[PyMOL] compiling pymol on Mac intel
Hi List! I am trying to compile pymol via 2 ways on my Macbook pro Intel: 1) Via fink: fink install pymol-py24 (installs version 0.99-1005) All seems to be ok, but when running /sw/lib/pymol-py24/bin/pymol, I got this: X Error of failed request: BadAlloc (insufficient resources for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Serial number of failed request: 19 Current serial number in output stream: 20 PyMOL: abrupt program termination. 2) Via SVN Pymol 1.0 python setup.py build Failed with: [...] gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/System/Library/Frameworks/OpenGL.framework/Headers -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/CoreFoundation.framework/Headers -I/System/Library/Frameworks/AppKit.framework/Headers -I/System/Library/Frameworks/ApplicationServices.framework/Headers -I/System/Library/Frameworks/Cocoa.framework/Headers -I/System/Library/Frameworks/IOKit.framework/Headers -I/sw/include/python2.4 -c layer5/main.c -o build/temp.darwin-8.10.1-i386-2.4/layer5/main.o In file included from layer0/os_gl.h:44, from layer5/main.c:27: /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290: warning: function declaration isn't a prototype layer5/main.c: In function 'launch': layer5/main.c:1484: error: 'MacPyMOLOption' undeclared (first use in this function) layer5/main.c:1484: error: (Each undeclared identifier is reported only once layer5/main.c:1484: error: for each function it appears in.) layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first use in this function) error: command 'gcc' failed with exit status 1 I am using: ri python24 2.4.3-1001 Interpreted, object-oriented language ii python24-shlib 2.4.3-1001 Interpreted, object-oriented language ii freeglut 2.4.0-1Opengl utility toolkit ii freeglut-shlib 2.4.0-1Opengl utility toolkit ii glut-shlibs3.7-1025 Opengl utility toolkit ii libpng31.2.18-1 PNG image format handling library ii libpng3-shlibs 1.2.18-1 Shared libraries for libpng3 package ii tcltk 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-dev 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-shlibs 8.4.13-3 Tool Command Language and the Tk toolkit ii freetype2 2.1.4-12 TrueType font rendering library, (dummy) ii freetype2192.2.1-4TrueType font rendering library, headers ii freetype219-sh 2.2.1-4TrueType font rendering library, shared libs And MacOSX OpenGL. I also tried with python 2.4.3 OSX Framework version, same error. My guess is it's trying to install MacPymol, but I don't know if I am even allowed (although I use pymol only visualisation and have several scripts written for it). Otherwise, how to tell setup to install pymol for X11? If I can use MacPymol (and compile it), that's would be great. So, any hint here would be very appreciated. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28
Re: [PyMOL] spectral coloring
Hi Martin, * Martin Höfling martin.hoefl...@physik.uni-muenchen.de [2007-06-26 15:15] wrote: Hi there, i am trying to map b factors on a surface representation. I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a way to fine tune the color spectrum, such as with the Midpoint and Offset sliders in vmd? My color_b.py script has some controls, although I'm not sure it will do quite what you want. It has a number of different gradients built in, plus you can adjust the overall saturation or value (brightness). Like the spectrum command you can set the minimum and maximum values to use, which can help to adjust the midpoint. It also has two modes, histogram, in which the spacing of B-values (or other values) is equal or ramp, in which the number of atoms in each bin is kept constant, but the widths of the bins vary. You are welcome to modify it to add new features, of course. You can find it at: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
[PyMOL] How to dislocate independently each structure when you have loaded two structures?
Hi, I have loaded two structure and tried to dislocate one independent on the other, but I couldn't. Is it possible to do thit? I would like to know how to dislocate independently each structure when you have loaded two structures? Thanks, Julio Cesar da Silva -- SAXS / Studies of protein Structure using SAXS Brazilian Synchrotron Light Laboratory Brazil Phone: +55 19 3512-1115
Re: [PyMOL] How to dislocate independently each structure when you have loaded two structures?
* Andreas Henschel a...@biotec.tu-dresden.de [2007-06-27 15:49] wrote: Hi Julio, If I understood you right, you can simply use translate, eg.: translate [20,0,0], mol_to_dislocate The important thing is that turn and move modify the camera, while translate and rotate modify the coordinates. Cheers, Andreas Júlio César wrote: Hi, I have loaded two structure and tried to dislocate one independent on the other, but I couldn't. Is it possible to do thit? I would like to know how to dislocate independently each structure when you have loaded two structures? Or you can put the mouse in editing mode (click in the bottom corner of the main graphics window where the mouse functions are described) and you'll now see that Shift middle-button is labelled MovO and Shift left-button is labelled RotO. So you can use Shift middle-button to translate one object and Shift left-button to rotate one object relative to the other. You just have to be careful that you pick your atom carefully if the two objects are superimposed. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
Re: [PyMOL] Sticks and distances with individual transparencies
Tsjerk, Sometimes the archives can be misleading... Actually, settings do now work on selections and bonds as well (with set_bond). However, only a small set of per-atom and per-bond settings are currently implemented, since each can require a significant amount of new code. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Tuesday, June 26, 2007 9:26 PM To: Dr. Mark Mayer Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Sticks and distances with individual transparencies Hi Mark, You could've found this one in the archives of this list. Settings work on objects, not on selections. The solution is to make an object for the solid sticks and one for the transparent sticks, using create. Cheers, Tsjerk On 6/26/07, Dr. Mark Mayer may...@mail.nih.gov wrote: Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is being set. PyMOLset stick_transparency=0.2, /sca//A/228 and !mc Setting: stick_transparency set for 5 atoms in object mol1. I'd also like to draw selected H-bonds with control of transparency with the rest solid, but have no idea how to do this. -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] compiling pymol on Mac intel
Alan, Hmm...the Darwin setup.py build is definitely broken...I'll need to look into why -- it shouldn't be trying to link to any MacPyMOL symbols (MacPyMOL is beyond the scope of the open-source project). In the meantime, you can probably try an in-place autotools-based compile instead. ./configure make make install Note that make install just installs into the current source directory. As for the Fink build, that looks like an X11 / OpenGL / GLX problem on your system. Does the precompiled X11 build work? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Alan Sent: Wednesday, June 27, 2007 4:46 AM To: Pymol Subject: [PyMOL] compiling pymol on Mac intel Hi List! I am trying to compile pymol via 2 ways on my Macbook pro Intel: 1) Via fink: fink install pymol-py24 (installs version 0.99-1005) All seems to be ok, but when running /sw/lib/pymol-py24/bin/pymol, I got this: X Error of failed request: BadAlloc (insufficient resources for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Serial number of failed request: 19 Current serial number in output stream: 20 PyMOL: abrupt program termination. 2) Via SVN Pymol 1.0 python setup.py build Failed with: [...] gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/System/Library/Frameworks/OpenGL.framework/Headers -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/CoreFoundation.framework/Headers -I/System/Library/Frameworks/AppKit.framework/Headers -I/System/Library/Frameworks/ApplicationServices.framework/Headers -I/System/Library/Frameworks/Cocoa.framework/Headers -I/System/Library/Frameworks/IOKit.framework/Headers -I/sw/include/python2.4 -c layer5/main.c -o build/temp.darwin-8.10.1-i386-2.4/layer5/main.o In file included from layer0/os_gl.h:44, from layer5/main.c:27: /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290: warning: function declaration isn't a prototype layer5/main.c: In function 'launch': layer5/main.c:1484: error: 'MacPyMOLOption' undeclared (first use in this function) layer5/main.c:1484: error: (Each undeclared identifier is reported only once layer5/main.c:1484: error: for each function it appears in.) layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first use in this function) error: command 'gcc' failed with exit status 1 I am using: ri python24 2.4.3-1001 Interpreted, object-oriented language ii python24-shlib 2.4.3-1001 Interpreted, object-oriented language ii freeglut 2.4.0-1Opengl utility toolkit ii freeglut-shlib 2.4.0-1Opengl utility toolkit ii glut-shlibs3.7-1025 Opengl utility toolkit ii libpng31.2.18-1 PNG image format handling library ii libpng3-shlibs 1.2.18-1 Shared libraries for libpng3 package ii tcltk 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-dev 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-shlibs 8.4.13-3 Tool Command Language and the Tk toolkit ii freetype2 2.1.4-12 TrueType font rendering library, (dummy) ii freetype2192.2.1-4TrueType font rendering library, headers ii freetype219-sh 2.2.1-4TrueType font rendering library, shared libs And MacOSX OpenGL. I also tried with python 2.4.3 OSX Framework version, same error. My guess is it's trying to install MacPymol, but I don't know if I am even allowed (although I use pymol only visualisation and have several scripts written for it). Otherwise, how to tell setup to install pymol for X11? If I can use MacPymol (and compile it), that's would be great. So, any hint here would be very appreciated. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE
Re: [PyMOL] compiling pymol on Mac intel
Alan, Okay, I found the glitch with the OSX defines -- my bad. However, I also rediscovered what the hidden difficultly is with compiling PyMOL under X11, and that is: Mac OS X's built-in python has an Aqua-based Tcl/Tk/Tkinter implementation NOT bound to X11 and which does not work with PyMOL due to conflicts in the threading and event model. So to compile PyMOL for X11 on Mac OS X, one needs a separate Python/Tcl/Tk/Tkinter instance that has been built for X11. Where you do get that? Fink. So the bottom line message is: Open-source PyMOL for X11 under Mac OS X must be compiled under the Fink environment, not straight Mac OS X. We need to fix the default setup.py to reflect this fact. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Wednesday, June 27, 2007 7:59 AM To: 'Alan'; 'Pymol' Subject: Re: [PyMOL] compiling pymol on Mac intel Alan, Hmm...the Darwin setup.py build is definitely broken...I'll need to look into why -- it shouldn't be trying to link to any MacPyMOL symbols (MacPyMOL is beyond the scope of the open-source project). In the meantime, you can probably try an in-place autotools-based compile instead. ./configure make make install Note that make install just installs into the current source directory. As for the Fink build, that looks like an X11 / OpenGL / GLX problem on your system. Does the precompiled X11 build work? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Alan Sent: Wednesday, June 27, 2007 4:46 AM To: Pymol Subject: [PyMOL] compiling pymol on Mac intel Hi List! I am trying to compile pymol via 2 ways on my Macbook pro Intel: 1) Via fink: fink install pymol-py24 (installs version 0.99-1005) All seems to be ok, but when running /sw/lib/pymol-py24/bin/pymol, I got this: X Error of failed request: BadAlloc (insufficient resources for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Serial number of failed request: 19 Current serial number in output stream: 20 PyMOL: abrupt program termination. 2) Via SVN Pymol 1.0 python setup.py build Failed with: [...] gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/System/Library/Frameworks/OpenGL.framework/Headers -I/System/Library/Frameworks/GLUT.framework/Headers -I/System/Library/Frameworks/CoreFoundation.framework/Headers -I/System/Library/Frameworks/AppKit.framework/Headers -I/System/Library/Frameworks/ApplicationServices.framework/Headers -I/System/Library/Frameworks/Cocoa.framework/Headers -I/System/Library/Frameworks/IOKit.framework/Headers -I/sw/include/python2.4 -c layer5/main.c -o build/temp.darwin-8.10.1-i386-2.4/layer5/main.o In file included from layer0/os_gl.h:44, from layer5/main.c:27: /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281: warning: function declaration isn't a prototype /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290: warning: function declaration isn't a prototype layer5/main.c: In function 'launch': layer5/main.c:1484: error: 'MacPyMOLOption' undeclared (first use in this function) layer5/main.c:1484: error: (Each undeclared identifier is reported only once layer5/main.c:1484: error: for each function it appears in.) layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first use in this function) error: command 'gcc' failed with exit status 1 I am using: ri python24 2.4.3-1001 Interpreted, object-oriented language ii python24-shlib 2.4.3-1001 Interpreted, object-oriented language ii freeglut 2.4.0-1Opengl utility toolkit ii freeglut-shlib 2.4.0-1Opengl utility toolkit ii glut-shlibs3.7-1025 Opengl utility toolkit ii libpng31.2.18-1 PNG image format handling library ii libpng3-shlibs 1.2.18-1 Shared libraries for libpng3 package ii tcltk 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-dev 8.4.13-3 Tool Command Language and the Tk toolkit ii tcltk-shlibs 8.4.13-3
