[PyMOL] Pymol 'n Cave

2002-11-28 Thread Tsjerk Wassenaar
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

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

2003-02-25 Thread Tsjerk Wassenaar
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] solid spheres

2003-03-28 Thread Tsjerk Wassenaar
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. -- :)

[PyMOL] Bonds

2003-06-27 Thread Tsjerk Wassenaar
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] Unit cell

2003-08-12 Thread Tsjerk Wassenaar
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] Unwanted artwork

2003-08-29 Thread Tsjerk Wassenaar
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

Re: [PyMOL] Restrict surface transparency to limited region

2004-01-15 Thread Tsjerk Wassenaar
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

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

2004-01-30 Thread Tsjerk Wassenaar
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,

[PyMOL] Povray

2004-02-19 Thread Tsjerk Wassenaar
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 viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop

Re: [PyMOL] 3d plotting in pymol

2004-05-24 Thread Tsjerk Wassenaar
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] Help/suggestions for illustrating lattice arrangement

2004-10-08 Thread Tsjerk Wassenaar
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] pymol + gromacs trajectories

2004-10-12 Thread Tsjerk Wassenaar
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] 2 colors for transparent surface and cartoon

2004-10-13 Thread Tsjerk Wassenaar
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] putty/sausage NMR figure

2005-07-22 Thread Tsjerk Wassenaar
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] antialiasing and povray

2005-07-26 Thread Tsjerk Wassenaar
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] unit cell and cell packing

2005-08-01 Thread Tsjerk Wassenaar
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] Pymol sessions

2005-08-03 Thread Tsjerk Wassenaar
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] Shadows

2005-08-12 Thread Tsjerk Wassenaar
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] How could I modify the secondary structures after superimpose of 2 or more structure?

2005-10-09 Thread Tsjerk Wassenaar
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] Adjust radius of sphere

2005-10-24 Thread Tsjerk Wassenaar
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

2005-10-24 Thread Tsjerk Wassenaar
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

2005-10-24 Thread Tsjerk Wassenaar
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] Selecting residue from object

2005-10-30 Thread Tsjerk Wassenaar
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] getting pov-ray temp files

2006-01-24 Thread Tsjerk Wassenaar
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] getting pov-ray temp files

2006-01-26 Thread Tsjerk Wassenaar
...@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] Multiple origins possible?

2006-02-20 Thread Tsjerk Wassenaar
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] models with reduced coordinate sets

2006-03-01 Thread Tsjerk Wassenaar
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

[PyMOL] cmd.get_povray stereo segfault

2006-03-11 Thread Tsjerk Wassenaar
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

[PyMOL] Bug: spheres with negative x-coordinates don't show up

2006-03-17 Thread Tsjerk Wassenaar
Hi Warren, I just ran into a bug with pymol 0.99 rc1 on SUSE 10 Linux on my Acer TravelMate 800, which has an ATI Radeon video card. The problem is that for atoms with negative x-coordinates the spheres don't show up. When I shift the coordinates using alter_state the spheres show up again. This

Re: [PyMOL] question about ca trace

2006-04-14 Thread Tsjerk Wassenaar
Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol just traces through all c-alphas in the object, regardless of chains or distances. So, selecting the linked residues and hiding the trace should solve your problem. Also, creating two files will do the trick.

Re: [PyMOL] changing individual sphere sizes

2006-04-15 Thread Tsjerk Wassenaar
Hi Laura, You can change the van der Waals radii of atoms using alter selection, vdw=newradius Alternatively, you can use the setting sphere_scale (set sphere_scale,factor), which changes all radii by the given factor. Note that you need to create different objects to use different factors for

Re: [PyMOL] RE: povray image mapping and default pigments

2006-04-19 Thread Tsjerk Wassenaar
Hi, Actually, one of the first of these images I made was of conotoxin floating above a see. Will that do? I'd still have to add the sunset though ;) O, and the checkered beach... In regards the problem of Seth, it's good you've solved it. It is possible though to remove all statements about

Re: [PyMOL] Question on rotation

2006-04-26 Thread Tsjerk Wassenaar
Hi Terry, There's a bit more to it. In the pymol view, the camera is located at the origin, so to rotate your coordinates you first have to move the center to the origin, do the rotation and move the thing back. I've scripted this in Povray. If you're interested, I can send you the script. You

Re: [PyMOL] biological unit

2006-05-19 Thread Tsjerk Wassenaar
Hi Surendra, split_states is a native Pymol command. If you download from the PDB the biological unit coordinate file, you can show it using split_states OBJECT Cheers, Tsjerk On 5/18/06, surendra negi negi...@yahoo.com wrote: Hello pymol, Is it possible to create biological unit of a

Re: [PyMOL] assigning properites

2006-05-23 Thread Tsjerk Wassenaar
Hi Frank, These settings apply to objects, if specified. set cartoon_trace,1,object1 will make it apply only to object1 Cheers, Tsjerk On 5/23/06, Frank Murphy f...@mrc-lmb.cam.ac.uk wrote: Hello, I was wondering if anyone out there has connived a way to assign different properties to

Re: [PyMOL] Is there any way to show the coordinates?

2006-05-23 Thread Tsjerk Wassenaar
Hi Ron, Check the commands get_view set_view Cheers, Tsjerk On 5/23/06, Ronald Chiu rccom...@gmail.com wrote: Hello All, Is there any way to show the coordinates for the orientation that a protein is in? Lets say you tweak (rotate and turn) a protein in to a particular orientation, is

Re: [PyMOL] unset surface colors

2006-05-24 Thread Tsjerk Wassenaar
Hi Natasja, That should be done with (IIRC) set surface_color,-1 Tsjerk On 5/24/06, Natasja Brooijmans broo...@wyeth.com wrote: I accidently used the set surface_color, x command, and then unset. Now the full surface is colored white. Rather, I want the surface to be colored by the color

[PyMOL] Edge thickness in ray_trace_mode 2 and 3

2006-05-30 Thread Tsjerk Wassenaar
Hi Warren et al. I really like the ray_trace_modes 2 and 3. However, I'd like to fiddle around with the thickness of the edges, but can't find a setting to do so. Am I overlooking something, or isn't there any (yet)? By the way, ray_trace_mode 2 is great for making colouring pictures to get the

Re: [PyMOL] error in loading pdb file

2006-06-30 Thread Tsjerk Wassenaar
Hi Dong, My guess is (but ofcourse Warren knows best) that pymol chokes in the full pathname, including the spaces. Note that under windows the actual pathname would be D:\DOCUME~1\1LTL.pdb The long pathname is an alias. Cheers, Tsjerk On 6/29/06, LIU Changdong cd...@ust.hk wrote: Dear all:

Re: [PyMOL] spheres representation and atomic / ionic radii

2006-06-30 Thread Tsjerk Wassenaar
Hi Michael, The answer to the second question is: yes alter selection,vdw=1.0 will change the radius of selected atoms to 1.0 angstrom. Cheers, Tsjerk On 6/30/06, Michael Weber web...@staff.uni-marburg.de wrote: Hi, I have a question concerning the spheres representation. According to my

Re: [PyMOL] PyMol question?

2006-07-03 Thread Tsjerk Wassenaar
Hi, You can do this using alter_state: alter_state 1,selection,(x,y,z) = (a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2, a31*x+a32*y+a33*z+d3) where a11-a33 are the matrix elements (check whether they have to be transposed) and d1-d3 are the elements of the shift vector. It may

Re: [PyMOL] script error? SyntaxError: invalid syntax

2006-07-07 Thread Tsjerk Wassenaar
Hi Petro, run expects a python script (.py), whereas you're trying to run a pymol script (.pml). For that you nead '@': @c:\pict.pml Cheers, Tsjerk On 7/6/06, Piter_ x.pi...@gmail.com wrote: Hi all I have some errors if I run script: PyMOLrun c:\pict.pml Traceback (most recent call last):

Re: [PyMOL] running Python scripts with options

2006-07-14 Thread Tsjerk Wassenaar
Hi Mikael, As far as I'm aware that is not possible (and definitely not with run, see 'help run'). What you can do is to define a function in test.py, which takes the arguments you want. Then, after running the script you can use the function as you please. If, in addition, you add to the end of

Re: [PyMOL] movie with 3 molecules

2006-07-21 Thread Tsjerk Wassenaar
Hi Adrien, You don't really need the double loop, I'd say. What about: for i in range(1,20): cmd.load(o.%03d.1.pdb%i,m1) cmd.load(o.%03d.2.pdb%i,m2) cmd.load(o.%03d.3.pdb%i,m3) cmd.hide(everything) cmd.show(spheres) cmd.ray() cmd.png(o.%03d.png%i) By the way, note that

Re: [PyMOL] Stereo image labeling

2006-07-27 Thread Tsjerk Wassenaar
Hi Hasan, Have a look at label... (and read the manual :)) Cheers, Tsjerk On 7/27/06, Demirci, Hasan hasan_demi...@brown.edu wrote: I have a cross-eye stereo image generated by PYMOL. Is there an easy way of custom labeling the residues by using PYMOL ? Or should I use a photo editor

Re: [PyMOL] problem: choking on big files

2006-07-28 Thread Tsjerk Wassenaar
Hi Philippe, Pymol isn't very good at handling many spheres. However, Povray is extremely efficient with raytracing scenes consisting of spheres and if you know the perspective you want to have the image from, you can convert your atom set to spheres (with desired radii) and apply the view from

Re: [PyMOL] nmr files

2006-07-29 Thread Tsjerk Wassenaar
Hi Chandra, 1. Just load the file on the command line or through the interface (load). Then to show all structures use 'set all_states,1' or 'split_states' if you want to have them as separate objects. 2. First create an object of the selection. 3. Please read the manual, search the archives

Re: [PyMOL] Change clipping plane only for one object

2006-08-16 Thread Tsjerk Wassenaar
Hi Paul, This is not possible at present (as has been mentioned in this mailing list several times...). Tsjerk On 8/16/06, Paul Wilhelm Elsinghorst p...@uni-bonn.de wrote: Hi guys, let's say we have a scene with two objects. Can I have different clipping planes for these two objects? For

Re: [PyMOL] PyMOL transparent backgound possible?

2006-08-17 Thread Tsjerk Wassenaar
Hi Michael, Use: set ray_opaque_background, off Cheers, Tsjerk On 8/17/06, Michael Weber web...@staff.uni-marburg.de wrote: Hi guys, for preparation of a figure I need to combine a PyMOL image export file (.png) with another image. Is it possible to export the PyMOL data with a

Re: [PyMOL] Select residues from multi chains

2006-08-17 Thread Tsjerk Wassenaar
Hi Binbin, Remember that computers understand things different than we usually do. You need: select (resi 367 and chain c) or (resi 366-379 and chain a) And gives intersection, or gives union... Tsjerk On 8/17/06, bm...@leeds.ac.uk bm...@leeds.ac.uk wrote: Hello there, I'd want to select

Re: [PyMOL] Problem

2006-08-24 Thread Tsjerk Wassenaar
Hi Mahesh, There is no way to see whether two atoms are connected. Pymol guesses the connectivity based on the distances between the particles. But to be certain whether atoms are bonded, you have to look in the PDB file, which should mention covalent attachment of a ligand. At the end of the

Re: [PyMOL] showing peptide planes

2006-08-28 Thread Tsjerk Wassenaar
Hi OJ, I don't know if someone has implemented it already, but it's not a hard thing to do if you know a little python. You basically need to fetch the coordinates of the OCNH atoms from a selection and build planes with CGO (you can have a look at Gareth Stockwells walls.py:

Re: [PyMOL] How to write the select residue around in script

2006-09-16 Thread Tsjerk Wassenaar
Hi Dong, The second argument to cmd.select has to be a string giving the selection _exactly_ as you would give your second argument on the command line (but then quoted). Try cmd.select(name, all within 3.2 of (resi 2 and chain A)) Cheers, Tsjerk On 9/15/06, XUESONG DONG

Re: [PyMOL] bug in selections for set ribbon_color

2006-09-18 Thread Tsjerk Wassenaar
Hi Tom, Settings (thriugh set) apply to objects and not to subsets of objects. Try creating an object from your selection first or change the colors using color. Best, Tsjerk On 9/17/06, Thomas Stout tst...@exelixis.com wrote: Has anyone successfully set colors for ribbons via a

Re: [PyMOL] drawing missing region

2006-09-21 Thread Tsjerk Wassenaar
Hi Rinku, Such a feature is not present in pymol out of the box. It is possible to write a python script to create a CGO object joining two given points (with a control point for each) with a smooth dashed line. Sorry if this doesn't help you further. Best, Tsjerk On 9/20/06, Rinku Jain

Re: [PyMOL] cartoon representation error

2006-10-24 Thread Tsjerk Wassenaar
Hi Eva, It may be that the secondary structure information is not set (assuming that you have some secondary structure). You can try to run 'dss' or if that fails you can try to resort to 'util.ss' which may do the trick. Alternatively, you can set the secondary structure information manually,

Re: [PyMOL] Fwd: two-dimensional 3D images

2006-11-02 Thread Tsjerk Wassenaar
Hi James, Maybe you can try another route. The ray_trace_mode, 3 gives very eye-catching pictures. Make one image intended only to grab attention and place it large in the centre of your poster. Make another image you can use to fill your background (chose the x/y-ratio of your poster for

Re: [PyMOL] cones in pymol?

2006-11-02 Thread Tsjerk Wassenaar
Hi Martin, You may also be interested in this script which you can use to draw an arrow from point A to point B: cgo_arrow( start, end, radius, head_radius, head_length, name, state ) start = [ x1, y1, z1 ], end = [ x2, y2, z2 ] For lots of arrows you can use: cgo_arrows( X, radius,

Re: [PyMOL] A command for color by chain?

2006-11-06 Thread Tsjerk Wassenaar
Hi Pernille, You're looking for the command: util.cbc Best, Tsjerk On 11/6/06, Pernille Haste Andersen p...@cbs.dtu.dk wrote: Hi Everybody, I frequently use the color by chain option available in the PyMOL viewer GUI, however I haven't managed to find a corresponding command to be used in

Re: [PyMOL] bond distance in pymol

2006-11-24 Thread Tsjerk Wassenaar
Shivesh, Well, what would you think of the command 'dist'? You could have read the manual... Tsjerk On 11/24/06, shivesh kumar shivesh_...@yahoo.com wrote: Dear all, Is there anyway to calculate the bond distances in pymol and to show the bond distances also... thanx in advance S shivesh

Re: [PyMOL] CGO Raytrace color problem

2006-12-05 Thread Tsjerk Wassenaar
Hi DeVill, If you're building a CGO structure with triangles, you have to make sure that the normal vectors are correct. These will determine the inside and outside of the object (and hence the coloring). Cheers, Tsjerk On 12/4/06, DeVill dev...@cs.elte.hu wrote: Hi! I have created a

Re: [PyMOL] cmd.label, custom labels, script

2006-12-19 Thread Tsjerk Wassenaar
Hi Rafael, You can use cmd.label(selection,'objectname-+resn+resi') Do mind the quotes.., the label string is _eval_uated. Of course, if objn = objectname, it also works as cmd.label(selection,'objn+-+resn+resi') Cheers, Tsjerk On 12/19/06, Rafael Najmanovich rafael.najmanov...@ebi.ac.uk

Re: [PyMOL] change the sphere size of a chosen atom ?

2007-01-11 Thread Tsjerk Wassenaar
Ni Hao Feng, First of all, please do not include an complete daily digest in a question (or reply) on this or any user list. If required, cut out only that part which connects to your question or reply. Then, in addition to Bobs comments, you can also use the terminal or a script, using the

Re: [PyMOL] Pymol cone shape?

2007-01-11 Thread Tsjerk Wassenaar
Hi William, Maybe the attached python script will be of some use. It contains a function (and some helper functions) to draw a CGO arrow in PyMOL. It contains code for drawing a cone for the head of the arrow. Hope it helps, Tsjerk On 1/10/07, William Scott wgsc...@chemistry.ucsc.edu wrote:

Re: [PyMOL] create covalent bond between different objects

2007-01-14 Thread Tsjerk Wassenaar
Hi Magnus, Fuse takes two arguments, you've only given one: (ret and name c15) and (protein and resi 219 and name n). What you intended was probably: fuse ret and name c15, protein and resi 219 and name n By the way, not any of my business, but what bacteriorhodopsin is this? Usually, the bond

Re: [PyMOL] selecting Na+ in pymol

2007-02-02 Thread Tsjerk Wassenaar
Hi Abhi, Actually, it was a bit surprising to me to see you're right. Now, for showing/hiding, it has been dealt with in the code, by allowing the + to be left out. However, for selecting (and alter_ing) that doesn't go, apparently. A workaround is to use cmd.select(selectionname,r. na\+) or

Re: [PyMOL] selecting Na+ in pymol

2007-02-02 Thread Tsjerk Wassenaar
. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Friday, February 02, 2007 2:23 AM

Re: [PyMOL] mesure line width

2007-02-20 Thread Tsjerk Wassenaar
Hi Mike, Easy, add the object name after the set command: set dash_width,3,dist01 set dash_width,10,dist02 Colouring works normally on objects: color red, dist01 color green, dist02 Cheers, Tsjerk On 2/19/07, Mike Summers summ...@hhmi.umbc.edu wrote: This works great! Is there any way I

Re: [PyMOL] WRL Output

2007-03-02 Thread Tsjerk Wassenaar
Hi Markus, You can export the scene to pov-ray format, for which you should be able to find a converter for vrml. Best, Tsjerk On 3/2/07, Markus Wahl mw...@gwdg.de wrote: Dear all, I wondered whether there is a possibility in PyMol to export the rendered polygon data in any kind of 3D format

Re: [PyMOL] protein cartoon/floating sidechains/ligands

2007-03-07 Thread Tsjerk Wassenaar
Hey, In addition, you may also want to set cartoon_smooth_loops,0 in order to have your loops nice and wiggly, attaching to your side-chains. Cheers, Tsjerk On 3/6/07, Andreas Forster docandr...@gmail.com wrote: Hey Gary, in order to have sidechains be attached to your cartoon

Re: [PyMOL] Calcium Phosphates

2007-03-23 Thread Tsjerk Wassenaar
Vala, What do you mean by Calcium Phosphates pymol files? If you mean structures of calcium phosphate..., try to find them on the web, searching for pdb files or other formats. Pymol is a molecular viewer.., it doesn't really come with such files from itself. Alternatively, since calcium

Re: [PyMOL] question on state

2007-03-28 Thread Tsjerk Wassenaar
Hi David, The state sort of refers to the frame or model in case of a multiframe/multimodel (multistate) system. You don't need to use it with set, it's optional. Just note that dash_length and dash_length are quite different things. Best, Tsjerk On 3/28/07, David Shin dav...@scripps.edu

Re: [PyMOL] translating cgo text

2007-04-02 Thread Tsjerk Wassenaar
Hi, A workaround may be to wrap the cgo object in a python object, with a reload function, as well as with transformation functions. class CGOWrap: cgoObject = [] name= [] def translate(self,vector): def rotate(self,matrix): def reload(self) ...etc... The most difficult thing is

Re: [PyMOL] ray-traced stero figurea

2007-04-03 Thread Tsjerk Wassenaar
Hi Richard, Why not set stereo_mode,3 and raytrace as it is on the screen? You can set stereo_angle and stereo_shift to modify the scene. Cheers, Tsjerk On 03 Apr 2007 10:57:36 -0500, Richard Baxter rbax...@alumni.uchicago.edu wrote: Dear All, I used the following commands to generate a

Re: [PyMOL] How to make different colour on backbone cartoon and sidechain stick

2007-04-07 Thread Tsjerk Wassenaar
Hi Adiphol, It would have been better to state several questions as subjcts, but ok... 1. I would like to show side chain one colour by stick and its backbone by cartoon another colour. So I tried to create to same molecules. One with normal backbone (no1) and the other with backbone and a

Re: [PyMOL] Mesh object features

2007-04-17 Thread Tsjerk Wassenaar
Hi Giacomo, If you type 'set meshtab', you'll get a listing of the mesh-related settings. With get mesh_something, you'll get the current (default) value. Best, Tsjerk On 4/17/07, Giacomo Bastianelli gbast...@pasteur.fr wrote: Dear Users, I would like to change (using the API Pymol

Re: [PyMOL] Showing periodic images

2007-04-20 Thread Tsjerk Wassenaar
Hi Gianluca, Unfortunately, Pymol offers no such functionality intrinsically. But this is where python comes in handy. Attached you find a script I wrote for the purpose. It allows you to shift objects or selections over the periodic lattice: run lattice.py create ObjectCopy,MyObject shift

Re: [PyMOL] Surface vertex list

2007-04-20 Thread Tsjerk Wassenaar
Hi Jim, Hmmm. I think your best option is to color the surface according to the atoms and write the surface in povray format. This will give you all the vertices. Just another thought springing to mind, you could cycle over the atoms using a script, writing away only the part of the surface

Re: [PyMOL] Showing periodic images

2007-04-21 Thread Tsjerk Wassenaar
Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 On Apr 20, 2007, at 9:30 AM, Tsjerk Wassenaar wrote: Hi Gianluca, Unfortunately, Pymol offers no such functionality intrinsically. But this is where python comes in handy. Attached you

Re: [PyMOL] unnatural aminoacid

2007-04-22 Thread Tsjerk Wassenaar
Hi Justin, If you have a pdb file of your coumarin derivative (which you can obtain e.g. with the PRODRG server), you can use 'fuse' to attach it to some amino acid side chain. By the way, it may be a good idea to try and polish your english a bit. A question clearly phrased will help people on

Re: [PyMOL] 3d pdf

2007-05-21 Thread Tsjerk Wassenaar
Hi William, In contrast to Nick, I read your question as inquiring after a 3D probability density function. In case I get it wrong, just ignore this mail. It is well possible to generate 3D pdfs and display them in Pymol. Actually, for one project I'm doing that right now. I have modified a

Re: [PyMOL] Sticks and distances with individual transparencies

2007-06-26 Thread Tsjerk Wassenaar
Hi Mark, You could've found this one in the archives of this list. Settings work on objects, not on selections. The solution is to make an object for the solid sticks and one for the transparent sticks, using create. Cheers, Tsjerk On 6/26/07, Dr. Mark Mayer may...@mail.nih.gov wrote: Dear

Re: [PyMOL] movie script

2007-08-14 Thread Tsjerk Wassenaar
Hi Hasan, Start with the structures superimposed and translate/rotate one/both away from the/each other. Glue the images together in reversed order and no one will see the difference... By the way, it might be nice to start with small translations/rotations and have them increase quadratically in

Re: [PyMOL] bonds persisting in movie

2007-09-10 Thread Tsjerk Wassenaar
Hi kmeatball, If you append all structures to the same model, which is what you do by loading each under the same name into different states, the connectivity will be determined by the first state. That is, the topology information (read bond map) is global, and applies to all states. If you want

Re: [PyMOL] arrow objects

2007-09-14 Thread Tsjerk Wassenaar
Hi Gianluca, It would have been worthwhile checking the archive of the mailing list: http://sourceforge.net/mailarchive/message.php?msg_id=8ff898150701110024y4b111ab2ic195813792c4b8d%40mail.gmail.com It's a script of mine; if you encounter any problems or have suggestions, feel free to contact

Re: [PyMOL] dash_color

2007-09-19 Thread Tsjerk Wassenaar
Hi, There's not actually a way to get the default back. Distances are stored as objects, so you can just use color. Best, Tsjerk On 9/19/07, Lari Lehtio lari.leh...@ki.se wrote: I do not know how to set the default, so I just use color grey50, dist* ~L~

Re: [PyMOL] succinct secondary structure 'readout'

2007-10-08 Thread Tsjerk Wassenaar
Hi Frieda, There's no such command. You'll have to parse the output you get through a script which filters it in the way you want. This isn't difficult though (good python exercise :p). Best, Tsjerk On 10/9/07, Frieda Reichsman frie...@nsm.umass.edu wrote: Hi, I would like to get secondary

Re: [PyMOL] real time editing/moving of molecular structure from scripting interface

2007-10-09 Thread Tsjerk Wassenaar
#--- Python proof e-mail ;) --- # Hi Aaron, # You can get to the coordinates in the following way: # First make a model from the selection you want to work on: sel = cmd.get_model( object ) # Then you can get to the coordinates and modify them without affecting the view: for i in

Re: [PyMOL] succinct secondary structure 'readout'

2007-10-09 Thread Tsjerk Wassenaar
, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Frieda, There's no such command. You'll have to parse the output you get through a script which filters it in the way you want. This isn't difficult though (good python exercise :p). Best, Tsjerk On 10/9/07, Frieda Reichsman frie...@nsm.umass.edu

Re: [PyMOL] succinct secondary structure 'readout'

2007-10-09 Thread Tsjerk Wassenaar
Hi Gillean, For what it's worth, I experienced the same... No dashes in the numbers: 1-1 1--1 L 1-2 2--1 L 2-3 3--1 L ... etc. The double dash must come from the -1 value used as default for your SSE class. Better double check what's going on there :) Cheers, Tsjerk On 10/9/07, gilleain

Re: [PyMOL] succinct secondary structure 'readout'

2007-10-10 Thread Tsjerk Wassenaar
Hi Frieda, I had to rewrite the script to get the output desired, now also using a class definition :p It works fine for me: PyMOL@../..\ss.pml PyMOLclass SSList:\ PyMOLlist = []\ PyMOLdef purge( self, resi, ss ):\ PyMOLif not self.list or self.list[-1][0] != ss:\ PyMOLself.list.append( [ss,

Re: [PyMOL] identification of residue names

2007-10-20 Thread Tsjerk Wassenaar
Hi, I wouldn't use list, since that's a python keyword :S Use reslist or something. Cheers, Tsjerk On 10/19/07, Piter_ x.pi...@gmail.com wrote: Hi Martin May be this will help: from sets import Set list =[] cmd.iterate('het', 'list.append(resn)') residname =Set(list) print residname

Re: [PyMOL] How to move aligned objects apart

2007-10-22 Thread Tsjerk Wassenaar
Hi Dave, Use alter_state: alter_state 1,selection,x=x+25 or alter_state 1,selection,(x,y,z)=(x+10,y+10,z+10) By the way, alter_state allows all sorts of transformations of coordinates... Cheers, Tsjerk On 10/22/07, David Garboczi dgarbo...@niaid.nih.gov wrote: I have three molecules

Re: [PyMOL] drawing arbitrary object with pymol

2007-11-01 Thread Tsjerk Wassenaar
Hi Paride, You'll have to build up the plane-with-hole with triangles. Not difficult to do, but not completely trivial either, especially not if the CGO syntax is new to you :S Best, Tsjerk On 11/1/07, Paride Legovini legov...@spiro.fisica.unipd.it wrote: Warren DeLano wrote:

Re: [PyMOL] Generate Symmetry matrix

2007-11-04 Thread Tsjerk Wassenaar
Hi Nagarajan, I'm not sure whether this is the best way to get what you need. symexp is intended to regain the crystallographic symmetry, but it seem to me you want to have the biological unit. The pdb files in the RCSB PDB are usually also available as biological unit and it should be possible

Re: [PyMOL] sphere diameter

2007-11-26 Thread Tsjerk Wassenaar
Hi Mark, You can also directly change the vdw radius of sodium to its ionic radius: alter r. na\+,vdw=1.02 rebuild Cheers, Tsjerk On Nov 27, 2007 1:15 AM, Dr. Mark Mayer may...@mail.nih.gov wrote: hello, Can't find anything about this in docs or in settings: Where are sphere diameter

[PyMOL] Fwd: sphere diameter

2007-11-27 Thread Tsjerk Wassenaar
Hi Abhinav, Whitespace matters. In fact, the first two characters in the atom name field of the pdb file are usually considered indicating the element type. Pymol also does this. This means that NA will be considered of element type N, whereas NA will be interpreted as being of element NA.

Re: [PyMOL] density map

2007-12-07 Thread Tsjerk Wassenaar
Hi Steve, You'll need to provide more information if you want to have a chance on a helpful thought. Maybe you could link the .pdb file and the .xplor map and show what O does to it. Cheers, Tsjerk On Dec 7, 2007 3:57 PM, W.M. B. butiany...@gmail.com wrote: Hi, All I'm trying to make a

Re: [PyMOL] Changing Bfactors

2008-01-14 Thread Tsjerk Wassenaar
Hi Ramakrishna, On Jan 12, 2008 3:51 PM, 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

Re: [PyMOL] export the mesh or surface

2008-01-16 Thread Tsjerk Wassenaar
Hi Linda, You can export it to povray: open(surface.inc,w).write(cmd.get_povray()[1]) Cheers, Tsjerk On Jan 16, 2008 4:55 AM, Lu Lin l...@cs.hku.hk wrote: Hi all, Anyone can tell me whether I can export the mesh or surface into a file (e.g. .wrl/.obj etc.)? Thanks!! Linda

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