Re: [PyMOL] how to get RMSD from align command

the job. Cheers, Warren > -Original Message- > From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] > Sent: Thursday, October 29, 2009 4:56 PM > To: Warren DeLano > Cc: Thomas Evangelidis; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] how to get RMSD from ali

[PyMOL] Remember, PyMOL is for visualization, not analysis.

Dear PyMOL-Users: Today's questions regarding alignment RMS values suggest to me that I should re-emphasize what PyMOL is and is not good for: Please everyone keep in mind that PyMOL is intended to be just a "molecular graphics" program, to be used for displaying, comparing, and manipulating mole

Re: [PyMOL] how to get RMSD from align command

/29/2009 5:24 AM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] how to get RMSD from align command Hi Warren, Now I am more confused. I used align command to measure the overall RMSD between homologous structures. Apparently align is not appropriate if not

Re: [PyMOL] how to get RMSD from align command

Tom, The complication with cmd.align() is that it is doing a whole lot more than a simple alignment. The first number is in fact the RMS, but it covers only the subset of the input atoms remaining after refinement is completed. The count of aligned atoms is the second field. If you're looking

Re: [PyMOL] number of h-bonds

Hello Michael, Unfortunately, there is no programmatic way to get this information out of PyMOL -- my apologies! Cheers, Warren -Original Message- From: Michael Zimmermann [mailto:micha...@iastate.edu] Sent: Mon 10/26/2009 9:04 PM To: pymol-users Subject: [PyMOL] number of h-bonds Dea

Re: [PyMOL] Replace Coordinates in State

Sean, Unfortunately, there isn't any way at present to directly expose PyMOL's internal C coordinate array to Python in an accessible form. Yes, iterate_state and alter_state are highly inefficient - it would make more sense to provide a means of exporting and re-importing coordinate sets via

Re: [PyMOL] Pymol Align Command and RMSD Calculation ?

> 1. What type of RMSD is calculated with align comman i.e All Atoms or only Backbone? It depends on the input selections. If you don't restrict it to backbone atoms, PyMOL will perform the fit for all matched atoms. Also, it is important to understand that "align" is a combined sequence and

Re: [PyMOL] Upgraded computer, PyMol now unusable :^(

John, We have seen such problems with OpenGL-based applications, including PyMOL, running under ATI Radeon hardware & graphics with older versions of the OpenGL-based Compiz window manager. The easiest solution is to reconfigure Linux to disable compositing and/or use a conventional window

Re: [PyMOL] Saving high resolution images

Hi Tom, Actually this is how the "draw" command works in using the screen-based OpenGL renderer to create images of arbitrary size. However, the ray-tracer isn't currently set up to operate that way. Ray might work with an orthoscopic projection, but with perspective enabled, each frame woul

Re: [PyMOL] real time first person camera view / control

Nick, How would this be different from the existing Scene interpolation capability? You can use the Scene menu to Append a series of scenes of the molecule (views+representations) and then use Scene -> Next, PAGE-DN or the scene command to interpolate through them. Cheers, Warren ___

Re: [PyMOL] not getting a simple translation

Hi David, You have a rotate command in that script. Did you mean to 'turn' the camera rather than 'rotate' the atomic coordinates? Cheers, Warren > -Original Message- > From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] > Sent: Thursday, October 22, 2009 7:00 AM > To: pymol-users@li

Re: [PyMOL] Export trajectory

Andrea, Yes: save file-name.pdb, object-name, 0 For example: save multi.pdb, mytraj, 0 Cheers, Warren -Original Message- From: andrea carotti [mailto:and...@chimfarm.unipg.it] Sent: Thu 10/22/2009 5:02 AM To: pymol Subject: [PyMOL] Export trajectory Hi all, is there the possibilit

Re: [PyMOL] Secondary Structure Matching

Fred, You might try "super" instead of align (same syntax). Failing that, you can use "pair_fit" with explicit selections -- just make sure the number of atoms is the same in each of the selections. Cheers, Warren > -Original Message- > From: Kerff Frédéric [mailto:fke...@ulg.ac.be] >

Re: [PyMOL] axpymol for mac

Aysegul, No, unfortunately not. AxPyMOL (http://axpymol.org for the curious) is a Windows-only capability, and it is only intended for use inside PowerPoint at present. Cheers, Warren From: Aysegul Ozen [mailto:aysegulo...@yahoo

Re: [PyMOL] Saving high resolution images

Eva, You may be past the limit of what PyMOL can handle. Regardless, the 64-bit Linux builds are the best at handling large-memory tasks. Practice with something really simple: fragment arg as spheres ray 6000,9000 Also, two more things I'd suggest for such a large image (in order to cut dow

Re: [PyMOL] selecting multiple, non-adjacent chains

Sean, There is also a more concise option: select allothers, chain 0:4+C:J+L:Z Or even more concise, using selection macro: chain/residue/atom select allothers, 0:4+C:J+L:Z// Cheers, Warren -Original Message- From: Marius Retegan [mailto:marius.s.rete...@gmail.com] Sent: Thursday, Oc

Re: [PyMOL] Change location of measurement label

Switch the mouse into editing mode, then ctrl-left-click-and-drag on the label to reposition. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from an iPhone -- please forgive brevity and/or typos!) On Oct 14, 2009, at 8:03 AM, "Per Larsson" wrote: > Hi! > > I need to make

Re: [PyMOL] color functionality for mac versions

Mark (& indeed all Mac users) MacPyMOL can be launched in two flavors, based on the name of the executable: If the executabled is named MacPyMOL, PyMOL launches in the mode you're familiar with: a single-window Cocoa-based interface. If the executable is renamed PyMOLX11Hybrid, then PyMOL launc

Re: [PyMOL] change bond length

Jens, Unfortunately, those values are hardcoded. However, if you load a coordinate file into PyMOL with alternate bond distances, and only modify dihedrals or use the sculpting capability, then the input bond distances should be preserved (for the most part). Cheers, Warren -Original Mes

Re: [PyMOL] Sessions and Scope

Tsjerk, Great question with a crummy answer: you can't! But this seems like a really good idea, at least for primitives stored in ordinary built-in Python containers. Saving class instances would be problematic, since session files wouldn't necessarily be restorable in the absence of accompanyi

Re: [PyMOL] rmsd for multiple snaphosts

>Dear all, > >i have multiple conformations files (multi pdb) and would like to >compute for each one, the rmsd for each snapshot against the first >snapshot. >Is it possible with pymol to do such a task ? > >thank you in advance for the gain of time ... :-) > >nicolas floquet Yes, using a short P

Re: [PyMOL] Iterate Script Over States

) print len(my_dict['L']) etc. Cheers, Warren > -Original Message- > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > Sent: Tuesday, September 29, 2009 7:40 AM > To: Warren DeLano > Subject: Re: [PyMOL] Iterate Script Over States > > Hi Warre

Re: [PyMOL] DepthQ configuration in a classroom setting

Roger, That's a bit odd: usually it either works or it doesn't. Working for 20 seconds at a time may indicate defective hardware (projector, emitter, graphics card, connector, dead battery, etc.). But as a first test, pease try using some other stereo-3D-capable software (e.g. VMD or Chi

Re: [PyMOL] Iterate Script Over States

Sean, Yes, that is an alternate route. cmd.get_model is likely slower than cmd.iterate_state, but should work regardless. Cheers Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Monday, September 28, 2009 11:58 AM To: pymol-users@lists.sourc

Re: [PyMOL] Iterate Script Over States

Sean, I'm not sure what you have in mind other than something like (python code): for state in cmd.count_states(): cmd.iterate_state(state, selection, expression) where expression is accumulating coordinates from multiple states Cheers, Warren From

Re: [PyMOL] Stereo flipping in coot and pymol

I agree with Dirk - this is likely a hardware problem. From within PyMOL ,it can be worked around via the menu Display->Stereo->Swap Sides or by typing "st sw" (stereo swap) at the command line. Cheers, Warren From: Dirk Kostrewa [mailto:kostr...@genzentr

Re: [PyMOL] Pymol segmentation fault

Ian, Based on that traceback, it looks like you have two conflicting versions of Tcl (8.4 as well as 8.5) linked against and running in the same process...that could be the source of the crash. Cheers, Warren From: Ian Berke [mailto:ian.be...@yale.edu]

Re: [PyMOL] Loading PDB Files does not work with Linux

Joachim, PyMOL relies entirely upon Python's built-in proxy support (via urllib), so if you can get a Python script configured to work properly through your proxy, then PyMOL should work as well. http://www.python.org/doc/2.5.2/lib/module-urllib.html Cheers, Warren

Re: [PyMOL] mutation

Chandan, Apologies, but PyMOL can only mutate the standard 20 amino acids. Note that you have asked that second question before: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07211.h tml Again, there is no special "theory" behind PyMOL's mutagenesis wizard: the

Re: [PyMOL] Bond command not functioning in script

Stuart, For what's it's worth, I'm not able to reproduce the problem: Aside from automatic suppression of output when using the Python API, I'm getting the exact same behavior with # test1.pml cmd.pseudoatom("temp",pos=[0,0,0],name="A") cmd.pseudoatom("temp",pos=[0,0,5],name="B") cmd.bond("te

Re: [PyMOL] dash_radius

Craig, In the OpenGL viewer, dashes are always drawn using line primitives, so dash_radius has no effect until you issue the "ray" command. Note that dash_width is generally preferable to dash_radius since it controls both the OpenGL and ray-traced renditions (so long as dash_radius is zero). Ch

Re: [PyMOL] dihedral angle

Vivek, If there are multiple attached atoms, then there may be multiple dihedrals present. There is a visual indicator which shows what angle is being measured -- do those indicator match the displayed angle? Cheers, Warren > -Original Message- > From: Vivek Ranjan [mailto:vran...@gmai

Re: [PyMOL] Grid View of a Group

Yes, but it may not be the answer you want: avoid putting those objects into groups. At present, groups and grids are interconnected in a hard-coded manner. Cheers, Warren > -Original Message- > From: T. Andrew Binkowski [mailto:abinkow...@anl.gov] > Sent: Thursday, September 17, 2009 9

Re: [PyMOL] Pymol Symmetry Mates Naming

Fang, There is no relationship between ACT and PyMOL, so one wouldn't necessarily expect them to match in terms of how they name the resulting objects. However, I suspect there may also be a difference of intent: Based on a quick glance at PyMOL source code, PyMOL appears to convey a relative

Re: [PyMOL] Displaying electron density from maps output by Coot.

To Everyone: When posting such questions, please always indicate what specific vesion of PyMOL you are using, since the program continues to evolve with every release (to reflect numerous end-user suggestions, as enabled by contributions from our sponsors.) To Andy: PyMOL version 1.2r1 should sy

Re: [PyMOL] movie.roll in middle of movie

Note that this kind of stuff is much easier in PyMOL 1.2 without any scripting. (ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12 under "Complex Movie Creation" -- login first). Nevertheless, a possible answer is below: Cheers, Warren # PyMOL .pml file (tested against PyMOL 1

[PyMOL] nVidia Quadro / LCD Stereo 3D Info Link

For those looking to do Quadro-based stereo 3D under Windows with the new 120 Hz LCD displays, please pay careful attention to which card you purchase if you expect to do stereo 3D! nVidia has a page with the facts you need: http://www.nvidia.com/object/quadro_pro_graphics_boards.html Good lu

Re: [PyMOL] RMS

.n_cycles_run, rms_info.initial_rms, rms_info.initial_n_atom, rms_info.raw_alignment_score, rms_info.n_residues_aligned); Cheers, Warren From: Carlos Ríos Vera [mailto:crosv...@gmail.com] Sent: Saturday, August 29, 2009 4:08 PM To: David Hall Cc: Warren

Re: [PyMOL] Alignment Objects

Maia, select all_arg_lys, resn arn+lys Cheers, Warren > -Original Message- > From: Maia Cherney [mailto:ch...@ualberta.ca] > Sent: Friday, September 11, 2009 2:03 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Alignment Objects > > Hi, > Is it posible in pymol to sele

Re: [PyMOL] Morph Movies

Colin, Can you describe what you are trying to accomplish (overall) in more detail? There are different approaches one could take depending on the objective... The simplest, but limited approach is to use the mset and madd commands with variable numbers of frames: # show the initial state (1) f

Re: [PyMOL] Rigimol

Colin, Unfortunately, that is hard to do: there is no guarantee that the proposed (characteristic) path of motion which relates any two spacial orientations will possess reasonable chemistry or sterics. RigiMOL does make an attempt to resolve simple conflicts, and the refinement step can address

Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

LDEN or some of the other suites out there and I wanted to > try this with PyMOL. I've gone through the manual, the web, > pymolwiki, the "masking" and "protecting" options, and I've tried > examining the use of

Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

OLDEN or some of the other suites out there and > I wanted to try this with PyMOL. I've gone through the > manual, the web, pymolwiki, the "masking" and "protecting" > options, and I've tried examining the use of frames and > split_states, but I haven'

Re: [PyMOL] help about mutation

Chandan, PyMOL's mutagenesis wizard is purely geometric, and is intended to offer up Dunbrack rotamers as per: http://dunbrack.fccc.edu/bbdep/bbdepdownload.php Cheers, Warren From: Chandan Choudhury [mailto:iitd...@gmail.com] Sent: Wednesday

Re: [PyMOL] undisplaying residues

Bala, The trick is to leave the phosphate displayed for those residues where the backbone should still be shown: hide everything, resi 20-40 and not elem p Cheers, Warren From: Bala subramanian [mailto:bala.biophys...@gmail.com] Sent: Monday

Re: [PyMOL] broken

Joel, When using the PyMOL launch icons, it is only possible to have one active version installed (registered) under Windows. However, you can (1) copy and rename the Program Files \ DeLano Scientific \ PyMOL folder from a correctly installed version, then (2) edit the launch.bat file insi

Re: [PyMOL] APBS in pymol1.2

Hugo, If building PyMOL from source, then please get APBS in source or binary form from the APBS sourceforge project: http://apbs.sourceforge.net Cheers, Warren > -Original Message- > From: Hugo G. de Teran [mailto:hugo.te...@usc.es] > Sent: Thursday, August 27, 2009 10:06 AM > Cc: a

Re: [PyMOL] Inexplicable exception raised by cmd.color()

Stuart, Hmm...it appear that QuietException is being thrown when the input pattern fails to match any valid object name (but without an error message being printed). The easiest immediate workaround is to simply swallow the exception. for i in range(10): try: cmd.color(colors[i],

Re: [PyMOL] invoke ramp_new without drawing 'ramp' CGO

Stephen, ramp_new ramp-name, ... disable ramp-name Cheers, Warren > -Original Message- > From: Stephen Graham [mailto:steph...@strubi.ox.ac.uk] > Sent: Tuesday, August 25, 2009 10:09 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO

Re: [PyMOL] RMS

Carlos, The complication is that align outputs RMS values for only those atomic pairs remaining following sequence matching following by a refined structure alignment (which omits atoms above a cutoff), whereas rms outputs the value for all atoms matched by identifier (without any optimization)

Re: [PyMOL] Zalman 3D Monitor

Joachim, I think this is more an issue of driver support rather than hardware. However, the latest drivers do not necessarily support older cards. Please see nVidia's site for details: http://www.nvidia.com/Download/index.aspx?lang=en-us and click on the "supported hardware" tab after searching.

Re: [PyMOL] Calling scripted functions within alter_state

, etc.: cmd.alter_state(..., "cmd.my_fn(...)") Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 4:06 PM To: Warren DeLano Cc: pymol-users Subject: Re: [PyMOL] C

Re: [PyMOL] Calling scripted functions within alter_state

Hello Stuart, By default, alter_state expressions are evaluated in the "pymol" namespace of the current PyMOL instance, not the "cmd" (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in "pymol" by default, and thus, includes any functions you define. Try:

Re: [PyMOL] Stick Radius different for selected residues, possible?

Sean, Use set_bond instead of set for per-bond properties. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from a mobile device. Please forgive brevity and/or typos!) On Aug 20, 2009, at 4:18 PM, "Sean Moore" wrote: > Hello, > I am trying to change the stick_radius for a fe

Re: [PyMOL] Light Command Details needed

The light and lightN settings are direction vectors, not coordinates. Intensity (reflect setting) is averaged across all such directional sources. It has recently been suggested that we need better control over lighting. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from

Re: [PyMOL] Transparent surfaces and presets

Jose, Yes, you need to override the object-specific transparency specification from the preset: unset transparency, object-name Cheers, Warren From: Duca, Jose [mailto:jose.d...@spcorp.com] Sent: Wed 8/19/2009 10:33 AM To: pymol-users@lists.sourceforge.net

Re: [PyMOL] coordinate transformation

Vivek, Create a copy of the original chain, modify the chain, and fit the copy to the original. For example # PyMOL 1.2 .pml input fab AAA, orig create copy, orig set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180 unpick fit origCA, copyCA Cheers, Warren

Re: [PyMOL] Updated B-factor in trajectory

Oscar, Use the discrete=1 option to load each PDB state as a separate set of atoms (instead of as a trajectory -- the default behavior). load multimodel.pdb, discrete=1 Cheers, Warren From: S4C6Ar Chung [mailto:s4c...@gmail.com] Sent: Sat 8/15/2009 9:44 A

[PyMOL] AxPyMOL Updated: .MAE and .MOE support.

FYI, for Windows users who like to live "on the edge"... AxPyMOL is the PyMOL Active Control, which makes it possible to display live molecular content, including PyMOL PSE and PSW files inside of PowerPoint (on Windows only). Because we are still having trouble getting this Windows-based com

Re: [PyMOL] Displaying .kont files / Grid Users

Florian, Can you convert the files to Insight GRID ".grd" format? PyMOL can read those files directly. Alternatively, dependeing upon complexity of the task, you might be able to study the SVL .kont reader and create a Python equivalent for use with PyMOL. Cheers, Warren > -Original Mes

Re: [PyMOL] states for distance objects

Hello Bernd, The trick is to create the distance objects using atoms already present in the states you wish the distances to occupy. For example: # load NMR structure fetch 1nmr, async=1 # measure N to C distance in each frame distance demo, 1/N, 85/C # play set movie_fps, 1 mplay Cheers

Re: [PyMOL] Extracting Amino Acid Sequence from PDB File

Buz, # Yep, PyMOL 1.2: load $TUT/1hpv.pdb save 1hpv.fasta # or by selection save 1hpv_A.fasta, chain A # etc. Cheers Warren > -Original Message- > From: Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, August 13, 2009 2:39 PM > To: pymol-users@lists.sourceforge.net; ccp...@jiscm

Re: [PyMOL] pymol autodock plugin

Jed, With the 1.2 release of PyMOL, we have completely switched over to Numpy. So the first thing to try is to replace: from Numeric import * # with from numpy import * Cheers, Warren > -Original Message- > From: Jed Goldstone [mailto:jedg...@mit.edu] > Sent: Thursday, August 13, 200

Re: [PyMOL] Measure surface area

Mirek, PyMOL isn't the optimal tool for measuring surface area -- perhaps others on the list can suggest good alternatives. The only kind of surface area PyMOL can measure well is solvent accessible area, and it is a bit slow because all it does is sum up partial areas associated with discrete

Re: [PyMOL] de-speculating?

Hi Tom, set specular, 0 alone should be enough to do the job if all you want to do is turn off specular lighting -- you can ignore all those other spec_* settings. However, for a more matte appearance I'd be more inclined to try: set shininess,10 set specular_intensity, 0.2

Re: [PyMOL] problems with apbs/pqr

James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for

Re: [PyMOL] PI-bond distance

> I´m desperate to get some information about PyMol, I need to know it is > possible to measure a distance from a middle of a pi-bond to another atom? No, this isn't possible directly, but you can do something like the following: # copy & paste demo snippet load $TUT/1hpv.pdb pseudoatom pi_cen

Re: [PyMOL] Python Function with Unlimited Positional Arguments

Sean, You need a keyword argument list as well, so that the effective PyMOL class instance (_self) can be passed in by keyword (actual use of _self is only strictly required when you have multiple PyMOLs active in a single Python interpreter). # pml input: python def my_fn(*arg, **kwd): pri

Re: [PyMOL] Difference between create and select?

Dirk, "select" doesn't create object, it creates atom selections, which are essentially lists of atoms in actual molecular objects. Selections have almost no properties, settings, or anything else other than a name (if they are named selections) and a display state (pink dots, on or off). Per

Re: [PyMOL] about secondary structure assignement: help

Paola, True, PyMOL doesn't write secondary structure to PDB files, but it does save the current in both PyMOL sessions as well as in PKL (Python Pickle) files. load $TUT/1hpv.pdb as cartoon alter chain A, ss='S' alter chain B, ss='H' rebuild save example.pkl, 1hpv delete all load

Re: [PyMOL] Getting SCALE record within PyMOL

Stuart, Sorry, there is no way to do this at present (short of manually editing text files). But thank you for the suggestion! Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Saturday, July 18, 2009 1:58 PM To: pymol-users Subject

Re: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization .

Minor correction, for geeks who care about technical trivia. I previously wrote: > I don't think [VGA] Modeline timings have any meaning when > generating a true digital display signal... Apparently the modeline timings do still have significance in terms of digital information transport, which

Re: [PyMOL] WARNING: No Mac or Linux support for 120 HzLCD synchronization

shouldn't this just work? Malcolm From: Warren DeLano [mailto:war...@delsci.com] Sent: Friday, July 17, 2009 12:23 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization Just to make sure everyone understands

[PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization

Just to make sure everyone understands: Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due to the need of a special USB driver for the 3D Vision sync emitter. Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog DIN sync connector - it ju

[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (WinXP info)!

Continuing coverage... Although GeForce 3D Vision is not officially supported for Windows XP, I managed to get it to work with PyMOL. Assuming you have the following setup: - A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm - A recent Quadro series graphics card such as

[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (Vista info)!

Today nVidia issued their first public beta release of their 190-series driver. Although this release is officially for GeForce hardware, it seems to work fine for Quadro cards as well. So, if you have the following hardware setup, then you can at last now use PyMOL in Stereo 3D at full 1680x1050

Re: [PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit

Valentina, PyMOL has been known to work great with the Samsung 2233rz for quite some time, but nVidia had not publicly released any of the required 190-series drivers until today. Note that, officially speaking, you will need a Quadro graphics card in order to do OpenGL-based stereo 3D.

Re: [PyMOL] PyMOL 1.2r1 error report

this reflect changes in the cmd API setup? Regards, Stuart Ballard -- Message: 1 Date: Thu, 9 Jul 2009 13:34:53 -0700 From: "Warren DeLano"

Re: [PyMOL] Comparing B-factors of aligned residues

Donnie, Please try: load $TUT/1hpv.pdb extract chA, chain A extract chB, chain B # assign some B values onto chA from random import random alter chACA, b=random() # show for later comparison... iterate chA///1-10/CA, chain,resi,b # generate an alignment align chACA, chBCA, o

Re: [PyMOL] Shader support?

Justin, No changes were made -- just define _PYMOL_OPENGL_SHADERS Cheers, Warren > -Original Message- > From: Lecher, Justin [mailto:j.lec...@fz-juelich.de] > Sent: Thursday, July 09, 2009 12:06 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Shader support? > > Hi all,

[PyMOL] PyMOL 1.2r1 Released

Greetings, Mac, Windows, and Linux builds for 1.2r1 were posted early this morning. Current subscribers can download them via Direct download: http://delsci.com/ip/12 or via online docs: http://delsci.info/dsc/ip As usual, I recommend caution with upgrading. Please don't upgrade right

Re: [PyMOL] Label coordinates

Folmer, Sorry no, this is still a "to do" item. Cheers, Warren > -Original Message- > From: Folmer Fredslund [mailto:folm...@gmail.com] > Sent: Thursday, July 09, 2009 6:33 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Label coordinates > > Dear all, > > Is there a way

Re: [PyMOL] Pymol build from source

Robert & Joseph: I just updated and tested both of the distutils and autotools open-source build systems to match the current source -- you should be good to go. please "svn update" and retry Cheers, Warren > -Original Message- > From: Robert Campbell [mailto:robert.campb...@queensu.ca]

Re: [PyMOL] unexpected EOF while parsing

> To include > blocks you have to do more than indentation. You have to put a slash > in front of the for statement and end all but the of the blocks with a > backslash. Actually, nowadays you can just wrap Python blocks with the statements: "python" and "python end". For example: # example py

Re: [PyMOL] subversion revision for 1.2?

Michael, Sorry for the confusion: Although 32-bit 1.2r0 Windows and Linux builds have been announced, Mac builds, 64-bit Windows & Linux builds, as well as final updates to the open-source code & build scripts are still in process. Once the complete 1.2 release is ready, that fact will be

Re: [PyMOL] DCD Trajectories and Movie Panel

Sean, The movie panel operates on movie frames, not trajectory states, so you need to create a relationship between them. A one-to-one relationship can be created using the Python command: cmd.mset("1 -%d" % cmd.count_states()) Or alternatively, you can use the new Movie -> Program -> State L

Re: [PyMOL] ZM-M220W and TRIMON ZM-M220W

The difference? $769.99 - $354.99 = $415 exactly. But seriously, this is a question for Dell, not pymol-users. For what it is worth, mid $300's is the current per-unit pricing for the ZM-M220W display - but they originally hit the market at a 2-3X higher price, so one of those links is pro

[PyMOL] "Your Mom is Open Source" (Fun stuff -- hey, it's Friday!)

Have you heard? You Mom Is Open Source! No, that is not some veiled condemnation of maternal virtue, but rather the provocative title of Shane Hope 's latest Solo Exhibition at the Winkleman Gallery

Re: [PyMOL] is font_color universal?

Tom, # per-object: set label-color, color-name, object-name # per-atom: set label-color, color-name, selection # for example fragment arg label all, name set label_color, yellow, arg set label_color, red, elem c # note that the other label settings may not work below the per-object level

Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...

Linux X86_64 - Hardy Heron 8.04 Stereo glasses: > Crystal Eyes 3 with 3pin mini din connector > > > Thanks for your help in advance > Hari Jayaram > Brandeis University > > > > On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano > wrote: > > > > Donnie,

Re: [PyMOL] Animation/ Matrix Question

Zach, Can you wait a week or two? This sort of thing is about to get 100X easier in PyMOL... Cheers, Warren -Original Message- From: Charlop-Powers, Zachary [mailto:zachary.charlop-pow...@mssm.edu] Sent: Thu 6/18/2009 10:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ani

Re: [PyMOL] Disabling cartoon_highlight_color

set cartoon_highlight_color, default From: Roger Rowlett [mailto:rrowl...@mail.colgate.edu] Sent: Thursday, June 11, 2009 7:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Disabling cartoon_highlight_color How do you disable cartoon_highlight_

Re: [PyMOL] How to plot residu with a number > 9999

10123 Cheers, Warren > -Original Message- > From: Warren DeLano > Sent: Tuesday, June 09, 2009 12:26 PM > To: ABEL Stephane 175950 > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] How to plot residu with a number > > > Stephane, > > Okay,

Re: [PyMOL] How to plot residu with a number > 9999

V/IBITEC-S/SB2SM > 91191 Saclay, FRANCE > website: http://www.st-abel.com > ------ > > > > Message d'origine > De: Warren DeLano [mailto:war...@delsci.com] > Date: mar. 09/06/2009 02:01 > À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net > Objet : RE: [PyMOL]

Re: [PyMOL] Hi all...

As for the your general question: can you "import pymol; from pymol import cmd; pymol.finish_launching(); etc"? Answer 1: Yes, if you manually compile PyMOL open-source code into an existing Python interpreter. Or Answer 2: Yes, if you run your Python script using PyMOL's built-in Python inte

Re: [PyMOL] How to plot residu with a number > 9999

Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren > -Original Message- > From: Stephane Abel [ma

Re: [PyMOL] map smaller than in Coot

Greetings Michael, I suspect this is a question PyMOL automatically normalizing the map values, whereas the other programs might not. For historical reasons, PyMOL's default behavior is to normalize CCP4 map values upon loading. To prevent this, issue: unset normalize_ccp4_maps before loading t

Re: [PyMOL] Distinct labels on white background (ray tracing)? (JimRemington)

Sorry, I accidentally forgot to CC the list on my response to Jim. Yes, the culprist is one of the 600+ settings (ray_label_specular to be exact). Recipe for jet-black labels below... fragment methane zoom label all, name bg white unset depth_cue unset ray_label_specular set label_co

Re: [PyMOL] reorienting a chain

Wed 6/3/2009 9:26 AM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] reorienting a chain Hello Warren, Thank you very much for your advice. I guess I was not being very clear. what i meant was that i would also like to save the coordinates of this reoriented pol

Re: [PyMOL] Principal Axes of Rotation

Sean, Apologies for not understanding... You definitely need orthoscopic, but there's more to it. set orthoscopic fetch 1bna, async=0 orient 1bna cmd.matrix_copy(None,"1bna") reset from chempy.cpv import average cmd.origin(position=average(*cmd.get_extent())) center origin #

  1   2   3   4   5   6   7   8   >