[PyMOL] cylinder fuzzy color when ray traced

Hi All, I am trying to highlight a specific residue (black color) in a helix (orange color) displayed in cylinder mode. When I perform ray tracing, the black region becomes a fuzzy gradient on the ends. Is there a ray tracing setting to make a crisp, sharp transition from orange to black to o

Re: [PyMOL] Ca sphere size from b-factor value

> # fetch a protein > > fetch 1ejg, async=0 > > # show as spheres > > as spheres, n. CA > > # set the vdw radii = some factor of the b-factor > > alter n. CA, vdw=b/5 > > rebuild > > Cheers, > > -- Jason > > On Tue, Jul 31, 2012 at 3:3

[PyMOL] Ca sphere size from b-factor value

Hi All, I would like to set the sphere size for each Ca atom proportional to the b-factor value (the larger the b-factor the larger the sphere size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug

[PyMOL] c-alpha only model & show cartoon

Hi All, ( I am unable to search the PyMOL mailing list archives for this question, per this message: http://sourceforge.net/mailarchive/forum.php?thread_name=200807281639.m6SGcvAe006759%40apollo.hosting4less.com&forum_name=pymol-users ) How can a cartoon cylinder diagram be displayed for a

[PyMOL] distorted electrostatic surface color with PyMOL/APBS

Hi All, I am having some problems with surface display of the output from the APBS plugin distributed with PyMOL (version 1.1r0) using the "color by potential on sol. acc. surf." option. Steps to reproduce the problem: 1. Load in a structure. 2. Perform the APBS calculation (execute "Set

[PyMOL] cmd.distance

Hi All, What are the various options for the variable 'mode' when using cmd.distance? Thanks, Doug

[PyMOL] alignment in pymol

Hi All- If I have a protein with 150 residues (three 50 residue repeats; 1-50, 51-100, 101-150), and I want to align the first 100 residues (resi 1-100) to the last 100 (51-150) ... and try to run the following commands: load structure.pdb create s1, resi 1-100 and structure create s2, re

Re: [PyMOL] putty/sausage NMR figure

pymol, and voila. If the effect isn't enough, you could always multiply your RMS values by some value (eg. 10). Good luck! JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojeti

[PyMOL] putty/sausage NMR figure

Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage

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

Hi Warren- Thanks for the reply. Fink adds /sw/lib to the beginning of the DYLD_LIBRARY_PATH. Adding the following to the beginning of the shell script fixed the problem: DYLD_LIBRARY_PATH=/usr/local/lib Thanks, Doug On Jun 10, 2005, at 2:11 PM, Warren DeLano wrote: Doug, I can'

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

Hi All- I've been using a shell script called 'macpymol' to start PyMOL from the command line under OS X (pre-Tiger): #!/bin/sh /Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL $* usage: macpymol file.pdb I noticed if I use Fink to install an application under OS X (Tiger) t

[PyMOL] atom selection: wildcard

Hi All- Is it possible to select all oxygen atoms (backbone & sidechain) with a command similar to the following: select oxy, name o* I cannot seem to get any variation of that to work without specifying all atoms (e.g. o+oe1+oe2) Thanks, Doug

Re: [PyMOL] Getting Closer to Wiki Time!

While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? Doug

Re: [PyMOL] Getting Closer to Wiki Time!

Unless I've missed the documentation pages before, with respect to python integration: 1. When to use '@script.py' vs. 'run script.py' (I know this now, but others starting out may not) 2. List of all cmd.xxx() options. I've encountered a few pymol commands where cmd.xxx() is not support, b

Re: [PyMOL] Getting Closer to Wiki Time!

Another potentially useful category: Plugin/Modules --> ex. Michael George Lerner's APBS plugin --> other existing and future plugins This would make it easy for others to contribute tips/explanations/experiences/etc. to these extremely useful add-ons. On Feb 15, 2005, at 1:11 PM, Warren De

Re: [PyMOL] Getting Closer to Wiki Time!

Although the section may be small to begin, I'd like to see (and will hopefully contribute to in the future) a section about 'NMR Applications'. Thanks, Doug On Feb 15, 2005, at 1:11 PM, Warren DeLano wrote: - Crystallography Aplications - Symmetry - Electron Density

[PyMOL] pymol & apbs

I just download & compiled apbs on a G4 using the instructions found here: http://www.chemistry.ucsc.edu/~wgscott/xtal/programs.html (although I had to modify the fink files slightly, it was a relatively painless installation) Many thanks for the apbs_tools plugin -- very cool! Is there any

Re: [PyMOL] effect of number of pixels on ray image quality

Building on the two previous posts, is it necessary to use 'viewport' before executing 'ray'? this: ray 2000, 2000 instead of: viewport 700, 700 ray 2000, 2000 Thanks, Doug On Jan 20, 2005, at 10:11 AM, Ezequiel H Panepucci wrote: - so you should execute the command: vi

Re: [PyMOL] selection help + align question

Thanks for that one; it works as advertised. Another question: if I have 10 different structures read into PyMOL, what is the best (most accurate) method for aligning the structures as an ensemble? Currently, I'm aligning all to the first structure read in (i.e. 2>1, 3>1, etc.) using a for l

[PyMOL] selection help

Hi All- I'm having some problems with selection syntax w/ multiple objects. I've loaded four different PDB files (in sequence & structure): load 1.pdb, a1 load 2.pdb, a2 load 3.pdb, b1 load 4.pdb, b2 I wanted to create two new selections: one = a1 & a2 two = b1 & b2 I've

Re: [PyMOL] pymol crashes with very large structures?

I didn't keep track of how long it took (and it took a while), but I was able to successfully run the following commands under OS X using MacPymol 0.95 on a machine w/ 1.5GB RAM. load 1JJ2.pdb hide all show surface Doug On Jan 9, 2005, at 1:45 PM, Wulf Dirk Leuschner wrote: I use an AMD 2

Re: [PyMOL] Need Feedback & Testing: 0.98 beta 17

Is it possible to make this an option by means of a switch? i.e. set mouse_toggle=0 (or 1) Or manually configure each click-and-release? I see how it could be useful, however I often double click the left mouse button randomly when ... thinking ... and in this beta release I accidentally invo

Re: [PyMOL] Coloring gradient

Will this work for what you want to do? spectrum palette=green_yellow Dear All, I'm trying to color a protein cartoon structure from N- to C-terminal with a green to yellow gradient. Had a browse around and couldn't quite find the correct command. Any pointers are welcomed. Peter

Re: [PyMOL] transparent background

Works perfectly. Many thanks. If anyone has any strong arguments for Apple's Keynote over MS's Powerpoint, I'd be interested in hearing them (off list or on). Thanks again, Doug On Aug 12, 2004, at 12:11 PM, Cartailler, Jean-Philippe wrote: Set the ray_opaque_background to off The PNG fi

[PyMOL] transparent background

Hi All- Is it possible to create an image in PyMOL with a transparent background (without having to feed it through a second program, such as the ImageMagick suite)? rant: MS PowerPoint has the ability to make images transparent, however Apple's Keynote does not -- a missing feature that's

Re: [PyMOL] A couple of quick PyMOL + APBS notes

APBS using fink g77, that will be great. Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Jul 15, 2004, at 6:52 PM, Douglas Kojetin wrote: (this might be better suited on an APBS list, but i figured i'd give

Re: [PyMOL] A couple of quick PyMOL + APBS notes

(this might be better suited on an APBS list, but i figured i'd give it a shot here) I downloaded the Mac APBS binary, but I'm seeing this error when trying to run it: % ./apbs-0.3.1-g4 dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib (No such file or directory, errno

[PyMOL] selection of residues with negative numbers

Hi All- I cannot make PyMOL make selections of residues with negative (sequence) numbers. Any quick way around this? ex. that works: PyMOL>show sticks, //mod1//10/ ex. that fails: PyMOL>show sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 & i; :4 )<-- I found this post on the m

Re: [PyMOL] Powermate dial with Pymol on OS X

A great many thanks for this -- I went out to the local Apple store and purchased a Powermate specifically for this - and it's awesome! Now I just need to work on programming it to interface with NMRView ... Doug On May 6, 2004, at 4:50 PM, William Scott wrote: Thanks, Ezequiel! That is e

[PyMOL] pymol locks up - unix pipe

Hi All- I'm using PyMOL through a UNIX pipe within a Tcl/Tk script interface. The script make calls to highlight certain residues, and it also uses the 'dist' command. After the script makes a a few calls (>20) to PyMOL, my PyMOL session usually locks up. Anyone know what might be going on

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

one other option. if you use ssh (instead of telnet) ... use the '-X' flag and there's no need use the xhost command: ssh -X u...@hostname see 'man ssh' for all options -- your server may need to be setup to use this specific switch. if you are under windows, you can check out 'cygwin' to

Re: [PyMOL] pymol x-windows version for Mac OS X

Works great! Many thanks! Doug On Feb 26, 2004, at 12:56 AM, wgsc...@chemistry.ucsc.edu wrote: Howdie, Citizens: Jack Howarth very kindly got a current version of X-windows pymol working on Mac OS X via fink. These files work for 10.3 and python 2.3, and he also has some that work with py

[PyMOL] cartoon transparency & a possible 'native' bug

[i'm sending again; it seems the pymol sourceforge list was down when i tried to send this] Hi All- In reference to this post: http://sourceforge.net/mailarchive/message.php?msg_id=6977122 When I gave PyMOL this command, I got the following error: Error: unknown setting 'cartoon_transparency'.

[PyMOL] cartoon transparency & a possible 'native' bug

Hi All- In reference to this post: http://sourceforge.net/mailarchive/message.php?msg_id=6977122 When I gave PyMOL this command, I got the following error: Error: unknown setting 'cartoon_transparency'. Is this setting only available on newer versions of PyMOL? If so, anyone working on a *new

[PyMOL] cartoon transparency & a possible 'native' bug

[trying a third time] Hi All- In reference to this post: http://sourceforge.net/mailarchive/message.php?msg_id=6977122 When I gave PyMOL this command, I got the following error: Error: unknown setting 'cartoon_transparency'. Is this setting only available on newer versions of PyMOL? If so, a

[PyMOL] nmr ensemble alignment

Hi All- Will reading in a structural ensemble load pdb01.pdb, ens load pdb02.pdb, ens ... ... automagically align the structures? If not, do I need to run another command, such as ' intra_fit (name ca) ' ? Or should I use normal 'fit'? Also, what is the best method for determining th

[PyMOL] Select Atom & Change View

Hi All- Is it possible to do the following through the command line ... --> select an atom (say the CA of residue 25) and bring the view of the molecule within PyMOL so that 25.CA is 'up front' (or closest to the viewer's point of view)? Thanks for the input, Doug

[PyMOL] pymol 0.93, fink & source compile issues (os x)

Hi All- It's be over a month since pymol 0.93 has been released ... anyone know when a Fink distribution will be available? Or how to do it manually (using Fink, without the main/online Fink database knowing about it)? I tried compiling the source manually, but I got an error similar to the

Re: [PyMOL] non-related question & related: electrostatics

mport, rendition, and coloring. (2) no clue Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Douglas Ko

[PyMOL] non-related question & related: electrostatics

Hi All- I'll ask my related question first: does anyone know if/when electrostatic calculations might be incorporated into pymol? Or if you can import calcs from another (hopefully free) program? Unrelated question: does anyone know of a secondary structure prediction program that outputs "