[PyMOL] FW: [Jmol-users] Pymol, DSV, and Jmol

FYI / FTR -- my recent post on the Jmol list pertaining to feature duplication interoperability. -Original Message- From: jmol-users-boun...@lists.sourceforge.net [mailto:jmol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Wednesday, March 05, 2008 12:34 PM

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

Anders, No plans at present, but hey, it is still one whole week before a week before the deadline! Anyone out there with sufficient bandwidth to mentor? Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability would make a good SOC project? ;) Cheers, Warren -Original

Re: [PyMOL] matching colors

the objects in your schematic. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Patrick Loll Sent: Wednesday, March 05, 2008 2:17

Re: [PyMOL] Scripts on Mac

-- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Sadler, Evan Sent: Friday, February 29, 2008 7:17 AM To: gilleain torrance; pymol-users

Re: [PyMOL] Isotropic thermal ellipsoids

exactly what you're thinking about doing, so perhaps you could describe one or more of your intended use cases in a little more detail? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun

Re: [PyMOL] Color residues by b-factor

the current behavior, would you agree that using the numeric average of the value would make the most sense? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users

Re: [PyMOL] grid_mode?

Xavier, grid_mode can currently only be found in the open-source code, but it will be present in the next beta build. This feature was added directly in response to recent requests from people wishing to visualize two or more structures in a juxtaposed fashion. Cheers, Warren -- DeLano

Re: [PyMOL] Selecting single type amino acids within X angstrom fromeach other

(each expanded to a residue) # selecting all nearby HIS residues as we go into the result while cmd.pop(tmp, c_alphas): \ cmd.select(result, result or byres (his/ near_to 6 of byres tmp)) # then display the resulting selection enable result Cheers, Warren -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Isotropic thermal ellipsoids

measure of absolute RMS displacement in any sort of modeling or analysis work. It is probably safer to stick with relative, qualitative comparisons within a single structure, keeping in mind that vdw could be scaled by systematic biases. Cheers, Warren -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Mouse start-up setting

Jorge, You can create a .pymolrc file in your home directory to do this. From the MacOSX terminal window, issue: echo config_mouse one_button ~/.pymolrc Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol

Re: [PyMOL] RMSD between two ligands

Horacio, PyMOL cannot currently superimpose small molecules unless: 1. either the identifiers match between the two molecules (fit commmand) or 2. the pairwise correspondance between the two is explicitly specified (pair_fit command or pair fitting wizard) Cheers, Warren -- DeLano Scientific

Re: [PyMOL] Align output

Evan, You can save the alignment object resulting from an align command to an aln file: align sele1, sele2, object=aln_obj save alignment.aln, aln_obj Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol

Re: [PyMOL] Importing pymol modules into python

-source code into Fink / X11 / Python via distutils. This will enable 'import pymol' from within external python scripts. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] scenes and animate versus frames mdo

a particular matrix with a particular frame, and it is also what you use to interpolate between views. PyMOLwiki has some coverage at: http://pymolwiki.org/index.php/Scene Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From

Re: [PyMOL] Command-line arguments when using PyMOL to launch ascript

list / MIME artifact. -- 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 Michael Lerner Sent: Friday, February 15, 2008 8

Re: [PyMOL] pymol nstall problems

://www.pymolwiki.org/index.php/Windows_Install Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Wednesday

Re: [PyMOL] help with batch mode

(1i8eCA,1) output=open(output.txt,'wa') for rms in list: output.write(str(rms)+\n) output.close() Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users

Re: [PyMOL] Pymol capabilities

, then it should be possible to load such content into PyMOL for visualization and animation, and for sharing results with your scientific colleagues. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun

Re: [PyMOL] help with batch mode

functions available to users at the command prompt and in command scripts where feedback is typically desirable. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] strange pymol crash

workarounds been identified? Thanks, John -- Re: [PyMOL] strange pymol crash From: DeLano Scientific del...@de... - 2007-12-22 20:35 John, This is a bug we haven't yet been able to figure out yet. However, Jack Howarth has provided the following workaround

Re: [PyMOL] pymol error in linux - does not work

Praba, You need to install 32-bit compatibility libraries for X11, which should provide the file in /usr/lib or /usr/X11R6/lib Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] transparency of cgo plane

Robin, Try: obj.extend([ALPHA,0.5]) 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 Robin Owen Sent

Re: [PyMOL] Apply a transformation matrix to a selection

Tony, create a, resi cmd.transform_selection(a, [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]], homogenous=1) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol

Re: [PyMOL] .pse file and new pdb

David, So long as the PDB files match, you should be able to: load new_pdb.pdb, new_object update old_object, new_object delete new_object Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun

Re: [PyMOL] Small VRML export bug

Chris, Thanks -- fixed. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Chris Want Sent: Monday, January 28, 2008 9:04 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL]

Re: [PyMOL] algorithm for alignment

with high relative variability (e.g. 2 standard deviations from the cycle's mean deviance). super does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del

[PyMOL] PyMOL By Popular Demand Survey (Jan 2008)

- Secondary structure display in sequence viewer - Scene buttons / sorter - Movie slider ala Cinema4D/Maya/3DSMax - Drag drop programming of object motions - Fix ___ bug... -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info mailto:del...@delsci.info

Re: [PyMOL] export the mesh or surface

Or, with recent builds, simply save myscene.wrl or save myscene.obj Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, January 16, 2008 4:37 AM To: Lu Lin Cc:

Re: [PyMOL] two objects with synchronous rotation about their axes

Oganesyan, Sorry, no, this isn't possible with the current PyMOL release, but it could be added fairly easily if there is popular demand. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] Problems with space group recognition

-- 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 Mark Wehner Sent: Saturday, January 12, 2008 4:07 AM

Re: [PyMOL] algorithm for surface calculation?

Tom, PyMOL provides a discrete brute-force approximation to the molecular surface as defined by the atomic van der Waals radii and the surface of all possible 1.4 A spherical waters in contact with the molecule. Cheers, Warren -Original Message- From:

Re: [PyMOL] Problems with space group recognition

Mark, It sounds like the sglite module may not have compiled correctly. 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

Re: [PyMOL] Rigimol Output

Buz, Does anyone know the exact meaning of the output from the first rigimol processing step? Those tables were used for diagnostic output during development of RigiMOL. For instance, if I give the rigimol program two structures that are very similar (structure #1 and structure #2), the

Re: [PyMOL] strange pymol crash

John, This is a bug we haven't yet been able to figure out yet. However, Jack Howarth has provided the following workaround: [with] the compile flags... -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Out of those it

Re: [PyMOL] Cartoon mode not stored in scene description?

Carsten, Hmm...this could be a bug. In the meantime, the way to get this effect is to duplicate the object, and then configure one object one way, and the second, another. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net

[PyMOL] FW: Pymol question

I have a quick question for you. I am trying to look at the structure of the tetranucleosome (pdb file 1zbb). However, the structure is only composed by 2 nucleosomes. Is there a way to duplicate the image to 4? Based on the BIOMT records in the PDB file: REMARK 350 BIOMOLECULE: 1 REMARK

Re: [PyMOL] Precompiled pymol won't work on Fedora 6

that the version of PyMOL you are using is 1.0r2. If you do not have it, you should be able to d/l it by going to http://delsci.com/dsc from any UTSWMC on-campus computer. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol

Re: [PyMOL] obtaining coordinates of solvent-surface points

their top priority. Examples include GROMACS, MMTK, APBS, Rosetta, Modeller, DSSP, MSMS, PHENIX, CCP4, Maestro, MOE, Discovery Studio, and so on. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa

[PyMOL] Seeking an Experienced Java Developer

Dear PyMOL Users Developers, One of DeLano Scientific LLC's key collaborators is looking for an experienced Java developer to contribute to an exciting PyMOL-integrated software product serving the drug discovery informatics market. This is a start-up type endeavor -- a rare opportunity to get

Re: [PyMOL] manual or list of commands options ??

A considerable amount of FREE documentation on PyMOL can be found at: http://pymolwiki.org Additional official documentation is available to project sponsors at: http://delsci.info/dsc (subscription info at http://pymol.org/funding.html) -Original Message- From:

Re: [PyMOL] creating objects

distances) into a single one. group my_dists, dist01 dist02 or group my_dists, dist0* -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer

Re: [PyMOL] Communication with external program

Martin, Absolutely -- Python provides all of the socket / communication infrastructure needed to accomplish this. One such example is the RPC plugin developed by Greg Landrum. See examples/devel/xmlrpc01.py -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info

Re: [PyMOL] file format for homebrew MD software

alter_state. Then, the only additional trick to incorporate is to copy the first state before using alter_state to modify coordinates for the copied state. see examples/devel/particle02.py (just added) for a working example of what your code should do instead. Cheers, Warren -- DeLano Scientific

Re: [PyMOL] drawing arbitrary object with pymol

Take a look at cgo05.py and cgo06.py: http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/ sample image: http://delsci.com/img/pore.jpg -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On

Re: [PyMOL] 3D Glasses. Where to buy them ?

David, Even if displays were to accept a high referesh-rate signal, there are two other problems: (1) the publisheed response times are usually gray-to-gray, not full-on-to-full-off. At 120 Hz stereo 3D, the display needs to go full-off to full-on and back to full-off in 8.3 ms total (roughly

Re: [PyMOL] file format for homebrew MD software

Paride, One option is to simply create and modify coordinates real-time using Python. See example particle01.py http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/pa rticle01.py?view=markup for a live animation of a particle system. -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Non-orthogonal maps from Python code

Konrad, Sorry -- the curent brick code only supports orthogonal maps. The only way to accomplish this at present is to write a crystallographic map in one of the supported formats (XPLOR ASCII, CCP4 binary, or DSN6/BRIX) and then read that map into PyMOL. Cheers, Warren -- DeLano Scientific

Re: [PyMOL] pymol installalation

http://www.pymolwiki.org/index.php/Windows_Install http://support.microsoft.com/default.aspx?scid=kb;en-us;324767 -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of surendra negi Sent: Monday,

Re: [PyMOL] Trouble making pictures in a script

Michael, The -c option forces PyMOL to run in command-line-only mode which means it doesn't have access to the OpenGL hardware (used by cmd.draw and interactive graphics). In command-line-only mode, ray tracing (cmd.ray) is the only option. Cheers, Warren -Original Message- From:

Re: [PyMOL] Superposition and connect of two segment

)) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD

Re: [PyMOL] How to move aligned objects apart

David, Here's an example of using the translate command to achieve what you're seeking. fetch 1t46,async=0 fetch 1oky,async=0 as cartoon align 1t46CA, 1okyCA orient 1t46 and organic turn z,180 translate [50,0,0], 1oky zoom show sph, organic color white, organic and elem c Cheers, Warren

Re: [PyMOL] APBS - Net charge and contour level

not be all that informative. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor

Re: [PyMOL] is there bond ? How to check?

... iterate all, print (resn, resi, name, index) -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source

Re: [PyMOL] png

get) with respect to the OpenGL view. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open

Re: [PyMOL] Load command

Greg, Documentation on load can be found in the following ways: PyMOL load ? will list arguments PyMOL help load will provide additional usage information. The PyMOLWiki has a page on the load command: http://pymolwiki.org/index.php/Load and load is also covered in the official docs:

Re: [PyMOL] customized sleek looking isomesh

of a pixel (even if you render at a much higher resolution) -- PyMOL attempts to deliver WYSIWYG at displayed resolution. That may explain why you were getting a thicker mesh than you wanted. map_double map-name can be used to double the sampling density of an existing map. Cheers, DeLano Scientific LLC

Re: [PyMOL] Coloring subunits

Greg, To directly specify RGB colors, you can encode them as a hexidecimal string (0xRRGGBB): color 0xffcc11, chain A However, the advantage of using set_color is that you can change your mind later without having to edit every line in your script where you use the color -- just the one line

Re: [PyMOL] VRML color

inconvenient as compared to having it just work in competing VRML-capable products. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer

Re: [PyMOL] moving objects freely

The drag action provides an easier to use solution. Right click on the atom, select molecule/chain/object then drag. From that point on, shift-left, shift-middle, and shift-right click can be used to move those atoms. -- DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] APBS-electrostatics

Gianluigi, The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances in a single Python interpreter -- your wizard needs to be updated so that the init method takes a _self keyword argument: def __init__(, _self=cmd): ... -- DeLano Scientific LLC Subscriber Support

Re: [PyMOL] place atom at coordinates/screen center?

pseudoatom myobj, pos=[1.4,3.5,2.4] PyMOLpseudoatom ? Usage: pseudoatom object [, selection [, name [, resn [, resi [, chain [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label [, pos [, state [, mode [, quiet ] _ From:

Re: [PyMOL] Pymol apbs problem

Evan, This appears to be a problem with file format incompatibility between PyMOL and the psize.py script. I suspect that rounding off the atom coordinates will eliminate it: alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0) Cheers, Warren _

Re: [PyMOL] Per residue rms

Per, No, looking through the code, there doesn't seem to be anything like this available yet, other than 3D visualization of the alignment (lines drawn between atom centers). What you are presumably looking for is the length of those lines. hmm... Cheers, Warren -- DeLano Scientific LLC

Re: [PyMOL] Mutagenesis wizard

However, step 6. (apply) results in this: Selector-Error: invalid model and. ( ( Model and _mutate_sel ) )-- Anyone with any ideas? Unfortunately, model is a PyMOL selection language keyword. Everyone, please avoid naming your models model, if possible -- that will save you some

Re: [PyMOL] pymol in the background

Try redirecting stderr and stdout to a file -- the process may be getting suspended by the shell due to output. csh/tcsh: pymol -qc script.pml pymol.log sh/bash: pymol -qc script.pml pymol.log 21 _ From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] svn 1.0r2?

Bill, See Source code? under the 1.0r2 news item at http://pymol.sf.net (may need to refresh browser). Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of William Scott Sent: Friday,

Re: [PyMOL] Keyword in PDB to display a string in the viewer

For safety security reasons, it probaby isn't such a good idea to put code into PDB files. Fortunately, we have something called a .p1m file which provides for the reverse: embedding of PDB and other data files within a script. There are three such examples (embed0X.p1m) in the test/dat

Re: [PyMOL] PDB changed CONNECT records

Mark, set connect_mode = 0 is the default, and this uses both distance-based and explicit (CONECT-based) connectivity. set connect_mode = 1 uses only explicity connectivity we don't have a connect_mode = 2 yet (forcing use of distance-based connectivity only), so instead, you'll need to

Re: [PyMOL] PDB changed CONNECT records

[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Thursday, September 06, 2007 11:24 AM To: 'Mark A Saper'; 'Pymol' Subject: Re: [PyMOL] PDB changed CONNECT records Mark, set connect_mode = 0 is the default, and this uses both distance-based and explicit (CONECT-based

Re: [PyMOL] Problem with using Zoom command difficulty movingmolecules

Nicole, The difference between the two files is that one of them is a single monomer whereas the other contains all 60 copies of the virion capsid biological unit. The problems you are experiencing are related to that fact that you are loading about 320,000 atomic coordinates with the new file

Re: [PyMOL] Problem with using Zoom command difficulty movingmolecules

Nicole, As much as we may enjoy blaming the PDB for the various shortcomings of their files, I cannot imagine how the changes they implemented could be causing the behaviors you describe. Rather, it sounds to me like you may be having problems with either PyMOL itself, or the underlying OpenGL

Re: [PyMOL] Pymol 1.0 graphics bug

Roger, This isn't so much a PyMOL bug as a flaky characteristic of OpenGL under Windows XP, which eventually stops updating the screen when an application like PyMOL attempts to draw continuously for a long period of time without relinquishing control back to the operating system event loop.

Re: [PyMOL] More MacPro questions

Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Patrick Loll Sent: Monday, August 27, 2007 12:05 PM To: pymol-users

Re: [PyMOL] stereo on MacPro, part deux

with the -S option (hypen capital S). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source

Re: [PyMOL] Building pymol on Windows?

The goal is to produce a Pymol that uses native Windows graphics, not one that requires X11. David, Please note that the goal behind Open-Source PyMOL (as maintained by DeLano Scientific LLC) is to enable compilation under open-source operating systems, and primarily, Linux with X11/GLUT

Re: [PyMOL] Macintel stereo - fixed

/MacPyMOL -X -1000 ./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer

[PyMOL] Drug Discovery Today (and Tomorrow!)

Hi Folks, I'm demonstrating PyMOL in the Apple Booth today and tomorrow at the Drug Discovery Today conference in Boston, MA. The booh number is #512. Please stop by and say hi if you're attending! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] best linux distribution to run pymol

is targeted at Linux 8-)! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joris Beld Sent: Sunday, July 15, 2007 5:20 AM Cc: pymol-users

Re: [PyMOL] compiling pymol on Mac intel

list of the Fink dependencies required. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open

Re: [PyMOL] Sticks and distances with individual transparencies

Tsjerk, Sometimes the archives can be misleading... Actually, settings do now work on selections and bonds as well (with set_bond). However, only a small set of per-atom and per-bond settings are currently implemented, since each can require a significant amount of new code. Cheers, Warren

Re: [PyMOL] compiling pymol on Mac intel

. ./configure make make install Note that make install just installs into the current source directory. As for the Fink build, that looks like an X11 / OpenGL / GLX problem on your system. Does the precompiled X11 build work? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] compiling pymol on Mac intel

under the Fink environment, not straight Mac OS X. We need to fix the default setup.py to reflect this fact. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent

Re: [PyMOL] rotate about an abitrary axis

Minh, This type of use is now covered under the rotate command in the official documentation for PyMOL 1.0 ( http://delsci.info/dsc ) as well as in the current open-source code. Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber

Re: [PyMOL] Sticks and distances with individual transparencies - repost

Mark, Your confusion arises from the new set_bond command, which must be used when setting bond-specific properties. Please see the official docs on set_bond. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want

[PyMOL] PyMOL 1.0 and Official Docs

components and capabilities! Together we are all working together to ensure that PyMOL continues to thrive under terms that remain compatible with the open-source code. Enjoy! Cheers, Warren L. DeLano, Ph.D. DeLano Scientific LLC Sponsorship info at http://pymol.org/funding.html

Re: [PyMOL] dimension lock feature

Martin, That is a good suggestion! No, this capability does not yet exist. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Höfling Sent: Wednesday, June 20, 2007 3:30 AM To:

Re: [PyMOL] can't type into Tcl/Tk dialogs using RHEL5 Linux Client

Hmm... Well, RHEL is a Fedora-based Linux, so I guess this shouldn't be a surprise. What is frustrating is that this problem is so inconsistent -- some users experience it, and others (including us) do not. At the present time, the only advice I can offer is: do not count on being able to run

Re: [PyMOL] low-end graphics cards/laptops

David, As long as you run Windows XP and not Vista, most modern shared-memory GPU systems should have sufficient performance for PyMOL. If you're thinking of new systems, it is no secret that I unabashedly favor and recommend the Windows--Linux-capable PC laptops made by that

Re: [PyMOL] bug in pymol surface rendering?

Correction (for the record): flag ignore, clear, resn mse flag ignore, resn mse, clear -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Tuesday, June 12, 2007 11:04 AM

Re: [PyMOL] pymol pair_fit script size limit ?

Indraneel, Try something like: pair_fit 1p80_A///79-130+160-180/CA, 1gwe_A///14-65+95-125/CA instead, where hypen (-) is used for matchd residue ranges, and plus (+) is used for the unmatched (gap) ranges. Cheers, Warren -Original Message- From:

Re: [PyMOL] ray_trace_mode

Jianghai, The ray_trace_mode tracing mechanism operates at a per-pixel level. Thus, to get a small image with a nice outline, you simply render a large image and then shrink it down. Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] bug in pymol surface rendering?

load some_smet_containing.pdb flag ignore, clear, resn mse show surface (or rebuild if surface is already shown) -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your

Re: [PyMOL] disconnected disulfide residues

Preston, You may need to post a PDB snippet containing the residues in question... Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Preston Garrison Sent: Friday, June 08, 2007 5:05

Re: [PyMOL] Surface question

Jeff, Extract the ligand into a new object, and then show the surface on that object only: extract lig, ligand-selection show surface, lig Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf

Re: [PyMOL] Adding 'interactive' script to pymol

, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD -Original Message

Re: [PyMOL] Highty shinning

Ney, This is likely due to faulty OpenGL driver. Cheers, DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring

Re: [PyMOL] Adding 'interactive' script to pymol

Use spawn instead of run. Cheers, DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD

[PyMOL] Informal Email Survey RE: Molecular Modeling Suites

! Cheers, Warren war...@delsci.com DeLano Scientific LLC

Re: [PyMOL] SUMMARY: CRT/TFT dual configuration with the nvidia FX3500

Savvas, Thank you for aggregating and posting that information. Just so everyone knows, it is possible to do this on a CRT/LCD-dual-headed Mac Pro with the Quadro FX 4500 graphics card. Having recently set this up for myself, I can attest to the fact that it just works without mucking with

[PyMOL] Reading .MOE files in PyMOL 1.0 beta 23

development. PPPS. Maestro users, stay tuned... dot-MAE is next as soon as .MOE reading proves stable and complete. - DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa

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