Hello PyMOL users,
As suggested by Warren, i have made some improvements to the ScriptBox,
which should integrate better into PyMOL now,
I have written a small program that lets you select your favorite PyMOL
script from a comfortable box floating beside your PyMOL window.
The URL is
OK, heres what we've got:
The DSSP program is available for Linux and Windows from
http://www.cmbi.kun.nl/swift/dssp/ .
I have written a Python script that parses the output of DSSP and alters
the annotation in PyMOL. You just start the script, then You have a
dssp object
command available.
Dear fellows,
We would like to present some effort we have made to integrate some
structure analysis tools into PyMOL. I won't go into detail much, feel
free to test it out.
Additionally, i have written a script that provides PyMOL commands
making creation of smooth animations fairly easy.
Fei Xu wrote:
HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?
Dear Fei Xu:
1. You select an atom
2. You display it as a ball
3. You type:
set sphere_scale = 2.0
Here, the number is the size proportional to an
Hi David,
try this:
http://www.rubor.de/bioinf/pymol_tips.html#getcoord
Kristian
David wrote:
Hi,
How do I access the objects I load from files (e.g. pdb file) directly
(i.e. in a script)? If I want to print the coordinates of an atom, or
the value of at a point in the electron density
,Z, thickness, unknown, color
pos1 xyz, pos2 xyz, thick, start_color R,G,B, end_color R,G,B]
Happy New Year!
Kristian Rother
have been fixed
already. Particularly, installation under Windows is still a little
eXPerience.
Kristian Rother
and
distribute the source code, as long as the original notices are kept in.
We hope this program will serve You well,
Kristian Rother and Christoph Gille
Institute of Biochemistry
Humboldt University Berlin
import java.util.zip.*;
import java.io.*;
import java.util.*;
/**
Name:Pymol.java
Purpose
sphere_transparency,0.2,c1
Setting: sphere_transparency set to 0.2 in object 'c1'.
PyMOLset sphere_transparency,0.8,c2
Setting: sphere_transparency set to 0.8 in object 'c2'.
PyMOLrebuild
Kristian Rother
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dunno
7)
also.
Good luck,
Kristian Rother
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Hello PyMOL users,
the collection of tips and examples from this mailing list has been
updated. I also broke up the FAQ page because it has grown too large.
the location is unchanged on
http://www.rubor.de/bioinf/
Yours,
Kristian Rother
.
- access to the PDB from PyMOL.
- integration of external applications (DSSP, PASS, HBExplore, calc-surface)
- commands for easier creation of animations
As rTools is not really mature, i still like to hear of bugs in it
(kristian.rot...@charite.de).
Yours,
Kristian Rother
Protein Structure Theory
Hello,
There is a script which accesses a PDB server to get the weekly update
lists of PDB structures. It downloads the new and modified structures
and can be run as a cronjob under Linux.
The script is freely accessible from http://www.rubor.de/bioinf/
Cheers,
Kristian Rother
Dear Tony,
You can get quite far with the mvCmd command. The parser will get
confused if you issue complex commands that way, but there are workarounds.
Example:
You want to rotate one chain only over some movie frames.
Step 1) write a rotate.pml script, containing:
rotate x,5,chain A
Step
Dear Christian,
Summary:
From within the same PyMOL instance, the command
pdb 1n1m
works, but the script
from pymol import cmd
time.sleep(1)
list = ('1n1m')
for strc in list:
pdb strc
does not.
(IMO, the import is not necessary here).
Analysis:
You use the code above as a PyMOL .pml
. However, it's far away from being a wiki. Neither it is complete
in any way.
http://www.rubor.de/bioinf/pymol_tips.html
Yours,
Kristian Rother
Humboldt Universität Berlin
. Users will add things where aproppriate, anyway.
Thus, in a heavily used Wiki its definitely easy to get lost.
my 2cents.
Kristian Rother
Charite - Medical University of Berlin
,
Kristian Rother
Charite - Universitätsmedizin Berlin
Dear PyMOL users,
there will be a PyMOL training in the area of Berlin,
Germany, soon. It is scheduled for October 19th, 15.00
at the beamlines of the BESSY II synchrotron.
Please contact me for details.
Kristian Rother
Charite - Universitaetsmedizin Berlin
kristian.rot
--- Chung-Ming Yu yucm...@gate.sinica.edu.tw wrote:
Dear all:
I changed the topology of secondary structures with
'alter' commands and then
I used 'rebuild' command to show the new topology of
secondary structures in
multiple structura alignment. I pointed out three
structures for
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