Re: [PyMOL] b-factors?

2002-05-24 Thread Robert Campbell
Dear PyMOLers, Nat Echols n...@mail.csb.yale.edu [2002-05-23 10:25] wrote: Can PyMOL do coloring by B-factors? I didn't see anything about this in the manual. If not, I'll go ahead and write a new function, unless someone else is working on this. * DeLano, Warren

[PyMOL] Coloring by B-factors

2002-05-31 Thread Robert Campbell
Dear PyMOLers, I've revised the B-factor colouring script that I published on this list back on May 24th. The function now allows you to choose the style of colour ramp (blue-magenta-red or rainbow), the way in which the B-value ranges are chosen (histogram or smooth ramp) plus the number of

[PyMOL] Bug in CGO cylinder drawing code?

2002-07-17 Thread Robert Campbell
Warren, I have found a CGO-drawing problem for which I cannot find a solution. I've been trying to perfect my script for drawing symmetry axes of crystal structures. I noticed that the script wasn't drawing all of the axes that it should have (i.e. not all of those that were listed by the

Re: [PyMOL] g: cgo label orientation

2002-08-20 Thread Robert Campbell
* dee...@iastate.edu dee...@iastate.edu [2002-08-20 07:03] wrote: On Sat, Aug 17, 2002 at 10:23:46PM +0200, Bartholomeus Kuettner wrote: Hello there! I followed mailing list instructions to create cgo based labels via a python script. Unfortunately, the labels are not in plane but more

Re: [PyMOL] Reading CCP4 maps

2002-09-05 Thread Robert Campbell
Quyen, * Quyen Hoang hoa...@mcmail.cis.mcmaster.ca [2002-09-05 15:32] wrote: I would like to read CCP4 electron-density maps into PyMol, but I don't know how (explore maps loaded fine). Would someone please give me a quick summary of the procedure. Thank you! simply doing: load

Re: [PyMOL] how to show the map in wall-side stereo way

2002-12-17 Thread Robert Campbell
Hi, * xiaofeng qian xiaofengq...@hotmail.com [2002-12-16 20:47] wrote: Does anybody know how to display the electrondensity map in the wall-side stereo way(not cross-eye way)? You can switch to wall-eyed, by changing the sign of the stereo angle. You will need to alter the stereo_shift as

Re: [PyMOL] PovRay file export

2003-02-26 Thread Robert Campbell
Hi, On 2003-02-26 14:54 Andreas wrote: how to write the PovRay file out? (I do not want to embed PoyRay as the renderer.) I also don't use povray directly as I like to edit the povray input file. I use the following script: # make_pov.py

Re: [PyMOL] coloring stick and atoms

2003-02-26 Thread Robert Campbell
Hi, On 2003-02-26 11:36 Mathews wrote: I am looking for a way to change the stick color by maintaining the atom color. Extra info: Using the set color_sphere command to change the colors of the spheres, changes the colors of the atoms to one specific color. I would like to have

Re: [PyMOL] helix width

2003-02-27 Thread Robert Campbell
* cheom-gil cheong cheomgilche...@hotmail.com [2003-02-27 12:37] wrote: I want to reduce the width of helices and the strands and the thickness of the strand to make better-looking figures. Does anyone did that before? It must be some setting parameters but I cannot find it in my manual.

Re: [PyMOL] color by B-factor?

2003-02-28 Thread Robert Campbell
Hi Cameron On 2003-02-28 12:48 you wrote: If possible, how does one color a PDB representation in PyMOL by the B-factor field?? Yes, have a look at my color_b.py script in the PyMOL part of my web site: http://biophysics.med.jhmi.edu/rlc/work/pymol You need to do a run color_b.py first,

Re: [PyMOL] coloring surfaces

2003-04-02 Thread Robert Campbell
Rajarshi and Gareth, * Gareth Stockwell gar...@ebi.ac.uk [2003-04-02 08:40] wrote: Rajarshi, With a bit of work you could add such a feature to the script, by using compiled graphics objects (CGOs). The PyMOL documentation explains how to use them. Gareth On Tue, 2003-04-01 at 21:42,

Re: [PyMOL] POVRay output

2003-04-15 Thread Robert Campbell
* Armand Tepper wjwtep...@yahoo.com [2003-04-15 04:09] wrote: Dear all, 1) In a future version of Pymol, would it be possible to parametrize the POVray output such that all textures, finishes etc. are declared once as variables (e.g. something like #declare carbon_texture = texture) ?

Re: [PyMOL] how to change all carbon atoms to yellow

2003-04-21 Thread Robert Campbell
* yibin xu yibin...@jcu.edu.au [2003-04-21 13:30] wrote: A little question. I want to color all carbons of my ligand to yellow and keep oxygen-red and nitrogen-blue. How to do that? Thanks in advance. color yellow , (ligand and e;c) where ligand is some method of selecting your ligand. It

Re: [PyMOL] color by ss

2003-04-29 Thread Robert Campbell
Hello, * cami...@mrc-lmb.cam.ac.uk cami...@mrc-lmb.cam.ac.uk [2003-04-29 14:08] wrote: Hello Pymol community, I'm experiencing a problem when colouring a pdb by secondary structure. The colour bleeds from the ends of helices and sheets into loop. for example, if I were to

Re: [PyMOL] ligand rendering

2003-05-13 Thread Robert Campbell
* Nat Echols n...@bioinfo.mbb.yale.edu [2003-05-13 15:38] wrote: I'm new with Pymol and I would like your help in the following problem: I have a receptor image that I want to emphasize the ligand in its interior. I'm a big fan of transparent surfaces for this, e.g.:

[PyMOL] New PyMOL-related scripts

2003-05-23 Thread Robert Campbell
Hi Folks, Some of you may have been using my color_b.py script for colouring by the value of the B-factor. Thanks to the stimulus of one user, I've updated it to have a variety of colouring gradients. You can now select from the following options: Gradients: 'bwr' blue-white-red (like

Re: [PyMOL] nonbonded

2003-06-19 Thread Robert Campbell
* Stefan Reinelt stefan.rein...@mpimf-heidelberg.mpg.de [2003-06-19 15:19] wrote: Hey there, I try to get a nonbonded as a simple ball without any sticks out of it. Any ideas ? Try: hide nonbonded, selection if desired show nb_spheres, selection if desired Cheers, Robert -- Robert L.

Re: [PyMOL] alternative method for loading coordinates

2003-09-11 Thread Robert Campbell
Warren, * Warren L. DeLano war...@delanoscientific.com [2003-09-09 17:42] wrote: If you're willing to switch into Python, there is an undocumented read_pdbstr function which can take a PDB file as a string variable. See modules/pymol/importing.py for the code. Temporary files are

Re: [PyMOL] A couple of movie questions

2003-09-18 Thread Robert Campbell
Hi Stephen, * Stephen Graham steph...@mail.usyd.edu.au [2003-09-18 21:02] wrote: First up: Is there any way to tell PyMol *not* to change its view when loading a PDB file? For viewing in general, and for movies w/ morphs (etc.) in particular it would be nice to not have to re-set the view

Re: [PyMOL] Creating hydrophobic surfaces

2003-10-01 Thread Robert Campbell
Hi Jason, * jkyano jky...@scripps.edu [2003-10-01 11:51] wrote: I am looking for a free program or script that can spit out sidechain hydrophobicity in the B factor column so that I can color a surface by hydrophobicity using the color_b.py script. I have a data2bfactor.py script that will

[PyMOL] Drawing symmetry operators

2003-10-10 Thread Robert Campbell
Dear PyMOLers, It was brought to my attention recently that the draw_cell.py and draw_symops_cctbx.py scripts on my web site were broken due to changes in the cctbx interface. It had been a while since I used the scripts myself, and I hadn't kept abreast of Ralf's changes ... Then Warren kindly

[PyMOL] CGO drawing bug (was Re: Drawing symmetry operators)

2003-10-10 Thread Robert Campbell
* Robert Campbell r...@post.queensu.ca [2003-10-10 13:04] wrote: snip all that stuff about the new scripts P.S. Warren, there is still a problem with drawing CGO cylinders and sausages along the (1,-1,1) direction -- they don't appear unless you ray trace the image: As an example: load

Re: [PyMOL] custom pymol scripts

2003-11-17 Thread Robert Campbell
Jack, * Jack Howarth howa...@bromo.med.uc.edu [2003-11-11 11:17] wrote: What exactly is the recommended approach for installing and maintaining custom pymol python scripts? While I have seen messages describing custom pymol scripts, their installation isn't described. Should I put them

Re: [PyMOL] Fog and ray-tracing

2003-12-05 Thread Robert Campbell
Hi Loic, * Loic BERTRAND l...@cryst.bioc.cam.ac.uk [2003-12-03 18:42] wrote: I want to generate a ray-traced image with a white background and a very strong fog effect. I tried to play around with the ray_trace_fog, ray_trace_fog_start and fog parameters but could not manage to do it.

Re: [PyMOL] assign secondary structure?

2003-12-17 Thread Robert Campbell
* Michael Bovee mbo...@uvm.edu [2003-12-16 14:27] wrote: Hmm. When I try this I get a syntax error: __ PyMOLload EcHRSade.pdb Executive: object EcHRSade created. PyMOLhide PyMOLshow cartoon PyMOLdss EcHRSade Traceback (most recent call

Re: [PyMOL] get_dihedral multiple objects

2004-02-11 Thread Robert Campbell
Leigh, * le...@rsvs.ulaval.ca le...@rsvs.ulaval.ca [2004-02-11 15:18] wrote: I am trying to use the get_dihedral routine. If I've got just one object it works as expected. For example: PyMOLget_dihedral 9/C, 10/N, 10/CA, 10/C (I type in) cmd.get_dihedral: -49.721 degrees. (pymol

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Robert Campbell
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)

Re: [PyMOL] Povray

2004-02-19 Thread Robert Campbell
* 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

Re: [PyMOL] restoring default surface coloring

2004-03-02 Thread Robert Campbell
* Lieven Buts lie...@ultr.vub.ac.be [2004-03-02 09:03] wrote: On Tuesday 02 March 2004 07:56, Matt Franklin wrote: [...snip...] I then realized that I had absolutely no idea how to restore the default surface coloring! (Except by quitting and restarting...) set surface_color, default

[PyMOL] New color_b.py and data2bfactor.py scripts

2004-03-04 Thread Robert Campbell
To the PyMOLers out there. This isn't particularly exciting news, but if you use my color_b.py and data2bfactor.py scripts, you may be interested in the update versions that I've just put on my web site. There is now a function in data2bfactor.py that loads data into the occupancy column,

Re: [PyMOL] New color_b.py and data2bfactor.py scripts

2004-03-05 Thread Robert Campbell
* Robert Campbell r...@post.queensu.ca [2004-03-04 16:24] wrote: To the PyMOLers out there. This isn't particularly exciting news, but if you use my color_b.py and data2bfactor.py scripts, you may be interested in the update versions that I've just put on my web site. Ops

[PyMOL] Yet another new script in my PyMOL script archive

2004-03-11 Thread Robert Campbell
Hi PyMOLers, I've added a new script to my PyMOL script archive. Have you ever wanted to highlight in the display a particular sequence and couldn't be bothered to look up the residue numbers? Me, too. So I wrote a little script called seq_select.py that creates a named selection of an object

[PyMOL] Bugs squashed in my scripts

2004-04-08 Thread Robert Campbell
Dear PyMOLers, It was brought to my attention yesterday that 2 of my scripts had problems with their selection routines, so I've put repaired versions up on my web site. They are: color_by_attype.py seq_select.py The problems arose if you had more than one object up with multiple chains and

Re: [PyMOL] Selections

2004-04-15 Thread Robert Campbell
Hi Jason, * Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote: Master Users, I'm a bit new to PyMol and still trying to master selections. I've read the documentation and played with quite a few macromolecules now and still have some problems with selections. For example, I

[PyMOL] New (repaired!) draw_symops scripts

2004-05-21 Thread Robert Campbell
Dear PyMOLers, A couple of users of my scripts had contacted me about problems with my draw_symops_cctbx.py and all_axes_new.py scripts. I've (I think) solved those problems and added a new functionality requested by one of them. The main problem was getting anything using cctbx to run properly

Re: [PyMOL] surface/grid questions

2004-08-27 Thread Robert Campbell
Dear Marcelo, * castilho casti...@if.sc.usp.br [2004-08-23 17:02] wrote: My name is Marcelo and I am a basic-level pymol user. I work with docking programs and I am trying to make pymol our default program for analysing docking results...this brings me to some questions: Is it possible to

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

2004-10-07 Thread Robert Campbell
Hi Roger, * Roger Dodd rb...@cam.ac.uk [2004-10-07 16:33] wrote: I am trying to prepare a figure illustrating a fairly complex packing arrangement in a large H32 (R32) unit cell, where the packing may actually have some biological relevance. To try and show the packing I've been

Re: [PyMOL] importing multiple states using a script to avoid typing load file0.pdb, file1.pdb, etc.

2005-01-19 Thread Robert Campbell
Hi, * Jeffrey N. Agar a...@chem.uga.edu [2005-01-18 14:07] wrote: also, typing the following example from the users manual gives invalid syntax with an arrow pointing to the m in file_list =glob(mov*.pdb): 2) The following is a Python program (with a .py or .pym extension) which uses a

Re: [PyMOL] selecting side chains

2005-01-28 Thread Robert Campbell
Hi, * Lisa Craig licr...@sfu.ca [2005-01-27 20:43] wrote: How do I select side chains without selecting the backbone atoms? Add ! n. n+ca+c+o or in long form and not name n+ca+c+o to your selection. So to colour all arginine and lysine side chains blue: color blue, r. arg+lys ! n.

Re: [PyMOL] secondary structures, spheres and plugins

2005-03-04 Thread Robert Campbell
Hi Einat, * Einat Sitbon einat_sit...@hotmail.com [2005-03-03 14:27] wrote: 1) Secondary structure can be viewed as cartoons, or as colors. The problem is the boundaries are not the same. If I color a strand by secondary structure, it seems that the following loop is a strand as well. I?m

Re: [PyMOL] combine distance objects

2005-03-08 Thread Robert Campbell
Hi, Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote: I want to create a lot of distance objects (in the hundreds) between particular atomic pairs. Obviously I can make a script like the following, inserting the exact atomic selections that I want: distance distobj12 =

Re: [PyMOL] How to generate a DNA structure with given sequence?

2005-03-24 Thread Robert Campbell
To add to what Cameron said: * Cameron Mura cm...@ucsd.edu [2005-03-24 09:44] wrote: Hi Hyun-Chul, It's easy to use PyMOL to build protein fragments in standard geometries (Build menu in the Tcl/Tk GUI window), but I'm not sure about DNA. Three non-PyMOL methods that I'm aware of are:

[PyMOL] Fitting/alignment of non-identical sequences

2005-03-29 Thread Robert Campbell
Dear Folks, I know a number of people have stumbled over the difficulty of calculating RMSD values for structures of non-identical sequences. While teaching a class that introduced students to the use of PyMOL to look at protein structures and to the study of certain structurally homologous

Re: [PyMOL] Fitting/alignment of non-identical sequences -- UPDATE

2005-03-31 Thread Robert Campbell
Dear Folks, * I r...@post.queensu.ca [2005-03-29 16:27] wrote: After playing around with this I finally got tired of doing it manually, so of course I wrote a python script to do this. It uses the alter command (so it isn't fast!) to modify the alt, name, resn, resi, chain, and segi values

Re: [PyMOL] sticks with different radii

2005-04-13 Thread Robert Campbell
Hi Shohei, * Shohei Koide sko...@uchicago.edu [2005-04-12 15:39] wrote: Hi, I would like to use different stick radii for the backbone and side chains (e.g. thicker sticks for BB and thinner ones for SC). The command set stick_radius=X seems to set the global stick radius, so I cannot use

Re: [PyMOL] creating r3d files

2005-04-27 Thread Robert Campbell
Hi Paula, * Paula Salgado pa...@strubi.ox.ac.uk [2005-04-27 10:44] wrote: Hi, Is it possible to save an r3d file in pymol for exporting into other render programs like povray? I would like to test rendering in other programs... I use the following script to save an input file for povray:

Re: Subject: Re: [PyMOL] fit command

2005-06-21 Thread Robert Campbell
Andre, * tree javer...@utmb.edu [2005-06-20 23:31] wrote: The Wiki (http://www.pymolwiki.org/) has some information about this. It also shows you how to change some properties to make things easier to fit. Intra_Rms (http://www.pymolwiki.org/index.php/Intra_Rms), and Fit

Re: [PyMOL] list residues in a selection

2005-07-07 Thread Robert Campbell
Hi, * Michael George Lerner mler...@umich.edu [2005-07-06 09:28] wrote: with my editing to put the original e-mail in the correct location On Wed, 6 Jul 2005, Sebastien Gerega wrote: Is there a way to list the residues that are in a selection? For example if I use the command select near,

Re: [PyMOL] Name length in names panel

2005-07-28 Thread Robert Campbell
Hello Sebastien, * Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-07-28 08:47] wrote: Hello, Is there a way to expand the names panel to be able to read object and selection names larger than 16 characters ? At the bottom left corner of the panel, just to the left of the VCR

Re: [PyMOL] Problem with intra_fit

2005-07-29 Thread Robert Campbell
Hi Ramon, * Ramon Crehuet rcs...@iiqab.csic.es [2005-07-29 12:55] wrote: Hi all, I have a problem with intra_fit. After reading two (or more) pdb into the same molecule, it does not recognise atoms for other states. I always get the message (this is for a short example): PyMOLintra_fit

Re: [PyMOL] Name length in names panel

2005-08-02 Thread Robert Campbell
Hellow Sebastien, * Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-08-01 08:48] wrote: Hello Sebastien, Hello, Is there a way to expand the names panel to be able to read object and selection names larger than 16 characters ? At the bottom left corner of the panel, just to

Re: [PyMOL] Creating PDB files from Primary Sequence

2005-08-11 Thread Robert Campbell
Hi folks, * Warren DeLano war...@delsci.com [2005-08-10 16:41] wrote: James, PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used Just hold down ALT/OPTION and type in the peptide sequence. The numbering

Re: [PyMOL] Creating PDB files from Primary Sequence

2005-08-11 Thread Robert Campbell
Hi, I just felt like making a correction to the language I used. It seems a few words went missing! * Robert Campbell r...@post.queensu.ca [2005-08-11 11:28] wrote: I had already written a script to do this, but making it easier to specify the exact phi/psi angles to use. I borrowed bits

Re: [PyMOL] Creating PDB files from Primary Sequence

2005-08-11 Thread Robert Campbell
Hi Blanton, * Blanton Tolbert blanton_tolb...@urmc.rochester.edu [2005-08-11 11:53] wrote: Hi pymolers is it possible to generate a template nucleic acid structures from sequence in pymol? Not as far as I've found. There are other programs that can do this: B (aka Biomer)

Re: [PyMOL] question on cctbx and pymol

2005-08-23 Thread Robert Campbell
Hi Sabuj, * Sabuj Pattanayek sabuj.pattana...@vanderbilt.edu [2005-08-22 18:03] wrote: Hi, Thank you for replying. In fact this is what I did. Gentoo automatically compiles pymol (pymol ebuild) with all required dependencies against the system-wide python-2.4.1. I then manually

Re: [PyMOL] question on cctbx and pymol

2005-08-24 Thread Robert Campbell
Hi, * Jianghai Zhu z...@purdue.edu [2005-08-24 01:59] wrote: I could not get cctbx work under either MacPymol or PymolX11Hybrid in Mac OS X. Anywhere I can find some instructions to get cctbx work in OS X? There is a page on the cctbx with special instructions for using it on the Mac:

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

2005-10-17 Thread Robert Campbell
Sebastien, * Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-10-17 08:41] wrote: Sebastien, I cannot change the color for rendering modes I defined. I do not understand what you mean by this. Cheers, Warren I mean that the color, for cartoon view, is unchangeable when

Re: [PyMOL] Listing secondary structure assignments

2005-11-24 Thread Robert Campbell
* J. Evan Sadler esad...@im.wustl.edu [2005-11-23 13:08] wrote: I need a list of the secondary structure assigned to each residue by dss in pymol. Is there a simple way to write this information to a file, or dump it to the screen? To dump it to the screen, try: iterate object name n. ca,

Re: [PyMOL] Re: New spectral color pallette

2006-01-05 Thread Robert Campbell
Alexander, * alexander.paut...@bc.boehringer-ingelheim.com wrote: I would like to color my protein according to B-factor with a self-defined spectral palette (In this case I have put sequence conservation into the Bfactor this column). I found that spectrum b, blue_white_red,

Re: [PyMOL] What residues have I selected?

2006-02-09 Thread Robert Campbell
Hi Aaron, * Aaron New aaron...@gmail.com [2006-02-09 09:36] wrote: I have selected atoms near an object of interest, and extended this via byres to a selection of the other atoms that are part of the same residue. Is there any way to output a file that would have the coordinates of the atoms

Re: [PyMOL] delete/create bonds in pymol

2006-02-10 Thread Robert Campbell
Hi Vanessa, * Vanessa Oklejas vokle...@stanford.edu [2006-02-10 11:18] wrote: Hi All, Does anyone know how to delete bonds between atoms in PyMol? You can use the unbond command: PyMOLunbond ? Usage: unbond [ atom1 [, atom2 ]] You can pick the two atoms with the mouse (such that they

Re: [PyMOL] a scaling question

2006-04-20 Thread Robert Campbell
Hi Fei, * Fei Xu f...@rutchem.rutgers.edu [2006-04-19 11:55] wrote: Hi!: I met a scaling problem. I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal

Re: [PyMOL] D-ala

2006-04-28 Thread Robert Campbell
Hi Orla, * Orla O'Sullivan orla.osulli...@teagasc.ie [2006-04-28 11:37] wrote: Is there any way to change an L-alanine to a D-alanine in pymol Sure. In the build menu there is an entry: Invert (pk2)-(pk1)-(pk3) [Ctrl-E] pk1 is the atom whose configuration is to be inverted. pk2 and pk3

Re: [PyMOL] Problem loading chempy objects to pymol

2006-06-07 Thread Robert Campbell
Hello Raúl, * Raúl Mera butil_li...@yahoo.com [2006-06-07 04:32] wrote: Hello all, I'm writing a Pymol plugin which creates many chempy objects (of the class Indexed) and displays the objects as diferent states of a structure. The atoms in the objects are not standar (they are dummy atoms

Re: [PyMOL] debian: error in opening pymol

2006-06-08 Thread Robert Campbell
Hi Arvind, * Arvind Marathe arv...@mbu.iisc.ernet.in [2006-06-09 00:14] wrote: Hi all, my system is a newly installed debian-3.1 linux. 'pymol' seems to be part of the installed package. But when I try to open pymol, I get the following error:

Re: [PyMOL] align states

2006-07-19 Thread Robert Campbell
Hi, * Joel Tyndall joel.tynd...@otago.ac.nz [2006-07-15 14:29] wrote: Hi andrea, you can easily do this by split_states my_struct dele my_struct for the NMR ensemble, then I would use the action menu, align function and align them to state_1. This is in effect aligning the

Re: [PyMOL] How can I change the surface_quality of an electron density map surface?

2006-08-16 Thread Robert Campbell
Hi Jonathan, * Jonathan Stuckey sblood@yahoo.com [2006-08-15 12:03] wrote: How can I change the surface_quality of an electron density map surface? set surface_quality=-1 does not do anything. The surface_quality parameter affects the quality of molecular surfaces, not isosurfaces. To

Re: [PyMOL] Paths to loaded objects

2006-08-23 Thread Robert Campbell
Hi folks, * Michael Lerner mgler...@gmail.com [2006-08-21 12:26] wrote: I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). Perhaps what Ron needs to do is not use the cmd.load()

Re: [PyMOL] mesure line width

2007-02-02 Thread Robert Campbell
Hi Andrea, * andrea carotti and...@chimfarm.unipg.it [2007-02-02 14:13] wrote: Hi all, is there the possibility to change the line width of the distance measure between two atoms? set dash_width, 3 If you like using a white background like I do, you can also change the dash color using the

Re: [PyMOL] simple cgo question

2007-02-19 Thread Robert Campbell
Hi Richard, * Richard Gillilan r...@cornell.edu [2007-02-19 10:22] wrote: I'm probably making a simpler mistake here, or perhaps there is something wrong with my installation or paths. I'm trying to load and display the simple cgo example in the manual. I created a file named arrows

Re: [PyMOL] Question about electron density map with mtz file

2007-05-11 Thread Robert Campbell
Hi Adiphol * adi di adipho...@yahoo.com [2007-05-11 10:26] wrote: Dear all, I am trying to put on the electron density. I only have .mtz file but I have a look at the manual and the program need XPLOR file. How can I get the XPLOR file or do I need to convert the mtz file to this - if so

Re: [PyMOL] APBS

2007-05-30 Thread Robert Campbell
Hi Vaheh, * Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote: I did not get much luck with those recommendations either. I was doing exactly the same. Something is phishy with my pymol and/or APBS installation. I did check for different pdb files, so it is not pdb related.

Re: [PyMOL] low-end graphics cards/laptops

2007-06-14 Thread Robert Campbell
Hi David, * David A. Horita dhor...@wfubmc.edu [2007-06-14 11:52] wrote: Hi, While I've seen a number of examples of good graphics cards to use with Pymol, I'd like some feedback on what an acceptable low-end is for a Windows laptop computer. Specifically, is the Intel GMA950 completely

Re: [PyMOL] spectral coloring

2007-06-27 Thread Robert Campbell
Hi Martin, * Martin Höfling martin.hoefl...@physik.uni-muenchen.de [2007-06-26 15:15] wrote: Hi there, i am trying to map b factors on a surface representation. I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a way to fine tune the color spectrum, such as

Re: [PyMOL] How to dislocate independently each structure when you have loaded two structures?

2007-06-27 Thread Robert Campbell
* Andreas Henschel a...@biotec.tu-dresden.de [2007-06-27 15:49] wrote: Hi Julio, If I understood you right, you can simply use translate, eg.: translate [20,0,0], mol_to_dislocate The important thing is that turn and move modify the camera, while translate and rotate modify the

Re: [PyMOL] python for loop with pymol command usage

2007-07-04 Thread Robert Campbell
Hi Louis, * Clark, Louis louis.cl...@codexis.com [2007-07-04 12:01] wrote: Dear user-group, I'm trying to learn how to use python commands inside pymol .pml scripts. I seem to be missing some understanding about how the interface works. Could somebody tell me how to fix this command

[PyMOL] my color_b.py script

2007-07-30 Thread Robert Campbell
To all you colouring aficionados, I've updated the color_b.py script on my web page to include Mark Wall's addition of user-defined, 3-colour, gradients. Now you can type on the command line something like: color_b selection, gradient=user, user_rgb=(0.,.3,1.,.8,.8,.8,1.,.8,0.) to get

Re: [PyMOL] aligning multimodel pdb file

2007-08-23 Thread Robert Campbell
Hi Abhi, On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma abhinav1...@gmail.com wrote: I want to align different models of a multimodel pdb file. How can I do that without extracting models as identical pdb. cheers, Abhi Try the intra_fit command. Cheers, Rob -- Robert L. Campbell,

Re: [PyMOL] getting lists of resn, resi, and atom ID of a selection.

2007-09-18 Thread Robert Campbell
Dear Tomoko, On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa outp...@yahoo.co.jp wrote: Dear all I am a beginner in Python programming. I would like to get lists of resn (residue names), resi (residue identifiers) and atom ID of a selection. For example, in case of

Re: [PyMOL] moving objects freely

2007-10-04 Thread Robert Campbell
Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net wrote: From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a

Re: [PyMOL] obtaining coordinates of solvent-surface points

2007-11-22 Thread Robert Campbell
Hello John, On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ josh8...@yahoo.com wrote: Hello: Im new at pymol and would like to obtain the coordinates of the dots that make up the solvent-accessible surface. I can obtain the vertices using cmd.get_povray()[1], but that will give me a list of

Re: [PyMOL] Changing Bfactors

2008-01-14 Thread Robert Campbell
On Sat, 12 Jan 2008 20:21:37 +0530, rama krishna ram...@gmail.com wrote: Dear User, I need to color the Molecule based on generalized order parameter after running the script data2bfactor i used the command data2b_res 'mol','datafile' after that it shows that IOError: [Errno 2] No such

Re: [PyMOL] MSMS Cavity Visualization in Pymol

2008-01-30 Thread Robert Campbell
Hi Buz, On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com wrote: Does anyone know of a script that is capable of displaying the surfaces identified by msms in pymol? I have a script called msms_cgo.py that you can download from:

Re: [PyMOL] MSMS Cavity Visualization in Pymol

2008-01-31 Thread Robert Campbell
A little oops! On Wed, 30 Jan 2008 16:33:00 -0500, I wrote: Hi Buz, On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com wrote: Does anyone know of a script that is capable of displaying the surfaces identified by msms in pymol? I have a script called msms_cgo.py that you

Re: [PyMOL] merging many frames to one

2008-02-12 Thread Robert Campbell
Hi again, Dimitry, On Tue, 12 Feb 2008 09:10:23 -0500, Robert Campbell robert.campb...@queensu.ca wrote: Hello Dimitry, On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov gene...@gmail.com wrote: Hello, I have a .pdb1 file with biological unit. It consists of two frames

Re: [PyMOL] getting a list of main-chain hydrogen bonds

2008-05-05 Thread Robert Campbell
Hi Tomoko, On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa tmk.n...@gmail.com wrote: Thanks for kind advices. Whatif and PISA worked excellently, but I want to get the list within Pymol. By parsing the pymol modules, I found hb = cmd.find_pairs(((byres +sss1+) and n;n),

Re: [PyMOL] Spheres for metal ions

2008-05-20 Thread Robert Campbell
Hi Gary, On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter gary.hun...@um.edu.mt wrote: I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use showspheres Fine Somehow recently I must have done something to reset the vdw radius of

Re: [PyMOL] How to view electron densities from the PDB

2008-06-27 Thread Robert Campbell
Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com wrote: This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif.

Re: [PyMOL] coloring based on sequence identity

2008-08-25 Thread Robert Campbell
Dear Morri, On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman morrifeld...@gmail.com wrote: Dear Rob, I'm interested in using your variability script with a substitution matrix. Would you please send me an example of a substitution matrix file? Thanks for writing such a useful script.

Re: [PyMOL] I want to represent a domain of my molecule as a low resolution solid shape

2008-09-11 Thread Robert Campbell
Dear Pietro, On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi pietro.rove...@path.ox.ac.uk wrote: Dear everyone, I want to represent a domain of my molecule as a low resolution solid shape. I have chosen surface representation but the surface is clipped, exposing

Re: [PyMOL] Showing conserved residues

2009-01-29 Thread Robert Campbell
Hi Abhinav, On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar abhin...@slac.stanford.edu wrote: Is there someway to select and show conserved residues when a bunch of superimposed structures are loaded into Pymol? And if so, can identical and similar residues be selected separately? I don't

Re: [PyMOL] trouble with symexp command

2009-02-04 Thread Robert Campbell
Hi Dave, On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi dgarbo...@niaid.nih.gov wrote: I am examining packing in several space groups by issuing the command symexp foo, foo.pdb, sele, 10 If I select the whole reference molecule, I think that I should get all the symmates within 10 A

Re: [PyMOL] fitting problem

2009-03-02 Thread Robert Campbell
Hi Sébastien, On Mon, 02 Mar 2009 18:21:15 +0100, sconill...@chimie.u-strasbg.fr wrote: Hi all (for the second time today ...), I have a problem using the fit function. When I try to do this : fit (fittest1 and resn P and !h.), (2VT4 and resn P and !h.) I have this message error :

Re: [PyMOL] problem in showing the electron density map

2009-04-03 Thread Robert Campbell
Hi Peter, On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson peter.hudson.pe...@gmail.com wrote: Hello all I am trying to upload the ED map on pymol. but, it is not visible on the screen. Although i checked at pymol wiki and i did as it is given on the wiki. For example. I took ccp4

Re: [PyMOL] POVRAY Usage

2009-05-15 Thread Robert Campbell
Hi Tom On Fri, 15 May 2009 14:57:36 -0700, Thomas Stout tst...@exelixis.com wrote: What version of PyMOL does this work with? I've been trying your commands with versions 1.1 and 1.2b and while PyMOL reports that the primitives have been processed, nothing is written to the file protein.pov

Re: [PyMOL] surface for oligosaccharide chains

2009-07-03 Thread Robert Campbell
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi! Can somebody tell me why I can't create surfaces for the oligosaccharide chains? By default, the surface and mesh commands ignore all atoms in HETATM records in a PDB file. You can change that with: set

Re: [PyMOL] Pymol build from source

2009-07-07 Thread Robert Campbell
Dear Joseph, On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph andrejos...@gmail.com wrote: Dear Delano Scientific support I've been fetching source code from the sourceforge repositories yesterday. I've no error or warning during ./configure, make or make install steps. However, when I

Re: [PyMOL] Measure surface area

2009-08-10 Thread Robert Campbell
Hi Mirek, On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano war...@delsci.com wrote: PyMOL isn't the optimal tool for measuring surface area -- perhaps others on the list can suggest good alternatives. I like MSMS for this. I have a script that will calculate the area (both solvent exposed

Re: [PyMOL] Alignment Objects

2009-09-11 Thread Robert Campbell
Hi David On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com wrote: Is there any documentation on getting information out of alignment objects into scripts? I tried looking around the wiki, but I didn't see anything. I'm just wondering things like if I have a residue

Re: [PyMOL] spectrum

2009-11-09 Thread Robert Campbell
Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote: Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: snip Sean's extensive explanation I know I'm biased, since I wrote the color_b.py script, but I fail to see

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