--- Chung-Ming Yu 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 further
> processing wit
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
As always, i'm curious about your comments, and probably, bug reports.
Cheers,
Kristian Rother
or.de/bioinf/pymol_tips.html
Yours,
Kristian Rother
Charite - Universitätsmedizin Berlin
everything grow by itself. 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
on problems on
my homepage. 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
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
.
Yours,
Kristian Rother
Humboldt Universität Berlin
--- Jacob Corn wrote:
> This is, unfortunately, not the case. For our
> installation, rtools
> already starts automatically (it's in the
> pmg_tk/startup directory).
> Adding "run /rtools.py" to the .pymo
Hello,
the old code of the scriptBox was converted into a modern PyMOL plugin,
hopefully eliminating all installation problems and stripping down code
size to 3 KB.
It is also available from
http://www.rubor.de/bioinf/pymol_extensions.html
Kristian Rother
,
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 2
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
reate obj1, (resi 431)
create obj2, (resi 440)
show surface, obj1
show surface, obj2
results in two separate surface objects.
Regards,
Kristian Rother
> However,
> either I get only the last surface displayed or a joined surface using the
> command examples below:
>
> this one g
case listing processes with ps shows an S
(stopped) instead of R (running).
In our application we used InputStream but should have
BufferedInputStream.
Yours,
Christoph Gille & Kristian Rother
revives after
terminating the process-object in java with destroy.
Has anyone seen something similar?
Greeting,
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
Am Donnerstag, 17. Juli 2003 23:05 schrieb Vajdos, Felix:
> Is there a way to append states to objects within pymol?
>
> Here's the scenario:
> Now, each animation is 50 frames (states) long, and runs fine. What I
> would like to do is at the end of each animation sequence to simply have
> the fin
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
the PMGApp.py
modification)?
When PyMOL starts up, do You get any error messages in the text screen? (press
ESC).
We are looking forward to help You,
Kristian Rother
erties
> as well) from withing a python script?
Yes. Look at:
http://www.rubor.de/bioinf/pymol_tips.html#getcoord
> 6)
dunno
> 7)
also.
Good luck,
Kristian Rother
__
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gt;set sphere_transparency,0.2,c1
Setting: sphere_transparency set to 0.2 in object 'c1'.
PyMOL>set sphere_transparency,0.8,c2
Setting: sphere_transparency set to 0.8 in object 'c2'.
PyMOL>rebuild
Kristian Rother
__
Do you
y 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
Pu
t - the program or my command?
The latter, of course :-)
select cont,(/molA//s/401 around 4.0 and molA)
or
select cont,(/molA//s/401 around 4.0 and chain s)
Kristian Rother
Dear Matt,
There is a straighter way to do it. Try just
pymol.com pymol_script.pml
(This works at least on my Linux machine).
You can also try
cat pymol_script.pml | pymol.com -p
or even
tail -f pymol_script.pml | pymol.com -p
The latter allows one to append lines to the pymol script from a
class for that). What is important is that a
cmd.extend(x,y) call should be called somewhere in the script, otherwise
Python thinks the data will be no longer used and calls the Garbage
Collection.
Kristian
> - Original Message -
> From: "Kristian Rother"
> To: &quo
Dear Mike,
You can at least do the following:
*** first call of command ***
- parse the file
- store the data in an object (dictionary, list, etc.) - you can probably
store the Strings that make up the CGO object.
- refine the data using the cutoff
- create CGO object from refined data
*** seco
release, although many bugs have been fixed
already. Particularly, installation under Windows is still a little
eXPerience.
Kristian Rother
[CYLINDER, start_position X,Y,Z,
end_position X,Y,Z, thickness, unknown, color
pos1 xyz, pos2 xyz, thick, start_color R,G,B, end_color R,G,B]
Happy New Year!
Kristian Rother
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 gr
Dear Rajarshi Guha,
You could at least try to reconfigure Robert Campbell's Color-by-B-factor
script. It assigns each atom its own color according to another value.
http://www.rubor.de/bioinf/pymol_tips.html#bfac
Kristian
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 origina
Hello all,
In case somebody is new to the mailing list and wonders what problems
have already been solved, it might be a good idea to take a look at:
http://www.rubor.de/bioinf/pymol_tips.html
which is basically a collection of examples for doing things with molecules.
I have compiled a lot o
active site fills out all the screen
move z,-200 # zoom out
move x,50# move a little to the side
# Now your molecule is ready to come to the scene:
show cartoon# make the molecule visible
mvClear
mvSinmove 1-100,x,-50
mvSinmove 1-100,z,200
mvCmd 101,mstop
movie
best wishes,
Kristian Rother
Dear Will,
You wrote:
The camera
movement I would like to do is a little more than simple rotations or
spirals, so it would be very helpful to me to be able to rotate about
an arbitrary vector, rather than just the principle axes, in mdo
commands. Is there a way to do this?
There is. The mov
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.
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
command available.
The s
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 still
.
BTW, is there any collection of scripts on the internet to browse through?
Kristian Rother
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