RE: [PyMOL] nmr ensemble alignment

...@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 Douglas Kojetin Sent: Monday, January

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

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-ad...@lists.sourceforge.net [mailto:pymol-users

RE: [PyMOL] Ray Tracing Crash

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 (650)-346-1154 Fax

RE: [PyMOL] Ray Tracing Crash

...@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 Matt Franklin Sent: Tuesday, January 20

RE: [PyMOL] homologous alignments?

, 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.sourceforge.net

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.com Warren L

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 L. DeLano, Ph.D

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

-- 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 Steven F. Killen

[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-users-ad...@lists.sourceforge.net

RE: [PyMOL] Display of electrostatic potential surfaces

, 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 Roger Dodd

[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] unsetting cartoon_colors

...@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: Thursday

[PyMOL] RE: Stereo on G4 Laptop?

/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 (650)-593-4020 -Original

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

...@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 Michal Bozon Sent: Saturday, December 13

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

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 Scientific LLC Voice (650)-346-1154

RE: [PyMOL] assign secondary structure?

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-users- ad...@lists.sourceforge.net

RE: [PyMOL] electron density settings

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 Scientist DeLano Scientific

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

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

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)-593-4020

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

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] Object orientation matrices

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 Pearl Sent: Tuesday, December 02, 2003 5

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, December 02

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

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] Viewing homotetramers with PyMol

, 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-users- ad

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

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 [mailto:pymol-users

RE: [PyMOL] detecting the existence of a selection

...@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 Tina Li Sent: Monday, December 01, 2003 11

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

-- 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

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, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

[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 screen or

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

RE: [PyMOL] surface area calculation

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 DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From

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] DSSP

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. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original

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

. 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] labeling atoms in GUI

...@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 rbax...@uchicago.edu Sent

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.sourceforge.net] On Behalf

[PyMOL] RE: Writing info to files

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

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-users-ad

RE: [PyMOL] solvent accesible 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...@lists.sourceforge.net

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

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)-346-1154 Fax (650)-593-4020 -Original

[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

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

-- 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, October 17, 2003 3:18 PM

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

...@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 Paulo Lai Sent: Tuesday

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: Robert

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] 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)-346-1154 Fax

[PyMOL] 2004 PyMOL Budget Reminder

://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] Using PyMol as a library - no GUI

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 Voice (650)-346-1154 Fax (650)-593

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+h

RE: [PyMOL] Underside of surface color

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: Friday, October 10, 2003

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

Shu-hsien Sure, instead of cmd.select, use cmd.do(select ligand, resn XYZ) cmd.do(select protein, ! ligand ) etc. ./pymol -qc select_box.py Is the command line mode of PyMOL. pymol -qc can be used like python in most cases. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L

RE: [PyMOL] Pymol script screenplay

. 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)-593-4020

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

...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 Also note that by some conventions, 2OA2 in a PDB file really means atom OA22. I didn't know that. What conventions are those? Furthermore, in your example

RE: [PyMOL] Pymol script screenplay

-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- From: pymol-users-ad

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

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 Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users

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.sourceforge.net

[PyMOL] RE:

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. Principal Scientist DeLano Scientific

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 answers is

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] modifying atom coordinates

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- From: pymol

RE: [PyMOL] negative images

), a copy of the problematic PNG file. Thanks, 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

RE: [PyMOL] A couple of movie questions

First up: Is there any way to tell PyMol *not* to change its view when loading a PDB file set auto_zoom,0 Secondly: Below is an example of a small hack I have written when making one particular movie. This one overlays two molecules related by a 2-fold axis by doing a simple rotation.

RE: [PyMOL] alternative method for loading coordinates

_cmd isn't meant to be called by anyone except PyMOL. 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

RE: [PyMOL] modifying atom coordinates

by unpickling them in a Python interpreter. 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

RE: [PyMOL] Transparent cartoons?

visual artifacts will occur with standard OpenGL rendering. If you're on a PC, then you'll need to wait for the next big release, which will probably happen next week. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] pymol raytracing crash

Thomas, I tried running your script on the current development version and on a version 0.90 binary, and wasn't able to get PyMOL to crash. How is PyMOL installed on your system? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal

RE: [PyMOL] individual surfaces?

...@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 Dirk Kostrewa Sent: Monday

RE: [PyMOL] incorporation of unusual amino acids

Uwe, We plan a research project where we want to stepwise incorporate D-amino acids into a peptide. To determine the exchanges it would be very useful if PyMol could assist. If I might dream I would like to have D-amino acids (and maybe other un- usual amino acids) available in the

[PyMOL] PyMOL for Mac G5, with Demos

computer for research -- Apple's first in a long time, and hopefully more will come if we appropriately reward this one with our business. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC

RE: [PyMOL] adding a new external GUI

menu, which then creates it's own window in response to user requests. 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] Filled view for deoxyribose rings, bases in DNA ???

Raji, Sorry, PyMOL can't do that yet. However, since you are probably the 10th person to ask for this, so it has become high priority for a future version... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice

RE: [PyMOL] Re: cannot find _cmd module

. 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 Behalf

RE: [PyMOL] Python commands and variables

Yes, but you need to write in Python directly. For example: from pymol import cmd cmd.select(mysel,none) for i in range(10,20): cmd.select(mysel,mysel or resi %d%i) Would work in a .py file. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] linker errors on win32?

Tina, layer0/MemoryCache.c is missing from the list of sources in the setup.py file. If you add that in right after the layer0/MemoryDebug.c, it should build. Sorry about that! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

[PyMOL] RE: E-mail worm is going around

Jan, Thanks for that -- copy hereby sent to the PyMOL list. This is a relief. I was wondering why strange bounced email was coming back and had become concerned that infection had occurred here despite every precaution. SMTP-based email is indeed a hopeless cause. I vote

RE: [PyMOL] Pymol 3D printing

Thanks for your code! P.S. I wish this mailing list had archives ... But it does! http://sourceforge.net/mailarchive/forum.php?forum_id=60 You can search by keyword. Look for the text box upper-left. Cheers, Warren

RE: [PyMOL] Different symmetry positions

slightly. Are you finding otherwise? 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

RE: [PyMOL] Delete Bonds

Jose, Select the bond using Ctrl-right-click, then either unbond pk1,pk2 or hit Ctrl-D. 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] strand representation + free label

Tina, That would be very difficult to do at present...I'll take this as a suggestion for a future version. 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] cartoons through nonstandard residues

of PyMOL should not suffer from this problem. alter all.type='ATOM' alter name P,name='P1' sort Thanks for your help in quashing that bug! 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] electrostatic potential ramp

If I understand the question correctly, the answer is disable ramp-name Cheers, Warren Hello: Is there anyway to remove the colour ramp from an electrostatic potential figure via a script (help hide doesn't list anything reasonable for this and there is nothing that I can see in the

RE: [PyMOL] cartoons through nonstandard residues

David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type='ATOM' sort rebuild I'm thinking about disabling this behavior before the next release. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

RE: [PyMOL] cartoons through nonstandard residues

David, The problem: PyMOL sorts PDB hetatms apart from molecules. The solution: alter all, type=’ATOM’ sort rebuild I’m thinking about disabling this behavior before the next release… Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano

[PyMOL] Upcoming Rendering Changes. Comments?

can be restored by changing two settings (ray_oversample_cutoff-0 and antialias-0 or 2). If you have strong objections to these changes, please speak up. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154

RE: [PyMOL] comprehensive rules for selection-expressions

someone explain what the different elems CHNOS* represent? I'd really appreciate more comprehensive documentation. That's just the coloring for Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur, in the color pop-up menu. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

RE: [PyMOL] H-bond display

Gareth, CGO is currently the way to go... 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

[PyMOL] 0.90 Two Minor Bug Advisories

. Today I also added support for InsightII's ascii/formatted grid file (just in case anyone has some old Biosym GRD files lying around...). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

RE: [PyMOL] Interaction surfaces

...) -- 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 Becker, Joseph W Sent

[PyMOL] New Map Formats Coming...

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

RE: [PyMOL] pymol on OSX

John, The native OSX port is incomplete with respect to the user interface. You can get the complete package if you use the Fink version under X11. PyMOL doesn't export 3D data well at present. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D

RE: [PyMOL] Electrostatic potential maps in PyMOL

with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the enddian-ness of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific

RE: [PyMOL] ca trace

Jason, In version 0.90, there is a ribbon_trace setting which allows you to do this for the ribbon representation. In versions 0.91+, I've added the same thing for cartoons cartoon_trace. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

[PyMOL] RE: (no subject)

I just download PYMOL into my Linux and it's working very nicely but I want to check whether it is possible to move a pdb file within a 3D density map independently to get a best fitting. Yes, you can move the molecule, but not the map. First, get into editing mode: edit_mode (or select

RE: [PyMOL] Further functionality

1- calculation of surface potentials- will this be coming soon? Creation of a Possion-Boltzman solver is a bit of work, so this will not happen very soon -- probably not until we accumulate enough sponsorship to contract with someone to perform the task. But perhaps someone might volunteer to

RE: [PyMOL] can't initialize module sglite

this helps. 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

RE: [PyMOL] stereo parameters?

. For hardware or cross-eye, set stereo_shift, 4 For walleye, set stereo_angle, 1.95 set stereo_shift, 4 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 v0.90 Released

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

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