhouette rendering code. You could try putting in the command “unset silhouette” after the preset and see if that avoids the crash.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 3, 2018, at 3:48 AM, Zhe Wang wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Tom and Greg, <div class=""><br class=""></div><div class="">Thank you very much for your help. </div><div class="">It works now. I tried out the lines you have shown. It did work. I can produce the image I need.</div><div class=""><div style="font-size:small;text-decoration-style:initial;text-decoration-color:initial" class="">To see what was the problem, I test line by line in this script (<a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>). The problem came from "<code style="" class="">rc("<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/preset.html" class="">preset</a> apply publication 1")</code><span style="" class="">".</span></div></div><div class="">Here I post the debugging backtrace information I got. It seems related to the swrast rendering lib.</div><div class="">Though my problem solved, it will be good to know the reason of this too.</div><div class="">Thank you again for your informative help.</div><div class=""><br class=""></div><div class="">Best, </div><div class="">Zhe</div><div class=""><br class=""></div><div class="">
<span class=""></span><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">(gdb) bt</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#0<span class="gmail-Apple-converted-space"> </span>aa_general_rgba_line (ctx=0x9db160, v0=0x7fffeab809c8, v1=0x7fffeab80bb0) at swrast/s_aalinetemp.h:208</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#1<span class="gmail-Apple-converted-space"> </span>0x00007fffecafd9b9 in _swsetup_edge_render_line_tri (ctx=0x9db160, ef=0x14d4060 '\001' <repeats 50 times>, "@\001", e0=5, e1=6, e2=30, v0=0x7fffeab809c8, v1=0x7fffeab80bb0, v2=0x7fffeab83970) at swrast_setup/ss_triangle.c:80</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#2<span class="gmail-Apple-converted-space"> </span>0x00007fffecaffa7f in _swsetup_render_tri (render=0x7fffecafd8c0 <_swsetup_edge_render_line_tri>, facing=1, e2=30, e1=6, e0=5, ctx=0x9db160) at swrast_setup/ss_triangle.c:165</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#3<span class="gmail-Apple-converted-space"> </span>triangle_twoside_unfilled_rgba (ctx=0x9db160, e0=5, e1=6, e2=30) at swrast_setup/ss_tritmp.h:181</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#4<span class="gmail-Apple-converted-space"> </span>0x00007fffeca82feb in _tnl_render_triangles_elts (ctx=0x9db160, start=0, count=150, flags=<optimized out>) at tnl/t_vb_rendertmp.h:175</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#5<span class="gmail-Apple-converted-space"> </span>0x00007fffeca83f65 in run_render (ctx=0x9db160, stage=<optimized out>) at tnl/t_vb_render.c:320</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#6<span class="gmail-Apple-converted-space"> </span>0x00007fffeca78ccd in _tnl_run_pipeline (ctx=0x9db160) at tnl/t_pipeline.c:158</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#7<span class="gmail-Apple-converted-space"> </span>0x00007fffeca7ae0c in _tnl_draw_prims (ctx=ctx@entry=0x9db160, arrays=arrays@entry=0xa2ab20, prim=prim@entry=0x7fffffffb5d0, nr_prims=nr_prims@entry=1, ib=ib@entry=0x7fffffffb5e0, min_index=<optimized out>, max_index=49) at tnl/t_draw.c:445</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#8<span class="gmail-Apple-converted-space"> </span>0x00007fffeca7b125 in _tnl_vbo_draw_prims (ctx=0x9db160, arrays=0xa2ab20, prim=0x7fffffffb5d0, nr_prims=1, ib=0x7fffffffb5e0, index_bounds_valid=<optimized out>, min_index=0, max_index=49) at tnl/t_draw.c:375</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#9<span class="gmail-Apple-converted-space"> </span>0x00007fffeca6da4e in vbo_validated_drawrangeelements (indices=0x0, type=5125, count=150, end=4294967295, start=4294967295, index_bounds_valid=0 '\000', mode=4, ctx=0x9db160) at vbo/vbo_exec_array.c:661</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#10 vbo_exec_DrawElements (mode=4, count=150, type=5125, indices=0x0) at vbo/vbo_exec_array.c:755</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#11 0x00007fffeb8221d9 in molecule::ObjectInstances::drawPushMatrix(chimera::LensViewer const*, molecule::ObjectInstances::DrawType) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#12 0x00007fffeb822253 in molecule::ObjectInstances::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#13 0x00007fffeb823f84 in molecule::Shapes::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#14 0x00007fffeb84fb76 in molecule::MoleculeLensModel::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#15 0x00007fffee09e3f9 in chimera::LensModel::xformDraw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#16 0x00007fffee09a8f4 in chimera::Lens::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#17 0x00007fffee0a6e09 in chimera::LensViewer::drawSilhouette(chimera::Array<int, 4ul> const&, chimera::LensViewer::DrawPass, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#18 0x00007fffee0a8b69 in chimera::LensViewer::drawScreenBoxes(chimera::Array<int, 4ul> const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#19 0x00007fffee0a8e9d in chimera::LensViewer::draw() const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#20 0x00007fffee0ab551 in chimera::LensViewer::pilImages(int, int, char const*, int, bool) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#21 0x00007fffee0dc98c in LensViewer_pilImages () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#22 0x00000000004ad05f in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fffffffc150, func=<optimized out>) at Python/ceval.c:4571</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#23 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc150) at Python/ceval.c:4379</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#24 PyEval_EvalFrameEx (f=f@entry=0x296b7d0, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#25 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x1de02d8, kwcount=10, defs=0x7fffe69c57b8, defcount=19, closure=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#26 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffc390, func=<optimized out>) at Python/ceval.c:4452</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#27 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc390) at Python/ceval.c:4377</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#28 PyEval_EvalFrameEx (f=f@entry=0x1de0090, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#29 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7ffff7f8a068, argcount=<optimized out>, kws=kws@entry=0x7fffe70e7968, kwcount=kwcount@entry=1, defs=defs@entry=0x7fff975f1458, defcount=defcount@entry=11, closure=0x0)</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#30 0x000000000051e205 in function_call (func=0x7fff96df7b90, arg=0x7ffff7f8a050, kw=0x7fffe6d94280) at Objects/funcobject.c:523</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#31 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fff96df7b90, arg=arg@entry=0x7ffff7f8a050, kw=kw@entry=0x7fffe6d94280) at Objects/abstract.c:2547</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#32 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffc6a0, func=0x7fff96df7b90) at Python/ceval.c:4671</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#33 PyEval_EvalFrameEx (f=f@entry=0x1f9acc0, throwflag=throwflag@entry=0) at Python/ceval.c:3033</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#34 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=2, kws=kws@entry=0x16dad00, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#35 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffc8d0, func=<optimized out>) at Python/ceval.c:4452</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#36 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc8d0) at Python/ceval.c:4377</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#37 PyEval_EvalFrameEx (f=f@entry=0x16daae0, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#38 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fffe715bf68, argcount=<optimized out>, kws=kws@entry=0x7ffff7f8a068, kwcount=kwcount@entry=0, defs=defs@entry=0x7fff96dcb2a8, defcount=defcount@entry=1, closure=0x0)</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#39 0x000000000051e205 in function_call (func=0x7fff96b5fed8, arg=0x7fffe715bf50, kw=0x7fffe710fb40) at Objects/funcobject.c:523</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#40 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fff96b5fed8, arg=arg@entry=0x7fffe715bf50, kw=kw@entry=0x7fffe710fb40) at Objects/abstract.c:2547</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#41 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffcbe0, func=0x7fff96b5fed8) at Python/ceval.c:4671</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#42 PyEval_EvalFrameEx (f=f@entry=0x7fffe6d58960, throwflag=throwflag@entry=0) at Python/ceval.c:3033</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#43 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x7fffe70a5560, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#44 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffce10, func=<optimized out>) at Python/ceval.c:4452</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#45 call_function (oparg=<optimized out>, pp_stack=0x7fffffffce10) at Python/ceval.c:4377</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#46 PyEval_EvalFrameEx (f=f@entry=0x7fffe70a53d0, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#47 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co@entry=0x7fffe714d7b0, globals=globals@entry=0x7fffe710f168, locals=locals@entry=0x7fffe710f168, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0,<span class="gmail-Apple-converted-space"> </span></span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>closure=closure@entry=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#48 0x00000000004af4f2 in PyEval_EvalCode (co=co@entry=0x7fffe714d7b0, globals=globals@entry=0x7fffe710f168, locals=locals@entry=0x7fffe710f168) at Python/ceval.c:669</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#49 0x00000000004c41cc in PyImport_ExecCodeModuleEx (name=name@entry=0x7ffff04947fc "chimeraOpenSandbox", co=co@entry=0x7fffe714d7b0, pathname=pathname@entry=0x13a2a40 "test.pyc") at Python/import.c:731</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#50 0x00000000004c452e in load_source_module (name=0x7ffff04947fc "chimeraOpenSandbox", pathname=0x13a2a40 "test.pyc", fp=fp@entry=0x1292be0) at Python/import.c:1121</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#51 0x00000000004c48d7 in imp_load_source (self=<optimized out>, args=<optimized out>) at Python/import.c:3163</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#52 0x00000000004acb39 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffd200) at Python/ceval.c:4357</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#53 PyEval_EvalFrameEx (f=f@entry=0x13b0860, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#54 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fff97626668, argcount=<optimized out>, kws=kws@entry=0x7ffff7f8a068, kwcount=kwcount@entry=0, defs=defs@entry=0x7fffee43a1a8, defcount=defcount@entry=1, closure=0x0)</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#55 0x000000000051e205 in function_call (func=0x7fffee4469b0, arg=0x7fff97626650, kw=0x7fffe71495c8) at Objects/funcobject.c:523</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#56 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fffee4469b0, arg=arg@entry=0x7fff97626650, kw=kw@entry=0x7fffe71495c8) at Objects/abstract.c:2547</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#57 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffd510, func=0x7fffee4469b0) at Python/ceval.c:4671</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#58 PyEval_EvalFrameEx (f=f@entry=0x139e490, throwflag=throwflag@entry=0) at Python/ceval.c:3033</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#59 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=2, kws=kws@entry=0x897058, kwcount=1, defs=0x7fffee436068, defcount=12, closure=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#60 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffd740, func=<optimized out>) at Python/ceval.c:4452</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#61 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd740) at Python/ceval.c:4377</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#62 PyEval_EvalFrameEx (f=f@entry=0x896c20, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#63 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x7ffff7f1fac0, kwcount=0, defs=0x7ffff7ef0f80, defcount=16, closure=0x0) at Python/ceval.c:3589</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#64 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffd980, func=<optimized out>) at Python/ceval.c:4452</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#65 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd980) at Python/ceval.c:4377</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#66 PyEval_EvalFrameEx (f=f@entry=0x7ffff7f1f938, throwflag=throwflag@entry=0) at Python/ceval.c:2994</span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">#67 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co@entry=0x7ffff7f9d230, globals=globals@entry=0x7ffff7f5f168, locals=locals@entry=0x7ffff7f5f168, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0,<span class="gmail-Apple-converted-space"> </span></span></div><div 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, 0.901961);" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">---Type <return> to continue, or q <return> to quit---</span></div>
<br class=""></div><div class=""><br class=""></div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Wed, Aug 1, 2018 at 10:56 PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Works for me :-)</p><p class="">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 class="">
windowsize 512 512<br class="">
surf<br class="">
copy file test.png<br class="">
stop<br class="">
<br class="">
And it created the image file and exited without a problem.<br class="">
<br class="">
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 class=""><p class="">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 class=""> Good luck,</p><p class=""> Greg<br class="">
</p>
<br class="">
<div class="m_8647441965752161163moz-cite-prefix">On 08/01/2018 03:57 AM, Zhe Wang wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class="">Hi,
<div class=""><br class="">
</div>
<div class="">I am trying to using headless Chimera on RedHat linux
server 7.3 to produce some images. </div>
<div class="">But I end up with a segmentation fault. Does anyone have an
idea how it comes to this?</div>
<div class="">The headless chimera is from <a href="https://www.cgl.ucsf.edu/chimera/download.html" target="_blank" class="">https://www.cgl.ucsf.edu/chimera/download.html</a>
(64-bit daily build).</div>
<div class="">The test code was taken without changes from <a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" target="_blank" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>.</div>
<div class="">Any ideas will be appreciated.</div>
<div class=""><br class="">
</div>
<div class="">Best, </div>
<div class="">Zhe</div>
<div class=""><br class="">
</div>
<div class="">PS: OSMesa 11.2.2 has been installed. </div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<span class=""></span><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Executing
chimera_surface.py...</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Processing
6c7m.pdb</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Opening
6c7m.pdb...</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">#0,
chain A: kemp eliminase KE07</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">6c7m.pdb
opened</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Center
of rotation: 0.867528 -1.77985 11.157</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 2.000000 1</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-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" class="">ebi-cli-002.ebi.ac.uk</a></span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space"> </span></span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main, probe radius 1.4, vertex density
2</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>12 connected surface components</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent excluded surface area = 10612</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-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></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent accessible surface area = 11324.6</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-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></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main has 12 components</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 10.000000 1</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-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" class="">ebi-cli-002.ebi.ac.uk</a></span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space"> </span></span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">RESTART
FROM TRI: 1</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 5 goes from 1.880000 to 1.980000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 6 goes from 1.880000 to 1.980000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 1569 goes from 1.420000 to 1.520000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Partial
mode</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">/software/chimera_headless/bin/mscalc
1.400000 10.000000 0</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-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" class="">ebi-cli-002.ebi.ac.uk</a></span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Copyright
M.F. Sanner (March 2000)</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Compilation
flags <span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space"> </span></span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">RESTART
FROM TRI: 1</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 5 goes from 1.880000 to 1.980000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 6 goes from 1.880000 to 1.980000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">radius
of atom 1569 goes from 1.420000 to 1.520000</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Partial
mode</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Calculation
of some surface components failed.</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-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_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>additional components such as inside bubbles.<span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space"> </span>If
the desired surface is already shown, there is no need for
concern.<span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>However, if it is not shown, see below for possible
fixes.</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-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_8647441965752161163m_-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></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" target="_blank" class="">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a></span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main, probe radius 1.4, vertex density
10</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>1 connected surface components</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent excluded surface area = 10036.7</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_8647441965752161163m_-6911996100271192826gmail-Apple-converted-space">
</span>Total solvent accessible surface area = 11266.5</span></div><div 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, 0.901961); min-height: 17px;" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br class="">
</div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Surface
6c7m.pdb, category main has 1 components</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Rendering
high resolution image...</span></div><div 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, 0.901961);" class=""><span class="m_8647441965752161163m_-6911996100271192826gmail-s1" style="font-variant-ligatures:no-common-ligatures">Segmentation
fault</span></div>
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</pre>
</blockquote>
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</div>
</blockquote></div></div>
_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>