Re: [PyMOL] Leap Motion

Hi Tsjerk, unfortunately I can't answer your question, but my former lab has done some work with the leap motion to control molecular graphics that you might find useful (not PyMOL though): video: https://www.youtube.com/watch?v=XU_6TWM9ke8 paper:

Re: [PyMOL] Active site in Pymol

Hi, you can use the Measurement Wizard to get distances between atoms. PyMOL will also print the residue type in the console if you click on any atom. Best, Julian On Tue, Aug 23, 2016 at 8:45 AM Farzaneh Namazifar < f.namazifar706...@gmail.com> wrote: > Hi Dear all; > I am a PyMol user. I

Re: [PyMOL] error message for forster resonance calcualtor

Hi Andina, did you try to run 'import Forster_distance_calculator.py' from the Pymol command line? Have you tried to do 'run Forster_distance_calculator.py' instead, then 'forster ...' ? Cheers, Julian On Mon, Sep 19, 2016 at 9:52 AM Andina Diana wrote: > Hello

Re: [PyMOL] Pymol Command window not displaying

Hi, are you trying to run PyMOL remotely, i.e. via ssh from your cluster? This might work if you forward X11 to your local machine, though I'm not sure if it supports OpenGL. Looking at the error message, another possibility might be a missing tcl/tk library? Good luck, Julian On Tue, Sep 20,

Re: [PyMOL] What's wrong with my pymol script?

Hi, adding a 'refresh' (http://www.pymolwiki.org/index.php/Refresh) seems to work: ``` from pymol import cmd cmd.fetch('1nmr', async=0) for i in range(1, cmd.count_states()+1): cmd.set("state", i) cmd.png("%d.png" % (i), width=1000, height=1000, dpi=300) cmd.refresh() ``` On

Re: [PyMOL] difficulty using Python scripts in PyMOL

Hi Mohsen, I'm a Mac user and haven't installed PyMOL on Windows lately, but have you tried following the installation instructions on the Wiki: http://www.pymolwiki.org/index.php/Windows_Install ? Cheers, Julian On Sun, Jul 31, 2016 at 5:28 PM Mohsen Chitsaz < mohsen.chit...@flinders.edu.au>

Re: [PyMOL] Finding the surface residues using code

Dear Leila, you can download the respective script using the link shown on the top right of the wiki page: https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/findSurfaceResidues.py Run this script in PyMOL by invoking 'run findSurfaceResidues.py' (using the path you downloaded the

Re: [PyMOL] Help Download structural alignment

Hi Clarisa, you can save an alignment using the create and save commands, e.g.: fetch 1oky 1t46, async=0 as ribbon align 1oky, 1t46 create aligned, all save aligned.pdb, aligned You can also save the alignment in clustalw format, see http://pymolwiki.org/index.php/Align. I hope this is what

Re: [PyMOL] Getting Started

Hi Melanie, have you gone through the 'movie school' ( http://www.pymolwiki.org/index.php/MovieSchool) ? I know that biomedical animators also like to work with the molecular flipbook (https://www.molecularflipbook.org/) or bioblender ( http://www.bioblender.eu/). Cheers, Julian On Wed, Jun 8,

Re: [PyMOL] Run pymol from source or compile?

Hi Martin, you need to compile PyMOL in order to see effects of code changes. The installation instructions on the wiki include some information on how to compile PyMOL from source. Cheers, Julian On Tue, May 24, 2016 at 7:54 PM Martin

Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

Hi, in case you haven't solved this yet, the following command prints the residue number and secondary structure: iterate n. CA, print resi + ':' + ss Cheers, Julian On Fri, May 13, 2016 at 10:40 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear PyMol friends, > I would like to export the

Re: [PyMOL] Color coded script

Hi, are you referring to the code examples? I think the coloring scheme is just a source code syntax highlighting, where all strings for example are in red, comments are in green, and functions are blue. Cheers, Julian On Tue, Nov 10, 2015 at 3:15 PM, wrote: > Hi, > >

Re: [PyMOL] Current and up to date manual

Yes, the Wiki is the most current manual for non-subscribers, though it is community driven and therefore not always up to date. If you point me to outdated pages I'll try to fix them ASAP. Cheers Julian On Sun, 8 May 2016, 00:09 Martin Hediger, wrote: > I found this manual

Re: [PyMOL] different distance calculated for same atoms

Hi You're passing more than one atom per selection to the cmd.distance() function, in which case the function returns the average between the measured distances (http://pymolwiki.org/index.php/Distance#PYMOL_API ). On a side note, this could be done much simpler: fetch 2nuz, async=0 h_add resn

Re: [PyMOL] Appending a pdb file

Hi Mohsen, if you want to superimpose structures, have a look at the align command: http://pymolwiki.org/index.php/Align Cheers, Julian On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi > > > > In order to superimpose two protein sequences, I am

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Hi all, translate does seem to work with CGOs if you use named arguments (note the 'object=' in the argument list): cmd.translate([x,y,z], object='membrane') Here's an example that you can copy and paste into pymol: --- python from pymol.cgo import * from pymol import cmd from

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Hi Annemarie, Have you tried the following? cmd.translate([x,y,z], object='membrane') replace x,y,z with your translation vector. Cheers, Julian On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie wrote: > I am trying to show some cell surface receptors and to indicate

Re: [PyMOL] superimposition of 2 ligand molecules

Hi, have a look at the 'align' command: http://pymolwiki.org/index.php/Align Best, Julian On Thu, Jan 28, 2016 at 7:13 AM, leila karami wrote: > Dear pymol users, > > I have 2 ligand molecules having similar backbone. There is little > difference between them. When I

Re: [PyMOL] on PDB display and calculation

Hi Smith, are you looking to visualize symmetrie axes? Then this might be a starting point: http://www.pymolwiki.org/index.php/SuperSym Cheers, Julian On Mon, Nov 23, 2015 at 4:15 PM, Smith Liu wrote: > Dear All, > > Once I have displayed a tetramer PDB by pymol, is any

Re: [PyMOL] on coloring residues based on residue conservation

Hi Smith, if you have a value for the conservation for each residue, you can use the spectrum command as described here: http://www.pymolwiki.org/index.php/Spectrum to color residues by that value. In the 'intermediate' example, replace newB with your value for conservation. Hope this helps.