Re: [PyMOL] problem: choking on big files

> Pymol isn't very good at handling many spheres. Slanderous! ...but true with default settings. However: ./pymol -O 1 monster_large_file.pdb Will enable PyMOL to display, manipulate, and render at least a million spheres per GB of RAM. Also try -O values up through 5 for alternate approach

[PyMOL] Installion Issues on DELL (solved)

Folks, In case there is anyone out there still stuggling to get PyMOL installed on their new DELL system, below is the latest word on how to work around the problem (graciously passed along by one of our users): Cheers, Warren "I found the solution, apparently the installer gets screwed up by s

Re: [PyMOL] atom selector problems

Arthur, Are you running in 24 or 32-bit color mode? Sometimes PyMOL has trouble resolving atom picks in 16-bit color mode. Also, some PDB files reuse residue numbers, which can cause PyMOL to include other atoms as well. Cheers, DeLano Scientific LLC Email Support Services > -Origi

[PyMOL] Booth #327 at the San Francisco ACS Meeting!

your convience to learn more PyMOL or to simply chat about the project, about molecular visualization and animation, about open-source business, or anything else of relevance to PyMOL. We hope to see you there! Cheers, DeLano Scientific LLC Email Support Services

[PyMOL] Help for X.org-based Stereo 3D on Linux?

ether or not it works, and if so, some information on how to get it to work. According to reports, simply adding Option "Stereo" "3" to Xorg.conf (as we have done for XFree86 in the past) isn't sufficient... Thanks in advance for any help you can offer! Cheers, DeLano Scientific LLC Email Support Services

Re: [PyMOL] PyMol on MacBook

> Has anyone benchmarked or tried PyMol out on the new MacBook > (not MacBook pro)? Raytracing performance is excellent on all Core Duo-based systems. However, the vanilla MacBooks are underpowered when in comes to OpenGL. For heavy PyMOL use, go with the MacBook Pro. Cheers,

Re: [PyMOL] PDB loader

in..." option under the Plugin Menu. We will most likely need to issue an updated 0.99 release candidate in order to restore the fetch command (the usual way of direct-loading PDBs over the internet with MacPyMOL). DeLano Scientific LLC Email Support Services > -Ori

Re: [PyMOL] PDB loader

s, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of DeLano Scientific > Sent: Wednesday, October 18, 2006 8:27 AM > To:

Re: [PyMOL] dissappearing model

Kelvin, Those are clipping planes -- try using the scroll wheel on your mouse to increase the slab depth. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.source

Re: [PyMOL] Unit of contour level in density map

Nian, What kind of map format is it? One of the two programs may be normalizing the map, but not the other. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-u

Re: [PyMOL] more color in pymol

Shivesh, New colors defined in the color editor can subsequently be used in "color" commands. color myNewColor, resi 100 Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mail

Re: [PyMOL] Bug in pymol log file?

y while using the program so that you don't lose too much time if you make a mistake. Do note, however, that writing PML scripts manually is still the best way to generate reusable "protocols" that can be applied over and over again to new structures. Cheers, DeLano Scientific L

Re: [PyMOL] undefined symbol: ObjectGroupAsPyList

Donnie, Hmm...it seems "ObjectGroup.c" was left out of setup.py. It should be fixed now. Thanks for the reminder! Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mail

Re: [PyMOL] Support for gromacs trajectories and cube files

trajectory. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Tsjerk Wassenaar > Sent: Wednesday, October 25, 2006 1:32 AM >

Re: [PyMOL] problems using "within" in selections

Anne, There is definitely a problem with PyMOL here: that ZnA object is not behaving correctly with respect to any of the distance-based selection operators, and so for it is not yet clear why. However, create nearZnA, 1q74 within 6 of (ligands and chain A) does work. Cheers, DeLano

Re: [PyMOL] problems using "within" in selections

Anne, Okay, the problem has been identified and fixed in the open-source code. It was an all-or-nothing failure to expand geometry in situations where the sole target atoms are one or both last two atoms in the source object (a rare scenario). Cheers, DeLano Scientific LLC Email Support

Re: [PyMOL] Support for gromacs trajectories and cube files

tpr" loaded > as "topol.tpr". > PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc Skip the tpr -- PYMOL can't read that at all. Try load ProtOut.pdb, your-object-name load ProteinTraj.xtc, your-object-name where your-object-name is the same object. Cheers,

Re: [PyMOL] color in pymol

lor, red Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of shivesh kumar > Sent: Saturday, October 28, 2006 4:33 AM > To:

Re: [PyMOL] Persistent PyMOL pipes? Preventing a call to 'cmd.quit()'.

Edward, Add a "K" keepalive option along with the -p: pymol -pK Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Ed

Re: [PyMOL] Persistent PyMOL pipes? Preventing a call to 'cmd.quit()'.

, that thread will message the main thread to terminate via 'cmd.quit()' when standard input is closed. For the actual code, see 'stdin_reader' in modules/pymol/parser.py. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: edward.d

Re: [PyMOL] color in pymol

as it once was. While it absolutely correct that command scripts are the most effective way of controlling PyMOL, the menus, when combined with the sequence viewer, selection modification actions, and wizards, can be pretty powerful too. Cheers, DeLano Scientific LLC Email Support Service

Re: [PyMOL] simply list selected atoms

iterate sele, print chain,resn,resi,name Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Jurgen F. Doreleijers > Sent: Wedn

Re: [PyMOL] cones in pymol?

Martin, The PyOpenGL included with PyMOL is probably out of date. It hasn't seen much use since it cannot interface with PyMOL's built-in ray tracer. In contrast, CGO primitives can be ray traced, but as noted, CGOs are limited to lines, spheres, cylinders, and triangles. Cheer

Re: [PyMOL] differential helix transparency

surface show cartoon set transparency, 0.5, chain A And for bonds: as sticks set_bond stick_transparency, 0.8, not name N+CA+C, all ray Unfortunately, per-atom cartoon_transparency is not yet supported. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- &

Re: [PyMOL] Ligand Surface Representation

faces. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of matthew.frank...@imclone.com > Sent: Thursday, November 02, 2006 7:43 AM

Re: [PyMOL] freeglut problem

eGLUT and your graphics driver. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Hugo Gutiérrez de Teran > Sent: Friday, Novem

Re: [PyMOL] pymol licensing questions

Clarification: PyMOL is BSD-style open source code, not GPL. > May I re-distribute the compiled program? Yes, but: The key condition of redistribution is that modified PyMOL code (source or binary) must be plainly distinguished from the version DeLano Scientific LLC maintains & dist

Re: [PyMOL] Latest version?

group objects, and improved mutagenesis are currently undergoing testing in the 1.00 beta series. Precompiled 1.00 beta builds are available to subscribers, and the current open-source code may be accessed via SVN on SourceForge. Cheers, DeLano Scientific LLC Email Support Services

Re: [PyMOL] set_dihedral command

nstead rotates the entire cyclic structure about the central bond of the dihedral. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf >

[PyMOL] Eight-core Mac Pro on ZDNet.co.uk

multiprocessing performance than Windows XP on identical four-core and eight-core hardware. Too bad they didn't test Linux too! Cheers, Warren L. DeLano, Ph.D. DeLano Scientific LLC

Re: [PyMOL] chempy documentation

code and its usage. Cheers, DeLano Scientific LLC Email Support Services > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of bgbg bg > Sent: Monday, November 20, 2006 4:59 AM &g

Re: [PyMOL] weird crashes inside /home/$USER

PyMOL may somehow be importing a conflicting .py or .so. Is "." in your path? It may be in PyMOL's default sys.path...hmm... Also note that > ${PYMOL_PATH}/__init__.py $* is better as > ${PYMOL_PATH}/__init__.py "$@" Cheers, DeLano Scientific LLC Email Sup

Re: [PyMOL] chempy documentation

.NET. Several proprietary examples of this design exist, and they are all quite successful. We need an open-source equivalent! Cheers, Warren DeLano Scientific LLC > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourc

Re: [PyMOL] installation trouble

-Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Angelo D Favia Sent: Monday, December 11, 2006 9:39 AM To: pymol-users@lists.sourceforge.net Subject: [P

Re: [PyMOL] installation trouble

d Hilvert Group, ETH Zürich Angelo D Favia wrote: I already tried all of the solution at the website but they didn't work for me. The error message still appears. A. DeLano Scientific wrote: <http://www.pymolwiki.org/index.php/Windows_Install> <http://ww

Re: [PyMOL] Copy a selection for a new molecule?

Esben, load molA.pdb select selA, resi 100-200 create molAcpy, molA select selAcpy, selA in molAcpy Note that this will only work if the atom identifiers: name, resi, resn, segi, chain are all unique. The "in" operator does not distinguish based on the "alt" (alternate conformer) property, so al

Re: [PyMOL] surface coloring fails with gradient loaded

, then "gradient ?" for usage. Note that this feature will not be supported by DeLano Scientific until after the 1.0 release. As for your question, "mdo" movie commands should be limited to localized state changes within PyMOL. Performing I/O or running external system calls

Re: [PyMOL] Why does the sculpting feature not work?

Matt, Three points: (1) PyMOL's sculpting feature isn't a forcefield, so it is best to clean up any pose you" sculpt" with a molecular mechanics forcefield minimization afterwards (using external software, such as the Swiss PDB viewer). (2) Unless bonding information is provided in the file, PyM

Re: [PyMOL] A suggestion on molecule selection

Frank, set state, state-number, object-name set state, obj1, 1 set state, obj2, 3 You can also use the freeze and thaw options in the object's action menu to freeze an object into the current state independent of the global state. Cheers, Warren From: pymol-u

Re: [PyMOL] A suggestion on molecule selection

Whoops, I goofed that example! meant set state, 1, obj1 set state, 3, obj2 -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Friday, December 15, 2006 4:27 PM To: 'S. Fran

Re: [PyMOL] symmetry generation P21/n?

> Perhaps Warren can post to the mailing list the clear text table of space group names that are acceptable. PyMOL still uses Ralf Gross-Kunstleve's old sglite toolkit for decoding spacegroups. Thus, there is no static list of acceptable forms. However, included below are the most of the string

Re: [PyMOL] cmd.label, custom labels, script

label selection, model+"-"+resn+resi _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Rafael Najmanovich Sent: Tuesday, December 19, 2006 3:04 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cmd.label, custom la

Re: [PyMOL] Outline in cartoon mode

Pernille, The algorithm PyMOL uses to generate outlines is discrete and based on actual pixels. Thus the maximum thickness is one pixel, but you can get a thinner outline by increasing the antialiasing setting to simply render more pixels: set antialias, 2 -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Pymol installation probs on ubuntu

Christoph, The message "Could not find platform independent libraries Consider setting $PYTHONHOME to [:]" indicates that Python is not being initialized properly. You may need to set PYTHONHOME explicitly in the pymol startup script. Cheers, Warren -- DeLano Scientific LLC

Re: [PyMOL] rmsd calculation of homologous structures

Marcela, Sorry, PyMOL can only compute rmsds on pairs of structures, not ensembles. 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

Re: [PyMOL] mutagenesis

Jamaine, That is the percentage of structures with that particular rotamer out of the population sampled (either the backbone bin or for the residue type as a whole). PyMOL presents the rotamers in order of decreasing prevalence. Cheers, Warren -- DeLano Scientific LLC Subscriber Support

Re: [PyMOL] Sequence view size

Aaron, Unfortunately, there is no good way to do this at present. A very ugly hack would be to save the current image and then measure its dimensions. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but wa

Re: [PyMOL] Merge PDB files

pdb symexp sym, 1hpv, 1hpv, 5.0, segi=1 create merged, all save merged.pdb, merged dele all load merged.pdb 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

[PyMOL] Builds for Educational Usage

PyMOL Teachers: If you are planning to use PyMOL in a classroom setting over the next six months, please let us know so that we can be sure that you and your students have access to current precompiled PyMOL builds. Cheers, DeLano Scientific LLC Subscriber Support Services mailto:del

Re: [PyMOL] CE Align & Wiki

Congratulations to Jason on his release, and having now run the code myself I can say that this is a pretty darn nifty tool: Quick protein structure alignment right within PyMOL without reliance upon sequence similarity! Amazing. Cheers, Warren -Original Message- From: pymol-users-boun.

Re: [PyMOL] pymol slow on linux PC

Joris, Unfortunately, Linux is usually the slowest and least-stable operating system for OpenGL visualization. Identical hardware often performs noticably better running under Windows XP (and nowadays, Mac OS X). I've seen up to 3X better performance on proprietary OSes. But that is not Linux's

Re: [PyMOL] pymol slow on linux PC

the way, configuring any system to triple boot can be a serious pain! Win/Lin is easy, and Mac/Win is easy, but getting all three going at once is a serious chore. Virtualization is a far better way to go. Cheers, Warren -Original Message- From: Peter Adrian Meyer [mailto:pa...@corn

Re: [PyMOL] future pymol-py problems

://pymol.sf.net under the Jan 14 news item. There is nothing in the license terms that prohibits redistribution of PyMOL in source and/or executable form. That is legal reality, and it will not change for the forseeable future. However, as a matter of intent, DeLano Scientific LLC's current focus

Re: [PyMOL] OT: platform discussion

Martin Höfling Sent: Saturday, January 20, 2007 8:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] OT: platform discussion Am Samstag, 20. Januar 2007 00:55 schrieb DeLano Scientific: Hi all, > Of course not: cost is a pragmatic consideration, but cost should not > solely b

Re: [PyMOL] problems by importing different docking pdb-files with poses in one session

ether or not you can open the file from "c:\". If that isn't the cause, then it might be some problem with the PDB file itself, in which case, please send me copy for troubleshooting. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.inf

Re: [PyMOL] Suggestion?

Hello Frank, Yes, you can group objects and drag them to reposition in the latest 1.0 beta series code. group group-name, space-separated-list-of-objects There is no molecular spreadsheet yet, though that too is a common request. Cheers, Warren -- DeLano Scientific LLC Subscriber

Re: [PyMOL] Xmlrpc listener

Geoff, There are a couple of minimal example files in the examples/devel directory. This module was written by Greg Landrum in his previous position at Rational Discovery -- it may not actively maintained at this point. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] Labeling CGO objects

d-coded at the C level as measurement objects. -- 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] dock one protein into another?

Richard, Probably the easiest way to do this is with the "drag" command. However, all of the atoms to be drag must be contained within a single molecular object. It is not currently possible to move multiple objects at once using the mouse. drag object-name Then move object with shift-(left or

Re: [PyMOL] Labeling CGO objects

> | CGO labels are currently insufficient and need work. Right > now, the > | only way to access high-quality labels (using scalable > TrueType fonts) > | is to create fake atoms and then label them. > > What's the recommended way to do this? Can you just put them > anywhere you like, irres

Re: [PyMOL] Command:turn

JP, > According to the manual, it is also supposed to be > constrained to the origin as well but doesn't appear to do > so, at least not in my hands Are its constraints possibly > overridden by such commands as center, orient, origin? origin position=[0,0,0] turn axis,angle can change the ori

Re: [PyMOL] Side by side views

David, This does not exist at present, but thank you for suggesting it. 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. Than

Re: [PyMOL] Stereo on Sharp LCD

, does not require customized software builds to drive it. 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 yo

[PyMOL] Windows Vista Released: CAUTION.

ask for Windows XP. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info

Re: [PyMOL] ImportError: No module named _cmd

Yun, Precompiled PyMOL builds for Windows run inside their own Python interpreter. Thus, to access PyMOL from Python, you need to run your script from within PyMOL. An easy way to do this is to give your script a ".pym" extension. Cheers, DeLano Scientific LLC Subscriber Suppor

Re: [PyMOL] selecting Na+ in pymol

t;r. na\+") which actually works, but probably shouldn't. 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.sourcefor

Re: [PyMOL] attach_amino_acid

Kirk, Just FYI, you are outside the realm of what PyMOL has been designed to do (so far). Regardless, editor.attach_amino_acid("junk/94/C","trp") seems to work with current versions (0.99rev8 and the latest 1.00 beta code). Cheers, Warren _ From: pymol-users-boun...@lists.sourc

Re: [PyMOL] movie in pymol

DeLano Scientific gives away without any expectation of reciprocity. With respect to obtaining assistance, the PyMOL user community will happily provide hints, exchange limited know-how, and point you at existing resources (such as Slerpy). However, it is unrealistic to expect one's peers

Re: [PyMOL] function keys

there was a function key > (keystroke) shortcut for stereo? Not built-in, but you can add such a key as follows: cmd.set_key('F1',lambda:cmd.stereo({'on':0,'off':1}[cmd.get('stereo')])) -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.

Re: [PyMOL] Using server CPU instead of client GPU?

/server setups. set use_display_lists, 1 might help a bit when displaying surfaces and other complex geometries. -- 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

Re: [PyMOL] image metadata plugin

ass in a multi-line string using Python: cmd.scene("001","store","This is the view of the binding site.\nPlease note the ligand in yellow.") We have much work to do to make annotations more general and more accessible... Cheers, Warren -- DeLano Scientific LLC

Re: [PyMOL] "inverse" carve command

Jan, Try using a negative number for the "carve" argument. Cheers, Warren > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Jan Lipfert > Sent: Saturday, February 10, 2007 12:40 AM > To: pymol-use

Re: [PyMOL] Slider for movies?

PI function enabling similar functionality to be developedas a plugin, such as an MD-specific browsing interface. 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

Re: [PyMOL] Distance Label Format

Anthony, In the latest 1.0 beta open-source code and builds, you'll find a label_digits setting that can control the number of digits after the decimal place. The new default is one digit. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info &qu

Re: [PyMOL] trouble selecting residues with mouse

This problem is usually caused by running out of colors used to encode atoms during interactive selection -- that can happen when the display is in 16-bit (thousands of colors) as opposed to 24/32-bit (millions of colors). Please double-check the Display settings in System Preferences. > -O

Re: [PyMOL] reload modified wizard

I believe this is a limitation of Python: once a code module is loaded and initialized, it is difficult to reload it...you might be able to hack it though. > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behal

Re: [PyMOL] Projecting shadows onto a background.

wizard box (choose plane) (click auto-position 99%) (use mouse to rotate) (toggle points) (use scroll wheel to increase clipping slab width) ray -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the pr

Re: [PyMOL] WRL Output

Tsjerk & Markus, Just by way of correction: PyMOL nowadays has VRML2 output -- simply "save my_file.wrl" from the command line. Cheers, DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the

Re: [PyMOL] contour levels in pymol

do not, then figuring out why not. 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 sponsorin

Re: [PyMOL] problems using selection wildcards?

note that PyMOL will then be unable to distinguish C2 in the base from C2* in the sugar, etc. However, if you issue this first, alter all, name=string.replace(name,"*","'") Then you will be able to distinguish C2 from C2' and still have your atom name wildcards!

Re: [PyMOL] plug-ins on Mac OSX - X11?

enabled by default. Once X11 is installed, then subsequent updates can safely be reinstalled. Perhaps someone else on the mailing list knows of an alternate way of getting X11 onto an existing Mac? -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From

Re: [PyMOL] plug-ins on Mac OSX - X11?

From: Frieda Reichsman [mailto:frie...@nsm.umass.edu] Sent: Tuesday, March 06, 2007 5:09 AM To: DeLano Scientific Cc: 'Users List PyMOL' Subject: Re: [PyMOL] plug-ins on Mac OSX - X11? Thanks, this sounds do-able at some po

Re: [PyMOL] cyclic structures

Unfortunately, this is not something PyMOL can do at present, and we were not able to come up with a workaround previously. In short, the code needs to be modified at a fundamental level, but the cartoon generator in PyMOL is about as bad as it gets: deeply nested code, 1-2 letter variables names

Re: [PyMOL] delete states

_traj, old_traj, 7, 3 create new_traj, old_traj, 8, 4 etc. The other workaround in terms of playing a movie would be to define the movie frames skipping those states you wish to exclude from playback: mset 1 15 -60 90 -120 etc. Thank you for the feature request! -- DeLano Scientific LLC Subsc

Re: [PyMOL] min_mesh_spacing

Dirk, That setting is for the molecular mesh representation, not maps, and it is also constrained by other factors. If you want to supersample maps, first load the map, then issue: map_double map-name -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not

Re: [PyMOL] problems with command line

receiving events inside a GLUT-based OpenGL window. Can someone else chime in with FC6 experiences? Is this problem rare, common, or universal with that distro? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but wa

Re: [PyMOL] question on "state"

load updated.pdb update original,updated delete updated unset suspend_updates Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info I'm interested prototyping some interactive molecular modeling and simulation code using pymol. I know one can chang

Re: [PyMOL] translating cgo text

Jennifer, Having glanced at the code, this is clearly not yet possible -- only molecule objects, atoms, and labels can currently be dragged about. However, eventually it will be possible to drag and animate all object types. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services

Re: [PyMOL] rigimol and morphing

This is where movie-making in PyMOL can get exceedingly complex, but here are the kind of commands one could use to accomplish something like that (assuming a 30 frame morph and a 12-second loop at 30 FPS): mset 1 x60 1 -30 30 x60 30 -1 1 x60 1 -30 30 x60 30 -1 movie.roll 1,360 > -Original

[PyMOL] Apple News / NIH event on April 12

tp://delsci.com/misc/mol_mod_inv.pdf Non-NIH-affiliated outsiders are quite welcome, but please register ahead of time! I hope to see you there. Cheers, Warren L. DeLano, Ph.D. DeLano Scientific LLC Molecular Modeling, Computational Chemistry, and Pathway Analysis on a Mac You're in

Re: [PyMOL] Single transparent sphere

Pre 1.0: fragment methane, mysph remove hydro and mysph alter mysph, vdw=2.0 as spheres, mysph set sphere_transparency, 0.5, mysph Post 1.0: pseudoatom mysph, vdw=2.0 as spheres, mysph set sphere_transparency, 0.5, mysph Cheers, Warren _ From: pymol-users-boun...@lists.sourcef

Re: [PyMOL] transparency cross-fading

By default, PyMOL only shows the front-most transparent surface. set transparency_mode, 1 and ray to reliably combine all transparent surfaces in all displayed objects. DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but

Re: [PyMOL] How can I the coordinates of the mesh representation of a protein in PyMol?

Not exactly, but if you hide everything except the mesh and then save as either PovRay (.pov) or VRML2 (.wrl), you can get the coordinates by parsing those files. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -Original Message- > From: pymol

Re: [PyMOL] distances and selections within states?

> "Find me the distance between atom1 and atom2 in state 4" print cmd.get_distance("atom1","atom2",4) > "select all waters that are within 5.0 angstroms of residue > 15 during state 7" Hmm...not easily done. The problem is that distance-based selection criteria apply to all states, giving you

Re: [PyMOL] "report" or "clone" settings?

Tom, This isn't currently possible without "hacking" the session files, and doing so is not something I can encourage as a "supportable" activity. Use a script! Cheers, Warren _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Be

Re: [PyMOL] vrml export normals

Just FYI -- use the latest open-source code or recent beta builds for current VRML export, since older versions export faulty VRML. Cheers, Warren > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of a

Re: [PyMOL] (no subject)

Martin, No, sorry, you will need an external tool to do this. 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. Than

Re: [PyMOL] building centroids for residues

Andreas, Thank you for posting that script. One of the new features in the PyMOL 1.0 betas is the pseudoatom command which has a similar behavior. pseudoatom object-name, selection show spheres, object-name In terms of finding the center of mass, try: center selection print cmd.get_position()

Re: [PyMOL] Using "slice" on a map

Evan, By default, the slice tracks with the 3D center of the camera view. If you turn off tracking, then you can rotate the camera independently of the slice. Then, with the mouse in 3-button-editing mode you can manipulate it with shift-click-and-drag actions. Height map is self-explanatory (o

Re: [PyMOL] failure to save coordinates adjusted with edit tool

Stuart, Empty PDB files can result from writing a file while PyMOL's global state number is set to a numerical state that does not actually contain the coordinates. Note that by default, single state objects are displayed in all states (unless static_singletons is disabled), which can cause some

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