Re: [PyMOL] weird visualization of a peptide structure

Annalisa, If bonds are not explicitly provided in the input file, then PyMOL infers bonding based on distance. Are the input coordinates valid? It looks like the atoms may be too close together in space... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp

Re: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

Buz, alter elem Na, elem='K' iterate elem K, print vdw show spheres, elem K alter elem K, vdw=1.4 rebuild iterate elem K, print vdw color yellow, elem K Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From

Re: [PyMOL] surface properties

Mark, PyMOL does not have such abilities at present. Can such concepts even be defined in a precise, objective, and unambiguous fashion? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Mark Collins

Re: [PyMOL] adding python modules for MacPyMOL

approach is to compile the Open-Source PyMOL source code for X11 instead of using MacPyMOL/PyMOLX11Hybrid. Unfortunately, the Python C ABI is just too fragile for anything else to be practical... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] PyMol memory vs. computer memory

-- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Crystal K. Chuang [mailto:ckchu...@lbl.gov] Sent: Tuesday, December 16, 2008 5:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMol memory vs. computer memory Hello

Re: [PyMOL] Ray Tracing A Protein Gallery

# and save save struct001.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, December 15, 2008 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray

Re: [PyMOL] B-factor putty tube representation

# unfortunately, the above does not in fact work because there is a bug in the code when all B factors are the same...you get a radius of 1 instead. # regardless, setting non-identical B factors should currently work: alter chain A, b=0.2 alter chain B, b=0.4 rebuild Cheers, Warren -- DeLano

Re: [PyMOL] y axis rock and mplay frame rate

Seth, set sweep_speed, 3.5 set movie_fps, 3 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: Seth Harris [mailto:set...@gmail.com] Sent: Monday, December 01, 2008 2:18 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL

[PyMOL] FW: 19th WCPCW Registration Now Open!

Attention Crystallographers: DeLano Scientific LLC will be exhibiting at the 19th WCPCW meeting April 5-8 in Asilomar, California with our usual setup: laptop, LCD, and plenty of time to talk PyMOL. But in addition, we are also settin up a WCPCW PyMOL event: most likely a 2-3 hour workshop

Re: [PyMOL] Dihedrals: Not a bug, though might cause misunderstanding

likewise for nucleic acids. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: DimitryASuplatov [mailto:gene...@gmail.com] Sent: Thursday, November 13, 2008 4:53 AM To: pymol-users@lists.sourceforge.net Subject

Re: [PyMOL] another odd PyMOL question....

Tom, label all, color will display the numeric color identifiers which can be used in place of color names. You can also use iterate to fetch them back out as a list: stored.list = [] iterate all, stored.list.append(color) print stored.list Cheers, Warren -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Camera Orientation

Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: QT [mailto:rdirect...@gmail.com] Sent: Monday, November 10, 2008 12:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Camera Orientation Hello everyone, I have a question

Re: [PyMOL] Camera Orientation

=spin).start() python end Cheers, Warren From: QT [mailto:rdirect...@gmail.com] Sent: Monday, November 10, 2008 10:04 PM To: DeLano Scientific Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Camera Orientation Ah thank you Warren, that gave

Re: [PyMOL] Camera Orientation

QT, No, unfortunately, it is more complicated than that...see the community wiki: http://pymolwiki.org/index.php/Get_View Also, for sectioning, you may wish to disable depth_cue unset depth_cue Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] Viewing gromacs in pymol

As an aside: If building current versions from source, there is now an additional performance hack for displaying trajectories using the simplest representations: lines, sticks, nonbonded, spheres, ribbon. set defer_builds_mode, 5 This will enable PyMOL to be more RAM and performance

Re: [PyMOL] question about checking the performance of PyMOL

). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling: cmd.refresh() After cmd.show. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message

Re: [PyMOL] export surface

Vahdati, The short answer to this is no. However, for the application you describe, try: zoom print cmd.get_position() Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Vahdati N. [mailto:nad...@soton.ac.uk] Sent

Re: [PyMOL] System freezes in cause of memory abuse

Christian, PyMOL's default behavior is to pre-compute and cache molecular geometry in RAM. Although this provides optimal performance for small numbers of molecular states, due to RAM usage, it is an unworkable approach for viewing long MD simulations. So, set defer_builds_mode, 3 before

Re: [PyMOL] incompletely drawn cartoon strands

Daniel, This is just a guess, but I suspect that there is a problem with identifiers and/or residue ordering in the structure which may be confusing PyMOL. A command like label name ca, segi+-+chain+-+resi may help reveal what is going on. Cheers, Warren -- DeLano Scientific LLC

Re: [PyMOL] zoom relative and absolute

that point. Cheers, Warren _ From: Joachim Reichelt [mailto:joachim.reich...@helmholtz-hzi.de] Sent: Thursday, September 18, 2008 7:35 AM To: DeLano Scientific Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] zoom relative and absolute So there something missing

[PyMOL] Plan for FreeMOL: APBS/PQR2PDB + MENGINE + MPEG movie creation

Baker Sent: Thursday, September 18, 2008 11:54 AM To: DeLano Scientific Cc: apbs-us...@lists.sourceforge.net; gilles.tr...@cgm.cnrs-gif.fr; pymol- us...@lists.sourceforge.net Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS Hi Warren -- Strictly speaking, the issue may

Re: [PyMOL] Strange behaviour with APBS

Gilles, The PyMOL and APBS programs have differing views as to whether PDB PQR files are column-based or space-delimited, respectively. We must eventually sort this out, because it causes continued grief for our users in common. For now, however, the workaround is to make sure no B-factors

Re: [PyMOL] zoom relative and absolute

). load obj1.pdb center obj1 zoom center, 20 ray png img1.png delete all load obj2.pdb center obj2 zoom center, 20 ray png img2.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

, or something else is going on. Gilles, what versions of PyMOL and APBS are you using? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Nathan Baker [mailto:nathanaba...@mac.com] Sent: Wednesday, September 17, 2008 6

Re: [PyMOL] install/upgrade

Joel, Does PyMOL 1.1 fail to even launch? If so, then your libc is probably older than the one required by that build. Note that we have posted an older glibc23-based linux build as well (measurably slower, but more compatible with older linux). pymol-1_1r1-bin-linux-x86-glibc23.tgz

[PyMOL] MacPyMOL Stereo 3D is back! (on Leopard)

Great news Mac users: The just-released Mac OS X 10.5.5 patch fixes the longstanding Stereo 3D compositing problems under Leopard. So, if MacPyMOL is the primary application for which you require Stereo 3D, then as of today, you can safely buy a new Quadro-equipped Mac Pro or upgrade your

Re: [PyMOL] select residues/atoms

in 24 or 32-bit color mode...aka. millions of colors. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of rdegr

Re: [PyMOL] Mutate serine to phosphoserine?

Ben, P-Ser and P-Try aren't currently built in to PyMOL. You could of course build the chemistry up atom by atom using the builder, but the resulting atom names wouldn't match standard PDB conventions. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp

Re: [PyMOL] Launch parameter -d with string

Christian, That limitation was fixed ages ago, spaces in commands such as: ./pymol -d 'help selections' should work fine with any recent unix-based PyMOL build, open-source or commercial. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] I want to represent a domain of my molecule as a lowresolution solid shape

of increasing the blur effect. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Pietro Roversi Sent: Thursday

Re: [PyMOL] uninstall plugins?

Sure. Done. It is now in the open-source code, and it will be present in version 1.2 builds. -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Matthew O'Meara Sent: Thursday, September 11, 2008 10:24 AM

Re: [PyMOL] ATOM and CONECT..

Yose, By default, PyMOL guesses connectivity based on proximity, based on the empirical observation that two atoms of a given radius will not be generally closer than a certain distance unless they are bonded. Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] curved cylinders in PyMOL

Michael, Sorry, this isn't something PyMOL is presently capable of doing. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] protein contact potential

the low-dielectric interior and the high-dielectric exterior (solvent region). I think it would be great if someone who knows far more than myself about PB electrostatics would address this issue in a rigorous fashion at some point. Cheers, Warren -- DeLano Scientific LLC Subscriber Support

Re: [PyMOL] Script for iterated `align`ment

Dimitry, cmd.align returns a list of numbers, the first of which is the final RMS value for atoms in the final cycle of alignment. You can of course use that result in a script. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original

Re: [PyMOL] combine opening pymol -- never mind

of sys.argv Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of David Shin Sent: Thursday, September 04, 2008 2:26

Re: [PyMOL] Molecule galleries

I'll second that. While applying PyMOL to generate millions of molecular renderings in an automated fashion may be a cool demonstration of open-source databases technology, using 2D molecules as inputs kind of misses the point: PyMOL is a 3D viewer, optimized for depicting 3D

Re: [PyMOL] Can't PNG a morph

Brian, This should work, so there is clearly some kind of problem. What version of MacPyMOL are you using? Also, have you tried setting ray_trace_frames before exporting? (save first -- that might take a while!). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] problem with pymol on FC6

on early versions of Mac OS X). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jhon Thomas Sent

Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3

OJ, I think Photoshop (or Gimp?) is probably the tool for this -- PyMOL's ray_trace_mode cannot distinguish between the underlying representations, but you could probably accomplish this through recoloring select portion of a single rendering or through composition of multiple renderings.

Re: [PyMOL] map outside the unit cell

expanded (e.g. a CRYST record was present in the input PDB file). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Rahul

Re: [PyMOL] sheared spheres for dots in dot representation

I think he means: sheared as in garden :) Creating a separate object is one route. Another would be: flag ignore, not rep dots rebuild But do note that this would affect surfaces or meshs as well. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] dot representation transparency setting

Nope, sorry: a quick look at the code confirms that no provision has yet been been made for a transparent dots representation. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun

Re: [PyMOL] independent positioning of two proteins, in preparation for RosettaDock?

(in other words, the objects will appear to move together). Also, if the molecules are part of the same object, then it is particularly important to right-click directly on the target chain, and then chain menu item and drag sub-menu-item. Hopefully that helps! Cheers, Warren -- DeLano

[PyMOL] FW: Python training for cheminformatics

From: owner-chemis...@ccl.net [mailto:owner-chemis...@ccl.net] Sent: Thursday, August 07, 2008 8:43 AM To: Warren DeLano Subject: CCL: Python training for cheminformatics Sent to CCL by: Andrew Dalke [dalke.:.dalkescientific.com] Hello all, I will be teaching a two-day training course in

Re: [PyMOL] resize to span 2 outputs on OS X

768 You'll need to adjust WH appropriately. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of aaron bryden Sent

[PyMOL] New Lower-Cost 3D Projector

pounds it fits under your arm and takes less than 5 minutes to set up Expected shipping to begin mid-September www.depthq.com or call +1 206 784 1385. -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] dots representation

the size of the sphere that the dot representation uses? I adjustable this through using alter, and changing the vdw setting for a selection (or object)... (then a rebuild)... Is this the best way? Yes. Cheers, Wawrren -- DeLano Scientific LLC Subscriber Support Services mailto:supp

Re: [PyMOL] label with arbitrary string

Richard, label (residue 200 and name ca), My favorite C_alpha The command you provided works as written, so what are you asking exactly? Is is that you want us to add a GUI way of doing this? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] Searching mailing list

the problem will be fixed soon! -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Boon Hoe Lim Sent: Saturday, July 26, 2008 9:10 AM To: pymol

Re: [PyMOL] move density

matrix_copy mol2, map2 isomesh mesh1, map1 isomesh mesh2, map2 etc. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] c-alpha only model show cartoon

Doug, Unfortunately, I do not think is not possible: PyMOL requires a full backbone in order to reliably generate cartoon geometries other than a simply backbone tube. Sorry! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message

Re: [PyMOL] ray and mpng

Doug, set ray_trace_frames before issuing the mpng command. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Bailey

Re: [PyMOL] distorted electrostatic surface color with PyMOL/APBS

Doug, Rotate transforms atomic coordinates (relative to the precomputed field). Try using turn to move the camera instead. turn y,180 etc. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun

Re: [PyMOL] .wrl Export

, then what you're seeing may be a shortcoming of the VRML viewer rather than of PyMOL. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.co mailto:supp...@delsci.com m _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun

Re: [PyMOL] .ccp4 map normalization - what does it mean?

Mike, Yes, that is the default behavior for PyMOL as well. To disable it, issue: unset normalize_ccp4_maps before loading your map file. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun

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

Petro, I am not sure this works in older versions, but set connect_mode,1 Should force current versions of PyMOL to only use connectivity information explicitly provided in the PDB file. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

Re: [PyMOL] movie between frames

Yes: unset movie_loop -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Weisel Sent: Saturday, July 05, 2008 4:07 AM

Re: [PyMOL] pdb-l: chain alignment tool

Inside a script, I would suggest adding ,async=0 so that the fetch command is forced to complete before the next command is read: fetch 1a25, async=0 show cartoon create chaina, chain a ... ... -- Subject: Re: [PyMOL] pdb-l: chain alignment tool Hi, There are many. One way is to use PyMol

Re: [PyMOL] How to display two or multiple eleectrostatic mapssimultaneously with PyMol?

at the molecular surface itself (which is less meaningful, since no atom could ever feel such a potential). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users

Re: [PyMOL] writing selection to a external file

Marius, Hmm...are you perhaps looking at the output before the file is closed and/or flushed? You should issue ndx.flush() or ndx.close() before attempting to use the output file. Cheres, Warren _ From: pymol-users-boun...@lists.sourceforge.net

[PyMOL] Reminder - still no 3D stereo under OS X 10.5

Hello All, Since I have long been such a big Mac stereo 3D proponent, it is especially important that I go on the record with an updated perspective. Based on all of the accumulated evidence to date, a verdict can now be rendered: we have lost the case. For stereo 3D visualization,

Re: [PyMOL] [SOLVED] python traceback from apbs plugin and one morequestion

light_count,10 set spec_count,1 set shininess, 10 set specular, 0.25 set ambient,0 set direct,0 set reflect,1.5 set ray_shadow_decay_factor, 0.1 set ray_shadow_deday_range, 2 unset depth_cue viewport 400,400 Then press ray. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] question on making movie between two scenes with differentpoint of view

are finally behind us. The only change I would suggest would be to allow at least 90 frames (3 seconds) between scenes so that the camera interpolation has time to complete. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From

[PyMOL] An Additional Stereo LCD Option: MIMO from Omnia

Last week I endorsed the Planar displays a promising alternative to CRTs. Martin Montgomery (MRC-DUNN) was kind enough to provide some insightful feedback on both Planar and Omnia displays, so I have included his comments below (with permission) along with a link to an image showing the two

Re: [PyMOL] NMR Chemical shift perturbation data to surfacerepresentation

yellow_white_red green_white_blue red_blue yrmbcg Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf

Re: [PyMOL] Question about PyMOL development

-- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of NeO Sent: Sunday, June 22, 2008 7:46 AM To: supp...@delsci.com; pymol-users@lists.sourceforge.net

Re: [PyMOL] Question about PyMOL development

in both the Python-based wizards and the Tcl/Tk GUIs. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _ From: DeLano Scientific [mailto:del...@delsci.info] Sent: Monday, June 23, 2008 9:31 AM To: 'NeO'; 'supp...@delsci.com'; 'pymol-users

Re: [PyMOL] Symmetry expanding electron density maps

symmetry records at present -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Engin Ozkan Sent: Thursday, June 19, 2008 4:34 PM

Re: [PyMOL] Appearance of nucleotides in DNA

Yes. set cartoon_side_chain_helper -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Alex Reynolds Sent: Monday, June 16, 2008

Re: [PyMOL] RMSD Calculations

Siddharth, align obj1CA, obj2CA, cycles=0 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of siddha

Re: [PyMOL] question about SUPER

Jianghai, That sounds like a bug, but it could be something specific about your script. Could you post (or email us) an example PyMOL script which reproduces the reported behavior? Thanks! Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original

Re: [PyMOL] Trouble with pymol tk GUI

Dimitry, From that traceback, it appears that you may not have successfully compiled _tkinter with your Python 2.5.1 build. To configure this manually, edit Setup.dist in the Modules directory of the Python source code distribution. Cheers, Warren -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Stereo output checkerboard format

to be no fundamental technical reason why desktop DLP displays shouldn't be able to do so as well. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users

Re: [PyMOL] problem picking atoms

Preferences). If not, then try to rotate the camera and adjust the clipping planes so that no other atoms are displayed near the atoms you wish to click on. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun

Re: [PyMOL] interior protein-surfaces

the above): set surface_color, white set surface_type, 2 unset ray_shadows Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun

Re: [PyMOL] [ccp4bb] While on the subject of stereo

Is there some way to increase the perspective-ness of the molecule being displayed (more so than the default perspective mode), I don't know whether this will work with the tracking software, but: set field_of_view, 50 zoom may do this trick. Cheers, Warren -- DeLano Scientific LLC

[PyMOL] Congratulations to Jason Vertrees, Ph.D.!

of Philosophy Club! In recognition of the critical enabling contributions Jason has made to the PyMOL Open-Source Project and to the community as a whole, and to further encourage and enable his future participation in the project, DeLano Scientific LLC is awarding Jason Vertrees the first PyMOL Open-Source

Re: [PyMOL] load script Mac

./script.pml or, if using a relatively recent PyMOL build, (3) force PyMOL to cd into the same directory as the script by using the following command sequence: cwd = sys.path.split(__script__)[0] if cwd: cmd.cd(cwd) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] Adding new states from data

()) # and rebuild the graphics objects cmd.rebuild(mov) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf

Re: [PyMOL] orientation-less scenes

Thanks for Andreas for this correction: scene store, F3, view=0 should be scene F3, store, view=0 -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: Andreas Forster [mailto:docandr...@gmail.com] Sent: Thursday, May 01, 2008 1:06 PM

Re: [PyMOL] appending metal ions

: pseudoatom my_enz, elem=Zn, name=Zn, resn=Zn, resi=2 And so forth. When you're done, write out the new pdb file. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] Color codes in mutagenesis wizard?

or slightly overlapping. Large red disks indicate signficant van der Waals overlap. Everything else lies between those extremes. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] PyMOL + Leopard + symlink

, MacPyMOL is itself set up to autoconfigure based on the name of the associated bundle. What is the intent behind using the symlink? Perhaps there is another way of meeting your need... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original

Re: [PyMOL] Embeding commands in PyMol session?

, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Schubert, Carsten [PRDUS] Sent: Friday, April 25, 2008 6:38 AM

Re: [PyMOL] Making transparent boxes with colored surfaces?

Pymol (at least up to 0.99rc6) has a problem with multiple transparencies in ray-tracing. That's news to me. Combination of multiple transparent surfaces is indeed broken in the OpenGL viewer up into 1.x. However, the ray tracer has been able to do this almost since the beginning. The

Re: [PyMOL] Keeping PDB ordering

Matrin, set retain_order before loading the input PDB file. Depending on the application, you may also wish to set pdb_retain_ids Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun

Re: [PyMOL] Problem Saving Molecules from batch mode

) However, a cleaner approach would be to run the Python script as the first argument to PyMOL followed by a -d statement. pymol -cq BuildHelix.py -d 'BuildMe(A)' Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message

Re: [PyMOL] Displaying multiple distances in MacPymol

the A action menu or use the set_name command. Or, if you like the old behavior: set auto_number_selections, on Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net

[PyMOL] ACS Mtg. New Orleans, April 7-9

Though DeLano Scientific LLC does not have its own booth at next week's American Chemical Society meeting in New Orleans, I will personally be joining our partner company Synaptic Science LLC in booth # 427 for much of the meeting. There we will be showing off recent progress integrating PyMOL

Re: [PyMOL] pseudoatoms and alignment

in the system but not necessarily visible in the 3D viewer. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf

Re: [PyMOL] Show sticks till a certain radius

(organic expand 5) color yellow, organic and elem c Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf

Re: [PyMOL] partial alignment (super?)

Carlo, If B is the chain ID for the matched seguments, then it should be as simple as: load file1.pdb load file2.pdb align file1//B//CA, file2//B//CA Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users

Re: [PyMOL] generating a labeled stereo image

Jong, Based on ChangeLog, draggable labels should be present in 0.99 and above. Control-left-click-and-drag on the label while in edit mode. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun

Re: [PyMOL] hardware stereo problem

Joris, We used to experience this problem occasionally on Linux, but not anymore. Your best bet is to update to the latest drivers. If that does not work, then this may be an unsolvable hardware issue on older cards. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] SISGL video memory error

(best), ATI (good), or Intel (acceptable) graphics chip. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Horacio Emilio

Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008?

Anders Others, Just FYI: On behalf of the PyMOL Open-Source Project, DeLano Scientific yesterday applied as a mentoring organization for the Google Summer of Code 2008. Google will publish the list of accepted organizations within a week -- we'll see what happens! In the meantime, the required

Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008?

that will impact the largest potential user base. So what hypothetical integrations would be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so on? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] How to combine serveral distance objects into one object

isn't yet in a FREE PyMOL build? Either: A. Compile the open-source code, B. Sponsor the project, (or) C. Wait a year or two. That's how the PyMOL project works! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From

[PyMOL] ActiveX PyMOL BETA Testing Development Club

, stay tuned -- ActiveX PyMOL BETA is now alive and kicking! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info

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