Re: [PyMOL] chain atom seq by cmd

On Wed, 03 Oct 2007 03:11:41 +0900, Hyunchul Kim wrote: > Hi, all > > How can I extract protein sequence from given pdb files by python API for > pymol ? > I want to get a sequence which is extracted from coordinates not the > annotated residue sequence in remarks. Assuming the protein has all

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

Dear Tomoko, On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa 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 1IEP_organic; > [

Re: [PyMOL] aligning multimodel pdb file

Hi Abhi, On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma 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, Ph.D. Senior Rese

[PyMOL] my color_b.py script

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 colours

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

Hi Louis, * Clark, Louis [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 below? > > > > PyM

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

* Andreas Henschel [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 coordinates. > > Cheers

Re: [PyMOL] coloring based on sequence identity

* Martin Höfling [2007-06-27 01:33] wrote: > Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee: > > Hi, > > > > I'd like to color a molecule based on its sequence similarity to another > > molecule. > > Can this be done in Pymol? > > If you can quantify "similarity" in a number you can write it into

Re: [PyMOL] spectral coloring

Hi Martin, * Martin Höfling [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 with the "Midpoint" and "Offset

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

Hi David, * David A. Horita [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 > useless or just

Re: [PyMOL] APBS

eports "i686" or "x86_64" Rob > > Steve > > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of > Oganesyan, Vaheh > Sent: Thursday, May 31, 200

Re: [PyMOL] APBS

Hi Vaheh, * Oganesyan, Vaheh [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. The roor > message is

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

Hi Adiphol * adi di [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 > how can I do

Re: [PyMOL] simple cgo question

Hi Richard, * Richard Gillilan [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" containing th

Re: [PyMOL] mesure line width

Hi Andrea, * andrea carotti [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 "Setting... -> Color.

Re: [PyMOL] problem getting kabsch.py to run

Hello Margaret, * Margaret Luk-Paszyc [2006-10-15 14:07] wrote: > Hello -- > > Can someone please advise me? > I'm a new user of PyMol trying to get the kabsch alignment > script to work. I only installed the main pymol installer > (v 0.99r6), and I have copied the kabsch.py script as the > w

Re: [PyMOL] Paths to loaded objects

Hi folks, * Michael Lerner [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() function but use hi

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

Hi Jonathan, * Jonathan Stuckey [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 change the smoothnes

Re: [PyMOL] align states

Hi, * Joel Tyndall [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 separate > states as

Re: [PyMOL] sphere_scale problem

Hi Vladimir, * Vladimir Potapov [2006-07-10 12:05] wrote: > Hi everyone, > > I need to set different sphere radius in my task - large CA and small CB > atoms. I use commands: > set sphere_scale=1.5, name ca > set sphere_scale=0.5, name cb > > What I see, that command affects all atoms, not jus

Re: [PyMOL] debian: error in opening pymol

Hi Arvind, * Arvind Marathe [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] Problem loading chempy objects to pymol

Hello Raúl, * Raúl Mera [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 > to represent a

Re: [PyMOL] loosen secondary structure

Hi, * O. J. Ganesh [2006-05-18 16:09] wrote: > > Hey PyMOL gurus: > > I have a 'perfect' helix. Is there some way to 'loosen' all of the > angles in the helix so instead of 3.6 residues per turn, I could > have, say, 8 residues per turn. My goal is to make the helix more > 'coil-like'. Is thi

Re: [PyMOL] That _cmd thing

Hello Atro, * Atro Tossavainen [2006-05-05 11:10] wrote: > > I've built pymol 0.99 manually according to the INSTALLATION VIA COMPILATION > instructions. I don't want to have a second copy of all the dependencies > which I already have anyway, and I want to have pymol for multiple flavours > of

Re: [PyMOL] D-ala

Hi Orla, * Orla O'Sullivan [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 are the two atoms atta

Re: [PyMOL] a scaling question

Hi Fei, * Fei Xu [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 size automatically >

Re: [PyMOL] delete/create bonds in pymol

Hi Vanessa, * Vanessa Oklejas [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: PyMOL>unbond ? Usage: unbond [ atom1 [, atom2 ]] You can pick the two atoms with the mouse (such that they are selected and

Re: [PyMOL] What residues have I selected?

Hi Aaron, * Aaron New [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 I have selected

Re: [PyMOL] Re: New spectral color pallette

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_whit

Re: [PyMOL] Listing secondary structure assignments

* J. Evan Sadler [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 & n. ca, print resn,resi,ss Cheers,

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

Sebastien, * Sebastien Moretti [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 'set > carto

Re: [PyMOL] question on cctbx and pymol

Hi, * Jianghai Zhu [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: http://cc

Re: [PyMOL] question on cctbx and pymol

Hi Sabuj, * Sabuj Pattanayek [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 installed cctbx, did "source >

Re: [PyMOL] question on cctbx and pymol

Hi, * Sabuj Pattanayek [2005-08-18 16:08] wrote: > Actually I was wondering the same thing, except how to set it up in > linux. I was able to compile the cctbx but I'm not sure how to get it to > show up as a python module so that Pymol scripts (e.g. Dr. Campbell's > draw_cell.py) can work. An

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi Blanton, * Blanton Tolbert [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") (http://www.scripps.edu/mb/case/Biomer/)

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi, I just felt like making a correction to the language I used. It seems a few words went missing! * Robert Campbell [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 of the I me

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi folks, * Warren DeLano [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 will be arb

Re: [PyMOL] Name length in names panel

Hellow Sebastien, * Sebastien Moretti [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 the left of the "

Re: [PyMOL] Problem with intra_fit

Hi Ramon, * Ramon Crehuet [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): > PyMOL>intra_fit name ca, 1 > Ex

Re: [PyMOL] Name length in names panel

Hello Sebastien, * Sebastien Moretti [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 controls" is a little vertical ba

Re: [PyMOL] list residues in a selection

Hi, * Michael George Lerner [2005-07-06 09:28] wrote: > > 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, sel01 around 6" how can I obtain a list > >of the residues in the "near" s

Re: Subject: Re: [PyMOL] fit command

Andre, * tree [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 > (http://www.pymolwiki.org/i

Re: [PyMOL] colouring surfaces according to molecular properties

Anders, * Anders Madsen [2005-06-21 16:33] wrote: > Dear PyMol users, > I would like to colour the beautiful > PyMol molecular surfaces according to > properties of the atoms involved. > Has anyone experimented with this? > > E.g. by accessing the coordinates that define > the surface and assign

Re: [PyMOL] rms_cur

Jason, * tree [2005-05-12 11:39] wrote: > PyMolers, > > The docs leave me stranded here. The wiki page > (http://www.pymolwiki.org/index.php/Rms_Cur) is the same as the docs. > > I'm trying to rms_cur two selections. I keep getting an > ExecutiveRMS-Error: No atoms selected. > error. > > I

Re: [PyMOL] creating r3d files

Hi Paula, * Paula Salgado [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: [PyMOL] atom number labels?

Hi Xavier, * Xavier Deupi [2005-04-20 10:49] wrote: > > I'm a new user, so my question is *extremely* basic... > > I want to display atom numbers as labels, but this property does not > appear in the list of properties that can be displayed using the command > 'label'. > > How can I do it?

Re: [PyMOL] dimer interface

Alex, * Alex Dajkovic [2005-04-15 10:30] wrote: > Dear all, > > I have a structure of a dimer and would like to see the surface at the > interface of the two proteins. Is there a way to do this in PyMol? Say the object has chains A and B: create chainA, object & c. a create chainB, objec

Re: [PyMOL] Creating one object from two

Hi Jacob, * Jacob Corn [2005-04-15 09:28] wrote: > Hi Robert, > You're exactly right. It's a chainid issue. If I load 2 PDBs with > different chainids, they "merge" without a problem. If they have a the > same chainid, lines display OK, but the sequence viewer and > ribbons/cartoon view makes

Re: [PyMOL] Creating one object from two

Jacob, * Jacob Corn [2005-04-13 16:40] wrote: > I am trying to create one composite object from two separate objects. > When I issue the command > > create objectx, object1 or object2 > > objectx is created and contains most of the two objects, but is missing > around 1/5-1/10 of the atoms (s

Re: [PyMOL] sticks with different radii

Hi Shohei, * Shohei Koide [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 this > comman

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

Dear Folks, * I [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 to match in > the

[PyMOL] Fitting/alignment of non-identical sequences

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 struct

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

To add to what Cameron said: * Cameron Mura [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: > > (1) T

Re: [PyMOL] combine distance objects

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

Re: [PyMOL] secondary structures, spheres and plugins

Hi Einat, * Einat Sitbon [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 > attaching a figure to

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 yo

Re: [PyMOL] selecting side chains

Hi, * Lisa Craig [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. n+ca+c+o Ch

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

Hi, * Jeffrey N. Agar [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 Python loo

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

Hi Roger, * Roger Dodd [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 generating symmetry

Re: [PyMOL] surface/grid questions

Dear Marcelo, * castilho [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 colour protein sur

Re: [PyMOL] showing sequence conservation on the surface

Hi Robert, On 2004-05-24 13:46 you wrote: > > I probably have a very stupid question. > How do I run the color_b.py script using the latest PYMOL on windows? > Just clicking on it does not work, I also tried to run it by calling it from > within pymol but this did not work either. Sorry if the i

Re: [PyMOL] showing sequence conservation on the surface

Hi Camille and Daniel, I heard my name mentioned, so I'll join in! * Daniel Rigden [2004-05-21 16:43] wrote: > Hi Camille > > The Espript server is the easiest way I know. Go here > > http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi > > choose Execute then Expert mode. SUpply an a

[PyMOL] New (repaired!) draw_symops scripts

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 f

Re: [PyMOL] Selections

Hi Jason, * Jason Vertrees [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 found a PDB onl

[PyMOL] Bugs squashed in my scripts

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 trie

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

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 cont

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

* Robert Campbell [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. Op

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

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, rather

Re: [PyMOL] restoring default surface coloring

* Lieven Buts [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" didn't wor

Re: [PyMOL] Povray

* Tsjerk Wassenaar [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 > loaded to the vi

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

Michael, * Michael Banck [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) > > > The sto

Re: [PyMOL] get_dihedral & multiple objects

Leigh, * 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: > > PyMOL>get_dihedral 9/C, 10/N, 10/CA, 10/C (I type in) > cmd.get_dihedral: -49.721 degrees. (pymol replies) > > But if

Re: [PyMOL] assign secondary structure?

* Michael Bovee [2003-12-16 14:27] wrote: > Hmm. When I try this I get a syntax error: > __ > PyMOL>load EcHRSade.pdb > Executive: object "EcHRSade" created. > PyMOL>hide > PyMOL>show cartoon > PyMOL>dss EcHRSade > Traceback (most recent call last)

Re: [PyMOL] Fog and ray-tracing

Hi Loic, * Loic BERTRAND [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. > The image generated thr

Re: [PyMOL] custom pymol scripts

Jack, * Jack Howarth [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 in the python directo

Re: [PyMOL] select only 1 of 4 identical resi's?

Hi Michael, * Michael Bovee [2003-11-11 16:08] wrote: > I think this is a question about syntax for the 'select' command. I > study a homodimeric enzyme, which has been crystallized in various > ligand-bound states. For example, I have loaded and aligned two > different pdb files, and so ther

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

* Robert Campbell [2003-10-10 13:04] wrote: 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 1avv.pdb run draw_symops_cctbx.py draw_symops 1avv O

[PyMOL] Drawing symmetry operators

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 a

Re: [PyMOL] Creating hydrophobic surfaces

Hi Jason, * jkyano [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 alter the B-val

Re: [PyMOL] writing out coordinates

Craig, * Craig Smith [2003-09-22 03:30] wrote: > > I've done a structural alignment of 2 domains using your align command. > How do I write out the new coordinates? Look at "help save". USAGE save file [,(selection) [,state [,format]] ] This will save the modified coordinates generated

Re: [PyMOL] A couple of movie questions

Hi Stephen, * Stephen Graham [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 each time I load a n

Re: [PyMOL] alternative method for loading coordinates

Warren, * Warren L. DeLano [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 unnecessary. This could

Re: [PyMOL] nonbonded

* Stefan Reinelt [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, show nb_spheres, Cheers, Robert -- Robert L. Campbell, Ph.D. Senior Research Associate

[PyMOL] New PyMOL-related scripts

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 g

Re: [PyMOL] ligand rendering

* Nat Echols [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.: > http://bioinfo.mbb.yale.edu/people/nat/mb

Re: [PyMOL] color by ss

Hello, * 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 > > color orange, a/

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

* yibin xu [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 could be by res

Re: [PyMOL] POVRay output

* Armand Tepper [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) ? Now the textu

Re: [PyMOL] coloring surfaces

Rajarshi and Gareth, * Gareth Stockwell [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, Rajarsh

Re: [PyMOL] color by B-factor?

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] helix width

* cheom-gil cheong [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. Yes they are there, b

Re: [PyMOL] coloring stick and atoms

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

Re: [PyMOL] PovRay file export

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

[PyMOL] rms fitting and align

Dear folks, I have a couple of questions about the alignment and fitting functions of pymol. I've been using the 'align' and 'fit' functions of pymol apparently quite successfully, but I found it difficult to make the 'rms' or 'rms_cur' functions actually report anything. I can take a structure w

Re: [PyMOL] nice povray settings?

Oooops I [2003-02-05 11:42] wrote: > > I typically use the following script (I call it make_pov.py) and > "run" it from pymol once to load the function, and then I do > "make_pov('povray.inp')" to create the povray.inp file. But of course I forgot to include the script, which is very short

Re: [PyMOL] nice povray settings?

Scott, * Scott Classen [2003-02-04 20:08] wrote: > I was wondering if anybody has some scene settings for povray that > produce nice depth-cued images. In particular I am making figures with > a white background and I would like to try povray instead of the built > in raytracer of PyMol

Re: [PyMOL] slimming down ray-traced loops

Hi, * Daniel John Rigden [2003-02-05 09:23] wrote: > I'm trying to make a figure of a superposition of various loops, each with > a different colour. I need a slim trace of the loops so that each may be > seen clearly. > > In normal view I can control the loop width using either > cartoon_loop_

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

Hi, * xiaofeng qian [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 well: set stereo_angl

Re: [PyMOL] pymol and povray

* Schubert, Carsten [2002-10-23 16:59] wrote: > Don't know about MACs but this works on PCs and SGIs: > - > Exporting Povray scripts from PyMol > > > The choice of the renderer is defined by the variable "ray_default_renderer". > A > value of 0 p

Re: [PyMOL] Need help with selections

Hello Aaron, * aaron.b.mil...@gsk.com [2002-10-11 15:36] wrote: > Hello, > > I am somewhat new to PYMOL and was trying to create a selection of atoms. > What I need to do is select all atoms of a protein that are within 5 > angstroms of an inhibitor (the protein and inhibitor are separate > mole

Re: [PyMOL] get_view

* Luca Jovine [2002-10-02 10:53] wrote: > On Wednesday, October 2, 2002, at 10:10 AM, Serge Cohen wrote: > > > PS: If any one as some info on the previous questions I asked (get_view > > blocks...), really don't fill shy about it. I did not have any answer > > (even off list) > > Actually, I

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