[PyMOL] Defining and Selecting molecules
I am wondering how to select molecules in Pymol. The system I am studying has an amide of interest (oleamide) in oil (At the moment just dodecane molecules). I have seen in the manual how to select individual elements, but is it possible to select either the Nitrogen or oxygen in my oleamide molecules, and then select all atoms which are bonded to this to therefore select the entire oleamide molecule. Or is it possible to define a molecule by defining a chain of elements (e.g. define a C12H36 chain for dodecane). I have tried just using the mouse to select individual molecules but find it very difficult to do depending on where in my system a particular molecule is. I'm probably just being really stupid, but I couldn't see it in the manual or the wiki. Thanks. Michael. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
hi all: could any one tell me how to get the coordinates for a specific atom in a particular amino acid using pymol commands is their a commant with can list the coordinates for each aminoacid in a protein molecule?? \ kindly clarify, thanking you in advance. - mohan -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] coordinates
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
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Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [PyMOL] Defining and Selecting molecules
Hi Michael, Have you had a look at 'help selections'? I am wondering how to select molecules in Pymol. What exactly do you mean here? The molecule for a certain atom? The molecule as in 'chain' (if it's a macromolecule), or as in 'residue' (if it's a ligand/cofactor/solvent)? The system I am studying has an amide of interest (oleamide) in oil (At the moment just dodecane molecules). I have seen in the manual how to select individual elements, but is it possible to select either the Nitrogen or oxygen in my oleamide molecules, and then select all atoms which are bonded to this to therefore select the entire oleamide molecule. Now, either/or sort of suggests logical XOR (exclusive or), which would mean nitrogen if only nitrogen is present (and not oxygen), oxygen if only oxygen is present (and not nitrogen), and none if none or both are present. But somehow logical XOR with such selections is not that logical to me. Do you want to have all atoms bonded to nitrogen or to oxygen (and assuming you don't have azides, peroxides and nitroxides of interest), then you'd probably want to do something like: select mysele, (not (e. n,o)) within 0.2 of (e. n,o) Or is it possible to define a molecule by defining a chain of elements (e.g. define a C12H36 chain for dodecane). I have tried just using the mouse to select individual molecules but find it very difficult to do depending on where in my system a particular molecule is. If you're dodecane molecules have unique residue ids than it should be trivial to use those: color yellow, resi 1 If this wasn't what you were after, please restate your question, clearly explaining what you want, what you tried and how that didn't do what you expected. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
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(e) jason.vertr...@schrodinger.com
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Re: [PyMOL] coordinates
Of course, you could just use the .pdb file as a text file:
grep CA .pdb | cut -f 2,4,7,8,9
will get you the amino acid number, the amino acid identity, and x,y,z
coordinates for the CA.
Jed
Jason Vertrees wrote:
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823
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Re: [PyMOL] installing pumol on suse
2010/3/22 Tatsiana Kirys nus...@mail.ru: I've installed it. But i have even more errors now: nus...@linux-3mpg:~/Download/trunk/pymol python setup.py build install bunch of stuff /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot find -lpng collect2: ld returned 1 exit status error: command 'g++' failed with exit status 1 This is the important error, all those others are just silliness. You need libpng-devel (which should also install some other package that starts with libpng that has the actual library) Interestingly, the pymol README claims pymol can be compiled without libpng. Assuming that isn't true any more, that probably should be corrected. -David -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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
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Re: [PyMOL] coordinates
Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
Of course you're all correct - Thierry Fischmann already emailed me to correct me :) I hadn't actually tested anything (mea culpa). I was just trying to point out for those of us less familiar with python that there were alternatives to doing this relatively simple thing outside of pymol. Apologies to the list, Jed Robert Campbell wrote: Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. Cheers, Rob -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
But it is very doable using grep/cut, you'll just have to use the -b flag that allows you to cut columns: grep CA .pdb | cut -b 13-26,30-54 Cheers, Tsjerk On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. 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: 613-533-6821 Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] installing pumol on suse
Looks like you don't have the python-devel package. This provides the header files such as Python.h you need for compiling python modules. -David On Fri, Mar 19, 2010 at 5:50 PM, Tatsiana Kirys nus...@mail.ru wrote: Dear All, i'm trying to install pymol on suse. i've checked that i have penGL, glut, libpng, tcl/tk, python, freetype2 installed. But when running python setup.py build install i got erroes could you please advise me what to do? thank you very much I've installed it. But i have even more errors now: nus...@linux-3mpg:~/Download/trunk/pymol python setup.py build install running build running build_py running build_ext building 'pymol._cmd' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -fomit-frame-pointer -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer3/Selector.c -o build/temp.linux-i686-2.6/layer3/Selector.o -ffast-math -funroll-loops -O3 In file included from /usr/include/python2.6/Python.h:8, from layer0/os_python.h:30, from layer1/PConv.h:20, from layer3/Selector.c:29: /usr/include/python2.6/pyconfig.h:1055:1: warning: _POSIX_C_SOURCE redefined In file included from /usr/include/malloc.h:24, from layer0/os_predef.h:193, from layer3/Selector.c:19: /usr/include/features.h:210:1: warning: this is the location of the previous definition gcc -pthread -fno-strict-aliasing -DNDEBUG -fomit-frame-pointer -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer4/Cmd.c -o build/temp.linux-i686-2.6/layer4/Cmd.o -ffast-math -funroll-loops -O3
Re: [PyMOL] installing pumol on suse
i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o build/temp.linux-i686-2.6/layer1/Setting.o build/temp.linux-i686-2.6/layer1/Shaker.o build/temp.linux-i686-2.6/layer1/Symmetry.o build/temp.linux-i686-2.6/layer1/Text.o build/temp.linux-i686-2.6/layer1/TypeFace.o build/temp.linux-i686-2.6/layer1/Wizard.o build/temp.linux-i686-2.6/layer1/View.o build/temp.linux-i686-2.6/layer2/AtomInfo.o build/temp.linux-i686-2.6/layer2/CoordSet.o build/temp.linux-i686-2.6/layer2/GadgetSet.o build/temp.linux-i686-2.6/layer2/DistSet.o build/temp.linux-i686-2.6/layer2/ObjectAlignment.o build/temp.linux-i686-2.6/layer2/ObjectCGO.o build/temp.linux-i686-2.6/layer2/ObjectCallback.o build/temp.linux-i686-2.6/layer2/ObjectDist.o build/temp.linux-i686-2.6/layer2/ObjectMap.o build/temp.linux-i686-2.6/layer2/ObjectMesh.o build/temp.linux-i686-2.6/layer2/ObjectMolecule.o build/temp.linux-i686-2.6/layer2/ObjectMolecule2.o build/temp.linux-i686-2.6/layer2/ObjectSurface.o build/temp.linux-i686-2.6/layer2/ObjectSlice.o build/temp.linux-i686-2.6/layer2/RepCartoon.o build/temp.linux-i686-2.6/layer2/RepCylBond.o build/temp.linux-i686-2.6/layer2/RepDistDash.o build/temp.linux-i686-2.6/layer2/RepDistLabel.o build/temp.linux-i686-2.6/layer2/RepDot.o build/temp.linux-i686-2.6/layer2/RepLabel.o build/temp.linux-i686-2.6/layer2/RepMesh.o build/temp.linux-i686-2.6/layer2/ObjectGadget.o build/temp.linux-i686-2.6/layer2/ObjectGadgetRamp.o build/temp.linux-i686-2.6/layer2/ObjectGroup.o build/temp.linux-i686-2.6/layer2/RepAngle.o build/temp.linux-i686-2.6/layer2/RepDihedral.o build/temp.linux-i686-2.6/layer2/RepNonbonded.o build/temp.linux-i686-2.6/layer2/RepNonbondedSphere.o build/temp.linux-i686-2.6/layer2/RepRibbon.o build/temp.linux-i686-2.6/layer2/RepSphere.o build/temp.linux-i686-2.6/layer2/RepEllipsoid.o build/temp.linux-i686-2.6/layer2/RepSurface.o build/temp.linux-i686-2.6/layer2/RepWireBond.o
Re: [PyMOL] Defining and Selecting molecules
The system I am studying has an amide of interest (oleamide) in oil (At the moment just dodecane molecules). I have seen in the manual how to select individual elements, but is it possible to select either the Nitrogen or oxygen in my oleamide molecules, and then select all atoms which are bonded to this to therefore select the entire oleamide molecule. PyMOL has some powerful selection operators, here are a few that might help you: (1) Select a complete residue based on one atom select aRes, br. someAtom (2) Select a complete molecule based on one atom: select aMol, bm. someAtom (3) Select all atoms bound to another atom: select boundTo, neighbor someAtom (4) Select organic small molecules select myLig, org So, if your case I would try: select oleamide, bm. anyOleoAtom If the ligand is bound to the protein, you'll get the entire object, so try br. instead to get just the ligand. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] installing pumol on suse
thank you for helping. I;ve installed it. But when i run it, is says OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.6) Traceback (most recent call last): File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line 432, in launch_gui __import__(self.invocation.options.gui) File /usr/local/lib/python2.6/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/local/lib/python2.6/site-packages/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw This error: creating /usr/local/lib/python2.6 error: could not create '/usr/local/lib/python2.6': Permission denied Means that you must run the compilation command as root (or with su privileges) The command: python setup.py build install Can be decomposed into: python setup.py build (this part has been completed in your case) and: python setup.py install (here it fails!). In this case you must have superuser privileges, try: sudo python setup.py install Or, if you don't have sudo on yout system, become root and execute the command as root. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o build/temp.linux-i686-2.6/layer1/Setting.o build/temp.linux-i686-2.6/layer1/Shaker.o build/temp.linux-i686-2.6/layer1/Symmetry.o build/temp.linux-i686-2.6/layer1/Text.o build/temp.linux-i686-2.6/layer1/TypeFace.o build/temp.linux-i686-2.6/layer1/Wizard.o build/temp.linux-i686-2.6/layer1/View.o build/temp.linux-i686-2.6/layer2/AtomInfo.o build/temp.linux-i686-2.6/layer2/CoordSet.o build/temp.linux-i686-2.6/layer2/GadgetSet.o build/temp.linux-i686-2.6/layer2/DistSet.o build/temp.linux-i686-2.6/layer2/ObjectAlignment.o build/temp.linux-i686-2.6/layer2/ObjectCGO.o build/temp.linux-i686-2.6/layer2/ObjectCallback.o build/temp.linux-i686-2.6/layer2/ObjectDist.o build/temp.linux-i686-2.6/layer2/ObjectMap.o build/temp.linux-i686-2.6/layer2/ObjectMesh.o
Re: [PyMOL] installing pumol on suse
You need to install Python Megawidgets (Pmw) http://sourceforge.net/projects/pmw/files/Pmw/ -- Jason 2010/3/22 Tatsiana Kirys nus...@mail.ru: thank you for helping. I;ve installed it. But when i run it, is says OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.6) Traceback (most recent call last): File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line 432, in launch_gui __import__(self.invocation.options.gui) File /usr/local/lib/python2.6/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/local/lib/python2.6/site-packages/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw This error: creating /usr/local/lib/python2.6 error: could not create '/usr/local/lib/python2.6': Permission denied Means that you must run the compilation command as root (or with su privileges) The command: python setup.py build install Can be decomposed into: python setup.py build (this part has been completed in your case) and: python setup.py install (here it fails!). In this case you must have superuser privileges, try: sudo python setup.py install Or, if you don't have sudo on yout system, become root and execute the command as root. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o build/temp.linux-i686-2.6/layer1/Setting.o build/temp.linux-i686-2.6/layer1/Shaker.o build/temp.linux-i686-2.6/layer1/Symmetry.o build/temp.linux-i686-2.6/layer1/Text.o build/temp.linux-i686-2.6/layer1/TypeFace.o build/temp.linux-i686-2.6/layer1/Wizard.o build/temp.linux-i686-2.6/layer1/View.o build/temp.linux-i686-2.6/layer2/AtomInfo.o build/temp.linux-i686-2.6/layer2/CoordSet.o build/temp.linux-i686-2.6/layer2/GadgetSet.o build/temp.linux-i686-2.6/layer2/DistSet.o build/temp.linux-i686-2.6/layer2/ObjectAlignment.o build/temp.linux-i686-2.6/layer2/ObjectCGO.o
[PyMOL] 1st Call For Papers, 17th Annual Tcl/Tk Conference 2010
17th Annual Tcl/Tk Conference (Tcl'2010) http://www.tcl.tk/community/tcl2010/ October 11 - 15, 2010 Hilton Suites/Conference Center Chicago/Oakbrook Terrace, Illinois, USA Important Dates: Abstracts and proposals due August 1, 2010 Notification to authors August 15, 2010 WIP and BOF reservations open August 1, 2010 Author materials due October 1, 2010 Tutorials Start October 11, 2010 Conference starts October 13, 2010 Email Contact:tclconfere...@googlegroups.com Submission of Summaries Tcl/Tk 2010 will be held in Chicago/Oakbrook Terrace, Illinois USA from October 11 - 15, 2010. The program committee is asking for papers and presentation proposals from anyone using or developing with Tcl/Tk (and extensions). Past conferences have seen submissions covering a wide variety of topics including: * Scientific and engineering applications * Industrial controls * Distributed applications and Network Managment * Object oriented extensions to Tcl/Tk * New widgets for Tk * Simulation and application steering with Tcl/Tk * Tcl/Tk-centric operating environments * Tcl/Tk on small and embedded devices * Medical applications and visualization * Use of different programming paradigms in Tcl/Tk and proposals for new directions. * New areas of exploration for the Tcl/Tk language This year is the third year that the Tcl community is participating in the Google Summer of Code. The conference program committee would like to encourage submissions that report on the Tcl projects selected for Google SoC 2010. Submissions should consist of an abstract of about 100 words and a summary of not more than two pages, and should be sent as plain text to tclconference AT googlegroups DOT com no later than August 15, 2010. Authors of accepted abstracts will have until October 1, 2010 to submit their final paper for the inclusion in the conference proceedings. The proceedings will be made available on digital media, so extra materials such as presentation slides, code examples, code for extensions etc. are encouraged. Printed proceedings will be produced as an on-demand book at lulu.com The authors will have 25 minutes to present their paper at the conference. The program committee will review and evaluate papers according to the following criteria: * Quantity and quality of novel content * Relevance and interest to the Tcl/Tk community * Suitability of content for presentation at the conference Proposals may report on commercial or non-commercial systems, but those with only blatant marketing content will not be accepted. Application and experience papers need to strike a balance between background on the application domain and the relevance of Tcl/Tk to the application. Application and experience papers should clearly explain how the application or experience illustrates a novel use of Tcl/Tk, and what lessons the Tcl/Tk community can derive from the application or experience to apply to their own development efforts. Papers accompanied by non-disclosure agreements will be returned to the author(s) unread. All submissions are held in the highest confidentiality prior to publication in the Proceedings, both as a matter of policy and in accord with the U. S. Copyright Act of 1976. The primary author for each accepted paper will receive registration to the Technical Sessions portion of the conference at a reduced rate. Other Forms of Participation The program committee also welcomes proposals for panel discussions of up to 90 minutes. Proposals should include a list of confirmed panelists, a title and format, and a panel description with position statements from each panelist. Panels should have no more than four speakers, including the panel moderator, and should allow time for substantial interaction with attendees. Panels are not presentations of related research papers. Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather sessions (BOFs) are available on a first-come, first-served basis starting in August 1, 2010. Specific instructions for reserving WIP and BOF time slots will be provided in the registration information available in June 2010. Some WIP and BOF time slots will be held open for on-site reservation. All attendees with an interesting work in progress should consider reserving a WIP slot. Registration Information More information on the conference is available the conference Web site (http://www.tcl.tk/community/tcl2010/) and will be published on various Tcl/Tk-related information channels. To keep in touch with news regarding the conference and Tcl events in general, subscribe to the tcl-announce list. See: http://aspn.activestate.com/ASPN/Mail/ to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC
Re: [PyMOL] installing pumol on suse
You must install Python megawidgets. Look for pmw on google, download and follow installation instructions (it is easy). I don't remember if you must build install again pymol after that or not. This is the last error you will have!! By the way, your PC is using MESA libraries. If you are using Nvidia or even ATI graphhics card, you should install propietary drivers in order to have a proper 3D acceleration. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru thank you for helping. I;ve installed it. But when i run it, is says OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.6) Traceback (most recent call last): File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line 432, in launch_gui __import__(self.invocation.options.gui) File /usr/local/lib/python2.6/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/local/lib/python2.6/site-packages/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw This error: creating /usr/local/lib/python2.6 error: could not create '/usr/local/lib/python2.6': Permission denied Means that you must run the compilation command as root (or with su privileges) The command: python setup.py build install Can be decomposed into: python setup.py build (this part has been completed in your case) and: python setup.py install (here it fails!). In this case you must have superuser privileges, try: sudo python setup.py install Or, if you don't have sudo on yout system, become root and execute the command as root. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o build/temp.linux-i686-2.6/layer1/Setting.o build/temp.linux-i686-2.6/layer1/Shaker.o build/temp.linux-i686-2.6/layer1/Symmetry.o build/temp.linux-i686-2.6/layer1/Text.o build/temp.linux-i686-2.6/layer1/TypeFace.o
Re: [PyMOL] installing pumol on suse
yes, thank you very much, it works now! Mon, 22 Mar 2010 14:49:02 -0400 письмо от Jason Vertrees jason.vertr...@schrodinger.com: You need to install Python Megawidgets (Pmw) http://sourceforge.net/projects/pmw/files/Pmw/ -- Jason 2010/3/22 Tatsiana Kirys nus...@mail.ru: thank you for helping. I;ve installed it. But when i run it, is says OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.6) Traceback (most recent call last): File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line 432, in launch_gui __import__(self.invocation.options.gui) File /usr/local/lib/python2.6/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/local/lib/python2.6/site-packages/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw This error: creating /usr/local/lib/python2.6 error: could not create '/usr/local/lib/python2.6': Permission denied Means that you must run the compilation command as root (or with su privileges) The command: python setup.py build install Can be decomposed into: python setup.py build (this part has been completed in your case) and: python setup.py install (here it fails!). In this case you must have superuser privileges, try: sudo python setup.py install Or, if you don't have sudo on yout system, become root and execute the command as root. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o build/temp.linux-i686-2.6/layer1/Setting.o build/temp.linux-i686-2.6/layer1/Shaker.o build/temp.linux-i686-2.6/layer1/Symmetry.o build/temp.linux-i686-2.6/layer1/Text.o build/temp.linux-i686-2.6/layer1/TypeFace.o build/temp.linux-i686-2.6/layer1/Wizard.o build/temp.linux-i686-2.6/layer1/View.o build/temp.linux-i686-2.6/layer2/AtomInfo.o
Re: [PyMOL] installing pumol on suse
THANK YOU, it works Mon, 22 Mar 2010 17:54:05 +0100 письмо от Hugo Gutierrez de Teran hugo.te...@usc.es: You must install Python megawidgets. Look for pmw on google, download and follow installation instructions (it is easy). I don't remember if you must build install again pymol after that or not. This is the last error you will have!! By the way, your PC is using MESA libraries. If you are using Nvidia or even ATI graphhics card, you should install propietary drivers in order to have a proper 3D acceleration. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru thank you for helping. I;ve installed it. But when i run it, is says OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.6) Traceback (most recent call last): File /usr/local/lib/python2.6/site-packages/pymol/__init__.py, line 432, in launch_gui __import__(self.invocation.options.gui) File /usr/local/lib/python2.6/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/local/lib/python2.6/site-packages/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw This error: creating /usr/local/lib/python2.6 error: could not create '/usr/local/lib/python2.6': Permission denied Means that you must run the compilation command as root (or with su privileges) The command: python setup.py build install Can be decomposed into: python setup.py build (this part has been completed in your case) and: python setup.py install (here it fails!). In this case you must have superuser privileges, try: sudo python setup.py install Or, if you don't have sudo on yout system, become root and execute the command as root. Hugo 2010/3/22 Tatsiana Kirys nus...@mail.ru i dont know why i'm so helpless, but i still got a bunch of messengees: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -shared build/temp.linux-i686-2.6/modules/cealign/src/ccealignmodule.o build/temp.linux-i686-2.6/ov/src/OVContext.o build/temp.linux-i686-2.6/ov/src/OVHeapArray.o build/temp.linux-i686-2.6/ov/src/OVHeap.o build/temp.linux-i686-2.6/ov/src/OVLexicon.o build/temp.linux-i686-2.6/ov/src/OVOneToOne.o build/temp.linux-i686-2.6/ov/src/OVOneToAny.o build/temp.linux-i686-2.6/ov/src/OVRandom.o build/temp.linux-i686-2.6/ov/src/ov_utility.o build/temp.linux-i686-2.6/layer0/Block.o build/temp.linux-i686-2.6/layer0/Crystal.o build/temp.linux-i686-2.6/layer0/Debug.o build/temp.linux-i686-2.6/layer0/Deferred.o build/temp.linux-i686-2.6/layer0/Err.o build/temp.linux-i686-2.6/layer0/Feedback.o build/temp.linux-i686-2.6/layer0/Field.o build/temp.linux-i686-2.6/layer0/Isosurf.o build/temp.linux-i686-2.6/layer0/Map.o build/temp.linux-i686-2.6/layer0/Match.o build/temp.linux-i686-2.6/layer0/Matrix.o build/temp.linux-i686-2.6/layer0/MemoryDebug.o build/temp.linux-i686-2.6/layer0/MemoryCache.o build/temp.linux-i686-2.6/layer0/MyPNG.o build/temp.linux-i686-2.6/layer0/Parse.o build/temp.linux-i686-2.6/layer0/Pixmap.o build/temp.linux-i686-2.6/layer0/Queue.o build/temp.linux-i686-2.6/layer0/Raw.o build/temp.linux-i686-2.6/layer0/Sphere.o build/temp.linux-i686-2.6/layer0/Tetsurf.o build/temp.linux-i686-2.6/layer0/Texture.o build/temp.linux-i686-2.6/layer0/Tracker.o build/temp.linux-i686-2.6/layer0/Triangle.o build/temp.linux-i686-2.6/layer0/Util.o build/temp.linux-i686-2.6/layer0/Vector.o build/temp.linux-i686-2.6/layer0/Word.o build/temp.linux-i686-2.6/layer0/os_gl.o build/temp.linux-i686-2.6/layer1/Basis.o build/temp.linux-i686-2.6/layer1/ButMode.o build/temp.linux-i686-2.6/layer1/Character.o build/temp.linux-i686-2.6/layer1/CGO.o build/temp.linux-i686-2.6/layer1/Color.o build/temp.linux-i686-2.6/layer1/Control.o build/temp.linux-i686-2.6/layer1/Extrude.o build/temp.linux-i686-2.6/layer1/Font.o build/temp.linux-i686-2.6/layer1/FontType.o build/temp.linux-i686-2.6/layer1/FontGLUT.o build/temp.linux-i686-2.6/layer1/FontGLUT8x13.o build/temp.linux-i686-2.6/layer1/FontGLUT9x15.o build/temp.linux-i686-2.6/layer1/FontGLUTHel10.o build/temp.linux-i686-2.6/layer1/FontGLUTHel12.o build/temp.linux-i686-2.6/layer1/FontGLUTHel18.o build/temp.linux-i686-2.6/layer1/Movie.o build/temp.linux-i686-2.6/layer1/Ortho.o build/temp.linux-i686-2.6/layer1/P.o build/temp.linux-i686-2.6/layer1/PConv.o build/temp.linux-i686-2.6/layer1/Pop.o build/temp.linux-i686-2.6/layer1/PyMOLObject.o build/temp.linux-i686-2.6/layer1/Ray.o build/temp.linux-i686-2.6/layer1/Rep.o build/temp.linux-i686-2.6/layer1/Scene.o build/temp.linux-i686-2.6/layer1/ScrollBar.o build/temp.linux-i686-2.6/layer1/Seq.o
Re: [PyMOL] animating symmetry
On Mon, Mar 22, 2010 at 4:27 AM, Harry M. Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Jason, I have tried to implement what you suggested, but seeing as I haven't made a movie in PyMOL in a long time (and was never very expert at it), I don't seem to have got it working. Here is what I did, on my Mac (10.4.11), with PyMOL 1.1r1 I loaded 1yme, which has space group P21. I then duplicated it from the Actions menu, and got obj01. I then generated symmetry mates within 4 A of 1yme, and displayed only 1yme_01000100 since this shows the 2 fold screw axis along b. Again, from the actions menu, for obj01 I did Align To Molecule 1yme_01000100. Then I issued the command mset 1 x120 followed by: mview store, 1, object=1yme frame 60 matrix_copy obj01, 1yme mview store, 60, object=1yme I then clicked on play. The movie ran through the 120 frames, but nothing happened on the screen. So, what did I do wrong? Thanks Harry Harry, I forgot the matrix_mode option. Here's a script that should get your first simple movie done for 1yme and help you with others. # fetch a protein with a great name fetch 1yme, one, async=0 # symmetry expand symexp foo, one, one, 4 # rename for easier use; call it two set_name foo01-100-1,two # remove others dele foo* # setup the camera view orient # set up a simple movie and save camera position mset 1x60 mview store # save mobile objects original position mview store, object=one # align the two objects align one, two, object=aln # grab the transformation matrix mm = cmd.get_object_matrix(one) # undo the transformation matrix_reset one frame 60 # this caused the problems set matrix_mode, 2 # move object one cmd.transform_object(one, mm) # store its new position which # PyMOL automaticaly reinterpolates for us mview store, object=one mplay Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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
