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

Re: [PyMOL] PyMOL compilation from source

Andreas, Try removing -D_FORTIFY_SOURCE=2 as a compiler option... PyMOL's macros sometimes choke on that. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Andreas Henschel Sent:

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] 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

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

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 a superset

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-users-boun

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 want

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:

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

/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 invited to a series

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] 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 change

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 yet

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 want

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

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

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 point. It will take me a few days to get to this. In the meantime, if someone knows of another solution, I'm all

Re: [PyMOL] problems using selection wildcards?

But then 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! Cheers, DeLano Scientific LLC

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

is not 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] contour levels in pymol

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 sponsoring this open-source endeavor! -WLD -Original

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 project

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.

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 Not yet

Re: [PyMOL] Slider for movies?

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 to quote your lab, school

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:

Re: [PyMOL] image metadata plugin

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 Subscriber Support Services mailto:del

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 to do

Re: [PyMOL] function keys

) 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.info Not yet a PyMOL Subscriber, but want to support the project? Email

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 your

Re: [PyMOL] selecting Na+ in pymol

, 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 Tsjerk Wassenaar Sent: Friday, February 02, 2007 2:23 AM

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] Windows Vista Released: CAUTION.

. 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 Support Services

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 you

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. Thank you

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

Re: [PyMOL] Labeling CGO objects

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-source endeavor

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, irrespective

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] 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

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 be defined in terms

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

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.info Not yet a PyMOL

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

Re: [PyMOL] pymol slow on linux PC

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...@cornell.edu] Sent: Friday, January 19, 2007 2:07 PM To: DeLano Scientific Cc: PyMOL-users

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] 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] 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 want

Re: [PyMOL] Merge PDB files

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 quote your lab

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] Pymol installation probs on ubuntu

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

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

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

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. Frank Yan

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 (e.g. APBS) within a movie command

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,

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:

Re: [PyMOL] installation trouble

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://www.pymolwiki.org/index.php/Windows_Install -Original

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 all

Re: [PyMOL] installation trouble

http://www.pymolwiki.org/index.php/Windows_Install -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:

Re: [PyMOL] chempy documentation

the 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 To: pymol-users

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 Support Services -Original Message

Re: [PyMOL] chempy documentation

. 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.sourceforge.net

Re: [PyMOL] set_dihedral command

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 Of Abhinav Verma Sent

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

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] 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 distributes

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 -Original

Re: [PyMOL] freeglut problem

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, November 03, 2006 1:30 AM

Re: [PyMOL] Ligand Surface Representation

You can, I believe, change this behavior so that Pymol will include HETATM records in surface calculations. I don't remember how, but Warren will probably chime in. set surface_mode, 1 and be prepared to split your structure into separate objects before showing surfaces. Cheers, DeLano

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. Cheers, DeLano

Re: [PyMOL] differential helix transparency

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- From: pymol-users-boun

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

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.dauver...@gmail.com [mailto:edward.dauver...@gmail.com

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 Edward d'Auvergne Sent: Sunday

Re: [PyMOL] color in pymol

, 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: PyMOL-users@lists.sourceforge.net Subject

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

/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, DeLano Scientific LLC Email Support Services -Original Message- From: pymol

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-users-boun...@lists.sourceforge.net

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 [mailto:pymol-users-boun

Re: [PyMOL] Bug in pymol log file?

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 LLC Email Support Services -Original Message

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 [mailto:pymol-users-boun

Re: [PyMOL] PDB loader

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 -Original Message- From: pymol-users-boun...@lists.sourceforge.net

Re: [PyMOL] PDB loader

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: 'surendra negi'; pymol-users@lists.sourceforge.net

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, DeLano

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

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

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

by at 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

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

[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

<    1   2   3