[PyMOL] Creating separate objects from a starting structure

show sticks,three This works very well. Maybe a wizard could be created to automatically split a structure into separate objects for the different chains? -- Lieven Buts Vrije Universiteit Brussel

Re: [PyMOL] Babel and File Format Conversion

://openbabel.sourceforge.net/. -- Lieven Buts Brussels Free University

Re: [PyMOL] molecular sculpting

try the sculpting demo in the Demo menu. You can then just drag atoms by left-clicking them while holding down the control key. The dragged atom moves, everything it is connected to is dragged along, and the structure tries to minimize its energy. Great fun! -- Lieven Buts Department

Re: [PyMOL] molecular sculpting

or intuitive way of manipulating the model than moving individual atoms or turning torsion angles. -- Lieven Buts Brussels Free University

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

) and slate). -- Lieven Buts Brussels Free University

Re: [PyMOL] color choices

whatever, ... -- Lieven Buts Department of Ultrastructure

Re: [PyMOL] you know what would be cool?

or so) and acos(cosom) fails. Also, omega and sinom become zero in this case, so the divisions by sinom fail. I added some checks to normalize this situation and stop the code from crashing, but we should look into what's causing this. -- Lieven Buts Department of Ultrastructure Vrije

Re: [PyMOL] Selecting a lot of residues

around the complete expression. This can be executed in PyMol by typing @list.pml and should select the indicated residues in the molecule protein. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Selecting a lot of residues

) which can be copied/pasted into PyMol, or read from the file with @list.pml. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] make cartoon from carbon atom trace?

wishes to all for 2004, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] H-bonds

(available at http://www.rubor.de/bioinf/pymol_rubor.html ) provide an interface to the HBExplore program at http://www.imb-jena.de/www_bioc/hbx/hbx.html. See the rTools documentation for more details. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Select Atom Change View

) for example). There are many abbreviations for long selections. Type help selections for more information. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] restoring default surface coloring

and set the carbon atoms to green. There's cbag for color by atom type, carbons green, cbaw for white carbons, cbay for yellow carbons and so on. Alternatively, you can use the color menu in the internal GUI. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit

Re: [PyMOL] Question about surface calculation

objects to generate exactly the surfaces you want. Cheers, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

LDFLAGS=${LDFLAGS} -L/usr/local/lib/i686-pc-linux instead. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Cavity display?

and got a surface picture of my cavities within literally a few minutes, as Lari already wrote. The rTools (http://www.rubor.de/bioinf/pymol_rubor.html) also contain a fucntion to interface PASS with PyMOL. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] unit cell

and/or change the clipping planes to show all of the unit cell. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] transformation matrix

the transformation matrices from the Dali report file. If someone has a way to use this matrix in PyMol, we'd be set: #!/usr/bin/env python # Script to extract 3x4 transformation matrices from Dali report files # Lieven Buts, 22-Oct-2004 import re,sys dali = open(sys.argv[1],r) pattern = re.compile(r

Re: [PyMOL] ribbon view of c-alpha only coordinates

with lines. Try set ribbon_trace,1. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel