On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> from pymol import cmd
> file=open("file.nam")
> for i in file.readlines():
> cmd.load(i)
You may have to strip the trailing newline ("\n") from each file name by using
"cmd.load(i.strip())"
f.close()
The first line opens a file for writing (overwriting the existing file, if
any). The second line generates PDB ATOM records for all the atoms in the
selection "(object)". The thrird line appends an "END" record, and the fourth
line closes the file, ensuring
't
> connect them with lines.
Try "set ribbon_trace,1".
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
racts 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]
ven know whether you
spell it with an s or a c :-) ), but a good source of information seems to be
at http://creativecommons.org/ .
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
zoom out and/or change the clipping planes to
show all of the unit cell.
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
S, recommended by Lari 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
DFLAGS were empty before I
started. If they are not, you may have to use
export LDFLAGS="${LDFLAGS} -L/usr/local/lib/i686-pc-linux"
instead.
Hope this helps,
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
atoms can
be quickly selected with a command like
select dummies,(name QA,QB,QD,QD1,QD2,QE,QE2,QG, \
QG1,QG2,QH1,QH2,QQD,QQG,QR,QZ)
The atoms can then be deleted using the "remove atoms" command on the
"dummies" selection in the PyMOL menu.
--
Lieven Buts
Department of Ult
racing, but it would only be beneficial on systems with
very recent graphics boards.
[1] http://graphics.stanford.edu/projects/brookgpu/index.html
[2] http://www.gpgpu.org/
I'm sure there are much more details to consider, but I hope this is a start.
--
Lieven Buts
Department of Ultrastr
luded for surface
generation. You can also create separate objects to generate exactly the
surfaces you want.
Cheers,
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
bject")
(note the parentheses and quotes) to color the object by
atom type 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,
more specific
("zoom (protein and chain A and resi 25 and name CA)" for example). There are
many abbreviations for long selections. Type "help selections" for more
information.
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
re complete criteria. The rTools for PyMOL (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
o not appear to get connected.
Best wishes to all for 2004,
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
into a single-line PyMol command
select group,(protein and chain A and resi 5,10,50,51,52,100)
which can be copied/pasted into PyMol, or read from the file with "@list.pml".
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
n and resi 50) or \
(protein and resi 51) or \
(protein and resi 52) or \
(protein and resi 100) )
Note the additional parentheses 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
(PDB 103L). At
residue 139, cosom becomes slightly larger than 1 (1.0008 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
wh
that you can use
color whatever, ...
--
Lieven Buts
Department of Ultrastructure
nge. When I try "util.ss protein", the cartoon changes immediately.
What am I missing?
--
Lieven Buts
Department of Ultrastructure
;(arg and n;cb)","(arg and n;ca)")
cmd.torsion("2")
cmd.unpick()
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.feedback('ena','sel','res')
else:
cmd.delete("arg")
--
Lieven Buts
Department of Ultrastructure
Brussels Free University
int.
Could you provide some more details on this procedure. So far I have
only managed to include an icon/object in PowerPoint that starts PyMol
in an extra window (with a specified script).
--
Lieven Buts
Vrije Universiteit Brussel
, cyan, salmon, purple, pink,
white (hydrogen) and slate).
--
Lieven Buts
Brussels Free University
l there, as it allows for a more
"physical" or
"intuitive" way of manipulating the model than moving individual atoms
or turning
torsion angles.
--
Lieven Buts
Brussels Free University
x27;t know about the script or the wizard (yet), but I did 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
abel
project at <http://openbabel.sourceforge.net/>.
--
Lieven Buts
Brussels Free University
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
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