Re: [PyMOL] caver plugin
Hi Yeping, unfortunately, the caver plugin doesn't take a selection expression, but only selection names. Regarding your selection expression, you miss the "name" operator. So this should work: PyMOL> select startsele, chain A and resid 21 and name CA In Caver: "Specify selection: startsele" Hope that helps. Cheers, Thomas sunyep...@aliyun.com wrote, On 07/23/13 02:31: > Dear pymol users, > > Does anyone use the caver plugin of pymol to analyze a ion channel? I > don't know how to specify selection for the starting of plugin. Should > the starting point be at the center of the channel where there is empty > and no atoms in the molecule? or should it be certain atom of the > molecule? If it should be the latter, what is the correct syntax of the > selection? For example, if I want to select CA atom of Try21 in chain A, > should I input the following command? > > chain A and resid 21 and CA > > But this is wrong and does not work. > > Could someone give me some tutorial? Thanks. > > Yeping Sun -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Residue numeration problem
Hi Gianluigi, I can only reproduce your problem with retain_order=1, not with retain_order=0 (which is the default). Could it be that in your pymolrc, you do "set retain_order, 1"? I don't think there is a difference between 1.6 and previous versions. Cheers, Thomas Gianluigi Caltabiano wrote, On 07/23/13 09:48: > Hi all, > > Since 1.6.0.0 on my Mac (OSX 10.8.4) I am experiencing an annoying > behaviour both when creating a new object from two existing and when > mutating a residue via mutagenesis wizard (both with Macpymol and X11) > > Creating a new object from two existing, mess up the two (different) chains. > set retain_order, 1 does not change this behaviour. > > As for the new object creating try to reproduce this: > > fetch 4DAJ > create MA, 4DAJ and chain A > create MB, MA > alter MB, chain='B' > create dim, MA MB > > > The new object is not ordered on a chain basis, but on residue number. > > Something very similar happens using mutagenesis wizard, in that case it > mess the new residue with the first residue. In this cases closing PyMol > and reopening (or chainging to Hybrid) often, but not always, works. > Still is a pain in the back. > > Any clues? > > cheers, > > Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Residue numeration problem
Hi Gianluigi, PyMOL might find more pymolrc files than you are aware of. Just to be sure, try this to get a hint: PyMOL> print invocation.options.deferred Also, check which plugins are installed and eventually disable them. Cheers, Thomas Gianluigi Caltabiano wrote, On 07/23/13 10:44: > Hi Thomas, > > thank you for answering so fast. > > I do not have set retain_order, 1 in my pymolrc, but you are right, if I > set retain_order, 0 the problem disappears. It is strange because I do > not generally use retain_order, but still I might have used it and for > some reason it have been kept by pymol. > > cheers, > > Gianluigi > > > Da: Thomas Holder > A: Gianluigi Caltabiano > Cc: pymol-users > Inviato: Martedì 23 Luglio 2013 9:27 > Oggetto: Re: Residue numeration problem > > Hi Gianluigi, > > I can only reproduce your problem with retain_order=1, not with > retain_order=0 (which is the default). Could it be that in your pymolrc, > you do "set retain_order, 1"? > > I don't think there is a difference between 1.6 and previous versions. > > Cheers, > Thomas > > Gianluigi Caltabiano wrote, On 07/23/13 09:48: >> Hi all, >> >> Since 1.6.0.0 on my Mac (OSX 10.8.4) I am experiencing an annoying >> behaviour both when creating a new object from two existing and when >> mutating a residue via mutagenesis wizard (both with Macpymol and X11) >> >> Creating a new object from two existing, mess up the two (different) > chains. >> set retain_order, 1 does not change this behaviour. >> >> As for the new object creating try to reproduce this: >> >> fetch 4DAJ >> create MA, 4DAJ and chain A >> create MB, MA >> alter MB, chain='B' >> create dim, MA MB >> >> >> The new object is not ordered on a chain basis, but on residue number. >> >> Something very similar happens using mutagenesis wizard, in that case it >> mess the new residue with the first residue. In this cases closing PyMol >> and reopening (or chainging to Hybrid) often, but not always, works. >> Still is a pain in the back. >> >> Any clues? >> >> cheers, >> >> Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] pymol fails to compile
Dear all, I'm installing PyMOL from svn on a RHEL 6.2 machine. This has always worked. Today, I get an "command 'gcc' failed with exit status 1" error (see below). Any suggestions? Is there something amiss with the source? Thanks. Andreas gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer3/Executive.c -o build/temp.linux-x86_64-2.6/layer3/Executive.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectMap.c:42:32: error: numpy/ndarraytypes.h: No such file or directory layer2/ObjectMap.c:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘MyArrayObject’ layer2/ObjectMap.c: In function ‘ObjectMapNumPyArrayToMapState’: layer2/ObjectMap.c:: error: ‘MyArrayObject’ undeclared (first use in this function) layer2/ObjectMap.c:: error: (Each undeclared identifier is reported only once layer2/ObjectMap.c:: error: for each function it appears in.) layer2/ObjectMap.c:: error: ‘pao’ undeclared (first use in this function) layer2/ObjectMap.c:5559: error: expected expression before ‘)’ token error: command 'gcc' failed with exit status 1 gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer4/Export.c -o build/temp.linux-x86_64-2.6/layer4/Export.o -ffast-math -funroll-loops -O3 -fcommon csbadmin@csb6 in pymol-src: layer2/RepSurface.c: In function ‘SurfaceJobRun’: layer2/RepSurface.c:4506: warning: ‘solv_map’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGOOptimizeGLSLCylindersToVBOIndexedImpl’: layer1/CGO.c:4344: warning: ‘org_colorVals’ may be used uninitialized in this function layer1/CGO.c:4337: warning: ‘col2[1]’ may be used uninitialized in this function layer1/CGO.c:4337: warning: ‘col2[2]’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGOProcessCGOtoArrays’: layer1/CGO.c:2815: warning: ‘normalValsDA’ may be used uninitialized in this function layer1/CGO.c:2815: warning: ‘accessibilityValsDA’ may be used uninitialized in this function layer1/CGO.c:2816: warning: ‘pickColorValsDA’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGORenderGL’: layer1/CGO.c:7954: warning: ‘normalVals_tmp’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGOOptimizeToVBONotIndexedWithReturnedData’: layer1/CGO.c:3371: warning: ‘normalValsDA’ may be used uninitialized in this function layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGORenderRay’: layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGOSimplify’: layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in this function -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___
[PyMOL] pymol fails to compile
Dear all, following up on my previous post, pymol-v1.6.0.0.tar.bz2 from http://sourceforge.net/projects/pymol/ compiles just fine on my machine. It's the most recent source from svn that doesn't. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol fails to compile
Hi Andreas, I recently made a small change regarding numpy support. Can you please send me the output of the following command: ls /usr/lib64/python2.6/site-packages/numpy/core/include/numpy Meanwhile, just disable numpy support by removing the try/except block in setup.py line 221. Thanks, Thomas Andreas Förster wrote, On 07/23/13 11:05: > Dear all, > > I'm installing PyMOL from svn on a RHEL 6.2 machine. This has always > worked. Today, I get an "command 'gcc' failed with exit status 1" error > (see below). > > Any suggestions? Is there something amiss with the source? > > Thanks. > > Andreas > > gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG > -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS > -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS > -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 > -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src > -Imodules/cealign/src/tnt -Ibuild/generated > -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src > -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include > -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer3/Executive.c > -o build/temp.linux-x86_64-2.6/layer3/Executive.o -ffast-math > -funroll-loops -O3 -fcommon > layer2/ObjectMap.c:42:32: error: numpy/ndarraytypes.h: No such file or > directory > layer2/ObjectMap.c:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or > ‘__attribute__’ before ‘MyArrayObject’ > layer2/ObjectMap.c: In function ‘ObjectMapNumPyArrayToMapState’: > layer2/ObjectMap.c:: error: ‘MyArrayObject’ undeclared (first use in > this function) > layer2/ObjectMap.c:: error: (Each undeclared identifier is reported > only once > layer2/ObjectMap.c:: error: for each function it appears in.) > layer2/ObjectMap.c:: error: ‘pao’ undeclared (first use in this > function) > layer2/ObjectMap.c:5559: error: expected expression before ‘)’ token > error: command 'gcc' failed with exit status 1 > gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG > -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS > -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS > -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 > -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src > -Imodules/cealign/src/tnt -Ibuild/generated > -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src > -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include > -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer4/Export.c -o > build/temp.linux-x86_64-2.6/layer4/Export.o -ffast-math -funroll-loops > -O3 -fcommon > csbadmin@csb6 in pymol-src: layer2/RepSurface.c: In function > ‘SurfaceJobRun’: > layer2/RepSurface.c:4506: warning: ‘solv_map’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGOOptimizeGLSLCylindersToVBOIndexedImpl’: > layer1/CGO.c:4344: warning: ‘org_colorVals’ may be used uninitialized in > this function > layer1/CGO.c:4337: warning: ‘col2[1]’ may be used uninitialized in this > function > layer1/CGO.c:4337: warning: ‘col2[2]’ may be used uninitialized in this > function > layer1/CGO.c: In function ‘CGOProcessCGOtoArrays’: > layer1/CGO.c:2815: warning: ‘normalValsDA’ may be used uninitialized in > this function > layer1/CGO.c:2815: warning: ‘accessibilityValsDA’ may be used > uninitialized in this function > layer1/CGO.c:2816: warning: ‘pickColorValsDA’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGORenderGL’: > layer1/CGO.c:7954: warning: ‘normalVals_tmp’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGOOptimizeToVBONotIndexedWithReturnedData’: > layer1/CGO.c:3371: warning: ‘normalValsDA’ may be used uninitialized in > this function > layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGORenderRay’: > layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in > this function > layer1/CGO.c: In function ‘CGOSimplify’: > layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in > this function -- Thomas Holder PyMOL Developer Schrödinger Contractor -
Re: [PyMOL] pymol fails to compile
numpy issue fixed in svn r4036. Cheers, Thomas Thomas Holder wrote, On 07/23/13 11:18: > Hi Andreas, > > I recently made a small change regarding numpy support. Can you please > send me the output of the following command: > > ls /usr/lib64/python2.6/site-packages/numpy/core/include/numpy > > Meanwhile, just disable numpy support by removing the try/except block > in setup.py line 221. > > Thanks, > Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Alpha Channels in Pymol Movies
Hello, I'm using MacPymol 1.5.0.4 When I save a ray traced .PNG file with set ray_opaque_background, 0 It does gives me a transparent background when I put the picture into other apps, e.g. Powerpoint. However, when I save it as a .mov file, I can see that pymol is trying for a transparent background (I can see each frame as a checkerboard), but the finished product is a solid black background that looks terrible. Has anyone encountered this problem and have a possible solution or workaround? Jordan -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
