[PyMOL] RE: making a movie
Hi, this works now fine and I get a movie. However, when trying to save it with "mpng mov" I I get a single frame only, and with "mpng mov #" I get a series of frames in which all pictures are overlayed sequentially. I.e. the first frame has the first picture, the second has the first plus the second picture one over the other and so forth. The very last picture is then a big blop of all states looking like a collection of all conformations as you might see it in a very bad NMR structure. What is wrong? Cheers, Dieter On 3 Feb 2005 at 15:26, Warren DeLano wrote: > Sorry, > > mdo syntax is weird for questionable reasons: you need a colon instead of a > comma after the first argument. > > > mdo 1: turn x,5; turn y, 5 > > cheers, > Warren > > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > > -Original Message- > > From: pymol-users-ow...@lists.sourceforge.net > > [mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of > > dieter blaas > > Sent: Thursday, February 03, 2005 2:12 PM > > To: pymol-users-ad...@lists.sourceforge.net > > Subject: making a movie > > > > Trying to make a simple movie I have followed the > > instructions given in "help mdo" i.e.: > > > > load test.pdb > > mset 1 > > mdo 1, turn x,5; turn ; > > y,5mplay > > > > however,already at the mdo command I receive the message "Error: > > invalid arguments for mdo command." > > what is wrong??? > > Thanx, Dieter > > > > > > > >
[PyMOL] Ver0.98: Regarding old configurations...
Is there anyone out there: 1) still running PyMOL on RedHat 6.2-7.1? or can we migrate out lowest-common-denomator Linux build to RH 7.2? 2) using Python 1.52 with PyMOL? 3) currently depending upon the Numeric or Numarray included with various PyMOL builds? If so, then which one? 4) running PyMOL under Windows NT, Win98, or Win ME? If so, then please speak up -- or forever hold your peace. Thanks for your feedback. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com
Re: [PyMOL] Desparate call for help
> I don't have red hat support yet. The problem appears to be that the > nvidia installer (nvidia...6629pkg2.run) is getting confused as to which > kernel is running. Just a couple of quick thoughts -- 1) Does /usr/src/linux point to the original installed kernel soruces or the updated kernel sources? Some software will look in /usr/src/linux for the headers, and if these aren't the headers for the kernel you're actually using the module won't load. 1b) The compiled kernel has the exact version number encoded in it, as does every module. Therefore, unless you have the source for 2.4.21-27.0.2.EL, there is no (easy, safe, and guaranteed) way to compile the module and have it work on your system. 2) Sometimes it is necessary to use an earlier driver. I had to go back several versions to get a friend's Inspiron 5150 to work - the newer drivers just froze X.
[PyMOL] Desparate call for help
Hi folks, Firstly sorry for the non pymol question, but if I can fix this I can use pymol in 3D. So the problem is that I can't get my nvidia driver to work! As I hear the groans...I have tried many things to no avail. Specs: linux RHE3-AS AMD-64 bit opteron dual processor nvidia quad 980 kernel 2.4.21-4ELsmp updated to 2.4.21-27.0.2.EL I'm using redhat for other proprietary software requirements so unfortunately I xcan't use anything else. (we could make it work on fedora core 2!) I firstly get the gcc_version check error. I can get around that by using export IGNORE_CC_MISMATH command. I then get this: "If you are using a Linux 2.4 kernel, please make sure you either have configured kernel sources matching your kernel or the correct set of kernel headers installed on your system." I don't have red hat support yet. The problem appears to be that the nvidia installer (nvidia...6629pkg2.run) is getting confused as to which kernel is running. Has anyone else had these issues/knows any hints. Many thanks in advance J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
[PyMOL] Centrosymmetric symmetry?
Has anyone ever been able to use PyMOL to expand the symmetry of a centrosymmetric space group? I have tried twice, once in P-1 and once in P21/c. Both attempts result in a core dump, but before asking Warren to examine his code, I thought I should check with everyone else and see if it works OK under other operating systems, other keyboard operators (i.e., not me), or what. I'm using PyMOL v0.98b27 under Win2000 on one box and WinXPsp1 on another Thanks, Tom
RE: [PyMOL] Default colors by element
Note also that PyMOL beta versions now match Jmol's colors element-for-element except for those few atomic colors previously defined in PyMOL (just C,N,O,H,S -- I think) Changing those colors is simply a matter of changing the associated color name: set_color helium, [ 0.4, 0.3, 0.7] recolor Carbons are the only exception, siince objects in PyMOL are given one of 40 default carbon colors in a repeating cycle so that separate molecules can be visually distinguished. To turn this off: set auto_color, off To get a Jmol-like carbon: set_color carbon, [0.564, 0.564, 0.564] load some_pdb_file.pdb Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Robert Campbell > Sent: Thursday, February 03, 2005 10:20 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Default colors by element > > Hi Frank, > > * S. Frank Yan [2005-02-03 10:10] wrote: > > > > Is there anyway to show the default color scheme of > different elements? > > The basics such as CHNOS are clear, but how about F, Cl, > Br, I, P, Na, > > Mg, Ca, etc? > > In the "Settings" menu on the external GUI, you can select "Colors..." > Then you will get a box with all the colours listed in it. > You can select a colour and then the "Edit" button (or just > double click the colour name) to see the colour. > > Otherwise you can look in the source in the file: > layer1/Color.c to see the complete colour listing at once. > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > > 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 > > > --- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > Reporting Tool for open source databases. Create drag-&-drop > reports. Save time by over 75%! Publish reports on the web. > Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Default colors by element
Hi Frank, * S. Frank Yan [2005-02-03 10:10] wrote: > > Is there anyway to show the default color scheme of different elements? > The basics such as CHNOS are clear, but how about F, Cl, Br, I, P, Na, > Mg, Ca, etc? In the "Settings" menu on the external GUI, you can select "Colors..." Then you will get a box with all the colours listed in it. You can select a colour and then the "Edit" button (or just double click the colour name) to see the colour. Otherwise you can look in the source in the file: layer1/Color.c to see the complete colour listing at once. Cheers, Rob -- Robert L. Campbell, Ph.D. 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] Default colors by element
Hi, Is there anyway to show the default color scheme of different elements? The basics such as CHNOS are clear, but how about F, Cl, Br, I, P, Na, Mg, Ca, etc? Thanks a lot, Frank
pymol-users@lists.sourceforge.net
> I need a few high-quality images of organic molecules for > teaching purposes. I've been playing with your latest > MacPyMol build all morning and can't seem to find a way of > displaying in ball & stick. I can either show spheres or > sticks, not B&S. I assume this can be done in MacPyMol. The > manual did not shed any light on the situation. Thanks. show sticks set valence, on set stick_ball, on set stick_ball_ratio, 3 set stick_radius, 0.12 You may wish to play with the exact values to get the look you want. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com
