RE: [PyMOL] PyMOL on Powerbook G4

2004-02-03 Thread Warren DeLano
Keana, This is a problem with at least one mac web browser...for some reason the .gz gets removed from the file upon download, but the file is still compressed. If you replace the .gz, then the file will uncompress and open properly when you double-click on it. Cheers,

RE: [PyMOL] Outline cartoon representation

2004-02-03 Thread Warren DeLano
Todd, Unfortunately that is not a problem PyMOL was designed to solve, and off the top of my head I can't think of any way to bend it around to do this -- you're talking about a different rendering scheme. I think it amounts to the following: trace every sharp edge, and outline every round

RE: [PyMOL] Surface triangulation of isopotential surfaces

2004-02-04 Thread Warren DeLano
Nuno, For a couple of reasons, I curently believe that electrostatic calculations based on point charge models are not valid near or within the protein surface -- you need to be at least one atom radius beyond the molecular envelope in order to draw physically meaningful interpretations.

RE: [PyMOL] different stick_radius for different residues

2004-02-04 Thread Warren DeLano
Frank, PyMOL's atom selection language is based on logical operators over sets of atoms. and is the intersection and or the union. You're looking for create forst2, (resi 1 or resi 32 or resi 356) Using macros, this can be reduced to: create forst, 1+32+356/ Please see the manual:

RE: [PyMOL] Zoom in a movie

2004-02-05 Thread Warren DeLano] On Behalf Of Jose Avalos Sent: Thursday, February 05, 2004 8:56 AM To: Warren DeLano Cc: 'Nat Echols'; 'Matt Franklin'; Subject: RE: [PyMOL] Zoom in a movie Sorry for the basic question, but I can't get the mdo command to work

[PyMOL] 2 Questions for the User Community

2004-02-06 Thread Warren DeLano
PyMOL Users: Regarding default setting:. 1) How many people will object if I change PyMOL's default cartoon settings so that loops are not initially smoothed? (cartoon_smooth_loop = off by default) The reasoning behind this is that gross smoothing is really only appropriate for

[PyMOL] Users Manual Printing Fixed

2004-02-09 Thread Warren DeLano
PyMOLers, In the past, some of you may have encountered a problem with printing the PDF version of the PyMOL Users manual. The problem has now been fixed -- so print away! Cheers, Warren -- Warren L. DeLano,

RE: [PyMOL] pymol on os x.3

2004-02-10 Thread Warren DeLano
Yunfeng, That is because the Mac still doesn't support Tcl/Tk out of the box. You'll either need to install Fink , X11, and the Fink version of PyMOL, or if you're willing to consider becoming a

RE: [PyMOL] get_dihedral multiple objects

2004-02-11 Thread Warren DeLano
Leigh, Get_dihedral can do what you need -- I think the problem is that you need to be more narrow in your atom selections. Otherwise, 9/C will match every atom named C, in every residue 9, and in every protein loaded. With two proteins loaded: load prot1.pdb load prot2.pdb You'll

RE: [PyMOL] save molecule format

2004-02-13 Thread Warren DeLano
Eric, For now, set retain_order, on Before writing out your PDB file -- that will insure that nothing changes. I'll look into whether the default behavior can be changed before the next release... Cheers, Warren -Original Message- From:

RE: [PyMOL] Labels not stored in scenes

2004-02-15 Thread Warren DeLano
Bjorn, Whoops! That is definitely an oversight -- I'll see what I can do to correct this. In the meantime, you may need to save a separate session file for each labeled scene. Cheers, Warren -Original Message- From:

RE: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread Warren DeLano
John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01,

RE: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread Warren DeLano
-Original Message- From: Charlie Sent: Wednesday, February 18, 2004 8:56 AM To: Warren DeLano Subject: Re: [PyMOL] selecting multiple atoms ie oxygen Warren DeLano wrote: John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names

RE: [PyMOL] using the build function

2004-02-19 Thread Warren DeLano
Dan, I think it's fair to say that PyMOL's currently molecular building capabilities are at the stage of a technology demonstration/proof-of-concept, but very little effort has yet been expended toward making them useful for real work. Part of that is because we don't yet have

RE: [PyMOL] Making the selection indicators bigger

2004-02-19 Thread Warren DeLano
Matt, Try: set selection_width, 6 set selection_width, 7 set selection_width, 8 Cheers, Warren -Original Message- From: [] On Behalf Of Matthew Zimmerman Sent: Thursday,

RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Warren DeLano
Morri has a good point: The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds should be capable of running on virtually any current x86-based Linux system: RH, SUSE, Debian, Fedora, or whatever. So, if you're having trouble with compilation or use of

RE: [PyMOL] molecular surface colored by hydrophobicity

2004-02-19 Thread Warren DeLano
Rongjin, PyMOL can certainly color surfaces by atom color and other properties. show surface color green, elem c color violet, elem n+o But Grasp's hydrophobicity function may be doing something more sophisticated then that... Cheers, Warren -Original Message- From:

RE: [PyMOL] drawing hydrogen bonds or dashes

2004-02-20 Thread Warren DeLano
-Original Message- From: [] On Behalf Of John Berrisford Sent: Friday, February 20, 2004 3:27 AM To: Warren DeLano; Subject: RE: [PyMOL] drawing hydrogen bonds

RE: [PyMOL] Are there limits for the number of coordinates accepted?

2004-02-25 Thread Warren DeLano
Dieter, Yes, there is a practical limit which depends on (1) the amount of RAM and (2) the operating system. For reasons I don't completely understand, PyMOL isn't able to get as much memory under Windows as under Linux or OSX on equivalent system. There are some things you can do to

RE: [PyMOL] Symmetry

2004-02-25 Thread Warren DeLano
Mads, The only way to accomplish this that I can think of would be to perform the normal expansion of all symmetry-related molecules within a cutoff and then use a Python script to delete those objects which don't fit a criteria. One such criteria might be the presence of a

RE: [PyMOL] sphere sizes

2004-02-28 Thread Warren DeLano
John, You're not doing anything wrong -- there's just a little confusion here about how settings work: they're global for an object or for the whole system. The current value is what is always used. To get different sphere sizes, use the alter command to change the vdw radii of the

RE: [PyMOL] selecting individual states

2004-03-05 Thread Warren DeLano
Neema, This is a fundamental limitation in PyMOL's current architecture... B factors are an atomic rather than a coordinate property. It may be possible to address this in the future, but not yet...sorry. The clusy workaround is to load each PDB file into a separate

RE: [PyMOL] How do I get PyMOL to keep TER cards?

2004-03-08 Thread Warren DeLano
Michael, PyMOL will only insert TER records when residue identifiers are non-sequential. Cheers, Warren -Original Message- From: [] On Behalf Of Michael George Lerner Sent: Monday, March 08,

RE: [PyMOL] 64-bit

2004-03-08 Thread Warren DeLano
Jason, Thanks for the kind words. It has been a while since anyone's tried to build/run PyMOL on a 64-bit may not currently be 64-bit clean. We don't currently have any Opteron hardware, but if you can build under -g, crash the program under GDB, and then send me the

RE: [PyMOL] PDB Insertion code (iCode) treatment by PyMol

2004-03-10 Thread Warren DeLano
Ilya, PyMOL treats insertion codes as part of the residue identifier: select my_sele, resi 324A Cheers, Warren -Original Message- From: [] On Behalf Of Ilya Venger Sent: Tuesday, March

[PyMOL] IRIX 6.5.18-6.5.21 Fix

2004-03-12 Thread Warren DeLano
Some users have reported problems with PyMOL on SGI hardware, particularly after upgrading IRIX. We now know what it going on: It seems that SGI broke the critical pthread library in several recent versions of IRIX. In order to get PyMOL and other pthread-dependent programs to run reliably on

RE: [PyMOL] Question about surface calculation

2004-03-15 Thread Warren DeLano
Fred, I think Lieven answered the second part, so I'll answer the first: PyMOL's surfaces are discrete approximations of the solvent contact surface (the surface of waters in contact with the protein at all possible positions). I generally think of the solvent accessible surface as being the

RE: [PyMOL] running PyMOL remotely - how to do it without GUI

2004-03-17 Thread Warren DeLano
Fred, Using the -c command line option will launch the command-line version of PYMOL (no display required). You may also wish to use -q to suppress the splash information. pymol -cq pymol_script.pml or pymol -cq Cheers, Warren -Original

RE: [PyMOL] CGO shading

2004-03-25 Thread Warren DeLano
Gareth, You need to provide normal vectors too. Otherwise OpenGL the raytracer won't be able to light them correctly. Cheers, Warren -Original Message- From: [] On Behalf Of Gareth

RE: [PyMOL] embeding pymol in a web page

2004-03-25 Thread Warren DeLano
Einat, That is a longstanding goal of the PyMOL project, but there are various hurdles to be surmounted, including creating an API for embedding PyMOL and a secure API/language-subset for controlling it via the network. Another problem is that each platform has a different optimal technology for

RE: [PyMOL] opaque interiors flag

2004-03-26 Thread Warren DeLano
Ken, set ray_interior_color, color-name eg: set ray_interior_color, grey30 To restore default: set ray_interior_color, -1 Cheers, Warren -Original Message- From: [] On

RE: [PyMOL] adding residues

2004-03-26 Thread Warren DeLano
Sergio, PyMOL probably isn't the best tool for doing this, but it can be done: To add to a free N-terminus, pick (ctrl-middle-click) the N-terminal nitrogen, and then press Alt-Letter (on Macs, Option-Letter) for the amino acid you want: For example: Alt-G adds a glycine To add onto the

[PyMOL] RE: Final testing of version 0.95

2004-03-29 Thread Warren DeLano
an official release... Cheers, Warren -Original Message- From: Warren DeLano [] Sent: Thursday, March 25, 2004 3:19 PM To: '' Subject: Final testing of version 0.95 PyMOL Users, I expect to announce

[PyMOL] RE: multi-instances of pymol on OS X

2004-03-30 Thread Warren DeLano
Sent: Tuesday, March 30, 2004 12:31 PM To: Warren DeLano Subject: multi-instances of pymol on OS X Hi, Warren, Is it possible that I can run multiple instances of pymol on OS X? After I opened pymol, if I double click pymol again it won't open a new pymol but just return

[PyMOL] RE: Some Ideas for PyMol

2004-03-31 Thread Warren DeLano
Franz, I agree that it would nice for PyMOL to handle this automatically, but I personally think that extra long CA-CB bonds look almost as goofy as sidechains hanging in space. As it stands, there are two ways to handle this annoyance manually, assuming that you're using version 0.95 beta:

RE: [PyMOL] bond connectivity

2004-04-01 Thread Warren DeLano
Thomas, The trick for handling these sorts of situations is to load the first PDB file into PyMOL using reasonable atom distances. So long as no new atoms are added in subsequent PDB files, PyMOL will continue to use the connectivity from the first state. The only way to

RE: [PyMOL] multiple atom selection by atom number

2004-04-02 Thread Warren DeLano
Lihua, You're correct: 'id' doesn't currently have the capability of selecting by range or even using a list. However, we can probably add that behavior in a future version. In the meantime, you could tap Python for the task, but it will be slow: select myrange, none for a in

[PyMOL] PyMOL 0.95 Released

2004-04-04 Thread Warren DeLano
PyMOLers: Yesterday marked DeLano Scientific's one year anniversary as a full-time business. In addition to popping the cork on a bottle of champagne, we celebrated with the release of version 0.95! Thank you to everyone who made the

RE: [PyMOL] [Fwd: labels]

2004-04-05 Thread Warren DeLano
Mado, PyMOL's current labeling is inflexible. The only way to change position automatically is to insert spaces at the front of the label: label (name ca), %s-%s%(resn,resi) The font selections are limited: normal: set label_font_id, 0 bigger: set label_font_id, 1 smaller: set

RE: [PyMOL] ray command

2004-04-05 Thread Warren DeLano
David, There isn't currently a programmatic way of doing this, but it wouldn't be too hard to make one. I'll put onto the todo list support for commands like: ray 1024; ray width=800; height=600; where the second axis is calculated. Note that we're currently missing an API function for getting

[PyMOL] RE: colors and states

2004-04-05 Thread Warren DeLano
load ref4.pdb, ref, discrete=1 then apply the overall coloring: spectrum b, selection=ref Cheers, Warren -Original Message- From: Tony Sent: Monday, April 05, 2004 2:08 PM To: Warren DeLano Subject: colors and states Warren, I have figured out how to move (rotate) my domains

RE: [PyMOL] save all not working for multiple objects from split_states?

2004-04-06 Thread Warren DeLano
Dan, That's the not expected result, but indeed you have a problem -- each of those subunits will have identical atoms. To resolve this, assign a unique segment identifier to each subunit: load 1c8e.pdb1, 1c8e split_states 1c8e delete 1c8e alter all, segi = model[-4:] rewind save

RE: [PyMOL] add hydrogens using different hybridization

2004-04-07 Thread Warren DeLano
Frank, PyMOL adds hydrogens based on the hybridization and formal charge of an atom...if you're not getting the right number of hydrogen, then you probably need to adjust either the valences of the bonds it participates in, or the formal charge. A) To adjust valences: 1) enable show valences

RE: [PyMOL] color

2004-04-08 Thread Warren DeLano
Yes, it's called spectrum...but it looks like the docs don't exist yet. PyMOLspectrum ? Usage: spectrum [ expression [, palette [, selection [, minimum [, maximum [, byres [, quiet ]]] eg: spectrum b spectrum q spectrum b, selection=my_obj spectrum b, minimum=5, maximum=60 spectrum count,

RE: [PyMOL] Series of general questions

2004-04-10 Thread Warren DeLano
1) I would like to show certain residues and have no problem getting the ones I want selected and displayed as sticks or whatever. The problem is color. When I change the color of the selection, it changes the color of the associated section of the ribbon. I would like to leave the

RE: [PyMOL] Ball and stick

2004-04-12 Thread Warren DeLano
Tony, First, enable stick_ball show sticks set stick_ball, on That will put rounded-ends on sticks. If you wall a ball stick representation, then also do something like the following: set stick_radius, 0.12 set stick_ball_ratio, 2 And if you want bond valences as well: set

RE: [PyMOL] picking atoms with latest version (0.95)

2004-04-13 Thread Warren DeLano
Ken's answer covers it...the following just provide a little more in-depth coverage: What has happened is that PyMOL now supports the picking of multiple atoms, so use of the lb and rb selections is less necessary. Picking and selecting are not the same thing in PyMOL. Selections are merely

RE: [PyMOL] set sphere_transparency?

2004-04-14 Thread Warren DeLano
Jason, The problem is that your script is changing the setting for the specific object-state by passing it an explicit object name and state number. cmd.set( sphere_transparency, str(val), spheres, 0, 1, 1 ) As an important compatibility consideration, I recommend for all API functions that

RE: [PyMOL] Selections

2004-04-15 Thread Warren DeLano
must I do c10+c11+c12...c50? Yes, unfortunately. However, this long selection: select tails1, r. pop n. c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca 1+ca2+c36 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50 Can be replaced with some Python code in your script:

RE: [PyMOL] Re: give unique chain identifiers

2004-04-15 Thread Warren DeLano
, Warren -Original Message- From: [] On Behalf Of Dr. Daniel James White PhD Sent: Wednesday, April 14, 2004 7:47 AM To: Warren DeLano Cc: Subject: [PyMOL] Re: give

RE: [PyMOL] movies in presentations

2004-04-16 Thread Warren DeLano
Mark, Despite the performance drop, I'm a big fan of presenting within PowerPoint -- I think it is simply the best solution for Windows. Note that within PowerPoint: - you can have your movie play automatically - you can start and stop the movie with a mouse click in order to discuss

RE: [PyMOL] movies in presentations

2004-04-17 Thread Warren DeLano
My thoughts on Yasara: I'm jealous! Yasara is beautiful, fluid, polished, and significantly ahead of PyMOL in several key technical areas. To me, Yasara seems like the Matrix of molecular graphics: its perceptive experience is a quantum leap beyond PyMOL, VMD, and other conventional programs,

RE: [PyMOL] 3D alignment viewer of RAPTOR ?

2004-04-19 Thread Warren DeLano
Joyce ( friends), I think that these kinds of RAPTOR-specific questions are best followed up with Bioinformatics Solutions ( ) first, rather than being posted to PyMOL-users. We're not (yet) familiar with how their interface works, so it is hard for

RE: [PyMOL] sphere scale

2004-04-21 Thread Warren DeLano
Mark, The sphere_scale setting is a multiplier of the atom's VDW radius. If you want to set exact radii, use alter: alter selection, vdw=number eg. alter (all), vdw=1.0 rebuild Cheers, Warren -Original Message- From:

RE: [PyMOL] sphere scale

2004-04-21 Thread Warren DeLano
Mark, The sphere_scale setting is a multiplier of the atom's VDW radius. If you want to set exact radii, use alter: alter selection, vdw=number eg. alter (all), vdw=1.0 rebuild Cheers, Warren -Original Message- From:

RE: [PyMOL] sphere scale

2004-04-22 Thread Warren DeLano
Mark, The sphere_scale setting is a multiplier of the atom's VDW radius. If you want to set exact radii, use alter: alter selection, vdw=number eg. alter (all), vdw=1.0 rebuild Cheers, Warren -Original Message- From:

RE: [PyMOL] (no subject)

2004-04-22 Thread Warren DeLano
Christian, This isn't implemented yet, but it is on the to do list. Cheers, Warren -Original Message- From: [] On Behalf Of Christian Rummey Sent: Thursday, April 22, 2004 2:35 AM To:

RE: [PyMOL] Does (PDB) size really matter? (Help!)

2004-04-24 Thread Warren DeLano
Ack! Sorry to hear this. The two things that determine memory usage when rendering are: 1) the total number of primitives (spheres, triangles, cylinder [i.e. lines] etc.) 2) the value of hash_max #1 may not be easily remedied for your scene #2 can be improved by setting hash_max to something

RE: [PyMOL] Does (PDB) size really matter?

2004-04-26 Thread Warren DeLano
Hi Jason, I see you have hash_max set to 400 -- that's the problem. In empirical testing, I found that there is rarely a reason to go above 200 with this setting. Having a hash table that is too finely sampled is no better than having one too coarsely sampled. PyMOL's default of 100 is

[PyMOL] Motion Blur

2004-05-05 Thread Warren DeLano
is there any way of showing movement of a molecule in a static image, for example as speed lines or a blur between the two states? If this makes any sense please let me know if you have some ideas!Mike, Motion blur in PyMOL is possible, but the process is a bit tedious. You need to

RE: [PyMOL] White surface problem

2004-05-07 Thread Warren DeLano
Einari, I can't get white surface look really white. Is there a way to do this ? Yes: increased the ambient light setting. set ambient, 0.4 ray Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] L-D amino acid conversion using pymol

2004-05-10 Thread Warren DeLano
Heinz-Uwe, For 0.95: The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert. For 0.93:

RE: [PyMOL] Creating cell surface

2004-05-10 Thread Warren DeLano
Tony, In order to enter multi-line Python code on the command line, you need to use explicit end-of-line continuations. Otherwise, PyMOL won't know where your Python code stops and PyMOL commands again begin. from pymol.cgo import * from pymol import cmd set cgo_sphere_quality, 3 def

RE: [PyMOL] GLX error

2004-05-11 Thread Warren DeLano
Michael, This is what can sometime happen when you update system libraries underneath vendor-supplied OpenGL drivers. If you reinstall your graphics drivers after the update, then the problem should go away. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] Moving Objects

2004-05-13 Thread Warren DeLano
Yes, Assuming you're running 0.95: Put the mouse into Editing Mode (Mouse menu or click on the mouse matrix). Insure that no atoms are currently picked (i.e. there are no pk selections). Click unpick if there are... You can now independently rotate and translate objects with

[PyMOL] Change in Selection Behavior

2004-05-14 Thread Warren DeLano
PyMOL-Users, I've been unhappy with the way the user interface for selection works in PyMOL and am planning a change. Going forward: 1) There will the concept of an active selection. 2) The enabled (visible) selection will be the active selection. 3) Only one selection can be enabled/active

RE: [PyMOL] Linux Beta Version with Sequence Viewer

2004-05-19 Thread Warren DeLano
To: Warren DeLano; Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer Hi Warren This is GREAT! I was going to suggest this for the future development, but (as usual :-) you're ahead. Very good points: * possible to chose between atoms

RE: [PyMOL] Creating a .pymolrc file in Windows

2004-05-19 Thread Warren DeLano
Actually, this too was anticipated ; ). On Windows: for PyMOL commands, simply use pymolrc (no extention -- I suppose pymolrc.txt or pymolrc.pml would've made more sense...) or for Python code: pymolrc.pym Cheers, Warren -- Warren

[PyMOL] 0.96Beta10 Bug Fix Notice

2004-05-20 Thread Warren DeLano
PyMOLer's, Lots of good feedback on the sequence viewer has been coming in -- thank you everyone, and please keep it up. I've got about a week's work of changes to make, but will continue to push out new releases as they are ready. I did want to draw your attention to the fact that up until the

RE: [PyMOL] using from native Python

2004-05-21 Thread Warren DeLano
Randy, For some reason this approach has turned out to be unstable, so I've basically placed it on unsupported status until someone with a better understanding of Python interactive mode than me can take a look at it. Are you aware that the PyMOL command line is also a Python

RE: [PyMOL] Rtools Question

2004-05-24 Thread Warren DeLano
Hi Tony Friends, I just wanted to draw your attention to the fact that rTools should (in theory) work with the 0.95 OSX-X11 hybrid version, which has an native Aqua-based OpenGL window and an X11-based Tcl/Tk gui. I specifically created that version to insure that Mac users wouldn't be

RE: [PyMOL] Cartoons from ca co-ordinates only

2004-05-27 Thread Warren DeLano
Hi Máire, PyMOL requires the other mainchain atoms to be present in order to generate a nice cartoon representation. The only exception to this is if you're willing to work with a simple tube, in which case you can enable the cartoon_trace setting (set cartoon_trace,on), followed by

RE: [PyMOL] Displaying of an NMR ensemble

2004-06-17 Thread Warren DeLano
Peter, set all_states, on Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From:

RE: [PyMOL] superposition of two molecules

2004-06-20 Thread Warren DeLano
Bill, Fit is an extremely finicky only works when the two objects have matched identifiers for each atom to be superimposed (name, resi, resn, chain, segi, alt). Align won't help you because you're using RNA. So you'll need to use pair_fit, which requires that you specify a

RE: [PyMOL] Electronic density maps

2004-06-21 Thread Warren DeLano
Konrad, There are several options for loading map data into PyMOL now: XPLOR (format=xplor) CCP4 (format=ccpy) O/BRIX (format=brix) In addition, you can use the following non-crystallographic formats: Delphi/Grasp PHI files (format=phi) AVS FLD files (as output from MEAD) (format=fld) and in

RE: [PyMOL] cartoon and alternates

2004-06-24 Thread Warren DeLano] On Behalf Of Robert Schwarzenbacher Sent: Wednesday, June 23, 2004 11:47 PM To: Warren DeLano Cc: Subject: [PyMOL] cartoon and alternates hi there, I get broken cartoons with alternate conformations. Is there a quick way

RE: [PyMOL] superposition of structures

2004-06-25 Thread Warren DeLano
(Warren DeLano) 2. cartoon and alternates (Robert Schwarzenbacher) 3. RE: cartoon and alternates (Warren DeLano) 4. Question about rotation (Qun Wan) 5. Questions about rotation view (Qun Wan) --__--__-- Message: 1 From: Warren DeLano To: 'Steve

RE: [PyMOL] superposition of structures

2004-06-25 Thread Warren DeLano
-Original Message- From: [] On Behalf Of Nalam, Madhavi Sent: Friday, June 25, 2004 1:48 PM To: Warren DeLano; Subject: RE: [PyMOL] superposition of structures

RE: [PyMOL] question about superposition

2004-07-02 Thread Warren DeLano
Qun, This is something that is easist to do with the Fitting wizard. Starting with the ATP, click successive matched pairs of atoms in the ATP and then the ADP. When you have enouch pairs, click Fit. That should be all you need to do. Cheers, Warren -- Warren

RE: [PyMOL] having problems with batch rendering

2004-07-05 Thread Warren DeLano
will hash_max 500 be even better? Thanks, Scott On Jul 5, 2004, at 10:56 AM, Warren DeLano wrote: Scott, The optimal hash_max is somewhat scenery-dependent, but values in the 180-250 range tend to be best for multiprocessor situations with lots

RE: [PyMOL] Showing electrostatics on surface ?

2004-07-06 Thread Warren DeLano
Vladimir, Michael and I have been working on streamlining the process for using ABPS with PyMOL and are almost at the point where PyMOL can generate the necessary PQR file (for proteins at least) from an ordinary PDB file lacking hydrogens, c-terminal carboxylates, etc. PyMOL can also

RE: [PyMOL] questions about electrostatics

2004-07-06 Thread Warren DeLano
Qun, PyMOL doesn't (yet) have the ability to calculate Possion Boltzmann electrostatic potentiallys. You'll need to use an external tool like GRASP or APBS to perform that task. If spectrum b doesn't produce the desired result, then there is probably some strange B-value present

[PyMOL] New Beta with Vacuum Electrostatics (for proteins)

2004-07-08 Thread Warren DeLano
PyMOLers, Electrostatics purists will undoubtedly question the wisdom of this action, but in the latest Windows beta version of PyMOL, I have added an experimental and as-yet-unvalidated automatic way to calculate and display vacuum electrostatic potentials (computed with a constant homogenous

RE: [PyMOL] selecting residues around

2004-07-10 Thread Warren DeLano
Jason Ah, I found the problem: Sticks represent bonds, not atoms. Normally, in order to see a bond, *BOTH* atoms involved have to have either sticks or lines shown. That's why you weren't seeing anything until increasing the radius of the selection sphere, which included the first bond atom

[PyMOL] PyMOL 0.96 Released

2004-07-12 Thread Warren DeLano
PyMOLers, The official 0.96 version of PyMOL had been released. As you've likely come to expect, this isn't so much a formal release as a quality-controlled build containing many of the recent beta features. Of greatest interest will probably be: 1) The sequence viewer. 2) Built-in support

[PyMOL] RE: sequences view

2004-07-13 Thread Warren DeLano
This question just came in about the sequence viewer...I'm anonymously copying it to the mailing list since it is bound to come up frequently: Hey Warren, I just downloaded the new version of PyMOL and was playing with the new sequence view. Is it possible to do a structural alignment

RE: [PyMOL] polar surface area with pymol

2004-07-13 Thread Warren DeLano
Ramesh, You can do something like this... For a solvent accessible PSA approximation: set dot_density, 3 remove hydro remove solvent show dots set dot_solvent, on get_area elem N+O get_area elem C+S get_area all For molecular PSA approximation set dot_density, 3 remove hydro remove solvent

RE: [PyMOL] pymol crash!

2004-07-14 Thread Warren DeLano
Ramesh, Thanks for this report. So far I haven't been able to reproduce the crash under Linux or IRIX... If other people encounter this same problem or other problems with the new releases, then please send a report to that includes your operating system details. If pattens

RE: [PyMOL] selection of residues with negative numbers

2004-07-15 Thread Warren DeLano
Douglas, I don't think PyMOL can handle negative selections yet. Just make them positive: alter all, resi=int(resi)+100 etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] sequence viewer problem on some PDB files

2004-07-16 Thread Warren DeLano
Dan, Yes, those files aren't really valid PDBs, but you can probably solve this by assigning a distinct chain to the waters and rebuilding: alter hoh/, chain='X' sort Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

[PyMOL] RE: [ccp4bb]: pymol and OS X v. 10.3.5 update -- a word of caution

2004-08-11 Thread Warren DeLano
Following up on Bill's report... We've updated to version 10.3.5 all the Mac's we have access to and have not been able to reproduce the reported problem. The configurations tested are: Mono on an LCD: MacPYMOL 0.95 on a dual G5 with an ATI Radeon 9600 (RV350) MacPyMOL 0.95 on a dual G4

[PyMOL] Sharp 3D Display (was:RE: [ccp4bb]: stereo glasses)

2004-08-12 Thread Warren DeLano
Ian, Yes, I have gotten PyMOL to work with the laptop version of this display (just Windows so far). The stereo effect is quite good. However, your head does need to be in just this right spot in order to get the effect. After 15 minutes, I learned to do this automatically, moving slightly off

RE: [PyMOL] Measuring Angles

2004-08-13 Thread Warren DeLano
Anthony, New in version 0.97 is a get_angle function that takes three single-atom selections. There is also a get_distance that is more efficient than the distance command (which creates objects)... See help get_angle To set up a loop, you'll need to generate a list of selections # for

RE: [PyMOL] line width

2004-08-19 Thread Warren DeLano
That's good advice, except that you'll lose any bonds between the two selections... the following example will keep those bonds (by duplicating atoms) create protein2, (selection_1) create protein3, ((not selection_1) extend 1) set line_width=1.2, protein2 set line_width=2.0, protein3 Cheers,

RE: [PyMOL] Negative residue index

2004-08-19 Thread Warren DeLano
Charles, It's a design limitation that hasn't yet been remedied. For the time being, please just shift residues into a positive range via a command such as the following: alter all, resi=int(resi)+100 Cheers, Warren Note that if you have alphanumeric residue identifers 110A, 110B, then you'll

RE: [PyMOL] PyMOL tutorial (moved and slightly updated)

2004-08-30 Thread Warren DeLano
Why do you think pymol cannot be sold? The copyright license does not seem to imply this[1], and such a restriction would render pymol not Open Source. Warren, can you tell us what you think on this? Michael Carly, Yes, in my world, open-source means available to all people and for all

RE: [PyMOL] Fast Coloring

2004-09-07 Thread Warren DeLano
) for atm in mdl.atom: atm.b = 10 cmd.load_model(mdl, new_obj) label new_obj, b Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-402 Thanks, Charlie Warren DeLano wrote: Charles

RE: [PyMOL] long loading times as the number of existing objects increases

2004-09-07 Thread Warren DeLano
Ben, Thanks for the great benchmarks! PyMOL is definitely showing non-linear behavior when it comes to loading a lot of objects...I don't know why this is exactly, but I can tell you that I didn't originally envision (and thus optimize PYMOL for) loading of so many objects. As it currently

[PyMOL] Latest beta

2004-09-09 Thread Warren DeLano
PyMOL Users who: 1. don't normally need to share session files with others 2. want to load a lot of structures into PyMOL 3. like living on the bleeding edge 4. will provide feedback on problems encountered may wish to try the latest 0.98beta05 executables for Win/Linux/Mac-X11 posted

[PyMOL] ATI Mobility Radeon 9000 Problems (?)

2004-09-13 Thread Warren DeLano
PyMOL Users, A major PyMOL sponsor is having problems with the Mobility Radeon 9000 chip on their Dell laptops under Windows XP. I am curious to know whether others have seen or are encountering similar problems with this chipset. The issue is as follows: When attempting to choose atoms using

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