[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

[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 l

[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.

[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

[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

[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 m

[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

[PyMOL] Stereo output checkerboard format

Hi, I was wondering if PyMOL will support so-called checkerboard stereo format output. This format is natively supported by the new DLP technology. We can finally get rid of the CRT monitors and put on the flat monitor and/or projection for the general audience, e.g. medicinal chemists. I th

[PyMOL] add hydrogens using different hybridization

Hi, I was wondering if there is a way to add hydrogens to a selected atom based on different hybridization, e.g., sp2, sp3, etc., in which way different number of hydrogens will be added with the corresponding geometry. Thanks, Frank __ Do you Yahoo!? Yahoo! Sm

[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

[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,

[PyMOL] Web plugin of PyMOL

Hi, I was wondering if there is a browser plug-in for PyMOL, which can be used to display molecules inside webpage with some limited manipulation tools. 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] 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 wan

[PyMOL] MovF and RotF problems

Hi, I was trying to use the MovF and RotF functions in the 3-Buttion Editing mode using version 0.98. The molecule is deformed with one single atom being totally out of the place during the movement. Does anyone have the same problem? Thanks a lot, 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

[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

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 wrote: > On Saturday 17 January 2004 03:25, Dr. S. Frank Yan > wrote: > &g

[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

Re: [PyMOL] different stick_radius for different residues

t; 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 &g