[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

[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

[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] 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

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

[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

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

[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: PyMOLshow sticks, //mod1//10/ ex. that fails: PyMOLshow sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 i; :4 )-- I found this post on the

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

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 it a shot here

[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] 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

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] 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

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. 21, 31, etc.) using a for

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:

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

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

[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

[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)

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

[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

Re: [PyMOL] putty/sausage NMR figure

, 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 Kojetin Sent: Tuesday

[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] 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.comforum_name=pymol-users ) How can a cartoon cylinder diagram be displayed for a

[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

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

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 3:36 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I would like to set

[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