RE: [PyMOL] question about _cmd.pyd

Wen, The only form of end-user PyMOL compilation we support on Windows is via Python's distutils facility. Assuming that your system paths are set up correctly, distutils compilations will work fine with msvc6 -- no Makefile is required. Your own c/c++ code should be built as a standalone

[PyMOL] RE: [PyMOL] Re： RE: [PyMOL] ques tion about _cmd.pyd

essage- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > wenming hu > Sent: Wednesday, August 24, 2005 6:29 PM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: [PyMOL] Re： RE: [PyMOL] question

RE: [PyMOL] Overlapping surfaces

Hugues, 1) PyMOL will not render identical overlapping surface triangles correctly -- it is a weakness in the current algorithm. 2) If the surfaces are truly distinct are distinct, then you'll only see one of the unless you select multilayer transparency, in which case you'll see both sides of

[PyMOL] Java Anyone?

PyMOL Users: We are looking to identify a few collaborators with existing Java application (not applet!) development efforts already in progress that would be ripe for inclusion of a simple real-time molecular visualization component. If this is you, then please make contact at your convenience a

RE: [PyMOL] Refinement in auto_sculpt

Mathieu, Deselect Sculpting from the builder menu or "unset sculpting" Note that if you're doing this a lot, then create some custom on/off function keys as follows: # F1 to turn on sculpting cmd.set_key('F1',lambda :(cmd.set("sculpting"),cmd.set("auto_sculpt"))) # F2 to turn off sculpting

RE: [PyMOL] Refinement in auto_sculpt

...@delsci.com > -Original Message- > From: Jim Nettles [mailto:jnet...@emory.edu] > Sent: Tuesday, August 30, 2005 6:00 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net; Mathieu Coincon > Subject: Re: [PyMOL] Refinement in auto_scu

RE: [PyMOL] out of memory with PyMOL in batch mode

Nicolas, PyMOL is probably running out of RAM during geometry construction, which is done by default for all 1000 frames (to enable fastest refresh rates). In your case, you want to disable that behavior and only generate geometry for the frame being rendered. This is something I added to 0.98:

RE: [PyMOL] out of memory with PyMOL in batch mode

September 08, 2005 5:32 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] out of memory with PyMOL in batch mode > > Warren, > I have tried my script after setting defer_builds_mode and/or > -D option to 2. PyMOL still crashes after approx

RE: [PyMOL] conformational states in the mutagenesis wizard

> I beleive the mutagensis wizard in the newer ( > 0.98) will > incorporate the Dunbrack library in some way or another. Indeed: the mutagenesis wizard in the latest betas incorporates the full bb-independent rotamer library and a sampled subset of the bb-dependent library covering populated reg

RE: [PyMOL] minor irreproducible bugs

Al, Bummer... Next time PyMOL won't start or is acting freaky, can you try launching PyMOL via command line as follows: Start Menu->Run then enter: cmd Assuming PyMOL is in the default location, paste in the following line: "c:\program files\delano scientific\pymol\pymolwin.exe" +2 And then p

RE: [PyMOL] Atom name and actual atom not consistent

Donald, Strange! Try making sure that you are running in "millions" of colors mode in the Display settings of System Preferences. If that doesn't solve your problem, then try the latest beta version http://delsci.com/beta to see if the problem still exists with the current code. Cheers, Warren

RE: [PyMOL] Atom labels problem

Alexey, Some video drivers don't draw fonts well as bitmaps, so try textures: set texture_fonts Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA .

RE: [PyMOL] Moving Selections

Lauren, Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific

RE: [PyMOL] rot+trsl matrices

Provided objects are moved in their entiretly, recent PyMOL betas may provide what you want via cmd.get_object_matrix(object-name) Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South

RE: [PyMOL] Global vars in Plugin name space?

Andreas, The trick here is that PyMOL symbols and the PyMOL command line operate in the pymol namespace, whereas Python modules and plugin each operate in their own "global" namespace. Try the following in your plugin: import pymol print pymol.colorDict Cheers, Warren -- Warren L. DeLano, Ph

RE: [PyMOL] alignment question

> is there any possibility to get a list of the pairs of atoms > that are matched using the align command? Not yet...sorry. Alignment objects are coming, but post 1.0. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite

RE: [PyMOL] How to change label size and font in pymol?

Xiang, We're working on better fonts & label display. In the meantime: set label_font_id, 4 For the biggest and heaviest font PyMOL currently supports. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suit

RE: [PyMOL] (no subject)

Yes, the create command provide you with this ability, though at the end of the process you end up with a new object. create new_object, old_object1 | old_object2 In some cases, new_object can be the same name as either old_object1 or old_object2: create old_object1, old_object1 | old_object2 A

RE: [PyMOL] From scenes to movies?

Pete & Dirk, Actually, I think Dirk is looking for something to convert the automatic scene-to-scene camera interpolation into movies...the immediate answer is no -- it isn't yet trivial to do, but we will be working on making that easier before the next release. Cheers, Warren -- Warren L. DeLa

RE: [PyMOL] transparency question

For various legacy reasons, the "transparency" setting only covers surface transparency. Try set sphere_transparency, 0.5 set stick_transparency, 0.5 etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., S

[PyMOL] Need Help with Stereo L/R Confusion

Folks, We are trying to track down and hopefully resolve a problem with the left and right images getting confused in stereo mode with PyMOL. I think this problem is limited to nVidia Quadro cards, but need more info. So... If (and only if) you use PyMOL in hardware stereo mode (with shutter gl

RE: [PyMOL] test in pymol scripting language

Use Python blocks! > Something like that: > if (count_atoms nt) == 0 > then cmd.delete("nt") if cmd.count_atoms("nt") == 0: \ cmd.delete("nt") Note the explicit use of "continuation" lines via backslashes. This ensures that PyMOL hands over both lines to the Python interpreter

[PyMOL] FYI: Windows Update issue for ATI cards

Folks, There is a broken ATI video driver making its way out through Windows automated update. I think it only effects the older ATI chips, such as the Radeon 7000, but if PyMOL suddenly stops working for you, then that is a likely cause. From what I understand, this can be fixed by reinstalli

RE: [PyMOL] Using the Pymol Run command

> Is there some recommended way to run a file of code? Gilleain is right on about the run command. On Windows and linux, you can also create .pym files that will specifically open into PyMOL. Another alternative is to use Python import capability. And of course, within pml files you can use blo

RE: [PyMOL] linux configuration

Andrew, What does PYMOL spit out on startup? Is it binding to the OpenGL drivers, or to Mesa? Also, you might set use_display_lists to take advantage of graphics card memory, etc. For example, on my dual Opteron/nVidia FX1100 based system, this option gives a 3X speedup in rendering. Cheers,

RE: [PyMOL] pymol problems with python after FC4 update

Stuart, It looks to me like you've got a mixed install with potentially old/incompatible files hanging around. For starters, see if the latest linux standalone build works http://delsci.com/beta pymol-0_99beta14-bin-linux-x86-glibc23.tgz That should help enable you to separate general PyMOL

RE: [PyMOL] Using the Pymol Run command

3 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: Terry Jones [mailto:tc...@hermes.cam.ac.uk] On Behalf > Of Terry Jone

RE: [PyMOL] Embedding pymol

Terry, We are very interested in this, but it is outside the scope of PyMOL 1.x. It will definitely be possible in PyMOL 2.x, but we'll need to break the API a bit for that in order to achieve an object-oriented usage paradigm. To accomplish this with current versions, it is necessary to launch

RE: [PyMOL] Embedding pymol

> 2 years ago I was involved with a project where we only > wanted to use pymol as a rendering widget, but it was > impossible. Our prototype used pymol's separate window, but I > recommended that the project look for another solution > because my impression was that the pymol project was more

RE: [PyMOL] how to show ribbon or cartoon

Li, If you load a protein structure without secondary structure assignments, PyMOL should assign then automatically. If not, then try running the "dss" command on the structure followed by "show cartoon". Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeL

RE: [PyMOL] Using a seperate python installation

There is always this trade off between (A) shipping PyMOL with its own Python, to guarantee reliable installation, or (B) using a system PyMOL install, for enabling integration and extensibility. One of PyMOL's advantages is that you aren't locked in to either approach, embedding or extension --

RE: [PyMOL] PyMol training

Emmanuel, There is a SF-Bay PyMOL mailing list for local annnouncements: http://groups.yahoo.com/group/pymol-sfbay/ We don't have any training events currently planned, but our next PUG (PyMOL Users Group) meeting will likely be on the 28th of Oct, focused on the version 0.99 release expected ar

RE: [PyMOL] PyMol segmentation fault while starting from external python program

Dmitriy, Due to problem with multithreading (especially with the Tcl/Tk external GUI), we haven't been able to get the "import pymol" approach to work in a stable robust manner across different OSes and environments. So sight now, as per comments in "modules/pymol/__init__.py", the only support

RE: [PyMOL] RGB values for preset colors in PyMol

Mark, print cmd.get_color_indices() will retrieve the color indices print cmd.get_color_tuple(index-number) will retrieve individual RGB components. set_color color-name, [r,b,g] will create a new color that will appear in the GUI list. From the open-source GUI you can use the "add" button in

RE: [PyMOL] PyMol segmentation fault while starting from external python program

din [mailto:brynd...@msu.edu] > Sent: Tuesday, October 11, 2005 5:06 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PyMol segmentation fault while starting > from external python program > > Warren > > It seems like PyMol should have

RE: [PyMOL] PyMol segmentation fault while starting from external python program

Update: With respect to "import pymol", I think all of the reported segmentation fault and race conditions have now been eliminated from the very latest source code. Since everyone doesn't have CVS access, I have posted a source tar-gz file on http://delsci.com/beta with updated instructions on b

RE: [PyMOL] lcd stereo

PyMOL can indeed drive this monitor, but a special build is required which includes Sharp's drivers. In fact, I just updated the Windows build for this product yesterday http://www.delsci.com/sharp3d For $600, I think this is defiinitely worth it -- but don't expect this product to replace your 2

[PyMOL] Need testers for new MacPyMOL on Tiger

For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its own copy (in part this is necessary preparation for Intel...). http://delsci.com/beta Please let me know how it works for you! Cheers, Warren

RE: [PyMOL] Re: Need testers for new MacPyMOL on Tiger

> My only request would be to add a > mechanism to stash the information panel if there isn't one > available --- I've gotten addicted to this capability for > presentations and teaching. You can manually collapse it by dragging the separator bar up to the top. Cocoa doesn't seem to provide a

[PyMOL] Geowall Testing

PyMOL Users: Regarding "geowalls" [also known as dual-projector passive stereo setups that use polarized lenses & glasses to deliver low-cost stereo 3D to large audiences]... Does anyone have one set up right now who might be able to test a new PyMOL build with improved geowall stereo support? C

RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

Michael d/l a recent build http://delsci.com/beta and use the "find"->"polar contacts" option under the objects Action "A" menu in the viewer window. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 21

RE: [PyMOL] How to raw_input() from windows Pymol?

Evangelos, This is architecturally impossible in PyMOL due to clash between the asychronous nature of GUI event handling and the synchronous nature of script execution using the main thread. Right now, the best thing you can do is add a new command into the language which calls your function foll

RE: [PyMOL] picking discrete coordinates

The best way to approach this is simply to build a small molecular object on the fly. See examples/devel/chempy_model*.py Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Fran

RE: [PyMOL] Pharmacophore visualizations

Andrew, It's either-or for now. Either you can render pharmacophores using CGOs or you can represent them as molecules and thus align them. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213

RE: [PyMOL] Geowall Testing

. South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourcefo

RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

; Sent: Tuesday, October 18, 2005 5:03 AM > To: pymol-users@lists.sourceforge.net > Cc: Warren DeLano; Michael Weber > Subject: Re: [PyMOL] automated H-bond computation & > visualization in pyMOL? > > hello, > > is this feature accessible from the command line as

RE: [PyMOL] feed value to pymol -qrc script.py

Andrea pymol -qrc script.py arg1 arg2 will work if you add a double-hyphen before the first argument in order to signal Pymol to stop interpreting arguments: pymol -qrc script.py -- arg1 arg2 Then your script can get these arguments as follows: from sys import argv my_argv = argv[argv.index("-

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

> But does this problem look like a bug ? No, it works as intended. The issue here is that the GUI just does not (yet) provide the capability of coloring representations, just atoms. So if you color representations directly using a command, then you'll need to use a command uncolor them. At

RE: [PyMOL] set_dihedral

> I guess that the moral of the story is that it's better to be > as specific as possible when making selections... Yes, this is an important thing to understand, and something I seen come up frequently with new users. The thing to remember is: As soon as you "create" a new object based on exis

RE: [PyMOL] Missing parts in cartoon mode

Kasper, Those regions show up fine with the latest beta versions (e.g. beta19 tested), so please upgrade. http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South

[PyMOL] Mac Stereo 3D: Breaking News

See "New Power Macs" on http://www.macworld.com/news/2005/10/19/liveupdate/index.php The first Quad-core Mac and the the first with a Quadro FX 4500 graphics card! Do you know what this implies? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scient

RE: [PyMOL] PyMOL featured on Apple Store site?

They've got MacPyMOL two places on this site: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D "in a window" down near the bottom. Amazing! The "Stereo 3D Matters to Me" campaign actually worked. Apple really *is* serious about meeting our needs

[PyMOL] Stereo 3D Monitors & Equipment

Here is some current information for those of you ordering yourself a new "Quad" Quadro-based Mac for doing Stereo 3D visualization. You will also need a good CRT, a stereo signal emitter, and shutter glasses. Stereo 3D glasses & emitters: - More expensive: StereoGraphics

RE: [PyMOL] Stereo

> Does this mean that until Apple release an OS / OpenGL driver > upgrade, stereo is still not possible on OS X even with new hardware? Not at all. Currently shipping hardware http://www.apple.com/powermac does stereo 3D in a window with currently shipping software http://www.delsci.com/macpymol

RE: [PyMOL] PyMol with MacOS 10.4

Konrad, Heads up: there are fundamental threading flaws inherent in Aqua/Tcl/Tk that currently preclude use of PyMOL with them. Basically, MacOS X can't feed events to multiple threads -- just a single thread. So, your either get interaction with the GLUT GUI, or the Tcl/Tk user interface, but

RE: [PyMOL] Re: Apple's tk and pymol

Bill, Are you using Framework GLUT or Fink/Xll GLUT? The latter might work because X11 actually runs as a separate process and has its own event queue which feeds into GLUT. If the former is working for you, then please provide some more specifics regarding OS version, etc. Cheers, Warren -- W

RE: [PyMOL] launching PyMol from a python function

Dmitriy, This is easily solved: PyMOL expects be imported at the global level as __main__.pymol, but you can spoof it by adding "__main__.pymol = pymol" as follows: def funct(): import __main__ __main__.pymol_argv = [ 'pymol', '-qx' ] import pymol __main__.pymol = pymol pymol.fini

RE: [PyMOL] Distnace objecs

Mirek, In recent versions (http://delsci.com/beta) , you can simply add measurements into a single object as you create them: dist my_measures, 14/ca, 16/ca dist my_measures, 17/ca, 16/ca dist my_measures, 19/ca, 16/ca angle my_measures, 14/n, 14/ca, 14/c dihedral my_measures, 10/n, 10/ca, 10/c,

[PyMOL] Mouse Zoom Change

Folks, I am going to flip the sense of the mouse camera zoom actions in versions 0.99 and beyond. Going forward, right-click-and-drag will zoom out with upward motion and zoom in with downward motion. Why the switch? (1) It is more intuitive: pulling the mouse toward you move the molecule towar

RE: [PyMOL] scenes and movies

Folks, Everyone wants and needs this functionality (including myself), but it doesn't quite work right (yet). Although some instructions were posted awhile back using the "mview" command, there are bugs in the current releases that prevent this from working the way it should when it actually come

RE: [PyMOL] cmd.quit() kills pymol together with the external python launcher

PyMOL can't be stopped and restarted within a Python -- it terminates the process. However, you can hide the graphics window as needed... cmd.window("hide") cmd.window("show") (in the future, pymol2 will support class-like behavior.) Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] .xyz file loading problem from chempy module

Dmitriy, The very latest beta versions of PyMOL can read .xyz files directly (via the "load" or "load_raw" commands). http://delsci.com/beta load_raw usage: my_xyz=open("some.xyz").read() cmd.load_raw(my_xyz, 'xyz', "my_xyz") I suspect the chempy XYZ file is limited to reading Tinker's fixed

RE: [PyMOL] Independent Rotation axis...

The "rotate" and "translate" commands can do this *if* you append the object=object-name to the command: Try typing in the following sequence of commands: fragment arg fragment glu translate [5,0,0], object=arg translate [-5,0,0], object=glu origin arg, object=arg origin glu, object=glu rotate

RE: [PyMOL] get color of atom ?

delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Indraneel Majumdar > Sent: Saturday, November 05, 2005 10:21 AM > To: pymol-users@lists.sourceforge.net > Cc: Warren DeLano

RE: [PyMOL] OS 10.4.3

MacPyMOL users: Just to let everyone know, we are aware of the screen fliker problem with the 10.4.3 update and working with Apple to resolve it ASAP. I have a favor to ask though: Could those who are expericing this issue please send me their machine info? Mac OS X has a comprehensive system p

RE: [PyMOL] Loading tetramer

Multiple ways to go: load tetramer.pdb1 set all_states is most memory-efficient However, load tetramer.pdb1 split_states tetramer delete tetramer Would give you the ability to manipulate each subunit independently. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Sc

[PyMOL] Mac Flicker Issue Workaround

Mac users: We lucked out and obtained a little help from an off-duty Apple engineer today who figured out how to work around the issue in 10.4.3. It was one of these combined bugs -- we weren't doing things sensibly in PyMOL, and the ATI driver wasn't quite complying with normal OpenGL behavior w

RE: [PyMOL] Discreet cartoon representation for overlapping secondary structure ?

> From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Indraneel Majumdar > Sent: Saturday, November 05, 2005 7:29 PM > To: pymol-users@lists.sourceforge.net > Cc: Warren DeLano > Subject: [PyMOL] Discreet cartoon

RE: [PyMOL] Mac Flicker Issue Workaround

. mailto:war...@delsci.com > -Original Message- > From: Jianghai Zhu [mailto:z...@purdue.edu] > Sent: Saturday, November 05, 2005 7:49 PM > To: Warren DeLano > Subject: Re: [PyMOL] Mac Flicker Issue Workaround > > I have problem to uncompress the data. Anybody

RE: [PyMOL] dna ladders

Mark, One of the great things about PyMOL is that you get the code right away. One of the worst things about it is that you get the code long before any documentation exists. Most of that code is new or overhauled as of yesterday. Here are some things to try: set cartoon_ring_mode, 1 (or 2 or 3

[PyMOL] MacPyMOL 0.99beta29

MacPyMOL Users, For those experiencing performance and/or flicker issues under 10.4.3, please update to 0.99Beta29 -- this should be the fastest, most stable MacPyMOL to date (~2-4X faster than betas 26-28). http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. P

RE: [PyMOL] MacPyMOL 0.99beta29

nday, November 07, 2005 8:03 PM > To: Warren DeLano > Subject: Re: [PyMOL] MacPyMOL 0.99beta29 > > Has anyone reported problems with these beta versions where > they launch but when you click on the windows, the > application seems to quit - using 10.4.3 but this problem > stem

RE: [PyMOL] movie from chempy objets

Raul, Load them in to the same object in a serial fashion -- i.e. where you specify the object state for each molecule loaded. You may also want to set the discrete object to 1 in order to avoid extra bonds. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] Wall Eye stereo widgets

Aaron, Very recent betas can do this: http://delsci.com/beta Use the command: stereo geowall and then stereo swap If you want crosseye instead of walleye. There is no developers manual yet... Cheers, Waren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Sci

RE: [PyMOL] File size?

Simon, Most likely you need to install vendor-specific OpenGL drivers to enable hardware acceleration (Linux can't ship with them because they aren't open-source). Refer to the web site for your graphics card vendor. Without such drivers, PyMOL falls back on software OpenGL rendering, which is

RE: [PyMOL] File size?

15, 2005 8:43 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] File size? > > Warren, > > Thank you for your answer. I have an Nvidia card on my > desktop with Nvidia drivers which I think include OpenGL > support. PyMOL is still

RE: [PyMOL] displaying protein with propeptide

A quick fix is to use the "retain_order" setting. set retain_order which will force PyMOL to honor the order of ATOMs in the PDB file over the numeric ordering of residue identifiers. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC

RE: [PyMOL] displaying protein with propeptide

only CONECT > lines in the pdb file instead of generating connectivity by distance? > > Eric > > Warren DeLano wrote: > > A quick fix is to use the "retain_order" setting. > > > > set retain_order > > > > which will force PyMOL to honor

RE: [PyMOL] Transparent background

Yes, in recent builds (http://delsci.com/beta). set opaque_background, off then draw or ray and then save the image. NOTE: Some graphics cards support this in OpenGL (draw command), other systems can only do transparent backgrounds via the ray-tracer (ray command). Cheers, Warren -- Warren

RE: [PyMOL] Light source questions

Chris, Multiple light sources will be in the next release -- the code is currently in CVS. For future reference: set light_count, 4 and modify the light, light2, and light3 vectors (if necessary) light0 is fixed along Z and has no default specular component. The Z axis light intensity is con

RE: [PyMOL] combine align and rms_cur to calculate rms for complexes

Andrea, PyMOL really can't do this job generally well because you'd need to specify an atom-by-atom correspondance between the two ligands. Unless the ligands are identical and have identical atom names, the numbers you get will be misleading. If that is in fact the case, then I think you're o

RE: [PyMOL] displaying protein with propeptide

0.147 33.200 19.269 0.00 30.41 > C > ATOM233 N ALA A 37 0.991 28.925 17.777 0.00 32.51 > N > ATOM234 CA ALA A 37 1.608 28.191 16.677 0.00 33.56 > C > > > Anne Mølgaard, Ph.D. > Center

[PyMOL] Workaround for Crash on MacPyMOL Startup

MacPyMOL Users, We have figured out why MacPyMOL was crashing for a select subset of users on start-up. It only happens if you extract our ".tar.gz" archive using StuffIt Extractor instead of Mac OS X's built-in extraction. The ultimate cause is rather esoteric: I had inadvertently enabled th

RE: [PyMOL] problem with amber trajectory

Dmitry, VMD may have the ability to shift and recombine the molecule relative to the periodic boundary in order to avoid this dismembered effect, whereas currently PyMOL does not. I believe ptraj can do this for you, though it has been ages since I have tried using PyMOL with Amber. Cheers, Warr

RE: Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)

> This is awesome. It looks like this has been a valid setting > for a *long* time, but I've never seen it. I look at a lot > of MCSS-type structures, and I have some really painful > scripts that get the bonds right once the structure is loaded > in PyMOL. Now, I can just stamp the CONECT r

[PyMOL] RE: NOTICE: mail delivery status

Now this has got to be the funniest bounce I've received to date as administrator of the PyMOL users list: > -Original Message- > From: pymol-users-ow...@lists.sourceforge.net > [mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of > postmas...@name-deleted-to-protect-the-innocen

RE: [PyMOL] Slowwwww ray

Michele, Did you just migrate from an older version? We switched PyMOL over to perspective-based rendering (WYSIWYG with OpenGL) as the default at some point in the past year. You can still render orthoscopically if you'd prefer: load 1alk.pdb show surface set orthoscopic set hash_max=160 ray

RE: [PyMOL] saving multiple object in one pdb file

FYI: In the development code, I've added a new "segi" option to "symexp" that will automatically assign a unique segment ID to symmetry-generated molecules. This will allow a use case such as follows: % pymol load $PYMOL_PATH/test/dat/1tii.pdb symexp s, 1tii, 1tii, 20.0, segi=1 save packing.pdb,

RE: [PyMOL] mixing ray_shadows states

Nat, ray_shadows is a global setting (only) -- changing it for individual objects has no effect. set ray_shadows, 0 ray will work. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Nat Echols Sent: Mon 11/21/2005 11:28 PM To: pymol-users@l

RE: [PyMOL] Raytracing interior surfaces. Problems in both PyMoland PovRay

Yep, Daniel's has it! To lessen the darkness of shadows, increase "direct" and if necessary, lower "reflect" get reflect get direct set reflect, 0.7 set direct, 0.4 ray Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster

RE: [PyMOL] How can I get the color ramp to show up in raytraced images?

Michael, There's a scaling bug for raytracing the ramp in perspective mode. set orthoscopic ray is the workaround. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Franc

RE: [PyMOL] EMizing an xray structure

Try a command sequence like this: alter all,b=10 set gaussian_resolution, 9.0 map_new dcalc, gaussian, 3.0 map_double dcalc isosurface dsurf, dcalc, 1.0 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 2

RE: [PyMOL] RE: EMizing an xray structure (Warren DeLano)

ct: [PyMOL] RE: EMizing an xray structure (Warren DeLano) > > Warren, > These commands (see below) go a long way toward solving the > problem of producing low resolution simple structures for my > textbook project. I have some questions: > > The first command elicits an er

[PyMOL] RE: ATI as a substitute to nVIDIA

John & Alain, I am not sure John really intended to cross-post that message, but now that the damage is done, I'll take it one step further: I believe the problem is our sacred open-source cow Linux, or rather that nasty amalgamation of diverse hardware, operating systems, and drivers collectivel

RE: [PyMOL] HETATM in pdb

Paul, rename object-name, force=1 will cause PyMOL to assign unique (though not necessarily sequential) atom names... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Franci

RE: [PyMOL] Problem with crashing

Occasionally PyMOL experiences problems due to a variety of factors, some of which are internal to the program, and others which are environmental in nature. If you encounter trouble, PyMOL may have a bug, or your computer's OpenGL graphics system may be at fault. To help those that seek to hel

RE: [PyMOL] Surface scribing in pymol?

Wulf, Just "show surface" for selected atoms: e.g.: hide surface show surface, resi 100 expand 5 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA .

RE: [PyMOL] Coloring "ladder" differently from "ribbon" in nucleic acid representation

Alex, Hmm...not exactly. you could set a uniform cartoon color for an object and then color the residue on a per-atom basis, or vice versa by setting the cartoon_ladder_color and relying on the atomic color for the cartoon, but there isn't a specific per-residue ladder or cartoon color (yet). Ch

RE: [PyMOL] translating and rotating protein in space

Vanessa, You're missing commas, and you need to issue the command in the model frame of reference (camera frame of reference is the default): translate [-14.911, -23.457, -1.534], camera=0 \ Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific

RE: [PyMOL] Iterative Magic Fit - Why not?

Shiven, "align" does indeed work just fine for 3hck and 2src... 3hck is an NMR structure ensemble, and PyMOL superimposes ensembles based on their average ensemble coordinates, not based on just one arbitrary structure (as is perhaps the case with DeepView?). The problem here is that mem

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