[PyMOL] cmd.get_povray stereo segfault

Hi Warren, First of all, I really love the stereoview rendering in Pymol 0.99. Still, I'd like some more control on the lighting and the surfaces and would like to output to povray. However, cmd.get_povray first processes the stereo scene, building the primitives for each panel (as desired), but

Re: [PyMOL] models with reduced coordinate sets

Hi Siv, It's possible, but requires some python programming. If you're atom sequence is like CA, CB, CA, CB it shouldn't be to hard... (unfortunately I don't have time now :S sorry). Tsjerk On 3/1/06, Siv Midtun Hollup s...@ii.uib.no wrote: Hi, I have pdb files with c alpha coordinates and

Re: [PyMOL] Multiple origins possible?

Hi Jon, It is also possible to use the origin command to set the origin to a specified position or to use a selection for determining the origin (origin selection). In that way you can get what you want by setting the origin for each molecule before doing a rotation. Cheers, Tsjerk On 2/20/06,

Re: [PyMOL] getting pov-ray temp files

...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Bhyravbhatla, Balaji Sent: Wednesday, January 25, 2006 9:50 AM To: Tsjerk Wassenaar Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] getting pov-ray temp files Thanks Tsjerk, I still have

Re: [PyMOL] getting pov-ray temp files

Hi Balaji, The temporary povray file is written to the working directory. However, you may want to use the attached script instead. This will write your scene in two parts, a .pov file containing all meta data, such as the lights, camera and #defaults, and an include file (.inc) which contains

Re: [PyMOL] Selecting residue from object

Hi Indraneel, For this you want the operator and; look at the sections on selection in the manual. select newObj, (resi 2-4) and oldObj2 Cheers, Tsjerk On 10/28/05, Indraneel Majumdar indran...@smartpatch.org wrote: Hi, How can I select residues from a particular object? eg. select

Re: [PyMOL] Adjust radius of sphere

Hi Anbang Li, If you want to show the spheres in a relative size, you can use set sphere_scale, 0.5 to scale down the size by half for example. To do this for a specific object, use set sphere_scale, 0.5, object Otherwise, if you want to change the actual radius, you can use alter selection,

Re: [PyMOL] non-pdb coordinate help

Hi Kristl, The pdb-file is column formatted. You can find a specification of the file format at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html The easiest is to write a python script to do the conversion. Hope it helps, Tsjerk On 10/24/05, Kristl Adams

Re: [PyMOL] question about ray after alter and rebuild

Hi Pete, Check on the sections clipped_by and bounded_by in the povray documentation. You can clip with a defined plane, and can actually do so using different planes for different objects. Alternatively you can use other objects to clip. Another possibility is to use CSG difference or

Re: [PyMOL] How could I modify the secondary structures after superimpose of 2 or more structure?

Hi Chung-Ming Yu, You can change the secondary structure identifiers as follows: alter helix_selection,ss='H' alter sheet_selection,ss='S' alter loop_selection, ss='L' The RMS deviation gives you information about the quality of the fit. The lower the number, the better the fit. Cheers,

Re: [PyMOL] Shadows

Hi Corinne, Sabuj, You're right with regards to the CGO. An example script (written by Gareth Stockwell) can be found at http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the raytracing, don't be fooled, I'd say this was Pymol's internal raytracer :) Hope it helps, Tsjerk On

Re: [PyMOL] Pymol sessions

Hi John, I've never met this problem, and have saved very large session files. Which version are you using? Tsjerk On 8/3/05, John Whitlow whitlow.j...@gmail.com wrote: I've been loading the results of my docking runs, which are multi-hundred SD files, into pymol and saving the session for

Re: [PyMOL] unit cell and cell packing

Hi Zhenbo, If you mean the triclinic unit cell, you can show it with 'show cell', given that it's provided in the pdb file. If you want a different representation, you need a script. Also for the cell packing, you'd need a script. If it's just a translation lattice, I think I have what you need,

Re: [PyMOL] antialiasing and povray

If you just type povray you'll get all command line options. Tsjerk On 7/25/05, andrea spitaleri andrea.spital...@gmail.com wrote: try povray +A0.3 file.pov zero -^ regards Cameron Mura wrote: hi, Is there anything special I need to do/set to achieve antialiased

Re: [PyMOL] putty/sausage NMR figure

Hi Doug, Well, you could write a function average(Object1, Object2, ...) which would return an object containing the average structure and the fluctuations from this average in the b-factor field.., I think :) Might be a useful feature, so if I'll find some time... (but feel free to try to beat

Re: [PyMOL] 2 colors for transparent surface and cartoon

Hi Gabriel, You can set a specific color either for the surface or the cartoon with set surface_color, color set cartoon_color, color or if you want to have more control over the colors you can create a new object and show one in cartoon and the other in surface: create newobj, obj show

Re: [PyMOL] pymol + gromacs trajectories

Hi Yunfeng Hu, Frankly, with Pymol, people don't as far as I know. What I usually do is determine for the first frame of the individual pdb files (obtained with trjconv -sep) the orientation, viewing point and appearance. This I save in a .pml script. Then with a bit of python code, looping

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, Unfortunately, there is no CGO ellipsoid. What you might try is represent the units in the lattice as arrows as to indicate their orientation (determined as the principal or principle ;) axis), and have one unit in (cartoon) detail, with a more slender arrow inside. I think it

Re: [PyMOL] 3d plotting in pymol

connected by one ribbon. Have a nice time in Rome. I wish to travel to Venice sometime. Thanks and Regards --Amit -Original Message- From: Tsjerk Wassenaar [mailto:t.a.wassen...@chem.rug.nl] Sent: Thursday, May 13, 2004 3:04 AM To: a...@sdsc.edu Subject: Re: [PyMOL] 3d plotting

Re: [PyMOL] show residues forming hydrogen bonds with each other

Hi Yunfeng Hu, You can try the following (which has surely been on the list before :) ): show sticks, (byres ((protA within 3.5 of protB) or (protB within 3.5 of protA))) You might want to make sure that you only have hydrogen bonds by adding additional terms. Hope it helps. Cheers,

Re: [PyMOL] Restrict surface transparency to limited region

Hi Warren, Wouldn't it be possible to change the [r,g,b] representation in Pymol to [r,g,b,t]. Then it would be trivial to have gradual transparencies in surfaces or other things. Since transparency is supported... Cheers, Tsjerk Warren L. DeLano wrote: Roger, This isn't

[PyMOL] Unwanted artwork

Hi Guys, Attached you find a nice piece of artwork produced by Pymol 0.90. This happens when I switch my screen under Linux RedHat 8.0 or when the screen saver starts, which is obvious on a 1944 frame movie ;) The images seem to get overlaid. Rendering would be an option if only double

[PyMOL] Unit cell

Hi :) Was wondering if somebody knows how to retrieve unitcell information in pymol. Thanks in advance, Tsjerk -- ~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical

[PyMOL] Bonds

Hi all! I've written a script to position all atoms into a simulation box, but the connectivity stays, thus generating a beautiful image of bonds all across the box. Though not too clear. Is there a way to update the connectivity directly (other than saving the coordinates and reloading)?

[PyMOL] solid spheres

Hi guys, Was wondering if it is possible to get the spheres filled when clipping. Couldn't find this in the mail archive. Sorry if I just overlooked. Cheers, Tsjerk -- ~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :)

[Re: [PyMOL] changing display during movie (mvSet??)]

Hmm, forwarding this to the list too. Maybe someone else also wants to use it... ---BeginMessage--- Hi Mike, You can add the following to the script movie.py from Kristian Rother. It will give you the possibility to fade colours over a given set of frames, as I understand you want. For

[PyMOL] Pymol 'n Cave

Dear everybody and Warren in particular, Thanks for the great program.., I've been persuading everybody in my group to use it for viewing and images! But what's on my mind is that it would be great to be able to use PyMOL in a CAVE environment. I don't know whether anyone is busy

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