Re: [PyMOL] Autodock/vina plugin for pymol on MAC
Hi, that means numpy is missing on your system. The easiest way to get rid of this problem is to upgrade to version 1.2 (I guess you're using the old 0.99). cheers, Daniel On Monday 07 June 2010 08:46:14 pm Sandip Bharate wrote: Hello , I have problem is installing ‘Autodock/vina plugin’ for pymol on Mac (Snow Leopard). I tried to install it …..i got the message that “Autodock.py plugin has been installed. Restart pymol to begin use” but it was not actually installed …the error message was…..”ImportError: No module named numpy. Error: unable to initialize plugin autodock” I read that Florian was able to install it successfully on Mac. Florian can you please help me in this matter? Help from any other will also be highly appreciated. Thank you !! Sandip -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Quick PyMOL Autodock/Vina Plugin advice
Hi Kristina,
this sometimes happens. I actually don't know why but if you set the
environmental variable ADPLUGIN_NO_OUTPUT_REDIRECT it should not happen
anymore.
Cheers,
Daniel
On Monday 07 June 2010 06:50:49 pm vivat mesin wrote:
Hi Everyone,
I am troubleshooting my Autodock/Vina Plugin installation, and I am able to
write the Vina input file, but when I try to run Vina, I get an Exception
in thread error in threading.py, autodock.py, and Tkinter.py. I have
pasted the error below.
If you have any advice, please let me know. I am running Lucid Lynx Ubuntu
10.04, but it is an installation within a loopmounted device (Wubi), so
this may also be contributing to my problem.
Thank you so much for your help!
Best,
Kristina
Exception in thread Thread-2:
Traceback (most recent call last):
File /home/kristina/Downloads/pymol/ext/lib/python2.5/threading.py,
line 486, in __bootstrap_inner self.run()
File /home/kristina/Downloads/pymol/modules/pmg_tk/startup/autodock.py,
line 199, in run self.status_line.configure(text = self.log_text)
File
/home/kristina/Downloads/pymol/ext/lib/python2.5/lib-tk/Tkinter.py, line
1208, in configure return self._configure('configure', cnf, kw)
File
/home/kristina/Downloads/pymol/ext/lib/python2.5/lib-tk/Tkinter.py, line
1199, in _configure self.tk.call(_flatten((self._w, cmd)) +
self._options(cnf))
TclError: out of stack space (infinite loop?)
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Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Vertrees jason.vertr...@schrodinger.com Subject: [PyMOL] FreeMOL To: pymol-users@lists.sourceforge.net Message-ID: 79558d781002181336x4216e157w7181f92f24cbd...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 PyMOLers, The FreeMOL website is back up as it was before (http://freemol.org). FreeMOL is still open-source, based off the original bioinformatics project. The only difference is the location of the webserver: it is now running from a Schrodinger server to give me better access (again, Warren's servers only had FTP access, we now have ssh). Please let me know if anything's missing. Thanks for being patient, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Message: 3 Date: Fri, 19 Feb 2010 01:37:24 -0800 From: Kin Sing Stephen Lee leek...@msu.edu Subject: Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 9 To: pymol-users@lists.sourceforge.net Message-ID: 23b94f8e-04b7-4718-8758-90b247c5d...@msu.edu Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Thank you Daniel, I finally found the Autodock tool path in Mac however, i got another error message: ImportError: No module named MolKit Is there any solution for this in Mac? Thank you very much Sing On Feb 18, 2010, at 10:56 AM, pymol-users- requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Autodock plugin (Kin Sing Stephen Lee) 2. Re: Autodock plugin (Daniel Seeliger) 3. Update Submitting Bugs (Jason Vertrees) 4. Re: Update Submitting Bugs (Christoph Gohlke) 5. Re: Update Submitting Bugs (Jason Vertrees) 6. Re: Update Submitting Bugs (Christoph Gohlke) 7. Regarding the Control panel in pymol (phani ghanakota) 8. Re: Regarding the Control panel in pymol (Jason Vertrees) 9. coordinate systems of pymol and povray (Gabriela Schlau-Cohen) -- Message: 1 Date: Tue, 16 Feb 2010 11:06:40 -0800 From: Kin Sing Stephen Lee leek...@msu.edu Subject: [PyMOL] Autodock plugin To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Message-ID: 333eebd7-7c78-48d5-90ae-ff9907837...@msu.edu Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing -- Message: 2 Date: Tue, 16 Feb 2010 20:26:00 +0100 From: Daniel Seeliger dsee...@gwdg.de Subject: Re: [PyMOL] Autodock plugin To: pymol-users@lists.sourceforge.net Message-ID: 201002162026.00620.dsee...@gwdg.de Content-Type: Text/Plain; charset=iso-8859-1 Hi Sing, take a look into ~/.ADplugin/pymol_autodock_plugin.conf and set the path to the autodocktools scripts correctly. Then the plugin should find them. Cheers, Daniel On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing
Re: [PyMOL] Autodock plugin
Hi Sing, take a look into ~/.ADplugin/pymol_autodock_plugin.conf and set the path to the autodocktools scripts correctly. Then the plugin should find them. Cheers, Daniel On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing --- --- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Use of PyMOL for inspection and saving of docking results from Autodock
Hi Msev, if you download the latest version you'll find what you're looking for. On the Score/Rank-page you can export docking scores and also docking poses in pdb format. If you save a list containing different ligands it might indeed look weired when you reload the file into pymol since pymol makes the bonds only based on the first model. But you can convert the poses.pdb to a mol2 file with babel and load that into pymol. That should look nice. Cheers, Daniel On Monday 15 February 2010 08:05:35 pm Marko S wrote: Hello, I'm quite a novice user of PyMOL but I am already impressed at the speed and beauty of the rendering. But I have some questions regarding it's use for viewing results of Autodock. So I normally proceed as follows, i open the PDB molecule say fetch BLABLA and i get the pdb file...Then i have two options, one is to simply open the .dlg file then i get only one ligand results which i scrool with the play button to see all the results, but there is also an option (i use the autodock plugin, and with that i get all of the results on the screen), but the problem is how to save everything together in one pdb. file. I tried with the write complex.pdb but it made a strange mess when i look with other pdb viewers such as Viewerlite. What can you suggest me to do? Thank you for the answers! Msev -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Getting information fron selected objects
Hi Phil, one option to get access to the coordinates is using the chempy model of a given selection ( named (sele) if you clicked it). m = cmd.get_model((sele)) the chempy model contains a list of atom objects which contain most properties you might need. for atom in m.atom: print atom.id, atom.name, atom.resn, atom.resi, atom.coord To extract the coordinates of all atoms you can simple do: coords = map(lambda a: a.coord, m.atom) or if you need the coordinates as numpy arrays use: from numpy import * coords = map(lambda a: array(a.coord), m.atom) gives you a list of numpy arrays or: coords = matrix(map(lambda a: a.coord, m.atom)) will produce a numpy matrix with your coords. Then you might do whatever you want with the coordinates and update the coordinates of the chempy model. As far as I now, you can not transfer them back easily to PyMOL but you can do a little trick. Load the modified model as new pymol object: cmd.load_model(m,modified) and then update the original selection with the coords from the modified object. cmd.update((sele),modified) Then you can delete the modified object. cmd.delete(modified) Cheers, Daniel On Tuesday 19 January 2010 08:00:51 pm Phil Payne Local wrote: I am writing a Pymol plugin, in which I need to extract, manipulate, and replace the coordinates of selected atoms. Are there examples out there I could use as a prototype? For starters, what command(s) do I use to get the name strings of residues that I've selected with mouse clicks. I would like to assign these to a variable. Then the same question applies to coordinates. How do I assign the values of atomic coordinates to a list variable in my plug_in script? --- --- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Autodock/Vina Pymol Plugin Windows problem
Hi Jed,
sorry for the late reply.
The plugin so far doesn't work properly on windows and mac (at least that's
what users report. I don't have a windows PyMOL to test it).
Could you send me your input files? I'd like to test it on linux to see if
there's a problem with the files or something else.
Btw, did anyone get it to run on windows or mac? If yes, it would be nice if
you drop me a mail with some info about your system (operating system, program
version, how is pymol installed).
Thanks,
Daniel
On Thursday 07 January 2010 04:49:11 pm Jed Goldstone wrote:
I can't seem to get the autodock Pymol plugin to work correctly in
Windows (XP). I think it's a bug somewhere.
I'm using the latest version of autodock grid and dock, and MGL Tools
1.5.4 on Windows XP with Python25, and PyMol 1.2r1
I've emailed the author, Daniel Seeliger, but haven't gotten a reply.
Has any had experience with this?
I'm getting at least 2 different errors:
first, in setting up a receptor. When I click on the PyMOL Selection and
Generate Receptor I get the following error:
Batch: C:\Program Files\MGLTools
1.5.4\MGLToolsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r
C:\Program Files\PyMOL\.ADplugin\receptor.dr1a.pdb -o
receptor.dr1a.pdbqt -A checkhydrogens
'{' is not recognized as an internal or external command,
operable program or batch file.
second, if I Select as Flexible in the Autodock plugin a PyMol
selection, I get the following Pymol error in background function,
Error: 1
type 'exceptions.KeyError' Exception in Tk callback
Function: bound method Autodock.select_flexible_residues of
pmg_tk.startup.autodock.Autodock instance at 0x10941580 (type: type
'instancemethod')
Args: ()
Traceback (innermost last):
File C:\Program Files\PyMOL/modules\Pmw\Pmw_1_3\lib\PmwBase.py, line
1747, in __call__
return apply(self.func, args)
File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line
1800, in select_flexible_residues
receptor_object = self.receptor_dic[rec]
type 'exceptions.KeyError': ''
Jed
--
Dr. Daniel Seeliger
Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry
Tel. +49 (0) 551-201-2310
http://wwwuser.gwdg.de/~dseelig
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[PyMOL] pymol autodock plugin
Dear PyMOLers, there is a new version of the plugin on the web (http://wwwuser.gwdg.de/~dseelig/adplugin.html). It contains a bunch of new features, like: - setup and execution of complete docking runs - support for VINA (http://vina.scripps.edu), a great new Autodock spawn - viewing of Autodock grid maps in PyMOL - some lightweight virtual screening functionality So far it's only tested on Linux and by myself so I expect it to be somewhat buggy and unstable. Therefore please report bugs. Cheers, Daniel On Thursday 13 August 2009 22:36:14 Warren DeLano wrote: Jed, With the 1.2 release of PyMOL, we have completely switched over to Numpy. So the first thing to try is to replace: from Numeric import * # with from numpy import * Cheers, Warren -Original Message- From: Jed Goldstone [mailto:jedg...@mit.edu] Sent: Thursday, August 13, 2009 1:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol autodock plugin The autodock plugin written by Daniel Seeliger ceased to function (load) when I upgraded to Pymol 1.2r1. Although it is not compatible directly with Autodock 4, it did have the useful functionality of presenting an autodock 'box' that was readily tweakable, so that the parameters could be exported for Autodock Vina. I would LOVE to have this resurrected, but I don't know python - can anybody help with this? The specific failures I got were: File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line 16, in module from Numeric import * ImportError: No module named Numeric Error: unable to initialize plugin 'autodock'. Any help would be greatly appreciated. Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.mit.edu/people/jedgold/home.html (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net --- --- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: dsee...@gwdg.de web: http://wwwuser.gwdg.de/~dseelig -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pynmr plugin installation
Hi Cyril, obviously the Numeric package is not installed. This package is somewhat out of date and replaced by the numpy package. You could try to replace the line from Numeric import * by from numpy.oldnumeric import * Good luck, Daniel On Friday 13 June 2008 12:50:08 cyril gaudin wrote: Dear Pymol Users, I am trying to use the Pynmr plugin within Pymol on a Mac OS 10.4 intel machine either with the X11Hybrid or the fink version. But I am not able to make it run when I launch Pymol. What I have done is just downloaded the pynmr_0.37f_OSX.tar.gz file, untared it in my /modules/pmg-tk/startup directory and installed it entering 'install' in the new created pynmr directory. The result of that is 2 new plug_nmr.py(c) files in the /modules/pmg- tk/startup directory. But when starting Pymol, here are the error messages I have : This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. Detected 4 CPUs. Enabled multithreaded rendering. Exception in plugin 'pynmr' -- Traceback follows... Traceback (most recent call last): File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ PMGApp.py, line 159, in initialize_plugins mod.__init__(self) TypeError: argument 1 must be string, not instance Error: unable to initialize plugin 'pynmr'. Exception in plugin 'plug_nmr' -- Traceback follows... Traceback (most recent call last): File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ PMGApp.py, line 156, in initialize_plugins __builtin__.__import__(mod_name) File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ startup/plug_nmr.py, line 47, in ? from pynmr.pynmr import * File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ startup/pynmr/pynmr.py, line 67, in ? from superimp import * File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ startup/pynmr/superimp.py, line 35, in ? from rmsd import * File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/ startup/pynmr/rmsd.py, line 34, in ? from Numeric import * ImportError: No module named Numeric Error: unable to initialize plugin 'plug_nmr'. Does anybody have ever met this problem? Or can advice me some new things to test as I have no more ideas to use the plugin? Thanks. Best Regards, Cyril Gaudin. -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: dsee...@gwdg.de www.mpibpc.mpg.de/groups/de_groot/dseelig/index.html
Re: [PyMOL] link residues with different number
Hi Stephanie, you can simply select two atoms you want to connect with Ctrl+middle_mouse_button and type bond on the command line. With unbond you can delete the bond. Alternatively you can add a CONECT entry to your PDB file, e. g. CONECT 1200 1250 Cheers, Daniel On Thursday 08 May 2008 01:44:41 stephanie.g...@free.fr wrote: Hi all, I'm wondering if there is an easy tool to link some residues which have not the following number, like aa2 and aa10 ? thanks, Stephanie Gras - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/java one ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: dsee...@gwdg.de www.mpibpc.mpg.de/groups/grubmueller/start/people/dseelig/index.html
