Re: [PyMOL] pymol crashes - segmentation fault - PLEASE HELP
Hi all, As suggested by Peter, I tried compiling PyMol from src (pymol-0_99rc6-src.tgz). Unfortunately it fell over :( Attached is the output. The error occurs in layer0/Crystal.c. I've look at the file in vim and there does not seem to be anything untowards (weird characters etc...) in it. I tried to compile from pymol-0_99rc1-src.tgz and got the same error. Any pointers?? Many thanks Noel On Friday 25 August 2006 23:49, you wrote: snip Dose anyone have any idea's? This occurs when I single click left or right in the main display. If you're using the binary distribution, try using the source distribution and see if the problem persists (if compilation fails, then the error message might provide some information as to what's going on). You could also try different graphics drivers (if possible). Failing that, it sounds like an issue w\ the mouse event listener in the glut stuff. Unfortunately I don't know of an easy fix or work-around if this is the case (hopefully Warren will chime in on this). Good luck, Pete -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au website: http://vbc.med.monash.edu.au/~fauxn 13:13:12-fa...@~/software/pymol-0.99rc6$ python setup.py install 1 pymol_setup.log 12 running install running build running build_py creating build creating build/lib.linux-i686-2.4 creating build/lib.linux-i686-2.4/chempy copying modules/chempy/bond_amber.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/hetatm.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/lst.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_amber99.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/dictdb.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_mmff.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/arc.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_amber.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/water_amber.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/solvate.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/protein.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/models.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/water_residues.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/mmd.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/cex.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/io.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/charge.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/sdf.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/map.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/bond_mmff.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/mass.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/xyz.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/place.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/mol.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/gms.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/pdb.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/cc1.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/cpv.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/mae.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/pkl.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/neighbor.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/gamess1.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_residues.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/brick.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/__init__.py - build/lib.linux-i686-2.4/chempy copying modules/chempy/bonds.py - build/lib.linux-i686-2.4/chempy creating build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/commands.py - build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/realtime.py - build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/state.py - build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/util.py - build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/__init__.py - build/lib.linux-i686-2.4/chempy/bmin creating build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/formal_charges.py - build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/assign.py - build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/amber99.py - build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/__init__.py - build/lib.linux-i686-2.4/chempy/champ creating build/lib.linux-i686-2.4/chempy/fast copying modules/chempy/fast/__init__.py - build/lib.linux-i686-2.4/chempy/fast creating build/lib.linux-i686-2.4/chempy/fragments copying modules/chempy/fragments/__init__.py - build/lib.linux-i686-2.4/chempy/fragments
Re: [PyMOL] pymol crashes - segmentation fault - PLEASE HELP
HI all, This is a follow on from the e-mail below. Frequently I'm also getting this error when pymol crashes: *** glibc detected *** /home/fauxn/software/pymol/pymol.exe: double free or corruption (!prev): 0x0aaef170 *** === Backtrace: = /lib/libc.so.6[0xc69d88] /lib/libc.so.6(__libc_free+0x78)[0xc6d25f] /usr/lib/libGL.so.1[0x5bd8e5a] === Memory map: 00101000-001fa000 r-xp fd:00 11326935 /usr/lib/libX11.so.6.2.0 001fa000-001fe000 rwxp 000f9000 fd:00 11326935 /usr/lib/libX11.so.6.2.0 001fe000-0020 rwxp 00:0f 1254 /dev/zero 0020-00214000 r-xp fd:00 12931879 /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so 00214000-00216000 rwxp 00013000 fd:00 12931879 /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so 00216000-00219000 r-xp fd:00 12905453 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so 00219000-0021b000 rwxp 2000 fd:00 12905453 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so 0021b000-00224000 r-xp fd:00 12905473 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so 00224000-00227000 rwxp 9000 fd:00 12905473 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so 00227000-0022c000 r-xp fd:00 12905440 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so 0022c000-0022d000 rwxp 4000 fd:00 12905440 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so 0022d000-00231000 r-xp fd:00 12905478 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so 00231000-00232000 rwxp 4000 fd:00 12905478 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so 00232000-00234000 rwxp 00:0f 1254 /dev/zero 00234000-00236000 rwxp 00:0f 1254 /dev/zero 00236000-00238000 rwxp 00:0f 1254 /dev/zero 00238000-0023a000 rwxp 00:0f 1254 /dev/zero 0023a000-0023c000 rwxp 00:0f 1254 /dev/zero 0023c000-0023e000 rwxp 00:0f 1254 /dev/zero 0023e000-0024 rwxp 00:0f 1254 /dev/zero 0024-00242000 rwxp 00:0f 1254 /dev/zero 00242000-0024b000 rwxp 00:0f 1254 /dev/zero 0027c000-0028 r-xp fd:00 12905441 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so 0028-00281000 rwxp 3000 fd:00 12905441 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so 002b3000-002b6000 r-xp fd:00 12905457 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so 002b6000-002b7000 rwxp 2000 fd:00 12905457 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so 002f3000-002f4000 r-xp 002f3000 00:00 0 [vdso] 002f4000-0030d000 r-xp fd:00 1669685/lib/ld-2.4.so 0030d000-0030e000 r-xp 00018000 fd:00 1669685/lib/ld-2.4.so 0030e000-0030f000 rwxp 00019000 fd:00 1669685/lib/ld-2.4.so 00311000-00a87000 r-xp fd:00 11326754 /usr/lib/libGLcore.so.1.0.7182 00a87000-00aa3000 rwxp 00775000 fd:00 11326754 /usr/lib/libGLcore.so.1.0.7182 00aa3000-00ab8000 rwxp 00aa3000 00:00 0 00aba000-00abb000 r-xp fd:00 15615182 /usr/lib/tls/libnvidia-tls.so.1.0.7182 00abb000-00abc000 rwxp fd:00 15615182 /usr/lib/tls/libnvidia-tls.so.1.0.7182 00ad3000-00ad7000 r-xp fd:00 12905474 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so 00ad7000-00ad9000 rwxp 3000 fd:00 12905474 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so 00b14000-00b17000 r-xp fd:00 12905449 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so 00b17000-00b18000 rwxp 3000 fd:00 12905449 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so 00b4a000-00b52000 r-xp fd:00 11326936 /usr/lib/libXrender.so.1.3.0 00b52000-00b53000 rwxp 7000 fd:00 11326936 /usr/lib/libXrender.so.1.3.0 00b6-00b64000 r-xp fd:00 11327016 /usr/lib/libXfixes.so.3.0.0 00b64000-00b65000 rwxp 3000 fd:00 11327016 /usr/lib/libXfixes/home/fauxn/software/pymol/pymol: line 14: 10660 Aborted $PYMOL_PATH/pymol.exe $@ Dose anyone have any idea's? This occurs when I single click left or right in the main display. On Tuesday 22 August 2006 13:46, Noel Faux wrote: Hi all, Recently I finally managed to install the Nvidia driver (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 Pro/AGP/SSE2) on my Fedora Core 5 box. When I try and run pymol it crashed after I load a pdb file and try and either right or left click on the main display. Here is the output from the pymol run: PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation
Re: [PyMOL] pdb files with many chains
Hi Siv, Try giving each chain a unique identifier. As pymol might believe that all the fragments belong to chain ' '. Cheers Noel On Wednesday 23 August 2006 22:40, Siv Midtun Hollup wrote: Hi, Hope this is the correct place for this question :) I have a pdb file with many small fragments in addition to a longer chain. These are not numerated in any way, only separated by TER (example below). In pymol, only two 'chains' appear, one with the long chain, and the other with all the fragments mixed together. Do chains need to be separated by anything else than lines containing TER? If I try to visualise the same pdb file in rasmol, the separate chains are drawn up (for instance with ribbon). Also, is there a limit to how many chains pymol can handle? I might have 1000 shorter chains in one pdb file. I run pymol 0.99rc6 for linux. Any help appreciated :) Sincerly, Siv Hollup -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au website: http://vbc.med.monash.edu.au/~fauxn
[PyMOL] pymol crashes - segmentation fault
Hi all, Recently I finally managed to install the Nvidia driver (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 Pro/AGP/SSE2) on my Fedora Core 5 box. When I try and run pymol it crashed after I load a pdb file and try and either right or left click on the main display. Here is the output from the pymol run: PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro2 Pro/AGP/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.82 Adapting to Quadro hardware. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. HEADERSCOP/ASTRAL domain d1a5ug2 [29269] 08-MAY-03 CmdLoad: /home/fauxn/results/SCOP_90_results/d1a5ug2.pdb loaded as d1a5ug2. /home/fauxn/software/pymol/pymol: line 14: 7203 Segmentation fault $PYMOL_PATH/pymol.exe $@ Any pointers welcome! Cheers Noel -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au website: http://vbc.med.monash.edu.au/~fauxn
Re: [PyMOL] odeling a sequence over a structure
Also try Modeller: http://www.salilab.org/modeller/ Cheers Noel ge...@embl-grenoble.fr wrote: Hi all ... I'm not sure weather the pymol mailing list is the best place to ask this but anyway ... I would like model a structure of a protein. I have a sequence of interest and I have a related structure which shares a very low sequence identity but is suppose to have a common fold. Do anyone knows how to deal with this ? Thanks, Tibo --- All the advantages of Linux Managed Hosting--Without the Cost and Risk! Fully trained technicians. The highest number of Red Hat certifications in the hosting industry. Fanatical Support. Click to learn more http://sel.as-us.falkag.net/sel?cmd=lnkkid=107521bid=248729dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- PhD student Department of Biochemistry and Molecular Biology Monash University Clayton 3168 Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au begin:vcard fn:Noel Faux n:Faux;Noel org:Monash University;Biochemistry and Molecular Biology adr:;;;Clayton;Vic;3800;Australia email;internet:noel.f...@med.monash.edu.au tel;work:+61 03 9905 1418 url:http://vbc.med.monash.edu.au/~fauxn version:2.1 end:vcard
[PyMOL] Proxy config plugin
Hi all, While building another plugin, I needed a way to access the net through our proxy and was unable to see any settings in pymol. So I wrote my own config plugin. There is a small security flaw, the password is saved by default as plain text (I'm currently looking into encrypting the password, any suggestions welcome). As the information is just a pickled tuple, other plugins are able to use it and connect via urllib2. The pdb loader plugin is such a plugin which would benefit from this (I'm in the process of modifying the code). To download please visit: http://vbc.med.monash.edu.au/~fauxn/pymol_plugin/plugin.html Is it possible to have this as part of pymol and placed in the Settings menu? All comments are more than welcome. Cheers Noel begin:vcard fn:Noel Faux n:Faux;Noel org:Monash University;Biochemistry and Molecular Biology adr:;;;Clayton;Vic;3800;Australia email;internet:noel.f...@med.monash.edu.au tel;work:+61 03 9905 1418 url:http://vbc.med.monash.edu.au/~fauxn version:2.1 end:vcard
[PyMOL] mutagenesis via python?
Hi all, I'm in the process of creating a plugin for pymol, however I've hit a small wall. Is there a series of python calls I can make in my code to perform a mutation without the loss of the original residue? I've tried to follow the commands the wizard returns but I'm unable to follow what is being done. Cheers Noel begin:vcard fn:Noel Faux n:Faux;Noel org:Monash University;Department of Biochemistry and Molecular Biology adr:;;;Clayton;Victoria;3800;Australia email;internet:noel.f...@med.monash.edu.au title:Mr tel;work:+61 3 9905 1418 url:http://vbc.med.monash.edu.au/~fauxn version:2.1 end:vcard
