Re: [PyMOL] wild card
Beware of sweeping statements - I work with nucleic acids (mostly
bound to proteins) and I am continually irritated by the use of * in
nucleic acid names, and I think I qualify as anyone.
Now that the ASCII code has settled down somewhat, ' could take
it's rightful place in PDB files, liberating * to its otherwise
universal role as wild-card.
Laurence Pearl
On Wednesday, February 18, 2004, at 05:25 pm, Eric Zollars wrote:
Anyone who works with nucleic acids will certainly prefer the current
situation. From the PDB format guidelines:
* The asterisk (*) is used in place of the prime character (') for
naming atoms of the sugar group. The prime was avoided historically
because of non-uniformity of its external representation.
Eric
David A. Horita wrote:
Warren,
Personally, I'd much rather have wild-card selections in atom names
and have to deal individually with the ill-conceived PDB files than
the other way around.
Regards,
David Horita
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren
DeLano
Sent: Wednesday, February 18, 2004 10:56 AM
To: 'John Berrisford'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] selecting multiple atoms ie oxygen
John,
color red, 5paa and elem o
The problem with using asterices as wildcards in atom names is that
some ill-conceived PDB files actually use them in atom names.
However, PyMOL does support the use of a terminal wildcard in some
cases, such as with the delete command...
create obj01, none
create obj02, none
delete obj*
And with residue names
color red, as*
color blue, gl*
color pink, hi*
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
John Berrisford
Sent: Wednesday, February 18, 2004 3:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selecting multiple atoms ie oxygen
I wish to select multiple oxygens (labelled O1, O2 etc..
within my pdb file) and colour them red for example. Is there
any easy way of doing this other than typing out a list of
all the oxygens I wish to select?
eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p))
I know in molscript its posible to use a o* label to select
all oxygens, is such a switch possible in pymol. It doesn't
work, or I am using the wrong syntax if its possible.
Any thoughts would be appreciated.
John
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--
Laurence H. Pearl
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
Phone +44-207-970 6045 : Secretary +44-207-970 6046
FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk
--
Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin
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Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Michael, * Michael Banck mba...@gmx.net [2004-02-19 12:24] wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. Just as another data point. I use the CVS version of PyMOL (currently version 0.94) under Debian testing (using gcc-3.3.3 20040125). I haven't seen any crashes. (In case it makes a difference: Athlon XP+ 2500 and Radeon 9500 Pro graphics). Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
Re: [PyMOL] Povray
* Tsjerk Wassenaar t.a.wassen...@chem.rug.nl [2004-02-19 04:30] wrote:
Hi Guys,
I seem to have some trouble rendering with povray. The render starts and
finishes fine, and the image is created, but Pymol crashes with a
segmentation fault as soon as the rendering is done. The image is not
loaded to the viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop
(Intel Centrino) with SuSe 9.0. I have changed povray_exe in povray.py
in modules to povray.
I never use the povray rendering directly from within PyMOL. I find the
PyMOL ray-tracer is great for most things and if it isn't sufficient, I
want to be able to edit the povray input as you suggest below.
Any hints?
Yes!
Than to Warren probably, it would be great if Pymol would be able to
write a povray object (include file) from a given selection. That would
combine the strong points of pymol where it comes to showing the thing
as you want it, with those of Povray, where it comes to lighting,
positioning, colouring, textures and so on. Since Pymol is already
capable of producing povray input it wouldn't be very hard I would guess?
It can do this. I use a simple little script that I call make_pov.py:
##
# make_pov.py
from pymol import cmd
def make_pov(file):
(header,data) = cmd.get_povray()
povfile=open(file,'w')
povfile.write(header)
povfile.write(data)
povfile.close()
##
Load the file with 'run make_pov.py' and then within pymol do:
make_pov('povray.input')
Then outside PyMOL feed this file to povray with whatever command-line
options you need. You do need to look at the size of the image reported
by the make_pov. It looks something like:
PyMOLmake_pov('povray.input')
RayRenderPOV: w 1100 h 900 f 63.349 b 102.310
RayRenderPOV: vol -17.316 17.316 -14.168
RayRenderPOV: vol 14.168 63.349 102.310
RayRenderPovRay: processed 714 graphics primitives.
Ray: total time: 0.03 sec. = 123885.9 frames/hour. (0.03 sec. accum.)
You'll need to use the same width and height (or the same ratio) to
make your povray output have the correct width to height ratio, e.g.:
povray +Ipovray.input +W550 +H450
Cheers,
Rob
--
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] using the build function
Hello everyone, I'm trying to build some model proteins for a diagram showing a protein unfolding over several steps. I'm using the build function in the 0.95beta10 release. The main problem is that I can't control the angle of the protein chain, so the chain just goes off in one direction only, unless proline is placed in the middle of a helix at which point it goes off at a new angle. This makes me think that it can be specified, but I just don't know how to do it. Any help would be appreciated, Dan
RE: [PyMOL] using the build function
Dan, I think it's fair to say that PyMOL's currently molecular building capabilities are at the stage of a technology demonstration/proof-of-concept, but very little effort has yet been expended toward making them useful for real work. Part of that is because we don't yet have a general back-end modeling engine inside of PyMOL (molecular sculpting is a pure GIGO kind of thing). That is still an important long-term goal. But the other reason is that I don't really have a clear idea in my mind for how such a builder should operate. What I would like to get from you and all other interested PyMOL users are wish-lists for how PyMOL's molecular builder should work (better). No hurry though -- feedback over the next month or two should be fine, and anyone attending MUG or CUP is welcome to give me an ear-full next week. Basically, a major goal is to evolve PyMOL into a builder that can be useful across the board for biology and drug discovery: for proteins, small molecules, nucleic acids, carbohydrates, solvent, and so on. As a general tool, it should be capable of supporting crystallography-oriented building, manual homology modeling, and hypothetical hand modeling of small molecules, as well as simple illustrative tasks such as the one you're working on. Of course, specialty tools like O, Quanta, Modeller, and MacroModel will always be superior in their respective niches, but I hope PyMOL can become eventually become good enough for simple common molecular building tasks... Questions to consider: What are the best builders out there today that we should learn from? What are the key functions PyMOL must absolutely have to be a builder? What other extra attractive feature should PyMOL seek to emulate? How can we make the best use of what is already in PyMOL, unique or otherwise? What are the biggest holes in the current versions? Things that are already on the radar: Rotamer-libraries. A 1-D sequence viewer with alignment and editing capabilities. An integrated builder tutorial. Finding an existing force-field provider to work with... Back and forth 2D to 3D for small molecules. Dan, It sounds like a feature you would like is that ability to aim the chain being built towards a certain direction. In the meantime, to accomplish your task, build the chain first, then turn on Auto-Sculpting in the Sculpting menu, put the mouse into editing mode, then control-left-click-and-drag to move the chain where you want it to go. Ctrl-middle-click to pick one (or more -- in the latests betas) joints...and then shift-left-or-middle click-and-drag, or control-left-click-and-drag to move the resulting fragments. If your chain is small, increase the number of Cycles per Update to accelerate convergence. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Moriarty, Daniel Sent: Thursday, February 19, 2004 9:47 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] using the build function Hello everyone, I'm trying to build some model proteins for a diagram showing a protein unfolding over several steps. I'm using the build function in the 0.95beta10 release. The main problem is that I can't control the angle of the protein chain, so the chain just goes off in one direction only, unless proline is placed in the middle of a helix at which point it goes off at a new angle. This makes me think that it can be specified, but I just don't know how to do it. Any help would be appreciated, Dan --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id56alloc_id438op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] drawing hydrogen bonds or dashes
I have searched the manual and forum and cannot find how to draw a hydrogen bond between two specific atoms. I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; which draws a line between two atoms A97 OE1 and Mn200. So not a hydrogen bond but a specific line. Is this possible in pymol? I have read posts on changing the thickness of a dash and the number of dashes in a line. But none on how to draw the line. Can anyone help me, i'm a new user by the way! thanks John
[PyMOL] cartoons
dear all, i am new to pymol and i have a question about cartoons. i saw the demo of cartoon ribbons and really liked it, but i haven't been able to get my protein displayed that way. when i give the command cartoon automatic all i get is a simple line that apparently traces the backbone of my protein chain. cartoon loop does the same thing. with cartoon tube i get a thicker line. how do i set the parameters so that i get nice helices and sheets like the ones showed in the demo? thanks, alex
[PyMOL] Making the selection indicators bigger
Hello -- So I've installed PyMOL onto a new system, and I'm having trouble with the little pink indicators that pop up when you make a selection. On this machine they appear to about a single pixel wide, which on a 1280x1024 resolution screen makes them practically invisible! I've tried poking about in the options a little but I don't know what to change... Any guidance? -- Matt Matthew Zimmerman Interdisciplinary Biophysics, University of Virginia http://www.people.virginia.edu/~mdz4c/ Lab: 4-223 Jordan Hall, 1300 Jefferson Park Avenue, Charlottesville, VA 22908 (434)924-2948 Home: 2655-C Barracks Road Charlottesville, VA 22901 (434)244-7989
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Hi Michael, I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. When I run this copy rather than the .deb version I am able to ray trace lines without a crash. Best, Morri On Thu, 19 Feb 2004, Michael Banck wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. Michael --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Making the selection indicators bigger
Matt, Try: set selection_width, 6 set selection_width, 7 set selection_width, 8 Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Matthew Zimmerman Sent: Thursday, February 19, 2004 2:46 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Making the selection indicators bigger Hello -- So I've installed PyMOL onto a new system, and I'm having trouble with the little pink indicators that pop up when you make a selection. On this machine they appear to about a single pixel wide, which on a 1280x1024 resolution screen makes them practically invisible! I've tried poking about in the options a little but I don't know what to change... Any guidance? -- Matt Matthew Zimmerman Interdisciplinary Biophysics, University of Virginia http://www.people.virginia.edu/~mdz4c/ Lab: 4-223 Jordan Hall, 1300 Jefferson Park Avenue, Charlottesville, VA 22908 (434)924-2948 Home: 2655-C Barracks Road Charlottesville, VA 22901 (434)244-7989 --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Morri has a good point: The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds should be capable of running on virtually any current x86-based Linux system: RH, SUSE, Debian, Fedora, or whatever. So, if you're having trouble with compilation or use of distribution-specific packages on Linux and simply want to use PyMOL as a standalone tool, then downloading those binaries is an easy way to get going. Installation is trivial and you don't need root privileges. 1) tar zxvf pymol-(version)-bin-linux-libc6-i386.tgz 2) cd pymol 3) ./setup.sh 4) ./pymol.com Cheers, Warren FYI: those builds are built using GCC 2.96 under RedHat 6.2 for maximum compatibility -- they're not the fastest PyMOL binaries in the world, but they do run without a hassle. -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Morri Feldman Sent: Thursday, February 19, 2004 3:18 PM To: Michael Banck Cc: pymol users Subject: Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2 Hi Michael, I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. When I run this copy rather than the .deb version I am able to ray trace lines without a crash. Best, Morri On Thu, 19 Feb 2004, Michael Banck wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. Michael --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] molecular surface colored by hydrophobicity
Rongjin, PyMOL can certainly color surfaces by atom color and other properties. show surface color green, elem c color violet, elem n+o But Grasp's hydrophobicity function may be doing something more sophisticated then that... Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of gu...@umbi.umd.edu Sent: Wednesday, February 18, 2004 7:12 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] molecular surface colored by hydrophobicity Dear all, I am preparing a figure of a molecualr surface, colored by the hydrophobicity of surface residues. Can pymol do this job? How about showing atom C* in a color, and N* and O* in another color? In fact I have tried GRASP but failed in coloring the surface. I used r=hyd, but could not color the surface of those redisues. This is an old version of grasp (1.0?). I am not familiar with this program. If anybody can tell me the correct way of doing it in grasp, it will also be greatly appreciated. Rongjin Guan --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] cartoons
Alex try typing: dss this will assign secondary structure to your PDB and then the cartoon will show you the sheets and helices you desire. Scott On Feb 19, 2004, at 1:44 PM, ALEX DAJKOVIC wrote: dear all, i am new to pymol and i have a question about cartoons. i saw the demo of cartoon ribbons and really liked it, but i haven't been able to get my protein displayed that way. when i give the command cartoon automatic all i get is a simple line that apparently traces the backbone of my protein chain. cartoon loop does the same thing. with cartoon tube i get a thicker line. how do i set the parameters so that i get nice helices and sheets like the ones showed in the demo? thanks, alex --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
