[PyMOL] Using Python 3.4.3 Shell

amed 'pymol' I would very appreciate your help. -- *Tom Aharoni* *PhD student @ Tel Aviv Uni.* *kuwari.tau.ac.il/Home.html <http://kuwari.tau.ac.il/Home.html>* -- Presto, an open source distributed SQL quer

[PyMOL] Plotting a rectangle to show clipping slab

/pictures/2003/frimanThesis03/frimanThesis03.png ' ). I have searched for the last few days and cannot seem to find anything simple to do this task. Does anyone know if there is a small script somewhere that can plot a 'plane' as defined by the clipping slab? Cheers, Tom -- *Thomas J Carruthers

[PyMOL] Loading multiple ligands into a single view

Hello all, I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains multiple ligands. I'd like to open this one file and see them all at once. It currently loads each ligand into its own state. Is there a way to over-ride this behaviour? Tom

Re: [PyMOL] Moveable Camera

. Is there a way to turn the look at vector x degrees horizontal and y degrees vertical? Tom -Original Message- From: Bard, Joel [mailto:joel.b...@pfizer.com] Sent: Wednesday, 12 May 2010 11:38 PM To: Tom Dupree; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Moveable Camera Tom- Take

[PyMOL] algorithm for surface calculation?

Hi all, Anyone know which algorithm PyMOL uses to calculate the surface representation of a molecule? Thanks, Tom Tullius

[PyMOL] Real Time movie making

Hi, I hoping to get into the molecular movie making business, and I'm wondering whether, rather than specifying each movement of an object, PYMOL can record object movements that are created using the mouse and/or keyboard. Thanks, Tom Leyh Professor of Biochemistry

[PyMOL] moving objects freely

From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a simple, intuitive way to do this? Thank a lot, Tom Leyh Professor

[PyMOL] installation on FC2

: *** [python] Error 2 What is wrong here? Tom Lee

[PyMOL] problem in installation

of Python. Anyway, I reinstalled Python again, but it doesn't help. Does anyone have this problem? Tom Lee

[PyMOL] set commands

Can someone point me to a list of the current set commands with explanations. -TIA -Tom -- __ Tom Thompson, Ph.D.PH 847-467-4049 Northwestern University 2205 Tech Drive Evanston IL 60208-0001

[PyMOL] Zoom Movies in pymol and record

I was wondering how one would go about making frames that shows a simple zoom. Also is there a feature that allows you to manually manipulate the model and push this to a movie. If not I think this would be a great feature for those who don't have python coding experience. -Tom

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

this is to run util.ss but this can be slow if you have a lot of structures. Is there a way in the API to tell whether a PDB file you've loaded contains secondary structure records, so that you can avoid an unnecessary call to util.ss? Tom Walsh

[PyMOL] Applying a rotation matrix to coordinates

Hi, I want to superimpose two structures using a translation vector and rotation matrix. Is the transform_object() function the best way to do this? Thanks, Tom Walsh

[PyMOL] show spheres

Hi, I have iron atoms in the ligand. When I ask PyMol to show spheres of the ligand, the iron atoms don't show up. Is it because the radius for iron hasn't been defined? If so, how can I define it? Tom Lee