[PyMOL] MacPyMOL Beta 2 Announce/Caveat

set your MacPyMOL expectations low -- this code will get better soon. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] SGI Crystal Eyes Problem

rhaps the same is true of your system?) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforg

RE: [PyMOL] nmr ensemble alignment

s, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf

[PyMOL] RE: c-alpha traces

Michal, Unfortunately, beautiful backbones require N and C coordinates as well, because PYMOL uses AA geometry to determine orientation vectors. The best you can do with CA only is a tube. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

RE: [PyMOL] translucent proteins

Lesley, set cartoon_transparency, 0.6 should do the trick. Note that you may need to ray-trace the image to avoid transparency artifacts. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax

RE: [PyMOL] Help for user-defined functions

Thanks for the suggestion, and the solution. In Versions >= 0.95, cmd.extend will will adds new commands into the help dictionary. In the meantime cmd.help_sc.append('func_name') will work... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph

RE: [PyMOL] How to send pymol command to pymol by python interpreter

aunching the PyMOL thread from a standalone Python script, I'd sure like to hear it : )]. -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-

RE: [PyMOL] c-alpha traces

Yes, PyMOL can visualize CA-only models, perform CA-based alignments on CA models, visualize all-atom models, perform CA-based alignments on all atom models, and perform all-atom alignments on all-atom models. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

RE: [PyMOL] How to send pymol command to pymol by python interpreter

your question : ). Sorry for the complexity, but that's the price of flexibility. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- >

[PyMOL] Problems with PyMOL + XIG Summit2.2

l here and then track down the problem... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Dr. Daniel James White PhD [mailto:d...@chalkie.org.

RE: [PyMOL] Ray Tracing Crash

ct to Debian, in order to debug the problem, you might want to send me a PyMOL session file which crashes on your system when the next command issued is "ray". Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] Ray Tracing Crash

... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net

RE: [PyMOL] Cartoon does not display properly

o:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax   (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Daniel Moriarty Sent: Tuesday, Ja

RE: [PyMOL] working directory

Lesley, If you always want PyMOL to start in a different directory, you can create a ".pymolrc" file in you home directory with a command like cd /users/lesley/scripts Which will be executed every time you start PyMOL. Cheers, Warren -- mailto:war...@delanoscientific.co

RE: [PyMOL] homologous alignments?

r red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sour

RE: [PyMOL] mouse

fails, then please try saving a png file of what you see on the screen ("png filename.png"). If that PNG file exhibits any distortion or artifacts, then that's the cause of the problems. Otherwise, PyMOL may have a bug... Cheers, Warren -- mailto:war...@delanoscientific.com Warren

RE: [PyMOL] Restrict surface transparency to limited region

o:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar &g

RE: [PyMOL] Restrict surface transparency to limited region

Roger, This isn’t possible right now. The only way to do it is to create two objects, surfacing different atoms in each object, and then enabling transparency in just one of the two objects. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal

RE: [PyMOL] build instructions

rs, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf

[PyMOL] DeLano Scientific Closed Until Jan 7, 2004.

PyMOL Users, This is the final reminder that I am now off-line and away from DeLano Scientific (which will be closed) until January 7th. Everyone please have a wonderful holiday and a Happy New Year! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal

RE: [PyMOL] Question

Avram, set cartoon_highlight_color, red Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-us

RE: [PyMOL] unsetting cartoon_colors

o:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax   (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Thu

[PyMOL] RE: 3-button mice

PowerBooks) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Sent: Thursday, December 18, 2003 5:45 AM To: war...@delanoscientific.com Subject: pymol Hi, I plan

RE: [PyMOL] Display of electrostatic potential surfaces

t yet. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behal

RE: [PyMOL] electrostatic surface

Ruslan, PyMOL can't yet calculate the electrostatic surface, but it can display the potential as output by Grasp, Delphi, MEAD, or Zap. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154

RE: [PyMOL] expand to molecule (by connectivity)

arren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of

[PyMOL] RE: Stereo on G4 Laptop?

tions/PyMOL.app/Contents/MacOS/PyMOL -BGS Alternative, you could simply click on the "PyMOL Stereo" icon in the Demos folder. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax

RE: [PyMOL] About licensing

(war...@delanoscientific.com) since the user's list isn't really the right place for these discussions. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original M

RE: [PyMOL] assign secondary structure?

ldn't need to worry about them Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-

RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)

plore what data is ending up in the Map, before trying to use the color ramps. There may also be some code in the chempy brick stuff which could serve as an example for populating the list. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

[PyMOL] DeLano Scientific Downtime (Dec. 22-Jan 7)

mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] electron density settings

ad, which is in angstrom units. To display the density around a ligand, create a mesh using the "carve" option. load map.ccp4 load protein.pdb load ligand.pdb isomesh m1, map, 1.0, ligand, carve=2.1 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Sc

RE: [PyMOL] Unable to read Gamess-US output

applications. But if you still want to use PyMOL, then you'll need to convert your files into something like .mol or .pdb... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593

RE: [PyMOL] residues deviate from protein secondary catoon representation

rsion will provide an easier workaround for this... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [ma

RE: [PyMOL] Viewing homotetramers with PyMol

ate=2, target_state=1 dele 1f41_tetra Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:

[PyMOL] Clarification on "A Few Good MacPyMOL OS X Beta Testers"

atform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] cannot 'fit' a particular pdb file

...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Michael Bovee > Sent: Tuesday,

FW: [PyMOL] detecting the existence of a selection

(repost: the mailing list was down yesterday afternoon and this message never made it onto the list) -Original Message- From: Warren L. DeLano [mailto:war...@delanoscientific.com] Sent: Monday, December 01, 2003 3:21 PM To: 'Tina Li'; 'pymol-users@lists.sourceforge.n

RE: [PyMOL] Object orientation matrices

rs, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Laurence

[PyMOL] More on "A Few Good MacPyMOL OS X Beta Testers"

ve in synchronization with the cross-platform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] detecting the existence of a selection

t; in cmd.get_names("selections") True Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [m

[PyMOL] A Few Good Mac PyMOL OS X Beta Testers

ks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] electron density settings

map1 isomesh mesh1, map1, 1.0 will generate a mesh with half the spacing of the original map. Note that map_double can usually only be used once on a given map before averaging artifacts appear. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] dss & ribbon representation

eing a simple molecular object useful in straight Python, outside of PyMOL. All you need to do is have a copy of PyMOL's "chempy" module available in your PYTHONPATH from chempy import io model = io.pkl.fromFile("myprot.pkl") for atom in model.atom: print atom.name Cheers

RE: [PyMOL] Reference

http://pymol.sourceforge.net/faq.html#CITE -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad

[PyMOL] RE: Stereo parameters, again

> I still do not understand your stereo parameters: the > stereo_angle should > define the rotation (around the y-axis) between the pictures > for the left and > right eye, whereas the stereo_shift should define whether the > origin or > midpoint of the picture is within the plane of the scre

RE: [PyMOL] surface area calculation

of the arginines in the presence of the other atoms, whereas the second gives the area of the arginines in isolation. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original

RE: [PyMOL] surface area calculation

This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] Re:labeling atoms in GUI

) To show distances, use the distance wizard: wizard distance then ctrl-middle-clock on two atoms in succession. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Origi

RE: [PyMOL] homologous alignments?

x, y And this would do a CA-only alignment: align xca, yca To see which atoms are aligned, add and object name: align xca, yca, object=alignment Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (65

[PyMOL] RE: X11 1.0 instability

otein surface set surface_color, ramp, prot Now you can ctrl-middle click and drag on the ramp to change the range. You can also specify the red,white, & blue points precisely: ramp_new ramp, phimap, [-10.0, 0.0, 10.0] Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeL

RE: [PyMOL] aa residues disconnected from 'fancy helices'?

Michael, That's because sheet's aren't flat -- cartoons aren't reality. set cartoon_flat_sheets, off set cartoon_smooth_loops, off In order to force the cartoons to follow the true CA trace. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D.

RE: [PyMOL] DSSP

that governments, companies, and funding agencies will begin to back these kinds of efforts wholeheartedly with money and policies, and thus drive rapid progress and widespread benefits throughout the sciences. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Pri

RE: [PyMOL] DSSP

tions of secondary structure, be exactly described, be reproducible, and be available in an open-source reference implementation. Does DSSP meet these criteria? No, but STRIDE might (if one could find it), and "dss" probably could in time. Cheers, Warren -- mailto:war...@delanoscien

RE: [PyMOL] a couple of newbie questions

> > Hello all. > I am relatively new to pymol, so please excuse me if > these questions > are too simple for the list as a whole. I am running 0.90 on a Linux > system by way of introduction. > > 1) What is the easiest way to select one molecule out of > several on the > screen and tra

[PyMOL] PyMOL 0.93 Released

rovided such quick feedback on 0.92! Sixth, Thanks to PyMOL users for understanding that software releases aren't always perfect. http://pymol.sourceforge.net/ Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] labeling atoms in GUI

.set_key('F2',cmd.label) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pym

RE: [PyMOL] secondary structure assignment and surface potential calc/mapping

e a 0.92 function to calculate and map surface > potential? This would be useful beyond compare. I wish. Your choices for this are Grasp, MEAD, Delphi, or Zap. Only MEAD is freely available. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scient

RE: [PyMOL] secondary structure and movie

l Purpose Commands: 1: dss state=1 2: dss state=2 3: dss state=3 etc. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > F

[PyMOL] Bugs in 0.92 (WARNING)

h may be practically invisible to you. By the way, if you notice any other serious bugs with the new version, please report them ASAP -- I'd like to fix them in 0.93 if possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific

RE: [PyMOL] movies and secondary structure

> I would like to make a movie from a trajectory of 50 frames > with varying sec structure. Following Warren's advice in a > previous thread (see below) I load every pdb file into a > different object *and* state using > file_list1 = glob("*_first.pdb") > for file in file_list1: > cmd.l

RE: [PyMOL] How to load O/BRIX map

. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforg

RE: [PyMOL] Ray tracing dashed lines

Einat, with version 0.92: set dash_gap,0 set dash_length,1 seems to do the trick for me, raytraced or not. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

[PyMOL] RE: Writing info to files

ripts in order to accomplish tasks such as this. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

[PyMOL] PyMOL 0.92 Released

version will be the increased WYSIWYG behavior of the ray-tracer with respect to line widths. If the bonds in your figure just got thinner, that's the culprit. You can manually adjust the various *_width or *_radius settings to achieve the desired results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] solvent accesible surface

surface for a nice combination of the solvent and molecular surfaces. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@

RE: [PyMOL] Save session on Mac OSX latest version?

Douglas, Simply: save filename.pse ie save today.pse Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-us

[PyMOL] Release in progress...

(in a whisper) I'm still in the process of building binaries, but pioneers are welcome to start downloading 0.92, if your platform is represented. It has been a long time since our last release, so proceed with caution! http://sourceforge.net/project/showfiles.php?group_id=4546 Please bring an

RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

with this Tcl/Tk, and I'm not sure Python's Tkinter can even work with it. Does anyone out there have experience using Tkinter on OSX without X11? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-115

RE: [PyMOL] Using PyMol as a library - no GUI

arren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls A. > Tangstad > Sent: Friday, Octo

RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

Fred, The tkinter dependency is missing. RPM is supposed to check that, but I forget to add it to the list. Look for the tkinter RPM on your RH9.0 CDROM (or on the net). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] atom sphere radius

Robert, alter selection, vdw=number for example: alter elem fe, vdw=1.0 rebuild Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From:

RE: [PyMOL] Off screen drawing bug on a nForce 2 computer

arren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net]

RE: [PyMOL] Is it possible to tell if a loaded PDB file contains secondary structure records?

from pymol import cmd if cmd.count_atoms("ss H or ss S or ss L")==0: util.ss() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message-

[PyMOL] 2004 PyMOL Budget Reminder

our mission ( http://www.delanoscientific.com/about.html ). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] new error

Tom, Yes you're right: MGL's stuff messes with PYTHONPATH and possibly PYTHONHOME. These need to be undefined for PyMOL to work correctly. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-34

RE: [PyMOL] recommendations for G5

o now know whether or not the 9800 suffers this same limitation. Perhaps others can comment? There were some glitches with Stereo on the ATI series of cards, but these may have been fixed by now. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scient

RE: [PyMOL] Using PyMol as a library - no GUI

rpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Vo

RE: [PyMOL] transforming all atoms by a matrix

Tina, > 1. I want to superpose object1 and object2 on top of each other, and have > derived a rotation matrix to transform object2 by. How do I apply this > matrix > to all its atoms? Either I parse its PDB coordinates, multiply them by the > matrix, and load the object (which can be really slow),

RE: [PyMOL] make a bond from two different molecule

e object, while forming a bond from the amino nitrogen in ARG to the carbonyl carbon in GLU. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- >

RE: [PyMOL] Command line equivalent available?

Nick, > There are a few commands that I've been using for which I can't seem to > find a command line equivalent: This actions can be performed using selections with standard atom identifiers: > show/hide mainchain atoms show lines, object-nameca+c+n+o+h hide lines, object-nameca+c+n+o+

RE: [PyMOL] atom (sub) selections

Wolfram, select m1cha, mole1 and chain a select m2cha, mole2 and chain a You can then perform operations such as: color cyan, m1cha color yellow, m2cha align m1cha, m2cha Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] Applying a rotation matrix to coordinates

wards from what you might normally expect in C or Python. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sour

RE: [PyMOL] Underside of surface color

c.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes > Sent: F

RE: [PyMOL] Creating stereo figures for pub

> I am having a small problem creating stereo figures, probably a syntax > problem. > Using this set of commands returns an image that looks great in stereo, > but is > only 640X480 (default window size) Currently you're ray tracing twice... > ray 2000,2000 > ray angle=-3 should be ray 2000,20

RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)

> Two more questions: > Does the 'pymol -qc' takes command line variables (os.argv in python)? > For example, the first line of my script would be: > cmd.do('load %s' %os.argv[1]) That's not possible. In order to get this behavior (for now) you need to treat PyMOL as a module (see below). > Seco

RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)

n -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Shu-

RE: [PyMOL] Alpha channel support gone?

Jean, Did you set ray_opaque_background, 0 ? Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourcefor

RE: [PyMOL] slow ray-tracing since updating to 10.2.8 (mac os x)

Wataru, Yes, Apple's 10.2.7 and 10.2.8 broke auto-detection of the second processor. To fix this, manually set max_threads, 2 before ray tracing. The next release will fix the problem... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Prin

RE: [PyMOL] Pymol script screenplay

ixels, etc. Typically each ray-tracing scene will have a different optimum, but usually 140-180 gives the shortest overall rendering times. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650

RE: [PyMOL] why is PyMOL renaming my residues?

ed for amino acids, so in theory "OA22" would be legal for a non-amino acid, whereas "2OA2" is required if the residue is an amino acid. What a mess! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] Pymol script screenplay

-o mvc1ec2.avi -ovc lavc -lavcopts > vcodec=mpeg4:vbitrate=6000:vhq:keyint=30") Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message--

RE: [PyMOL] why is PyMOL renaming my residues?

Z NAP 164 30.554 66.174 18.275 0.00 1.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O Which is as close as I think PyMOL is going to get... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] drawing the surface correctly

Michael, Thanks for your question. flag ignore, atom-selection, set rebuild Will enable you to remove the surface from selected atoms. For example: show surface flag ignore, resn wat or resi 150, set rebuild Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

RE: [PyMOL] access space group and cell dimensions of stored molecules

capitalized, but the filename should be all lowercase. For example: pymol/modules/wizard/mywiz.py containing class Mywiz(Wizard): ... should work. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax

[PyMOL] RE:

0, 5.0, 6.0, # XYZ 2 2.0,# Radius 1.0, 1.0, 1.0, # RGB Color 1 1.0, 1.0, 1.0, # RGB Color 2 1, 1, # End caps (0=none, 1=flat, 2=round) ] ) cmd.load_cgo(obj,'my_cgo') Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Princi

RE: [PyMOL] two_sided_lighting

Meitian, Sorry, this is not possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourcefor

RE: [PyMOL] modifying atom coordinates

valent scaffold of peptides and arbitrary small molecules, but it knows nothing about forces and energies. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message-

RE: [PyMOL] bug in rpm?

Nat, Are you running stock RedHat 9.0? The threading library in RH90 is broke. You may need to apply the glibc patches released by RedHat in order to get a stable system. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650

RE: [PyMOL] getting color of a residue + selecting non-natural residues

Tina, > I have two operations that I want to perform, and am not aware of a simple > way > (if possible) of doing them. So here it goes: > > 1. how (if possible) to retrieve the color for a residue as identified in > an > expression, e.g. "resi 9"? Note that it's not a range so no multiple > answ

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