[PyMOL] Stereo on Sharp LCD
Hi, I'm testing the Sharp 3D LCD monitor (LL-151-3D) using PyMOL 0.99rc6. By simply pressing the 3D button on the monitor without enabling any stereo in PyMOL, it appears to show somewhat enhanced depth. However, if I enable the quad-buffered stereo in PyMOL, the picture is just smeared. I was wondering if special version of PyMOL is needed, as well as specific graphic cards. If so, is such version of PyMOL available for purchase or download. Or, this is just the best the monitor can do. Thank you very much. Frank
[PyMOL] Suggestion?
Hi, I was wondering if we can move and group the molecules in the upper-right molecule panel. Also, it would be even better if PyMOL can show properties stored in the molecule file (e.g. SDF). I guess a separate window may be needed, while in this way you can neatly organize all the related molecules from a project in one place. Sorry it may sound like a Schroedinger project table :-) Thanks, Frank
[PyMOL] A suggestion on molecule selection
Hi, When two SDF files, each of which contains multiple entries, are loaded, it seems PyMOL can only display the same frames from the two objects. It goes like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like frame 1 in obj 1 and frame 3 in obj 2. I was wondering if there is a way to get around. Thanks a lot, Frank
[PyMOL] separate views of different objects
Hi, I was wondering if there's a way in PyMOL to separate different objects. That is, different objects don't move together. When an object (molecule) is hidden it doesn't change the orientation no matter how the others move. This would be useful if you want to visualize a set of related targets but not conformationally connected. Thanks a lot, Frank
[PyMOL] A suggestion
Hi, I was wondering if PyMOL (with some plugin) has the capability to visualize a series of small molecules that are associated with a protein in a seamless way, e.g. poses from a docking exercise. Right now, what we can do is to combine all the structures into a single file and open with PyMOL. It would be a great tool to further advance PyMOL as a visualization tool. Thanks, Frank
[PyMOL] util.cba in a loop
Hi, I was trying a script similar to the following: for i in ragne(1,5): print i util.cba(26,resi 930-933) The loop seems to be only iterated once right after the util.cba. I tried other commands like cmd.show and cmd.hide, which are fine. Is it possible to use util.cba in a loop? Thanks, Frank
[PyMOL] Hidden residue selection
Hi, When I select a residue that is shown as stick, the usual magenta dots that highlight the residue seem to be hidden behind the stick rendering and are not visible. It is however okay when the residues are shown as lines. The latest beta version of PyMOL is used. Also, just a suggestion, is it possible to only highlight the atoms that are visible on selection in the case when the hydrogen atoms are hidden? It really obscures the view with those extra dots. Thanks, Frank
[PyMOL] Manually move one molecule relative to another
Hi all, I was wondering if there's a way to manually move a molecule relative to other molecules (such as in the case of manual docking) using the mouse. I searched the previous posts and found that MovF/RotF are the way to do that. But, when using these mouse functions to move the molecule, one atom of the molecule moves erratically and the molecule is then distorted. It appears to be a bug. Thanks a lot, Frank
[PyMOL] Molecular surfaces
Hi all, I was wondering if there are any simple tools to compute various molecular surface properties, such as electrostatic, polarizability, hydrophobicity, or even HOMO-LUMO, for small organic molecules. I understand Miguel from Jmol project is actively developing the surface feature. Just wanna be ready of the back-end computational tools. The apbs tool is surely great to compute electrostatic potential; however, it requires charges to be computed a prior, particularly in the case of unknown small molecules. I tried anteamber to compute the charge. Though it works most of the time, it is kind of slow for on-the-fly computation and visualization. Any suggestions? Thanks, Frank
[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] modeling in pymol
Hi, I was wondering if PyMOL has some simple modeling functionalities, such as rotate through a particular bond (change the dihedral angle), delete/form bonds, superimpose, etc., via mouse. These functions will be particularly useful for molecular modeling besides the wonderful graphics. Also, when I load certain PDB files, PyMOL automatically assign many bonds which are not supposed to be there. I understand it may base on distance rule for assigning molecular bonds; however, is there any way I can change the behavior of this? Thanks, Frank
[PyMOL] animation using pymol
Hi, I have two static frames of a loop structure, one is in an open form, the other is in closed form. I would like to make an animation which shows the transformation movement from open to closed. I was wondering if Pymol can handle this. Thanks, Frank
Re: [PyMOL] different stick_radius for different residues
Thanks a lot! I have a another question. Is there way to define a group of residues which are not linked to each other. I tried create forst2, (resi 1 and resi 32 and resi 356) but it doesn't work. Thanks, Frank --- Morri Feldman mfeld...@itsa.ucsf.edu wrote: Dear Frank, try: create forSticks1, resi 1-2 show sticks, forSticks1 set stick_radius, .25, forSticks1 create forSticks2, resi 12-15 show sticks, forSticks2 set stick_radius, .1, forSticks2 By using create, you create a new named object with its own settings database. The new object's settings can be set independently of other objects. Best, Morri On Tue, 3 Feb 2004, Dr. S. Frank Yan wrote: Hi, I was wondering if Pymol is capable of setting different stick thickness for different residues of a molecule. I tried set stick_radius=0.25 show sticks, resi 1-2 set stick_radius=0.1 show sticks, resi 12-15 It appears that the stick_radius variable is global, and it changes the thickness of all the sticks. Thanks, Frank __ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/ --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users __ Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online. http://taxes.yahoo.com/filing.html
[PyMOL] different stick_radius for different residues
Hi, I was wondering if Pymol is capable of setting different stick thickness for different residues of a molecule. I tried set stick_radius=0.25 show sticks, resi 1-2 set stick_radius=0.1 show sticks, resi 12-15 It appears that the stick_radius variable is global, and it changes the thickness of all the sticks. Thanks, Frank __ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/
Re: [PyMOL] hardware stereo using pymol
Hi, Thanks for the reply. We set them; however, it is still not working yet. I can see the pymol screen is flickering, but the emitter is apparently not turned on (no red light). --- Andreas Aemissegger aemisseg...@org.chem.ethz.ch wrote: On Saturday 17 January 2004 03:25, Dr. S. Frank Yan wrote: I'm using stereographics crystaleye with e-2 emitter and Quadro2 Pro graphics card, which does support the emitter. I am able to set the stereo on, and the screen starts to flick a little; however, the emitter is not turned on by the program and therefore no stereo. Stereographics claims that the emitter has to be turned on/off by application program when the stereo is enabled/disabled. I was wondering if anyone has experience with that. Thanks a lot, Frank Which OS is that? If you are on Linux, make sure you configure your X11 properly: 1) use the nvidia driver 2) load the glx module 3) remove the dri and GLcore modules 4) Most important: add Option Stereo 3 to the nvidia device section to turn on support for onboard stereo Regards Andreas -- Andreas Aemissegger, Laboratory of Organic Chemistry ETH Hoenggerberg - HCI F322, 8093 Zurich, Switzerland Phone: +41 1 632 2972, Fax: +41 1 632 1486 Mail: aemisseg...@org.chem.ethz.ch, WWW: http://www.protein.ethz.ch PGP key on request --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users __ Do you Yahoo!? Yahoo! Hotjobs: Enter the Signing Bonus Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus
[PyMOL] hardware stereo using pymol
I'm using stereographics crystaleye with e-2 emitter and Quadro2 Pro graphics card, which does support the emitter. I am able to set the stereo on, and the screen starts to flick a little; however, the emitter is not turned on by the program and therefore no stereo. Stereographics claims that the emitter has to be turned on/off by application program when the stereo is enabled/disabled. I was wondering if anyone has experience with that. Thanks a lot, Frank __ Do you Yahoo!? Yahoo! Hotjobs: Enter the Signing Bonus Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus
