Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

2011-06-17 Thread Schubert, Carsten [PRDUS]
To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to merge molecules in Pymol? Hi Carsten, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB

Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

2011-06-17 Thread Schubert, Carsten [PRDUS]
...@schrodinger.com] Sent: Friday, June 17, 2011 11:57 AM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol? Hi Carsten, PyMOL doesn't write non-coordinate records to disk. You'll need to write

[PyMOL] How to merge molecules in Pymol?

2011-06-16 Thread Schubert, Carsten [PRDUS]
Hi, Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with 'multisave' and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An

[PyMOL] New 16 char length restriction of object names in menu?

2011-05-19 Thread Schubert, Carsten [PRDUS]
Has the length of the object name entry in the right hand menu been restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed to have been no limit on the length of the entry. For instance cmd.load(reallylongmapnamehere, format=ccp4,object=reallylongmapnamehere) would truncate the display

Re: [PyMOL] New 16 char length restriction of object names in menu?

2011-05-19 Thread Schubert, Carsten [PRDUS]
Hi Jason, thanks for the follow-up. Let us know when the issue is fixed. Cheers, Carsten -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Thursday, May 19, 2011 12:11 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users

Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore -- fixed

2011-05-12 Thread Schubert, Carsten [PRDUS]
...@schrodinger.com] Sent: Wednesday, May 11, 2011 6:37 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore Hi Carsten, That's pretty odd. Can you please show us exactly what you're typing? Also

[PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore

2011-05-11 Thread Schubert, Carsten [PRDUS]
Hi, The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files from the command line anymore. Does anybody have the same problem? What am I missing? Cheers, Carsten -- Achieve unprecedented app

Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore

2011-05-11 Thread Schubert, Carsten [PRDUS]
worked. Cheers, Carsten -Original Message- From: Alvin Oga [mailto:pymol.l...@mail.linux-1u.net] Sent: Wednesday, May 11, 2011 5:49 PM To: Schubert, Carsten [PRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line

Re: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in aPyQt4 widget

2011-04-26 Thread Schubert, Carsten [PRDUS]
Kasper, not sure if this will help you, but I think the GLEW stuff was added recently in V1.4.x and it seems to be still somewhat experimental. May be to get you started you could switch to v1.3r1 from the repository and try to embedd that version. V1.3.x should not contain the new GL stuff.

Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Schubert, Carsten [PRDUS]
Joachim, I'm running into the same issue on a SuSe SLED10 box. The 32bit binary (on the 64bit OS) displays the same behavior, i.e. only the MESA libs were used. The 64bit version actually core dumps during startup. I opened up a bug report with Schrodinger and they were already working on it (I

Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Schubert, Carsten [PRDUS]
Nadine, Probably the command line is your best friend here. Look into the 'clip near,x' and 'clip far,x' command, which allows to move the front and back clipping planes in x increments. Positive values move towards you, negative values of x away from you. If that does not provide enough fine

Re: [PyMOL] write a script from pse file

2011-03-13 Thread Schubert, Carsten [PRDUS]
Maia, as far as I know a .pse is just a dump of the internal data structure of Pymol. You can save the molecules contained in the session, but the graphical representation and any modifications would need to be recreated. Hopefully Jason proves me wrong ... Cheers, Carsten -Original

Re: [PyMOL] Different color on each side of strand

2011-03-07 Thread Schubert, Carsten [PRDUS]
Not sure if this is possible but it would be a nice feature to have. Since it mimics the way helices are drawn, when cartoon_highlight_color is set. Cheers, Carsten -Original Message- From: Keitaro Yamashita [mailto:yamash...@castor.sci.hokudai.ac.jp] Sent: Sunday, March

Re: [PyMOL] labeling by a pseudoatom

2011-02-27 Thread Schubert, Carsten [PRDUS]
Roberto, partial answer to point 3. Adding a _ before an object name hides it from the panel. For points 1 or 2. Could you please expand on your question? Is this for interactive or scripted mode? For scripted mode you could modify the coordinates of the pseudoatom to be closer to the target

Re: [PyMOL] Color scale changed in APBS?

2011-02-22 Thread Schubert, Carsten [PRDUS]
Hi Wataru, in addition to what Jason mentioned: Have you tried to look at the potential mapped on the solvent accessible surface and display the molecular surface? If you display the potential like this the colors will be much more muted, on the other hand this is the setting you will find most

Re: [PyMOL] pymol movie scripting for beginners questions

2011-02-11 Thread Schubert, Carsten [PRDUS]
Aiko, I can't directly comment on your problem, but I had good experience with the eMovie plugin. May be give that a try. http://www.weizmann.ac.il/ISPC/eMovie.html HTH Carsten -Original Message- From: Aiko Matsumoto [mailto:aikomatsumoto1...@googlemail.com] Sent: Friday,

Re: [PyMOL] Independent Zooming in Grid Mode

2011-01-28 Thread Schubert, Carsten [PRDUS]
Sean, Just a thought, but the translate command looks like as if it should be possible to selectively modify the viewmatrix on a per object basis: translate translates the atomic coordinates of atoms in a selection. Alternatively, is modifies the matrix associated with a particular

[PyMOL] Wiki down?

2011-01-27 Thread Schubert, Carsten [PRDUS]
I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log

Re: [PyMOL] Wiki down?

2011-01-27 Thread Schubert, Carsten [PRDUS]
AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Working fine for me (using Safari on a Mac). -Nat

Re: [PyMOL] colors and font size while ray tracing

2011-01-21 Thread Schubert, Carsten [PRDUS]
Hi Madhavi, with regards to your first question: I usually add text after rendering the stereo figures. That gives much better control and has the advantage that label come out cleaner. Look into Canvas, Photoshop or GIMP to do this. As an additional tip you can control the depth of the labels

[PyMOL] 3D TVs experience with PyMOL?

2011-01-17 Thread Schubert, Carsten [PRDUS]
Hello List: Has anyone been able to put together a workable system where they can run PyMOL from a 3D HDTV using a regular workstation (Linux or Windoze) and the NVIDIA 3D Kit for presentation purposes? I did some preliminary research and while there is a wide range of 3D TVs out there I am not

Re: [PyMOL] Force of pure white background when ray tracing with fog

2011-01-05 Thread Schubert, Carsten [PRDUS]
my background to white and tested all ray_trace_mode settings (with fog on) and the background is pure white. Can you please provide a snippet of code that produces the effect? Cheers, -- Jason On Tue, Jan 4, 2011 at 8:22 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Hi

[PyMOL] Force of pure white background when ray tracing with fog

2011-01-04 Thread Schubert, Carsten [PRDUS]
Hi Pymolers, I just noticed that Pymol produces an off-whitish background when ray tracing a figure with fog enabled. The RGB values are (252,253,254) with my standard settings and are devilishly hard to spot on a monitor, but show up on some printers as a grayish background. Is there a setting

Re: [PyMOL] Start PyMOL session in web browser

2010-12-20 Thread Schubert, Carsten [PRDUS]
Hi Martin, not directly applicable to your question, but may be it directs your thinking into a different direction. If I remember correctly Warren pointed out a couple of year ago the p1m file format was supposed to support downloading of structural information from the web with some limited

Re: [PyMOL] Charged Surface Calculation at different pHs?

2010-04-07 Thread Schubert, Carsten [PRDUS]
Steve, you need to use PDB2PQR to generate your pqr file, with choice of pH and then run APBS on that file. I pulled reasonable defaults for APBS from the APBS plugin tool. PDB2PQR is accessible through the APBS website. HTH Carsten From: Soisson, Stephen M

Re: [PyMOL] stereo rotation lost with draw command

2010-02-06 Thread Schubert, Carsten [PRDUS]
Norbert, Try something like this for a side-by-side stereo image: turn y,3 draw png left_image.png turn y, -6 draw png right_image.png turn y,3 Caveat is that potential shadows may not be rendered correctly in stereo. That's why the angle option was implemented in ray. HTH Carsten

Re: [PyMOL] Whitespacing?

2010-01-26 Thread Schubert, Carsten [PRDUS]
Not much of a help, but WingIDE Professional Edition has a very good indentation manager, which takes care of the mixed/space tab issues. If you are working in python frequently it is a worthwhile investment. Cheers, Carsten -Original Message- From: Jason Vertrees

[PyMOL] New Feature Ideas

2010-01-21 Thread Schubert, Carsten [PRDUS]
Jason, here are my feature requests, only slightly biased by the fact that some of them would be useful for my paper now (-: 1) arbitrary clipping planes bound to an object with an intelligent gui to place them. Something akin to be found in Maestro or semi-transparent CGO objects which can be

[PyMOL] Preserving sec. structure in states for animation

2010-01-12 Thread Schubert, Carsten [PRDUS]
Hi, I am trying to make a movie form a set of morphed pdb files. Currently the individual files are loaded into the same object with increasing states, all pdb files contain the SHEET and HELIX record created by dssp. The object is then displayed as a cartoon. When I loop over the states I

[PyMOL] Viewport dimensions query

2009-09-24 Thread Schubert, Carsten [PRDUS]
Hi, Does anyone know how to get a hold of the viewport dimensions from within a script? I vaguely remember some posts about this subject, but could not find anything in my archive. Thanks Carsten -- Come build

Re: [PyMOL] Viewport dimensions query

2009-09-24 Thread Schubert, Carsten [PRDUS]
://www.mail-archive.com/pymol- us...@lists.sourceforge.net/msg05888.html Best regards, Folmer Fredslund 2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com: Hi, Does anyone know how to  get a hold of the viewport dimensions from within a script? I vaguely remember some posts about

Re: [PyMOL] label a stereo .png image in pymol

2009-09-07 Thread Schubert, Carsten [PRDUS]
Peter, here are some general considerations for stereo images A. The images should be ~63mm apart with respect to a point which you consider to be neutral, i.e. neither lies in front or in the back of the zero-plane B. The distance of the images also put restrictions on their

Re: [PyMOL] Smooth fading of surface in movie?

2009-09-01 Thread Schubert, Carsten [PRDUS]
Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface

Re: [PyMOL] object-specific Z-clipping

2009-05-02 Thread Schubert, Carsten [PRDUS]
planes. If we can achieve this in PyMol then the rest is fairly easy. Cheers, Carsten -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Friday, May 01, 2009 8:53 PM To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] object

Re: [PyMOL] object-specific Z-clipping

2009-04-30 Thread Schubert, Carsten [PRDUS]
Hi Warren, I would be interested to see the OpenGL version implemented, despite the lack of raytracing support. In a pinch the draw command could just be sufficient to produce a good picture. As for the implementation in a raytracer context I second Tsjerk's and Harry's thoughts on the subject.

Re: [PyMOL] pymol and bonds to symmetry related molecules

2009-04-07 Thread Schubert, Carsten [PRDUS]
Christian, as far as I know, PyMol is only able to draw bonds between atoms within the same object. The easiest way would be to combine the pdb files, probably a good idea to give the symm-mate a different chain or segid and then issue the bond command to draw the bond. HTH Carsten

Re: [PyMOL] Showing only part of a surface around a ligand

2009-03-25 Thread Schubert, Carsten [PRDUS]
Wulf, suppose you have this scenario: Protein in chain A Ligand in chain I Then create b-site, byres chain A within 5 of chain I show sticks, chain I show surface, b-site should get you close. HTH Carsten BTW If you replace the create command with select your surface will be

[PyMOL] Procedure for adding packages to pymol site-packages?

2009-03-06 Thread Schubert, Carsten [PRDUS]
Hi, how would I go about adding a package to the $PYMOL_PATH/ext/.../site-packages w/o screwing up the install? For most packages the mechanism is python setup.py install. Would this work to run this from within pymol? Thanks Carsten

Re: [PyMOL] selenomethionine

2009-01-21 Thread Schubert, Carsten [PRDUS]
Scott, the MSEs are probably HETATM records instead of ATOM records. You can either replace the HETATM records to ATOM records or set surface_mode to 1 which allows rendering of surfaces with HETATM records (I think, am a bit fuzzy on that) HTH Carsten -Original Message-

Re: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS

2009-01-16 Thread Schubert, Carsten [PRDUS]
Michael, play around with the hash_max value, which seem to partially control how much memory is used during rendering. You can also reduce the quality of the rendering Display-Quality, that should reduce memory requirements too. I know you don't want that, but do you really need max quality?

Re: [PyMOL] Making Stereo Pair Graphics

2008-11-24 Thread Schubert, Carsten [PRDUS]
Buz your image size will automatically be limited by the separation of two equal points in the respective images, which should be ~62 mm apart. Let me know if you need more details. Carsten -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, November 24, 2008 3:01

Re: [PyMOL] remove cartesian coordinate from w/in transparent metal ions

2008-10-29 Thread Schubert, Carsten [PRDUS]
Tom, you need to hide the 'nonbonded' representation of your ion, which shows up as a little coordinate system i.e. hide nonbonded, chain I#if your ion is in chain I show spheres, chain I set sphere_transparency=0.5, chain I Cheers, Carsten -Original Message- From: Thomas

Re: [PyMOL] Electron density map in pymol

2008-09-26 Thread Schubert, Carsten [PRDUS]
Jhon, all the newer builds of PyMol are able to read ccp4 maps, no need to convert to xplor format. As far as your commands are concerned, you are almost there. Try this: load mymap.ccp4, format=ccp4, mymap isomesh map, mymap, 2.0, site, carve=1.6 were map is the name of the map graphical

Re: [PyMOL] hydrogen naming

2008-08-21 Thread Schubert, Carsten [PRDUS]
phenix.reduce is an option -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita Sent: Thursday, August 21, 2008 3:32 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] hydrogen naming

Re: [PyMOL] How to disable automatic atom connection?

2008-07-14 Thread Schubert, Carsten [PRDUS]
I believe show valence=on,your_selection will do the trick. Where your_selection is the ligand or whatever you want to display. Good luck Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of

Re: [PyMOL] different transparency surfaces proteins

2008-07-09 Thread Schubert, Carsten [PRDUS]
Joris, you should be able to apply different transparency settings if your proteins are part of different objects i.e. set transparency=0.8, sel1 set transparency=0.5, sel2 HTH Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] drawing axes

2008-06-11 Thread Schubert, Carsten [PRDUS]
Just to add onto what Tsjerk had to say about running python snippets in a .pml script. You can also encapsulate the python code in blocks like this: python your python code here python end This works with all newer version of pymol (1.0) and enhances readability of the code quite a bit. HTH

[PyMOL] Embeding commands in PyMol session?

2008-04-25 Thread Schubert, Carsten [PRDUS]
Hi, is it possible to embed commands or scripts into a pymol session? I am routinely creating PyMol sessions for users who for the most part have no clue how to use PyMol. So I'd like to include a dialog or message, which gets displayed after the session has loaded and clues the user in how to

Re: [PyMOL] Embeding commands in PyMol session?

2008-04-25 Thread Schubert, Carsten [PRDUS]
] Sent: Friday, April 25, 2008 3:28 PM To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Embeding commands in PyMol session? Hi Carsten, The best way to share PyMOL content with novice users is via pre-defined scenes stored in a session file. Users

Re: [PyMOL] hardware stereo problem

2008-03-12 Thread Schubert, Carsten [PRDUS]
Joris, this is a well known problem with the NVIDIA cards. It gets better with the newer highend cards but does not go away completely. You may want to invest in such a card and play around with different drivers. Carsten -Original Message- From:

Re: [PyMOL] How to make the dashed line having more dots?

2008-03-04 Thread Schubert, Carsten [PRDUS]
JunJun there are a couple of settings which relate to dashes. Go to Setting-Edit All... and filter by dash. You need to play around with these settings to get the desired effect. Be aware, some of these changes only become visible after raytracing. Cheers Carsten -Original

Re: [PyMOL] Isotropic thermal ellipsoids

2008-02-24 Thread Schubert, Carsten [PRDUS]
Warren, this thread gave me an idea about an enhancement request I had for some time. Would it be possible to extend the molecular object module in a way that 2 or more general properties per atoms would be available in PyMol in addition to b and q. For instance in Grasp 2 properties (Prop1,

[PyMOL] Cartoon mode not stored in scene description?

2007-12-12 Thread Schubert, Carsten [PRDUS]
Hi I am trying to define 2 scenes, in one the protein is represented in cartoon automatic mode in the other with cartoon putty. Pymol (1.0 on Linux or 1.1b on Windows) both only draw the recalled scenes in putty mode. Is that expected behaviour? I would have thought that the cartoon mode is

Re: [PyMOL] displaying unit cell in PyMol

2007-05-08 Thread Schubert, Carsten [PRDUS]
Satinder, make sure you have the correct CRYST record in your file, then load it and in the graphics GUI under S(how) select the Cell menu item. That should do the trick. Cheers Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] Suse 10 and PyMOL crashes

2006-10-04 Thread Schubert, Carsten [PRDUS]
Joris, just an idea. Check if the /dev entry for your video card has the right permissions. For the nvidia board I observed that sometimes the entries (/dev/nvidia0 and/or /dev/nvidiactl) are crw-- instead of crw-rw-rw. Check if changing the permissions on these entries or changing the owner

[PyMOL] Newline character in scene annotation message

2005-08-12 Thread Schubert, Carsten [PRDUS]
Hi I am trying to combine a scene with annotations spanning several lines. So far something like scene new, store, message=Line1\nLine2 would produce some nice coloration effects but not a newline character. I was able to use the api function to do the trick mesg=line1\nline2

RE: [PyMOL] Stereo 3D News

2005-02-17 Thread Schubert, Carsten [PRDUS]
Hi All: just a quick follow up on Warren mentioning the Sharp 3D LCD display. After a couple of trials with various drivers I got the LCD to work under the following setup: Nvidia Quadro FX1100 with driver V67.22 Windows XP with all the latest SPs and patches installed (may not matter) One head