RE: [PyMOL] Opening FlexX multi files

Eric, PyMOL loads multi-model PDB, SDF, or MOL2 files as movies. You can use the VCR conrols/arrow keys to iterate through them. Alternatively, you can use the split_states command to create single objects out of each state. load multimod.mol2 split_states multimod I'm not sure if 0.97 will

RE: [PyMOL] Reconstructing selections

i) Is there any guarantee that atoms are stored internally in the same order that they appear in the PDB file? set retain_order sort However, that's not really necessary: ii) If so, is there any way to directly construct a selection containing e.g. atoms 1,3,8,10,11... of a given object?

RE: [PyMOL] Free text labels

Uwe, Yes: label 23/ca, This is the CA of residue 23 Right now, the only way to modify the distance at present is to insert spaces in the label: label 23/ca,This is the CA of residue 23 Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

RE: [PyMOL] modeling in pymol

Frank, Yes, PyMOL has molecular editing functions, but it doesn't yet have a clean-up ability. To rotate bonds, put the mouse into Editing Node and then control-right-click-and-drag on the end of the bond you wish to move. To delete bonds, control right-click and release on the bond, then type

RE: [PyMOL] saving transformed PDB files

Steve, Yes, in fact that's currently the only way it can save them. Just use the save command. You also might think about selections and loops: cnt=22 for a in range(1,cnt+1): \ cmd.load(FINALCNS_%d%a,MOL%d%a) select region,

RE: [PyMOL] Trouble with rendering in ball and stick

Jamie, # first, just show sticks hide all show sticks # for uniform-radius balls, use the stick_ball settings set stick_ball, on set stick_ball_ratio, 2.5 set stick_radius, 0.12 # for variable radius balls, use scaled spheres show spheres set sphere_scale, 0.2 set stick_radius, 0.12 Cheers,

RE: [PyMOL] align output

Andreas ExecutiveAlign: 2889 atoms aligned. ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=6.10). ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=2.98). means: 2889 atoms were aligned intially, then after looking at the quality of the alignment, 95 atoms were rejected as

RE: [PyMOL] CrystalEyes on a Mac

James, The trick with getting stereo on the Mac version is to copy and rename the MacPyMOL or PyMOLX11Hybrid executable to StereoPyMOL. On the Mac, there is currently no way of switching in or out of stereo. Either you launch in full-screen stereo (without the extenal GUI), or you get mono.

RE: [PyMOL] control panel colors

Chris, First, is there any way to add additional colors to the control panel list of colors? Not easily, and not in a portable way. If you know Python, you can edit the mol_color and sel_colr functions in modules/pymol/menu.py...but future versions of PyMOL may not work with your changes.

RE: [PyMOL] Bug: renaming objects causes 'show' not to work

Mikko, I think this bug was fixed a few beta versions back. You might want to try: pymol-0_98beta05-bin-linux-x86.tgz http://delsci.com/beta Which is the latest linux binary currently available... Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] How to apply state-specific colours?

Hubert, The trick for doing this is to load each state into a discrete object, which maintains separate atoms for each state. load $TUT/1hpv.pdb, discrete=1 load $TUT/1hpv.pdb, discrete=1 color red, state 1 color blue, state 2 Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D.

RE: [PyMOL] Swissprot

Jules, Right now (and for the foreseeable future) PyMOL's sequence viewer shows actual atoms in an object (whether or not they have coordinates). There isn't currently any way to retrieve that information other than by looking at atoms... model=cmd.get_model(object-name) for atom in model.atom:

RE: [PyMOL] Coloring gradient

count is the operator you're looking for: spectrum count, green_yellow, selection=50-100/ Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist, DeLano Scientific LLC, 400 Oyster Point Blvd., Suite 213, South San Francisco, CA 94080 Biz:(650)-872-0942

[PyMOL] MacPyMOL Beta

For those of you who prefer the MacPyMOL incentive version of PyMOL for the Mac, there is a new beta at: http://delsci.com/macbeta This copy will enable you to use the sequence browser without having to use X11 (via PyMOLX11Hybrid, Fink, etc.). Cheers, Warren -- mailto:war...@delsci.com Warren

RE: [PyMOL] wire-mesh spheres?

Sphere transparency example included below... ALPHA must preceed COLOR to be effective. PyMOL does not yet do a global sort of tranparent triangles, so there will be artifacts in OpenGL. Raytracing should look fine however. # from within a .py OR .pym file... from pymol.cgo import * from

RE: [PyMOL] Re: PyMOL-users digest, Vol 1 #749 - 8 msgs

Kostas, Some (all?) Logitech mice come misconfigured with the middle mouse button assigned to some goofy proprietary function. You can fix this on Windows, but I don't know about Mac. Personally, I no longer buy Logitech products for this exact reason. Microsoft Intellimice work fine with

RE: [PyMOL] RE: wire mesh spheres?

Actually, the setting is set transparency_mode = 1 It's a long story, but if you start using transparency a lot, you'll find that there are times when you prefer not to see multiple layers of transparent objects, such as convoluted surfaces, for the sake of clarity. PyMOL defaults to that

RE: [PyMOL] cmd.read_pdbstr segfault

Tom Charles, Tom, thanks for your attention to this issue -- actually, the problem is more narrow... Charles was (only) seeing a segfault with the read_pdbstr function and PDB file 1DT7, and indeed I have been able to reproduce this on Linux with version 0.97. However, the latest 0.98 betas

RE: [PyMOL] cmd.read_pdbstr segfault

python modules to my install for development reasons. Thanks, Charlie On Nov 20, 2004, at 5:53 PM, Warren DeLano wrote: Tom Charles, Tom, thanks for your attention to this issue -- actually, the problem is more narrow... Charles was (only) seeing a segfault

[PyMOL] Perspective Rendering (at last!)

PyMOL Users, Hooray -- PyMOL's ray tracer can finally do perspective rendering! Why is this such a good thing? Because (1) ray-traced images are now always what you see is what you get (WYSIWYG) versus OpenGL, (2) you can make rendered movies where molecules move around still look right, and

[PyMOL] RE: [ccp4bb]: GRASP

Lots of options nowadays! Just to clarify what you can or can't do with PyMOL, here are the choices: 1) PyMOL has an automated menu action that generates a local protein contact potential with a constant dielectric screening function. If all you want is a GRASP-like surface image to get a

RE: [PyMOL] macpymol beta bug

Hmm... The problems are fixed in MacPyMOL beta24 (http://delsci.com/macbeta). Also note that there is a new setting cartoon_side_chain_helper that greatly simplifies figure preparation when you mix cartoons and side chains. It takes care of making sure the cartoon goes through the CA position,

RE: [PyMOL] rendering pictures to publish

Alan, Right now, the only way to achieve such high resolutions is to ray trace using large width and height, save as PNG and then use a tool like Photoshop, GIMP, or Imagemagick save a TIF with the correct DPI value. For a 300 dpi rendered image at 4 by 3: ray 1200,900 save hi_res.png For

RE: [PyMOL] fedora core 3 and pymol

Wolfram, This could (at least in theory) be a bug in PyMOL, but I suspect it is a problem with either Mesa or the OpenGL drivers on your system. Seeing the backside of triangles look like the front is an indication that either PyMOL or the graphics driver is scrambling the order of vertices or

RE: [PyMOL] Coloring chemical elements with colors of your choice

Bianca, The latest win/mac betas have this capability -- all atomic elements now have colors. win: http://delsci.com/beta mac: http://delsci.com/macbeta Example usage: # to turn off the automatic carbon color sequence set auto_color, off # to define your preferred colors set_color aluminum,

RE: [PyMOL] animation in v. 0.98beta18

Tom, It was broken at first, but try increasing animation_duration to something in the range 1.5 to 3 set animation_duration, 2 Of course, you'll need an updated version http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano

RE: [PyMOL] Can't load file.pbd in MacPyMol

Jeff, MacPyMOL currently starts in the working directory of the calling process. If double-clicked, then it starts in /Applications (the directory which encloses the bundle -- which is silly and needs to be fixed). To get to your: home directory: cd ~ desktop: cd ~/Desktop documents: cd

[PyMOL] PyMOL on Dual-CPU Workstations

PyMOL Users: For those of you who like to keep up with the numbers, I just ran some new PyMOL CPU benchmarks on dual-processor unix workstations based on the Intel/Xeon, the Apple/G5, and our brand new AMD/Opteron. These aren't top models, but rather affordable systems with performance within

[PyMOL] Re: SGI Aquisition

From: Sean C. Garrick garr...@me.umn.edu To: Apple Scitech Mailing List scit...@lists.apple.com (snip) Sci-Vis is not a worthwhile business. (snip) I'll challenge you on that. There have been all kinds of developments in the professional 3D field, from affordable dual-use

RE: [PyMOL] Alignment objects

Andreas, It's not a stupid question -- its just a year or more ahead of its time. Right now aligment objects currently don't do anything other than show you which atoms were aligned in the 3D viewer. In time however, those objects will integrate with the sequence-viewer... Cheers, Warren

RE: [PyMOL] electron density map manipulation

blaas Sent: Friday, January 28, 2005 1:19 AM To: pymol-users@lists.sourceforge.net Cc: Warren DeLano Subject: RE: [PyMOL] electron density map manipulation Thanx Warren, perfect! But when entering: load map1.dsn6 slice_new slice1,map1 I get the message: Syntax Error: invalid syntax

RE: [PyMOL] Error opening saved .pse file

, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. RE: electron density map manipulation (dieter blaas) 2. RE: electron density map manipulation (Warren DeLano) --__--__-- Message: 1 From: dieter blaas dieter.bl

RE: [PyMOL] Multiple ATOM selection

Jon, To group the following atoms: ATOM688 CG ASP A 87 ATOM689 OD1 ASP A 87 ATOM690 OD2 ASP A 87 ATOM 1247 OG SER A 157 ATOM 1259 OG1 THR A 159 ATOM 1861 CZ3 TRP A 234 ATOM 1862 CH2 TRP A 234 select mysel, a/87/cg+od1+od2 |

RE: [PyMOL] split screen with their own repair

Geoui, This is something I definitely plan to implement in PyMOL, but it doesn't exist yet. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 .

RE: [PyMOL] How do I color and label unit cell

Lan, Try color color-name, object-name This action both sets the default object color which is used for the cell as well as coloring all of the atoms. Then you can recolor the atoms independently. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano

RE: [PyMOL] Web plugin of PyMOL

Frank, No, PyMOL can't do this. If you need molecules in a web page, I strongly recommend Jmol v10: http://jmol.sf.net , which DeLano Scientific officially endorses as the tool of choice for lightweight molecular viewing (in a browser). Jmol is open-source, high-performance, runs anywhere,

[PyMOL] Drug Discovery Today, today!

New open-source article: DeLano W.L. The case for open-source software in drug discovery DDT (2005) Volume 10, Issue 2. In press today -- if asked, I can forward you a copy ; ). Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC .

[PyMOL] RE: ballstick

I need a few high-quality images of organic molecules for teaching purposes. I've been playing with your latest MacPyMol build all morning and can't seem to find a way of displaying in ball stick. I can either show spheres or sticks, not BS. I assume this can be done in MacPyMol. The

RE: [PyMOL] chainbow on commandline

...@lists.sourceforge.net] On Behalf Of Robert Sent: Friday, February 04, 2005 9:32 AM To: 'Warren DeLano'; pymol-users@lists.sourceforge.net Subject: [PyMOL] chainbow on commandline ___ Robert Schwarzenbacher, PhD The Joint Center for Structural

[PyMOL] RE: [Jmol-developers] structure detection?

Nicholas, For example, each pattern that matches the following is alanine : a C bonded to CH3, NH2 and COOH. The algorithm must also deals with peptide bonds and disulfure bonds. It must also work when the H atoms are not int the xyz file. You're on the right track. In fact, most

[PyMOL] Stereo 3D News

Topic (1): If any of you are going to LinuxWorld next week in Boston, be sure to stop by the Emperor Linux booth (# 1821 - http://www.emperorlinux.com). They are slotted to demonstrate a new Linux-based laptop from Sharp Electronics that has their latest 15 autostereoscopic 3D LCD display --

[PyMOL] Documentation / Wiki Brain Storming

Is there some kind of pymol startup switch or environment variable to disable loading into a stereo window? Use the -M startup option (forces a mono OpenGL graphics context). Is this documented anywhere? Hmm no. Say, what do people think about the idea of creating a PyMOL Wiki to hold

RE: [PyMOL] cut-off distance

only the portion of the fitted density map that is located at a defined distance from my selection? This is what the carve option to isosurface and isomesh do: isomesh mesh-name, map-name, level, selection, carve=distance load map1.xplor load ref.pdb zoom ref and resn LIG, 3 isomesh mesh1,

[PyMOL] RE:

dude, what's a WIKI? Hah! Well, in case you're wondering it has nothing to do with... this http://www2.gvsu.edu/~oatesr/wookie.jpg this http://www.geocities.com/Area51/Corridor/8289/wicket.jpg this http://www.prairielights-croquet.org/wicket.jpg or this

RE: [PyMOL] Animated Zoom

Charles, I've added an animate option to commands like zoom, orient, origin, scene. reset zoom all,100,animate=1 orient animate=1 Cheers, Warren PS. Set animation_duration to control the length of the animation. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano

RE: [PyMOL] Coordinates for End Groups

Ramon, Though PyMOL's molecular editor is extensible in this way, there are some pieces missing when it comes to adding new fragments into the mix. What you hope to do will require general design improvements followed by some Python development. For example, one of the problems with the

[PyMOL] Stereo 3D by the Numbers

Thank you to all who replied to my Stereo 3D matters to me email response plea! With over 600 direct responses from almost 300 organizations, Apple now has convincing documentation that Stereo 3D is a make or break issue for the Mac in pro-3D visualization -- a market that spans a surprising

[PyMOL] Getting Closer to Wiki Time!

PyMOL Users, Jason Vertrees (UTMB) has volunteered to lead the creation of a PyMOL Wiki, and has found a suitable location for hosting. We now need your input on how the Wiki should be organized. Please summarize your ideas to the mailing list in the next 24-48 hours so that Jason has your

RE: [PyMOL] Re: PyMolWiki

Luca, (I can't believe PyMOL's cartoon command still does not recognise the most common 5' and 3' nucleotides!), Sorry, I neglected to send you an email about this: there was a new setting added to the beta called cartoon_nucleic_acid_mode set cartoon_nucleic_acid_mode, 1 If you set

RE: [PyMOL] Re: align proteins in pymol

The only difficulty I have with these movements is that when you do fragment rotation you never know exactly what the axis of rotation is going to be. Usually I have to play around with the overall camera view and the atoms I'm grabbing a few times before I can get the rotation I want.

[PyMOL] DeLano Scientific Doubles!

Hi all, I am overjoyed to announce that DeLano Scientific has grown, at last! *We* are now two people full-time: myself and Joni Lam (mailto:j...@delsci.com), who started today. Over coming weeks, Joni, as the Business Operations Manager ('da bom'), will be assuming responsibility for most

RE: [PyMOL] residue replacements / modified amino acids

1. Is there a simple way in pymol to replace an amino acid in a given structure? If so, how can you then check (other than visibly) if there are any glaring steric/electrostatic clashes? Yes, using the mutagenesis wizard. But no, there's no refinement/validation possible so it isn't as

RE: [PyMOL] combine distance objects

Daniel, This is a reasonable request, but no, it isn't possible right now -- sorry. If it isn't necessary to be able to turn the distances on and off, then you can name them using a preceeding underscore _ so that they are omitted from the object list. Cheers, Warren -- Warren L. DeLano,

RE: [PyMOL] Movie (one more)

Jmarie, The latest betas do this in real-time, but there isn't yet a facility to writing out a static movie of that form. As you might expect, there is broad agreement that such a capability is very much needed. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] visualizing electrostatic potential for clipped object

Keiko, Hmm...that is a neat idea, but no, it isn't possible. The best you can do is color a slice through the molecule. load pot1.phi ramp_new ramp1, pot1 load prot1.pdb show surface, prot1 set surface_color, ramp1, prot1 slice_new slice1, pot1 color ramp1, slice1 set transparency, 0.2,

RE: [PyMOL] Adding Hydrogens to GFP Chromophore

Buz, You must fix the bond valences manually... Mouse menu - 3 button editing mode Ctrl-right click on bond Ctrl-W to cycle valence (repeat as necessary to get correct valences) Then optinally remove hydrogens when done (use the action [A] menu on the object - remove hydrogens) Cheers,

RE: [PyMOL] Translating and rotating

Konrad, Yes, but it is currently awkward because you need to protect the other atoms in the object from moving first (action menu - movement - protect on the inverse selection), then you can drag the object moving just the atoms in the original selection. Cheers, Warren -- Warren L. DeLano,

RE: [PyMOL] How do you reset to default bonds/connectivity for all states in an object?

Paul, Set the discrete=1 option to the load command when loading multiple small molecules from a PDB. Otherwise, PyMOL will attempt to match them up atom for atom based on name, applying connectivity from the first state. Cheers, Warren PS. Humorous aside: Wow: factory settings -- I like

RE: [PyMOL] G5 and pymol flashing

Bill, I've noticed this happens on some machines (G5 imac) and not others (G5 dual, G4 powerbook, G4 tower). I may be a bug in Panther, since the problems seems to have been fixed in the Tiger beta, but...well...that's not out yet. It does seem to depend on whether or not any other programs

[PyMOL] San Francisco Bay Area Mailing List

Hi All, We are starting up regular PyMOL users group meeting and training sessions at our South San Francisco location. In order to avoid cluttering up the pymol-users mailing list, I have created a Yahoo group to handle local matters such as these meeting announcements. So, if you are a PyMOL

RE: [PyMOL] G5 and pymol flashing

MacPyMOL users: I believe that I have worked around the bugs in the latest nVidia drivers hardware. Beta at http://delsci.com/macbeta Flickering specular reflections and periodic multicolored flashes should no longer be a problem. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] psw files and powerpoint

The new pymol beta has been fun to play with. I like the scenes function but am having trouble importing the .psw file into PowerPoint. I can make a hyperlink as was suggested in the mail list, but this is not ideal. I need to go through two windows warnings about evil hyperlinks, the

RE: [PyMOL] atom reordering in pdb

set retain_order sort Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273

RE: [PyMOL] Problem with pml script and png command

Greg, Actually, this a fundamental problem with the way the GLUT library works -- it uses callbacks instead of events, which causes refresh issues on Windows. The problem has nothing to do with Python -- PyMOL is all C when it comes to OpenGL. Suffice it to say that we are aware of and working

RE: [PyMOL] setting for publications

How can I set, by line commands, cmyk colour space cmyk and maximum quality display util.performance(0) Also, would be very nice if pymol could show in a feedback log file ou screen the commands being executed when triggered by mouse on graphical menu. It would help a lot automatising

RE: [PyMOL] PDB parse error?

Gareth, Looking over the code, we're using sscanf for most of the PDB field reads...so there's no way around this short of changing the source code and recompiling. However, are spaces legal within PDB field entries? They would be expected cause problems because space is almost always used to

RE: [PyMOL] SEPs in pymol generated pqr

Jack, Editing the output PQR sounds like a sensible approach. As far as obtaining charges goes: in order to be quantitatively correct, the ligand would need to be parameterized using the same approach as the protein force field...(for Amber99, I think that means performing an ab initio quantum

RE: [PyMOL] orient the molecule

This is tricky because the view matrix isn't quite the same format as the coordinates translation matrix. Here's some code that will do what you want: # transform selection coordinates by the camera view cv=list(cmd.get_view()) cmd.transform_selection(all, \ cv[0:3]+[0.0]+ \ cv[3:6]+[0.0]+

RE: [PyMOL] Error report when I saved image

Yunbo, PyMOL wasn't unicode or utf8 compliant -- try saving the file in a directory path that only contains plain ordinary ASCII characters. Alternatively, the latest beta version might work for you since it runs in utf8 by default. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] Sausage ribbon

Yes, it's in there...called putty show cartoon cartoon putty unset cartoon_smooth_loops unset cartoon_flat_sheets Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco,

RE: [PyMOL] b-factor colors

Of course, For example: spectrum b, minimum=20, maximum=50 Or to color on a per-object basis: load myprotein.pdb spectrum b, selection=myprotein, minimum=20, maximum=50 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC .

[PyMOL] 0.98 update: Python-dependent builds for Windows

Hi All, Thanks to Mirek Cygler for pointing out a flaw with the first crop of PyMOL 0.98 Python-dependent builds for Windows. In addition to not correctly detecting the installed Python, then lack support for the new PyMOL show .psw session files. Note that if you downloaded one of the

RE: [PyMOL] the conserved residues can be overlapped?

Yunbo, Can I use pymol to superimpose two protein structures ? How should I do? You want the align command. Example usage with 2 pdb files: load prot1.pdb load prot2.pdb align prot1ca, prot2ca It may be necessary to restrict the alignment region to certain chains. For example,

RE: [PyMOL] PyMOL versus WinXP, SP2

Tom, FYI: The Toshiba laptop I cart everywhere I go is Win XP Service Pack 2 with an nVidia GeForce4 460 Go graphics chip. No problems whatsoever. I can't recall for sure, but I think that there may have been some confusion between XP SP2 and the problems seen with the nVidia drivers. As

RE: [PyMOL] Hybrid won't start

Einat,

RE: [PyMOL] Scene function

(ie microsoft error message blah blah blah, Don't send) and doesn't do what its supposed to when you double click on this ie open (or use the hyperlink from powerpoint). We'll need specifics in order to be helpful. As an initial guess, I'd say that the PSW file type may not be correctly

RE: [PyMOL] disappearing surface representation

Karen, Your problem is that opaque_background is turned off, so trasparency is being handled via alpha-channel, and not via blending. If you re-enable this setting (remove set ray_opaque_background, off) then I think you'll get the kind of effect you seek. Cheers, Warren -- Warren L. DeLano,

RE: [PyMOL] Labels

How can I get my labels to appear in front of a cartoon representation of a protein? By making your labels in PowerPoint or Photoshop after rendering in PyMOL. However, thank you for the suggestion -- better labels are a high priority. Cheers, Warren -- Warren L. DeLano, Ph.D.

[PyMOL] RE: Crashing PSW files: Likely Solution

PyMOL Users: There have been several reports of crashes when launching PyMOL show (PSW) files (ie. PSE files renamed PSW to trigger the full-screen mode). The common factor behind in these crashes seems to have been Intel Extreme Graphics chips and Windows XP Service Pack 2. We managed to

RE: [PyMOL] listing distance measurements

Stephanie, This is a very reasonable request, but unfortunately it is not one that PyMOL can meet at present -- it will require some significant changes within the C code for the distance command. Thank you for the suggestion. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] delete object states

Martin, Unfortunately this doesn't exist yet, but I agree that it is a necessary function. The best you can do right now is load a blank PDB file into that state. That should delete the coordinates for that state, but it doesn't actually delete the state. # to delete the coordinates for state

RE: [PyMOL] polar contact definition

Sergio, We use the term polar contacts because, as you correctly point out, some of the contacts shown don't meet strict hydrogen-bonding criteria. Of course, many macromolecular crystal structures aren't of high enough resolution to make definitive determinations anyway...so... With ideal

RE: [PyMOL] removing loops

hide cartoon, not ss H+S -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 .

RE: [PyMOL] Linux FC3 upgrade causing pymol core dump

...@delsci.com -Original Message- From: Michael Kutz [mailto:mk...@ttpharma.com] Sent: Thursday, May 26, 2005 8:29 AM To: Fischmann, Thierry Cc: 'Warren DeLano' Subject: RE: [PyMOL] Linux FC3 upgrade causing pymol core dump Thierry, The machine i have is a 6221 also. IBM's

RE: [PyMOL] v0.98 slow (includes: ray abort info...)

will be greatly appreciated Hari Jayaram Brandeis University On 5/27/05, Warren DeLano war...@delanoscientific.com wrote: Mark, 0.98 should rarely be more4X slower to ray-trace than 0.97 unless you are running out of RAM. To get the faster

RE: [PyMOL] Questions comments about CGO objects

Gergori, 1) what is the difference between LINES, LINE_LOOP, LINE_STRIP. If I understood correctly, LINES is to build single lines, LINE_LOOP will connect the first and the last point (VERTEX), but no clue about LINE_STRIP. 2) what is the difference between TRIANGLES, TRIANGLES_STRIP

RE: [PyMOL] NMR structures

To see them all at once: load my_struct.pdb set all_states Or if you want them separated into individual objects: unset all_states split_states my_struct dele my_struct Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster

[PyMOL] Problems with nVidia drivers on Windows?

If anyone else is experiencing a non-functional PyMOL with late-model nVidia drivers on Windows XP or similar, pymol-0_99beta96 contains a workaround that has been reported to eliminate the problem. http://delsci.com/beta Hopefully the next driver release for Windows will fix this problem just

RE: [PyMOL] definitions of secondary structure

Sergio, As is typical with PyMOL, the secondary structure assignment engine is ad hoc and empirically tuned to produce desirable aesthetics. Though there are some phi/psi's that are clearly helix/sheet and others that are clearly not, there are certain regions of phi/psi space were the

[PyMOL] Shader Fun Large System Support

PyMOL Users: If you are lucky enough to own a fancy new OpenGL graphics card that supports shaders, there is some fancy new OpenGL code in PyMOL that I'd like you to test (Win Mac). PyMOL now has sphere modes that are memory-efficient, can provide much greater image quality for interactive CPK

RE: [PyMOL] vdw volume

Binging, There aren't any volume computations in PyMOL... To set radii, use the alter command *after* loading the molecule alter elem c, vdw=1.9 alter elem n, vdw=1.8 alter elem o, vdw=1.7 rebuild Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist

[PyMOL] draw command

PyMOL Testers: 0.99beta07 also contains a new command: draw which creates an oversized OpenGL image using the current window. Usage: draw [width, height, antialiasing-level] Examples: draw 1600 will create an 1600-pixel wide image with an aspect ratio equal to that of the current screen.

RE: [PyMOL] labelling using single letter codes

1. Add this to your $HOME/.pymolrc file: # start $HOME/.pymolrc modification one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \ 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\ 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\

RE: [PyMOL] OSX: fink image libs, pymol and the command line

Doug, I can't be sure, but this looks like a problem with MacOS X binding PyMOL to the wrong shared object, quite possibly due to some change in the resolution order...your analysis is on track. To fix this, try to figure out what entry in PATH, LD_LIBRARY_PATH, (or whatever mechanism MacOS uses

RE: [PyMOL] background color

Jianghai, Try dividing all those numbers by 255.0 -- then it will work. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942

RE: [PyMOL] Pymol on MacMini: performances

Luca, We bought a Mini here in the office to use as an inexpensive, secure, stable, hassle-free CVS server. I hadn't tried running PyMOL on it until today... In a very small set of tests with surfaces, a $600 1.42 Ghz G4 Mini (ATI) has about 25% of the OpenGL performace and 60% of the

RE: [PyMOL] Pymol/ABPS

Dyda, By default, PyMOL uses charges and radii from the Amber99 forcefield, as per APBS. The PDB2PQR tool included with APBS enables you to use other charge/radius sets, such as CHARMM. Chain IDs need to be removed for PQR...though future versions of PyMOL do this automatically. Cheers,

RE: [PyMOL] Preset Views

Laura, Presents are simply miniature Python programs bound to menu items. To create your own while avoiding changes to menu.py which is overwritten during upgrades, you can wrap and replace the 'presets' function in the menu module at runtime. # file: add_preset.py # run add_preset.py to load

RE: [PyMOL] install_plugin(s)

Charles, Thanks for pointing this out -- yes, unfortunately plugin installation was broken in the early 0.98 release candidates, including the source distribution. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point

RE: [PyMOL] gradual transparency

Humberto, You've hit an insumountable limitation in PyMOL at present...sorry! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942

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