Re: [PyMOL] question about ray after alter and rebuild
--- 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 within all 12 structures. However, when I > try to ray the structural > resolution (only 3 of all 12 structures) to > 2000x2000 with 'ray 2000, 2000', I > always received a low resolution (as screen > resolution only) result. How could > I do? Thanks a lot! > > Fisher C.-M. Yu > > yucm...@gate.sinica.edu.tw > > > > --- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training > Course > Free Certification Exam for All Training Attendees > Through End of 2005 > Visit http://www.jboss.com/services/certification > for more information > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > __ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com
RE: [PyMOL] PyMol training
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...@charite.de __ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com
[PyMOL] rtools 0.7 release
Dear PyMOL users, i am happy to announce that the rtools package is out in a new polished version (finally). You can get it from http://www.rubor.de/bioinf rtools is a PyMOL plugin that has - a click-box for frequently used commands - commands for easily making - plugins for some external programs such as DSSP, HBEXPLORE, PASS - connections to the PDB and Columba databases (the latter is just being published, therefore you might not have heard of it yet http://www.columba-db.de). - some other stuff There are two major changes to version 0.6 - better installation - better documentation As always, i'm curious about your comments, and probably, bug reports. Cheers, Kristian Rother
Re: [PyMOL] Getting Closer to Wiki Time!
Hi, here's my 2cents on Wiki topics: * Displaying biochemical properties * Coloring molecules * Rendering molecules - I miss a topic like 'basics of displaying molecules'. - What about 'displaying basic chemical properties', like double bonds, h-bonds, bond angles and b-factors. - Modeling and editing structures. How to do electrostatics and energy minimization. - Launching PyMOL (has been asked often) - Some kind of 'script collection' would be very useful. Some examples on what could appear within these topics are found on http://www.rubor.de/bioinf/pymol_tips.html Yours, Kristian Rother Charite - Universitätsmedizin Berlin
[PyMOL] Re:Wiki Brain Storming
On Tuesday 08 February 2005 01:44, Warren DeLano wrote: > Say, what do people think about the idea of creating a PyMOL Wiki to hold > nuggets of information like this? Or is there a better alternative to > Wiki now available? As i have been maintaining sort of PyMOL FAQ for some time, i would definitely like a Wiki, too. Simply because it would take less time for me to update a Wiki rather than HTML pages. Thus, i strongly encourage setting up a Wiki, and i would like to transfer all the answers i have collected there. If anyone is wondering what i'm talking about, look at http://www.rubor.de/bioinf/pymol_tips.html I know Wiki's that suffer or starve from inactivity, but i never heard of one that got unusable because malevolent users permanently put *graffitti* on the pages. However, a good Wiki needs to be structured beforehand, rather than having 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
[PyMOL] Re: List participation commentary
On Monday 22 November 2004 18:49, Cameron Mura wrote: > >Ultimately the mailing list serves as a form of living manual to the > > program, so it would be nice to preserve as many of these insights as > > possible! Well, i have written up and sorted a number of answers to common 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
[PyMOL] Re: PDB-Codes
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 script. Thus, PyMOL will interpret each
command primarily as a PyMOL command. If no matching command is found, the
Python things will be tried.
Translation:
PyMOL probably thinks that 'strc' is the PDB-code rather than the variable. It
tries to download 'pdbstrc.ent' from the PDB server.
Question:
Does a script just containing
'pdb 1n1m' work? I guess yes.
Solution - Go Python:
script.py
---
from pymol import cmd
time.sleep(1)
list = ('1n1m')
for strc in list:
cmd.do('pdb %s'%(strc))
start it with:
run script.py
I hope that helps,
Kristian
Re: [PyMOL] rtools from .pml scripts
Dear Jacob and Andreas, The PyMOL launching procedure occurs IMO in three steps: 1) Start main PyMOL window and command processor 2) Start floating Tk window 3) Start plugins (it should be similar when you use PyMOL in batch mode). Thus, it may occur that commands from your .pml scripts are executed while the rtools plugin has not been initialized yet. A simple solution would be to issue a delay of 2-5 sec at the start of the script to make sure rtools is up and running. You could do this using: time.sleep(5) This is actually pure Python, but it works from the PyMOL cmd line as well. 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 .pymolrc does > not allow rtools to > be used from within the script. > > Jacob > > andr...@biochem.utah.edu wrote: > > Jacob, > > > > I believe rtool will always be usable if you put > > run /rtools.py > > into your .pymolrc file. > > > > > > Andreas > > > > > > > > > > > >>This is an odd concidence, since I was just about > to post about > >>something very similar. > >>I would like to use rtools commands from a .pml > that is read from the > >>command line (eg - with the -qc flag, instead of > using the graphical > >>interface). > >>When starting pymol normally, rtools loads and > everything is hunky dory. > >>However, even if I add a "run /rtools.py" > command to the .pml > >>script, none of the rtools commands are > recognized. Manually running > >>rtools.py from within the .pml produces no errors. > >>Is there a way to use rtools from within a script > that never sees the > >>graphical front end? > >> > >>Jacob > >> > > > > > > > > > > > > > --- > > This SF.net email is sponsored by: IT Product > Guide on ITManagersJournal > > Use IT products in your business? Tell us what you > think of them. Give us > > Your Opinions, Get Free ThinkGeek Gift > Certificates! Click to find out more > > > http://productguide.itmanagersjournal.com/guidepromo.tmpl > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > -- > Jacob Corn > UC Berkeley - Berger Lab > Lab: 510-643-8893 > Fax: 510-643-9290 > jc...@uclink.berkeley.edu > > > --- > This SF.net email is sponsored by: IT Product Guide > on ITManagersJournal > Use IT products in your business? Tell us what you > think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! > Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > __ Do you Yahoo!? Yahoo! Mail Address AutoComplete - You start. We finish. http://promotions.yahoo.com/new_mail
[PyMOL] Script Box 0.7 release
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
[PyMOL] Plugin: Protscale color gradients
Dear PyMOL users, One of our students and i have written a plugin that colors proteins by the amino acid scales on www.Expasy.ch. It is available at http://www.rubor.de/bioinf Also, i have updated the PyMOL tips pages to reflect some topics discussed here in recent months. Yours, Kristian Rother
Re: [PyMOL] Rtools Question
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) use it from mvCmd: mvCmd 1-100,@rotate.pml movie For more complex things (like using the sin()-smoothed movement features), you will probably need to hack into rtools/rMovie.py Yours, Kristian Tony Giannetti wrote: Hello all, This may have already been answered but I don't see it in the archives. I've got rTools working under MacPyMol and the effects are great. I'm working with a scene that has many objects loaded at once and I want to have some of them move independently over each other. So far I can only get rTools to apply rotations/translations to the whole scene, but not to individual objects. I can probably work around this using the alpha channel and then pasting the rendered images back onto the original scene in photoshop, but I'm wondering if there's a command scheme that will allow object one to rotate and translate according to rTools commands without altering the other objects in the scene. Thanks much, Tony --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] local PDB updates
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
Re: [PyMOL] individual surfaces?
Am Dienstag, 9. September 2003 09:14 schrieb Dirk Kostrewa: > Dear PyMol users, > > I'm currently trying to display individual surfaces around different > selections of a molecule to show how they contact each other. The trick is to define the selections as individual objects: create 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 gives only the surface of residue 440 > > show surface, ( resid 431 ) > flag ignore, ( not resid 431 ) > show surface, ( resid 440 ) > flag ignore, ( not resid 440 ) > rebuild > > whereas this one gives the joint surface of residues 431 and 440 > > show surface, ( resid 431 or resid 440 ) > flag ignore, ( not ( resid 431 or resid 440 ) ) > rebuild > > How can I display the individual surfaces separately? > > Alternatively, is there a command to display atoms in a CPK representation? > > Best regards, > > Dirk. ---
[PyMOL] Starting PyMOL from Java
Hello PyMOL and Java users, We have found a solution to the problem we reported last week. Bug: Pymol occasionally blocked when started with java.Runtime.exec. Description: The error was in our java-application since it is quite difficult to use the Process class properly. The error was hard to find because it only occured in some java-versions. When processes that write to stdout are launched with Runtime.exec(...) it is important to read the output into a BufferedInputStream. Otherwise the process is stopped after some amount of produced output because of pipe_wait. In this 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
[PyMOL] Starting Pymol from Java
Hello PyMOL users, We have problems with starting pymol from another application and are unable to find the reason. A short listing demonstrating the problem is here http://www.rz.charite.de/bioinf/strap/PymolBug.java The problem occurs only on some computers. On the computers where it occurs it is completely reproduce-able. On most computers pymol is correctly started and the protein given as argv[0] is loaded. However on one LINUX PC a problem occurs if and only if java version 1.4.2 is used. The same java version worked, however, on another LINUX PC with very similar configuration which has a faster CPU. The problem occurred also on an MaciBook, java1.4.1_01 The problem presents as follows: Pymol is started and feels fine until after 10s the load-command is send by the java program via standard input to pymol Immediately after receiving the data pymol is frozen and revives after terminating the process-object in java with destroy. Has anyone seen something similar? Greeting, Kristian Rother
[PyMOL] rTools 0.6.0 released
Hello PyMOL users, There are some recent improvements and bugfixes to the rTools suite available. The package rTools 0.6.0 can be regarded as beta, it is available from: http://www.rubor.de/bioinf New features include: - more detailed instructions for Win and MacOSX users. - states can be freely assigned to movie frames. - separate mvTurn and (as suggested by Richard Ball) - color fading in movies. (written by Tserk Wassenaar) rTools for PyMOL is a collection of useful stuff not yet contained in PyMOL itself. It includes. - some dialog boxes for rapidly running scripts etc. - 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 Group Institute of Biochemistry Humboldt University Berlin
Re: [PyMOL] appending states to objects
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 final state rock back and forth, as in with the "rock" button on the > Tcl window. However, I do not want to have the whole thing rocking during > the animation. Dear Felix, Though it may sound a little like advertisement, i recommend the rTools package for PyMOL. (http://www.rubor.de/bioinf). Here, you can issue some commands assigning states to frames, like mvRot 1-500:1-50,z,90 mvRot 501-1000:50-1,z,-90 Which will let states 1 to 50 be shown across the first 500 frames (however, state 50 is shown only in the last frame). In the second 500 frames, the order is reversed, i.e. the sequence plays backwards. You can also simply assign commands to frames, leaving the state untouched: mvSinmove 1001-1100,x,10 mvSinset 1001,1100,transparency,0.0,1.0 To play the animation, just type: movie And yes, you can get the structure rocking with these commands. I apologize it does not run perfectly yet, as a bugfix release of rTools is about to appear within a week. I hope that was not too confusing, Kristian
[PyMOL] Pymol Tips updated
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
Re: [PyMOL] Movement in animations: version 2
Dear Kelley, > created /tmp and /pdb directories It is meant to be in C:\tmp and C:\pdb, just in Unix-style notation. How would You say this in Mac? > I should state that several aspects of the install > instructions in regard to the directory structures in my system were > unclear. In fact, i don't know if anyone has ever used rTools on MacOS before. If there is one, could You please write me, how You got it running? --- debugging --- > In both versions of Pymol described above, when a simple move command is > inserted into a script as follows: > > mset 1 x100 > mvMove 20-40,x,80 > movie > > I get the following error messages: > > PyMOL>mset 1 x100 > PyMOL>mvMove 20-40,x,80 > Traceback (most recent call last): > File "/Applications/PyMOL/Darwin/modules/pymol/parser.py", line 234, in > parse > exec(com2[nest],pymol_names,pymol_names) > File "", line 1 > mvMove 20-40,x,80 > ^ > SyntaxError: invalid syntax OK, the mvMove command is apparently not known to Your PyMOL. Did You try to install it in $PYMOL/modules/pmg_tk/startup/rubor (without 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
Re: [PyMOL] command-line and python scripts
Dear Markus,
> 1) How can I supply arguments to a python script,
> when I invoke it from
> the pymol command line?
Write the python script like
def bla(arg1,arg2):
any.python.commands(arg1,arg2)
return
from pymol import cmd
cmd.extend('blacommand',bla)
Now you can call your function 'bla' from the PyMOL
command line:
PyMOL> blacommand pdb1cso,42
Which would be like in Python:
bla('pdb1cso','42')
> 2) Can I set user variables in the pymol command
> line and access them
> in a python script?
same answer as for 1).
> 3) Can I rerun a python script and use generator
> functions that I
> initialised in the run before?
Sorry, I did not understand this question completely
(might be same answer as above two).
> 4) Can I temporarily return control to pymol from
> within a running a
> python script and continue running the script after
> I have finished
> interacting with pymol?
You should probably check out the Script Box utility,
if You have not already (http://www.rubor.de/bioinf
> 5) Can I query the active state of a pymol object
> (and other properties
> 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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Re: [PyMOL] different transparencies
Michal Bozon wrote: I would like to have some spheres transparent, but some spheres leave opaque. Or to have spheres with different transparencies. Is it possible? Yes, it is. just tried it: PyMOL>set sphere_transparency,0.5 Setting: sphere_transparency set to 0.5. PyMOL>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 Yahoo!? Yahoo! Platinum - Watch CBS' NCAA March Madness, live on your desktop! http://platinum.yahoo.com
[PyMOL] Using PyMOL from Java
Dear PyMOL users,
We have written a Java class allowing to bind Java applications to use PyMOL.
It has been developed and tested on a SuSe Linux 8.0 machine, but migration
to other OS'es should be no problem.
It is hereby published using the Python License. Thus, You may modify 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: A class that allows to start PyMOL from Java programs and to
ship commands to PyMOL from an application.
Author: Kristian Rother and Christoph Gille
(kristian.rot...@charite.de, christoph.gi...@charite.de)
Created: 2003/02/17
Copyright: (c) 2003
Licence: Python License
This class was originally written to provide PyMOL support for Strap.
Strap is an application for editing structural alignments of proteins.
*/
public class Pymol {
public static String examples[]= new String[] {
"load pdb1cse.ent",
"color blue,pdb1cse",
"show sticks,pdb1cse",
"hide spheres",
"Color Molecule Atoms Specified Specification 0,255,255"
};
// Name of the PyMOL executable with command-line options
public static String customize[]= new String[] {
"pymol -p"
};
private static OutputStream stdin=null;
private static Runtime rt=Runtime.getRuntime();
private static Process process=null;
public Pymol() {}
//
public static boolean launch() {
String pymol=customize[0];
try {
process=rt.exec(pymol);
stdin=process.getOutputStream();
} catch(Exception e){
System.err.println("Pymol.java: Error launching Pymol");
return false;
}
try{Thread.currentThread().sleep(5000);}catch (Exception e){};
return true;
}
//
/**
When loadProtein is called the first time
process will be null;
When process already terminated process.exitValue() succeeds;
In both cases launch Pymol again.
*/
public boolean loadProtein(File pdb) {
// process terminated
try {
process.exitValue();
process=null;
}
catch(Exception e){};
if (process==null) launch();
if (process==null) {
System.err.println("Could not launch PyMOL.\nIs the path of the executable set right ?\nPlease type the complete path of the binary into the file "+customize[0]);
return false;
}
interpret("load "+pdb+",prot");
return true;
}
// -+---
public String interpret(String s) {
System.err.println(getClass().getName()+": "+s);
try {
stdin.write(s.getBytes());
stdin.write('\n');
stdin.flush();
}catch(Exception e){
System.err.println("Error in "+getClass().getName()+".interpret("+s+") \n "+e);
}
return "";
}
//
public void dispose() {interpret("delete all");}
public String[] getExamples() {return examples;}
//
/**
Example application of Pymol.java
*/
public static void main(String argv[]) {
int n=argv.length;
if (n<1) {
System.err.println("Demo: loads some proteins into pymol and renders the 2nd and 3rd residue with spheres");
System.err.println("Usage: java Pymol protein.pdb [protein2.pdb ...] ");
return;
}
Pymol pym=null;
for(int i=0;i
Re: [PyMOL] neighbor selection
Dear Nukri, > When I do > select cont,(/molA//s/401 around 4) > it sure selects all atoms from molA that are within 4 A from residue 401 > but it also selects > ALL other atoms from the current session (but not displayed) that are > within 4 A. > What needs improvement - 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
Re: [PyMOL] running pymol in command mode
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 an external program, which will be executed immediately. Kristian > I'm trying to use pymol to render a large number of complex images in > order to make a molecular movie. .. > > However, I'm having trouble getting the command mode to function. It > appears that one should launch pymol like so: > > pymol.com -c < pymol_script > > where "pymol_script" is a script file that you could otherwise invoke > from the GUI's command line by "@pymol_script". However, when I try > this with a simple script like:
Re: [PyMOL] Associating data structure with CGO object
Dear Mike, > Where would I store the reference to the object (containing my data) so > that I can retrieve it on the second call? Can I link it to the CGO object > or something? You can reference the object in Your Python script just like: my_data = [] (but i'd prefer using 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: "Mike Liang" > Cc: > Sent: Thursday, January 30, 2003 3:53 AM > Subject: Re: [PyMOL] Associating data structure with CGO object > > > 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 > > > > *** second call of command *** > > - delete CGO object > > - refine the data using the cutoff > > - create CGO object from refined data > > > > Message: You can create objects in Python scripts that are persistent as > long > > as PyMOL is running. > > This should work a lot faster than parsing the file several times. > > > > Kristian > >
Re: [PyMOL] Associating data structure with CGO object
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 *** second call of command *** - delete CGO object - refine the data using the cutoff - create CGO object from refined data Message: You can create objects in Python scripts that are persistent as long as PyMOL is running. This should work a lot faster than parsing the file several times. Kristian > What I want to do is parse a file that has a bunch of coordinates and draw > the spheres in PyMOL. But then I want to be able to adjust the cutoff for > which points are to be drawn. > > What I was doing now was first to run the script to bind the function to a > command. Then the function will load the file and draw the spheres at a > particular cutoff. If I rerun the function, it will delete the old CGO > object, parse the file again, and recreate a new CGO. But if the file is > really big, this becomes cumbersome. > > Or maybe what I need to do is create a "pymol object" and then have it > create the CGO object everytime it needs to be drawn. Then have my > function be able to update the cutoff parameter for the object. > > Thanks! > Mike >
Re: [PyMOL] ScriptBox
> If anyone has any suggestions they'd be most appreciated. I like ScriptBox > a lot so do you think there's any chance of incorporating this into PyMol > either as a GUI window or as its own dropdown scripts menu that could also > list all the scripts in a given directory?? Hello, There is a very recent (6.1.) package of rTools available from http://www.rubor.de/bioinf , where ScriptBox and some other tools are contained. Most things are accessible from menus, You can also add Your own scripts to the box using the add_script command. rTools 0.5.2 is still a Beta release, although many bugs have been fixed already. Particularly, installation under Windows is still a little eXPerience. Kristian Rother
Re: [PyMOL] recent problems
David wrote: 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 grid? http://www.rubor.de/bioinf/pymol_tips.html#getcoord Eric Hu wrote: >Hi, I wonder if anyone has had the similar problem. I >can see both the label and dash at normal window. >After raytracing there is only a yellow dotted line >between two atoms without the distance. How can I make >the distance shown on the raytracing picture? Thanks! As far as i know, the only way is to use CGO-Text for labels. This is tough, though. http://www.rubor.de/bioinf/pymol_tips.html#cgolabels -- Fei Xu wrote: >Would you like to tell me what kind of commands I can use to draw a line >in pymol, if I know the exact location of this line in 3D-space? You can use CGO objects from a python script like this: # cgo-example.py from pymol import cmd from pymol.cgo import * obj = [CYLINDER, 0.1, 0.1, 0.1, 10.0, 0.0, 0.0, 0.1, 0.0, 0.0, 1.0, 1.0, 0.0, 0.5,] cmd.load_cgo(obj,'hbonds') The values in the obj array are: [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
Re: [PyMOL] accessing objects directly
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 grid?
[PyMOL] Re: molecular surfaces
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
Re: [PyMOL] (no subject)
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 original size of 1.0. Unfortunately, settings for individual objects are not functional yet. Kristian
[PyMOL] practical PyMOL FAQ
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 of recent postings there. However, the topics around Stereo 3D and MacOSX were not included (i know nothing about both of them). Kristian
Re: [PyMOL] multi-step movie
Hello Gabriel,
Your Questions:
1. How can you make a molecule rotate 10 times only,
go to http://www.rubor.de/bioinf and download the movieScript module
and issue the following commands:
mvClear
mvRot 1-500,x,3600
mvCmd 501,mstop
movie
Explanation:
This tells movieScript to rotate the molecule in frames 1 to 500 around
3600 degrees, then calls the mstop command in frame 501.
2. Is there any script command, that put the script on
"hold" until you press the mouse or the keyboard
button ? This is useful for multi-step movie.
I think this should be done using the raw_input("press any key")
function from a python script.
3. Is there any possibility to do zoom-in , for
example, into the active site.
of course, there is (e.G. 'actsite' is your active site subselection):
hide all # molecule gets invisible
orient actsite # now the 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
Re: [PyMOL] rotation about an arbitrary vector?
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 movie.py script does exactly this: camera movements. Basically, any movement can be achieved by adding x,y and z rotations. You can specify how quick each axis is to be rotated and so on. Any camera movement can be smoothed, if You like. http://www.rubor.de/bioinf/pymol_movie.html As You wrote You are making movies of trajectories i assume that Your animation uses more than one state. Movie.py doesn't get alongt with them at the moment. This is because i don't know what would be useful. If You want to go with movie.py, write me, and we'll get something on that. Kristian
[PyMOL] rTools and Movie for PyMOL released
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. All the stuff can be found on: http://www.rubor.de/bioinf Authors : K. Rother, C. Froemmel et al., Institute: Protein Structure Theory Group, Charite Berlin http://www.charite.de/bioinf I am very curious to hear bug reports. Kristian
Re: [PyMOL] Secondary structure assignments
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 script can be found on my homepage, http://www.rubor.de/bioinf/pymol_extensions.html along with some useful stuff http://www.rubor.de/bioinf/index.html However, the script works for sure only on Unix. For Windows, i still need to figure out how to - redirect the output of Dssp on Windows - assign platform-independent Paths correctly. If someone could test the script, that would be great. Kristian
Re: [PyMOL] Update to ScriptBox 0.3 for PyMOL
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 the same: http://www.rubor.de/bioinf/scriptBox.html On my page, there is also a 'quick and dirty' hack for PyMOL. FilePipe.py allows to execute PyMOL commands from a shell. It starts its own thread and reads lines from a text file. This doesn't work well, but it works. Does anyone have a better idea to do this? If you want to have both GUIs running simulaneously, then try using the startup directory in modules/pmg_tk (you'll need to modify ScriptBox.py to have an __init__ method which creates the window, but simply returns instead of forking a thread or calling mainloop) Thanks, this works in fact really well. Kristian
[PyMOL] Release of ScriptBox 0.2 for PyMOL
Hello PyMOL users, I have written a small program that lets you select your favorite PyMOL script from a comfortable box floating beside your PyMOL window. ScriptBox 0.2 can be found at: http://www.rubor.de/bioinf/scriptBox.html Its my first release, so the program might still have bugs. BTW, is there any collection of scripts on the internet to browse through? Kristian Rother
