Re: [PyMOL] adding python modules for MacPyMOL

ended 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...@delsc

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 C

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 Messag

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] 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.

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] Ray Tracing A Protein Gallery

ender ray # 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.sou

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 that

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

entially display phi's, psi's, and chi's, and perhaps 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, Nov

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 Scie

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] Camera Orientation

cmd.move("z",-cmd.get_view()[11]) cmd.refresh() threading.Thread(target=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 Su

Re: [PyMOL] Camera Orientation

eld_of_view, 45 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 ever

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 competi

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

reference). 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 -

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 loadi

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 -- D

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

s- > boun...@lists.sourceforge.net] On Behalf Of Nathan 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

Re: [PyMOL] zoom relative and absolute

ning a box around 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 somethi

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

current code, 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, Sep

Re: [PyMOL] zoom relative and absolute

e same scaling (for a fixed aperture / window size / aspect ratio). 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

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 exc

[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 existin

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 http://

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 To

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

ent way 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

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...@

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 m

Re: [PyMOL] select residues/atoms

re running 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

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 [mailto:p

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.sourceforg

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] protein contact potential

in a PB calculation would be greatest due to discrete discontinuities between 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

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

files one by one through use 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: Thurs

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 representatio

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] Selecting Negative Residues

i=int(resi)-200 set seq_view # test selections indicate resi \-127 indicate resi \-136-\-129 A bit ugly, but it works! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforg

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] cylindrical representation

52-75/ca # resolved with "dss" dss The other approach would be to manually break the helix definition: dele all fetch 1u7k, async=0 as cartoon show ribbon set cartoon_cylindrical_helices alter 65/ca, ss='L' rebuild Cheers, Warren -- DeLano Scientific LLC Sub

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. Cheers,

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] independent positioning of two proteins, in preparation for RosettaDock?

e camera moves (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, Wa

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] 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 m

Re: [PyMOL] Can pymol indentify H-bonds and electrovalent bonds andshow them?

selection1, selection2, mode=2 eg.: dist pol_conts, chain A, chain B, mode=2 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 way

[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 Pyt

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

768 You'll need to adjust W&H 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 br

[PyMOL] New Lower-Cost 3D Projector

- At 6.9 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] 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.

Re: [PyMOL] dots representation

d way to adjust 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 Servi

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] 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] On

Re: [PyMOL] Searching mailing list

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] 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-

Re: [PyMOL] python/pymol malfunction on new Ubuntu installation

Try the following in a new shell: export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ python2.5 ${PYMOL_PATH}/__init__.py Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforg

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:

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] 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 (o

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 To

Re: [PyMOL] Problems with ray and high resolution

gain set antialias, 0 set ray_trace_gain, 2.5 ray 6000 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 Beha

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 [mailto:pymol-users-boun...@lists.sourc

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

he potential 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 [mai

[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, Open-sourc

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

te set 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

[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 displa

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

s 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-

Re: [PyMOL] Question about PyMOL development

e of the self_cmd argument, and you'll see similar constructs 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: Monda

Re: [PyMOL] Question about PyMOL development

arren -- 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.sourceforg

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 Of

Re: [PyMOL] Symmetry expanding electron density maps

have 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

[PyMOL] Endorsement: Planar Displays for Desktop Stereo 3D

Fellow stereo-3D addicts, I am endorsing Planar stereo 3D displays for use with PyMOL. Note that there is absolutely no relationship between DeLano Scientific and Planar, but I did see the product at the Schrodinger User Symposium and both Planar and Schrodinger were kind enough to allow me to

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 S

Re: [PyMOL] exploding proteins

set use_display_lists 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 Andreas Forster Sent: Saturday, Ma

Re: [PyMOL] Stereo output checkerboard format

e seems 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 [mai

[PyMOL] Stereo 3D still broken on MacOS X Leopard 10.5.3

loper relations at Apple that they are aware of the severity of the problem and have the issue appropriately prioritized. Unfortunately, there is just a bit too much good stuff going on with Apple these days... Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com

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] 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] [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 --

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

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] appending metal ions

due number: 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...@

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] Adding new states from data

dinates inside PyMOL stored.list.reverse() cmd.alter_state(2,"mov","(x,y,z)=stored.list.pop()") # and rebuild the graphics objects cmd.rebuild("mov") Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info &

Re: [PyMOL] load script Mac

pymol ./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 Serv

Re: [PyMOL] orientation-less scenes

Andreas, Yes, you can do this two ways by passing "view=0" to the scene store command. Either (1) save the scene without saving view information: scene store, F3, view=0 or (2) recall the scene while ignoring any view information: scene F1, view=0 Cheers, Warren -- DeLano Scie

Re: [PyMOL] Color codes in mutagenesis wizard?

t 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-

Re: [PyMOL] PyMOL + Leopard + symlink

OS/MacPyMOL bash: put in your ".profile" alias pymol=/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -Original Message- > From: Scott Shandler [mailto:shand...@mail.med.upenn

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

Re: [PyMOL] access to tkinter root for new Toplevel?

GUI as part of your initialization. The plugin approach is the safe way to add new functionality using Tkinter. See modules/pmg_tk/startup/__init__.py for example code to get you started. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info

Re: [PyMOL] Embeding commands in PyMol session?

t\nMy second line of text") 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 > Of Schubert

Re: [PyMOL] Problem Saving Molecules from batch mode

are superfluous with '-c'. B) 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 S

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-user

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 thi

Re: [PyMOL] wizard message

Jesper, No, sorry, there is not any way to configure the size or position of the message text at present. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -Original Message- > From: pymol-users-boun...@lists.sourcefor

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