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

2009-10-30 Thread Warren DeLano
-Original Message- From: Thomas Evangelidis [] Sent: Thursday, October 29, 2009 4:56 PM To: Warren DeLano Cc: Thomas Evangelidis; Subject: RE: [PyMOL] how to get RMSD from align command Warren, before I write something

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

2009-10-29 Thread Warren DeLano
:24 AM To: Warren DeLano Cc: 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 sufficient

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

2009-10-29 Thread Warren DeLano
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

Re: [PyMOL] Replace Coordinates in State

2009-10-26 Thread Warren DeLano
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] number of h-bonds

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

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

2009-10-25 Thread Warren DeLano
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 3D

Re: [PyMOL] not getting a simple translation

2009-10-22 Thread Warren DeLano
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 [] Sent: Thursday, October 22, 2009 7:00 AM To:

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

2009-10-22 Thread Warren DeLano
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] Saving high resolution images

2009-10-22 Thread Warren DeLano
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 would

Re: [PyMOL] Secondary Structure Matching

2009-10-21 Thread Warren DeLano
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 [] Sent:

Re: [PyMOL] Saving high resolution images

2009-10-19 Thread Warren DeLano
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

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

2009-10-17 Thread Warren DeLano
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 [] Sent: Thursday,

Re: [PyMOL] Change location of measurement label

2009-10-14 Thread Warren DeLano
Switch the mouse into editing mode, then ctrl-left-click-and-drag on the label to reposition. Cheers, Warren -- Warren L. DeLano, Ph.D. (Sent from an iPhone -- please forgive brevity and/or typos!) On Oct 14, 2009, at 8:03 AM, Per Larsson wrote: Hi!

Re: [PyMOL] color functionality for mac versions

2009-10-08 Thread Warren DeLano
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

Re: [PyMOL] rmsd for multiple snaphosts

2009-10-02 Thread Warren DeLano
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 Python

Re: [PyMOL] Sessions and Scope

2009-10-02 Thread Warren DeLano
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

Re: [PyMOL] DepthQ configuration in a classroom setting

2009-09-29 Thread Warren DeLano
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

Re: [PyMOL] Iterate Script Over States

2009-09-28 Thread Warren DeLano
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

Re: [PyMOL] Iterate Script Over States

2009-09-28 Thread Warren DeLano
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 [] Sent: Monday, September 28, 2009 11:58 AM To:

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

2009-09-24 Thread Warren DeLano
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. Cheers, Warren

Re: [PyMOL] Pymol segmentation fault

2009-09-24 Thread Warren DeLano
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

Re: [PyMOL] mutation

2009-09-23 Thread Warren DeLano
Chandan, Apologies, but PyMOL can only mutate the standard 20 amino acids. Note that you have asked that second question before: tml Again, there is no special theory behind PyMOL's mutagenesis wizard: the

Re: [PyMOL] dihedral angle

2009-09-22 Thread Warren DeLano
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

Re: [PyMOL] dash_radius

2009-09-22 Thread Warren DeLano
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).

Re: [PyMOL] Bond command not functioning in script

2009-09-22 Thread Warren DeLano
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)

Re: [PyMOL] Grid View of a Group

2009-09-18 Thread Warren DeLano
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 [] Sent: Thursday, September 17, 2009

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

2009-09-17 Thread Warren DeLano
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

Re: [PyMOL] Pymol Symmetry Mates Naming

2009-09-17 Thread Warren DeLano
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

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

2009-09-16 Thread Warren DeLano
Note that this kind of stuff is much easier in PyMOL 1.2 without any scripting. (ScreenCasts for PyMOL Sponsors at under Complex Movie Creation -- login first). Nevertheless, a possible answer is below: Cheers, Warren # PyMOL .pml file (tested against PyMOL

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

2009-09-12 Thread Warren DeLano
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: Good

Re: [PyMOL] Morph Movies

2009-09-11 Thread Warren DeLano
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)

Re: [PyMOL] Alignment Objects

2009-09-11 Thread Warren DeLano
Maia, select all_arg_lys, resn arn+lys Cheers, Warren -Original Message- From: Maia Cherney [] Sent: Friday, September 11, 2009 2:03 PM To: Subject: Re: [PyMOL] Alignment Objects Hi, Is it posible in pymol to select all


2009-09-11 Thread Warren DeLano
, 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 [] Sent: Saturday, August 29, 2009 4:08 PM To: David Hall Cc: Warren DeLano; pymol

Re: [PyMOL] Rigimol

2009-09-10 Thread Warren DeLano
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

Re: [PyMOL] undisplaying residues

2009-09-09 Thread Warren DeLano
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 [] Sent:

Re: [PyMOL] help about mutation

2009-09-09 Thread Warren DeLano
Chandan, PyMOL's mutagenesis wizard is purely geometric, and is intended to offer up Dunbrack rotamers as per: Cheers, Warren From: Chandan Choudhury [] Sent:

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

2009-09-09 Thread Warren DeLano
the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS where, as part of the demo, he showed off some toy example where he docked a ligand in by hand, complete with having PyMOL show red/green dots for steric

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

2009-09-09 Thread Warren DeLano
, pymolwiki, the masking and protecting options, and I've tried examining the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS

Re: [PyMOL] broken

2009-09-02 Thread Warren DeLano
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

Re: [PyMOL] APBS in pymol1.2

2009-08-27 Thread Warren DeLano
Hugo, If building PyMOL from source, then please get APBS in source or binary form from the APBS sourceforge project: Cheers, Warren -Original Message- From: Hugo G. de Teran [] Sent: Thursday, August 27, 2009 10:06 AM Cc:

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

2009-08-26 Thread Warren DeLano
Stuart, 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

2009-08-25 Thread Warren DeLano
Stephen, ramp_new ramp-name, ... disable ramp-name Cheers, Warren -Original Message- From: Stephen Graham [] Sent: Tuesday, August 25, 2009 10:09 AM To: Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO

Re: [PyMOL] Calling scripted functions within alter_state

2009-08-24 Thread Warren DeLano
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] Calling scripted functions within alter_state

2009-08-24 Thread Warren DeLano
.: cmd.alter_state(..., cmd.my_fn(...)) Cheers, Warren From: Stuart Ballard [] Sent: Monday, August 24, 2009 4:06 PM To: Warren DeLano Cc: pymol-users Subject: Re: [PyMOL] Calling scripted

Re: [PyMOL] Zalman 3D Monitor

2009-08-24 Thread Warren DeLano
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: and click on the supported hardware tab after searching.

Re: [PyMOL] Transparent surfaces and presets

2009-08-20 Thread Warren DeLano
Jose, Yes, you need to override the object-specific transparency specification from the preset: unset transparency, object-name Cheers, Warren From: Duca, Jose [] Sent: Wed 8/19/2009 10:33 AM To:

Re: [PyMOL] Light Command Details needed

2009-08-20 Thread Warren DeLano
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. (Sent

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

2009-08-20 Thread Warren DeLano
Sean, Use set_bond instead of set for per-bond properties. Cheers, Warren -- Warren L. DeLano, Ph.D. (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

Re: [PyMOL] coordinate transformation

2009-08-17 Thread Warren DeLano
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,

Re: [PyMOL] Updated B-factor in trajectory

2009-08-15 Thread Warren DeLano
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 [] Sent: Sat 8/15/2009 9:44

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

2009-08-14 Thread Warren DeLano
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

Re: [PyMOL] pymol autodock plugin

2009-08-13 Thread Warren DeLano
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 [] Sent: Thursday, August 13, 2009

Re: [PyMOL] Measure surface area

2009-08-10 Thread Warren DeLano
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?

2009-08-07 Thread Warren DeLano
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

2009-08-05 Thread Warren DeLano
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

Re: [PyMOL] PI-bond distance

2009-08-04 Thread Warren DeLano
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

Re: [PyMOL] Python Function with Unlimited Positional Arguments

2009-08-02 Thread Warren DeLano
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):

Re: [PyMOL] Getting SCALE record within PyMOL

2009-07-20 Thread Warren DeLano
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 [] Sent: Saturday, July 18, 2009 1:58 PM To: pymol-users

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

2009-07-17 Thread Warren DeLano
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

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

2009-07-17 Thread Warren DeLano
this just work? Malcolm From: Warren DeLano [] Sent: Friday, July 17, 2009 12:23 PM To: Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization Just to make sure everyone understands: Stereo 3D

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

2009-07-17 Thread Warren DeLano
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] PyMOL 1.2r1 error report

2009-07-16 Thread Warren DeLano
-- Message: 1 Date: Thu, 9 Jul 2009 13:34:53 -0700 From: Warren DeLano Subject: [PyMOL] PyMOL 1.2r1 Released To: pymol-users

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

2009-07-16 Thread Warren DeLano
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.

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

2009-07-16 Thread Warren DeLano
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

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

2009-07-16 Thread Warren DeLano
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

Re: [PyMOL] unexpected EOF while parsing

2009-07-07 Thread Warren DeLano
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 pymol

Re: [PyMOL] subversion revision for 1.2?

2009-07-04 Thread Warren DeLano
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

2009-07-02 Thread Warren DeLano
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 Loop

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

2009-06-30 Thread Warren DeLano
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

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

2009-06-26 Thread Warren DeLano
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 in

Re: [PyMOL] is font_color universal?

2009-06-24 Thread Warren DeLano
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...

2009-06-22 Thread Warren DeLano
in advance Hari Jayaram Brandeis University On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano wrote: Donnie, This tripped me up for a while too, but I think the stereo DIN is an output (for projector, Z-screens, etc.) not an input.   Suffice it to say

Re: [PyMOL] Animation/ Matrix Question

2009-06-19 Thread Warren DeLano
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 [] Sent: Thu 6/18/2009 10:11 PM To: Subject: [PyMOL]

Re: [PyMOL] Disabling cartoon_highlight_color

2009-06-11 Thread Warren DeLano
set cartoon_highlight_color, default From: Roger Rowlett [] Sent: Thursday, June 11, 2009 7:17 AM To: Subject: [PyMOL] Disabling cartoon_highlight_color How do you disable

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

2009-06-09 Thread Warren DeLano
structs, I suspect we could extend that to 7 characters plus a null without adversely impacting PyMOL's memory use characteristics... Cheers, Warren -Original Message- From: ABEL Stephane 175950 [] Sent: Tuesday, June 09, 2009 12:34 AM To: Warren DeLano

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

2009-06-09 Thread Warren DeLano
Cheers, Warren -Original Message- From: Warren DeLano Sent: Tuesday, June 09, 2009 12:26 PM To: ABEL Stephane 175950 Cc: Subject: Re: [PyMOL] How to plot residu with a number Stephane, Okay, I see -- you're just spilling the top digit

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

2009-06-08 Thread Warren DeLano
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

Re: [PyMOL] map smaller than in Coot

2009-06-08 Thread Warren DeLano
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

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

2009-06-08 Thread Warren DeLano
Stephane, As per , 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

Re: [PyMOL] Hi all...

2009-06-08 Thread Warren DeLano
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

Re: [PyMOL] Principal Axes of Rotation

2009-06-03 Thread Warren DeLano
Sean, orient selection followed by a 90 degree rotation about the camera's ]X-axis should give you a couple of views with the desired characteristics. turn x, 90 Cheers, Warren From: gilleain torrance [] Sent: Wed

Re: [PyMOL] Principal Axes of Rotation

2009-06-03 Thread Warren DeLano
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 #

Re: [PyMOL] reorienting a chain

2009-06-03 Thread Warren DeLano
:26 AM To: Warren DeLano Cc: 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 polymer. Let me

Re: [PyMOL] Selection/remove bug?

2009-06-02 Thread Warren DeLano
Hi Jim, B all by itself is a selection language keyword for the b-factor property: select high_b_factor, b 50 So just use a different selection name: select chB, chain B Cheers, Warren From: Jim Remington [] Sent:

Re: [PyMOL] reorienting a chain

2009-06-02 Thread Warren DeLano
You can save a copy of the original and then superimpose the copy back onto it # using fab command from the latest 1.2 beta to create poly-ala fab AAA, pol # create copy of the polymer create copy, pol # adjust a torsion set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60

Re: [PyMOL] wrl and dx files problem

2009-06-02 Thread Warren DeLano
Raluca, PyMOL transforms the output geometry in order to deliver a default view matching what's seen in the viewer window. To prevent that, you'll need to effectively eliminate PyMOL's camera transformation by restoring to a transformation-less identity matrix: cmd.reset()

Re: [PyMOL] update mesh level to custom value after deleting map object

2009-05-28 Thread Warren DeLano
Hari, isolevel mesh-name, level Cheers, Warren From: hari jayaram [] Sent: Wednesday, May 27, 2009 12:29 PM To: Subject: [PyMOL] update mesh level to custom value after deleting map object H I

Re: [PyMOL] Load Selection

2009-05-26 Thread Warren DeLano
Sean, You can save some time a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon after the load statement). load 1E3M.pdb; remove not A-C+F// Cheers, Warren From: Sean Law

Re: [PyMOL] surface of ligand

2009-05-26 Thread Warren DeLano
set surface_mode, 1 Cheers, Warren -Original Message- From: chaix denis [] Sent: Tuesday, May 26, 2009 3:55 PM To: Cc: Chaix Denis; support; Subject: [PyMOL] surface of ligand Dear users

[PyMOL] FYI: Mid-range stereo 3D projector / emitter / glasses bundle

2009-05-20 Thread Warren DeLano
Stereo-3D-enthusiasts, Ad include below, just FYI -- no affiliation with DeLano Scientific -- though we have used products from these companies and found them effective. It appears that you can now set up a small conference room for active-stereo 3D visualization with glasses for 4 people

[PyMOL] When in doubt, go with nVidia.

2009-05-20 Thread Warren DeLano
Folks, For quite some time now, we have ourselves experienced and continued to receive complaints regarding graphics artifacts and other glitches with ATI/AMD Radeon HD graphics chips on multiple platforms. Though we haven't had time to investigate everything to our satisfaction, it is worth

Re: [PyMOL] Documentation and advice for external GUI Movies commands?

2009-05-19 Thread Warren DeLano
Jean, Assuming that you are using the most recent PyMOL 1.2 beta build, first create a Scene for each display you wish to show. (To do that, show everything the way you want and then select Append from the Scene menu. Repeat the process for each view / color / representation you wish to

Re: [PyMOL] vacuum electrostatics

2009-05-18 Thread Warren DeLano
Denis, Sorry, PyMOL only has protein charges coded at present. Perhaps the APBS project's pdb2pqr utility might be able to assign charges to canonoical ligands (such as ATP)? Cheers, Warren -Original Message- From: Chaix Denis

Re: [PyMOL] create double bonds in small molecules

2009-05-14 Thread Warren DeLano
Tom, set valence edit_mode Ctrl-right-click on the bond Ctrl-W seems to do the trick. Perhaps there's a problem with the version of PyMOL you're using? Cheers, Warren From: Thomas S. Leyh, Ph. D. [] Sent:

Re: [PyMOL] Error: unknown type

2009-05-12 Thread Warren DeLano
Shiven, It appears the script was flawed: names = cmd.get_names(sel1) should be: names = cmd.get_names(selection=sel1) I've updated it on the Wiki. Cheers, Warren -Original Message- From: Shiven Shandilya [] Sent: Monday, May 11, 2009 4:47 PM To:

Re: [PyMOL] Vacuum electrostatics

2009-05-11 Thread Warren DeLano
Mark, Should be fixed now (in rev 3720). Cheers, Wawrren -Original Message- From: Mark Wehner [] Sent: Monday, May 11, 2009 12:11 PM To: Subject: [PyMOL] Vacuum electrostatics Hi everyone, in the newer version of

Re: [PyMOL] Non-planar clipping?

2009-05-07 Thread Warren DeLano
David, This is a weak area for PyMOL. One thing to try is to switch to an animation with multi-layered transparency, two_sided lighting (and other tweaks) to help show the entire binding site volume. The approach isn't perfect, but it may help: fetch 1gzm, async=0 remove not a//

Re: [PyMOL] Vector-Based Figure Export

2009-05-06 Thread Warren DeLano
Sean, We don't have vector export, but PyMOL can generate a high-resolution BW transparent-background raster image as illustrated below: load $PYMOL_PATH/test/dat/1tii.pdb as cartoon set ray_trace_mode, 2 set ray_trace_gain, 1 unset antialias unset opaque_background unset

Re: [PyMOL] Grid_mode - reference structure

2009-05-05 Thread Warren DeLano
Martin, set grid_slot, -2, object-name for the object you wish to spread across all grid slots. Cheers, Warren -Original Message- From: Höfling Martin [] Sent: Tue 5/5/2009 5:02 AM To: Subject: [PyMOL] Grid_mode - reference

Re: [PyMOL] diehedral angle

2009-05-05 Thread Warren DeLano
Vivek, # new command in 1.2b5 - fabricate peptide, ALA trimer: fab AAA # set a dihedral value ro 180 degrees. set_dihedral 1/C, 2/N, 2/CA, 2/C, 180 Cheers, Warren From: Vivek Ranjan [] Sent: Tue 5/5/2009 12:09 PM To:

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