Re: [PyMOL] To all PyMOL supporters, a message from DeLano Scientific
It is a very sad news. I've been asked to perform a PyMOL training next year in France. I will dedicate this session to his memory. If I can help anyway, tell me. Best regards, Jerome Pansanel Le jeudi 05 novembre 2009 21:27:38, Jason Vertrees a écrit : PyMOLers, I have been asked to send the following on behalf of Warren's wife, Beth: To all PyMOL supporters, a message from DeLano Scientific: Warren DeLano has passed away. We are not accepting new orders at the moment, while we plan our next steps. For those customers who have purchased support subscriptions, we are presently continuing to provide support via the email address designated for this purpose. Please do not send email to Warren's personal email address (war...@delsci.com). We thank everyone for their tremendous support over the years, both monetary and non-monetary, and ask you to please bear with us while we plan for PyMOL's future. Thanks, Elizabeth Pehrson (Warren's wife) -- 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
Re: [PyMOL] Adding python modules
Hi, You can get MySQL python from here: http://sourceforge.net/projects/mysql-python Jerome Le vendredi 9 mars 2007 15:22, DeVill a écrit : Hi! I end up with the same problem. Just like this plugin i tried: import MySQLdb but I get this error message, when starting up pymol: Exception in plugin 'dbsearch' -- Traceback follows... Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py, line 156, in initialize_plugins __builtin__.__import__(mod_name) File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py, line 54, in ? import MySQLdb ImportError: No module named MySQLdb Error: unable to initialize plugin 'dbsearch'. Bye DeVill 2007/3/9, Jerome Pansanel j.pansa...@pansanel.net: Hi, Take a look on this plugin: http://pymol-plugins.sourceforge.net/dbsearch.html Cheers, Jerome Pansanel Le vendredi 9 mars 2007 14:24, DeVill a écrit: Hi! I would like to use direct mysql connection to a database in a plugin. Can you please tell me if there is a way to add MySQLdb module to PyMOL? if yes, then how? Bye DeVill - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Adding python modules
Try to copy MySQLdb into: C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\site-packages\ Jerome Pansanel Le vendredi 9 mars 2007 19:54, DeVill a écrit : Hi! I know that as well... what I don't know is how to install it under PyMOL. If I were using simply python, than that would be no big deal, I did that a 1000 times: setup.py --build; setup.py --intall Presently I'm using the windows version of PyMol, and installing a separate python interpreter, and installing MySQLdb module didn't help. When I tried to start PyMOL and enter into command line: run setup.py --build, it didn't work as well, as it wants to find the file setup.py --build. Any other ideas? Thnx DeVill 2007/3/9, Jerome Pansanel j.pansa...@pansanel.net: Hi, You can get MySQL python from here: http://sourceforge.net/projects/mysql-python Jerome Le vendredi 9 mars 2007 15:22, DeVill a écrit: Hi! I end up with the same problem. Just like this plugin i tried: import MySQLdb but I get this error message, when starting up pymol: Exception in plugin 'dbsearch' -- Traceback follows... Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py, line 156, in initialize_plugins __builtin__.__import__(mod_name) File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py, line 54, in ? import MySQLdb ImportError: No module named MySQLdb Error: unable to initialize plugin 'dbsearch'. Bye DeVill 2007/3/9, Jerome Pansanel j.pansa...@pansanel.net: Hi, Take a look on this plugin: http://pymol-plugins.sourceforge.net/dbsearch.html Cheers, Jerome Pansanel Le vendredi 9 mars 2007 14:24, DeVill a écrit: Hi! I would like to use direct mysql connection to a database in a plugin. Can you please tell me if there is a way to add MySQLdb module to PyMOL? if yes, then how? Bye DeVill - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Plugin for Open Babel
Hello, I've developped a plugin that add the possibility to use Open Babel. This permits you to import all file formats supported by Open Babel. This plugin use the Python wrapper of Open Babel. You can get it here: http://sourceforge.net/project/showfiles.php?group_id=189996package_id=222732 Cheers, Jerome Pansanel
Re: [PyMOL] chempy documentation
Hi, Frowns is another Python-based chemical informatics library, but is no more maintained. A great idea would be to initiate such project. We could based the design on the CDK library (http://cdk.sourceforge.net/). Comments or suggestions ? Cheers, Jerome Pansanel Le lundi 20 novembre 2006 17:14, DeLano Scientific a écrit : Bgbg, The idea behind chempy was that it could eventually be developed into a Python-based chemical informatics library. In practice, however, its capabilites and performace are quite limited and so it mainly just exists for use by PyMOL. No, there is no documentation for chempy other than the code and its usage. Cheers, DeLano Scientific LLC Email Support Services -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of bgbg bg Sent: Monday, November 20, 2006 4:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] chempy documentation Hello, all. Is there any chempy documentation available? I've searched the web for a while, but couldn't find anything relevant. Do PyMol subscribers have access to extra documentation? Thank you -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] PDB loader
Hi,
I have post this bug for many time ago to the maintainer, but the change does
not appear in pymol v0.99-rc6 and earlier. Here is a part of the old code
(import urllib2, zlib) to replace:
***
- pdbFile = urllib2.urlopen('http://www.rcsb.org/pdb/cgi/export.cgi/' +
- pdbCode + '.pdb.gz?format=PDBpdbId=' +
- pdbCode + 'compression=gz')
- cmd.read_pdbstr(zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS),
pdbCode)
***
with this new code (import urllib2, StringIO, gzip) (works fine):
***
+ pdbFile = urllib2.urlopen('http://www.rcsb.org/pdb/files/' +
+ self.pdbCode + '.pdb.gz')
+ pdbStream = StringIO.StringIO( pdbFile.read() )
+ pdbData = gzip.GzipFile(fileobj=pdbStream)
+ cmd.read_pdbstr(pdbData.read(), self.pdbCode)
***
If you have problem to deal with such piece of code, I can send you the
complete plugin.
Cheers,
Jerome Pansanel
Le mercredi 18 octobre 2006 16:59, surendra negi a écrit :
Hi,
In pymol, PDB loader service is no longer working. My
self downloader script is also not working! They
changed
the file location. There is no more export.cgi in pdb
web site.
sn
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Re: [PyMOL] Hydrogen bonds
Dear Selvaraj, You will find useful resources about hydrogen bonding with PyMOL on: http://www.rubor.de/bioinf/tips_modeling.html#addhbond Regards, Jerome Pansanel Le mercredi 23 août 2006 22:48, selva raj a écrit : Dear Pymol users, Would anyone tell me how to draw hydrogen bonds between interacting atoms in a crystal structure of small molecule using Pymol. An attempt to do it through mentioning cutoff distance as 3.0, and mode as 0, failed. Command: distance (selection1),(selection2)[,3.0[,0]] This command is showing all possible distances from the selected atoms Thanking you, yours friendly. Selvaraj, - Here's a new way to find what you're looking for - Yahoo! Answers Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW
Re: [PyMOL] Displaying Disulphide bonds using Pymol
Hello, You can find some documentation about sulfur bonds on this page: http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory If you are not successfull by using this resource, don't hesitate to post again. Cheers, Jerome Pansanel Selon Nagesh Chakka nagesh.cha...@anu.edu.au: Hello everyone, I am unable to display disulphide bonds using PyMOL (version 0.97). My understanding is that PyMOL can connect Cys that are within bonding distance. The PDB file (ID 1AG2) defines residues involved in the SSBond formation. I also tried to use the command bond to connect the residues but without any success. I am not sure if I am doing anything wrong. Any suggestion in this regard is appreciated. Thanks Nagesh Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Mail sent through IMP: http://horde.org/imp/
Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title=Settings,
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry(500x400)
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
While we're discussing ways to make our favorite program a little
better, I had an idea I thought I'd throw out there...
While making some figures the other day, I found myself scrolling
endlessly through the edit settings menu (under Setting -- Edit All) a
number of times, mostly to locate a relatively small number of settings
related to ray tracing. This got me thinking about a way to improve
access to the many wonderful features that have been added to PyMOL.
The solution I came up with is a filter line which could be placed
directly above the window listing all the settings. Users could then
type a word, say ray or cartoon, and only the settings containing
this word would be shown.
The best example of a program containing this feature is the
about:config window in Firefox. When you open a browser and type
about:config instead of an address, a window containing hundreds of
settings appears. At the top is a filter bar which you can use to pare
down the number of settings listed below.
I think this would be a great addition to PyMOL and would help users
familiarize themselves with the many new settings which have been (and
will be) implemented. :)
Perhaps others have even better solutions to this problem. The use of a
filter is just the first idea which came to my mind. I think it would be
relatively easy to implement, although my python programming skills are
somewhat limited.
Thanks,
Michelle Gill
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Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title=Settings,
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry(500x400)
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
While we're discussing ways to make our favorite program a little
better, I had an idea I thought I'd throw out there...
While making some figures the other day, I found myself scrolling
endlessly through the edit settings menu (under Setting -- Edit All) a
number of times, mostly to locate a relatively small number of settings
related to ray tracing. This got me thinking about a way to improve
access to the many wonderful features that have been added to PyMOL.
The solution I came up with is a filter line which could be placed
directly above the window listing all the settings. Users could then
type a word, say ray or cartoon, and only the settings containing
this word would be shown.
The best example of a program containing this feature is the
about:config window in Firefox. When you open a browser and type
about:config instead of an address, a window containing hundreds of
settings appears. At the top is a filter bar which you can use to pare
down the number of settings listed below.
I think this would be a great addition to PyMOL and would help users
familiarize themselves with the many new settings which have been (and
will be) implemented. :)
Perhaps others have even better solutions to this problem. The use of a
filter is just the first idea which came to my mind. I think it would be
relatively easy to implement, although my python programming skills are
somewhat limited.
Thanks,
Michelle Gill
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Re: [PyMOL] Sequence view print out
Le Mardi 28 Février 2006 21:10, Joel Tyndall a écrit : Hi all, I'm not sure if this has been asked before and I'm not sure if its possible...but here goes anyway. Is there a way to print/export the sequences in the viewer window? It would be an easy way to translate actual secondary structure to a sequence alignment In the control window, you can get a subsequence corresponding to a secondary structure with : stored.list = [] for i in range(a,b): cmd.iterate( name ca and resi +str(i), stored.list.append(resn)) where a is the id number from the first amino acid in the secondary structure and b is (the id from the last amino acid +1) in the secondary structure. The stored.list variable contains now all the amino acids in the secondary structure. Then, you can use all the power of python to process this list as you want. Don't hesitate to ask for more features, Cheers, Jerome Pansanel Thanks J
Re: [PyMOL] Sequence view print out
Le Mardi 28 Février 2006 21:10, Joel Tyndall a écrit : Hi all, I'm not sure if this has been asked before and I'm not sure if its possible...but here goes anyway. Is there a way to print/export the sequences in the viewer window? It would be an easy way to translate actual secondary structure to a sequence alignment In the control window, you can get a subsequence corresponding to a secondary structure with : stored.list = [] for i in range(a,b): cmd.iterate( name ca and resi +str(i), stored.list.append(resn)) where a is the id number from the first amino acid in the secondary structure and b is (the id from the last amino acid +1) in the secondary structure. The stored.list variable contains now all the amino acids in the secondary structure. Then, you can use all the power of python to process this list as you want. Don't hesitate to ask for more features, Cheers, Jerome Pansanel Thanks J
Re: [PyMOL] output formats
Hi, I have work a little with .obj file. I've written a script that translates OBJ file to PDB file. It is quite simple to make the opposite. For more information on obj format, you can read this resume: http://www.fileformat.info/format/wavefrontobj/ You can also translate PyMOL CGO to OBJ file. Cheers, Jerome Pansanel Le Mercredi 08 Février 2006 05:03, scott_lu...@med.unc.edu a écrit : Is there any way to output in any of the following file formats? .max, .drf .3ds, .prj .ai .dem, .xml, .ddf .dwg, .dxf .fbx .htr .ige, .igs, .iges .ipt, .iam .ls, .vw, .lp .obj .shp .stl .wrl, .wrz You'll recognize the last two as VRML extensions. Thanks for your advice, Scott Lujan Redinbo Lab --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Python scripting for Pymol
Hi, I writing a small script in python, in order to export png picture from a MDL sdfile. Here is a sample of the function : def mol2png(ctfile,name): pymol.cmd.read_molstr(ctfile,name) pymol.cmd.set(valence,1) pymol.cmd.color(black,elem c) pymol.cmd.color(red,elem o) pymol.cmd.color(blue,elem n) pymol.cmd.color(yellow,elem s) pymol.cmd.bg_color(white) pymol.cmd.zoom(name) pymol.cmd.png(name) time.sleep( 1 ) pymol.cmd.delete(name) It works fine only if I have the function time.sleep(1). If not, I have only empty pictures. Is there another solution to delete the molecule only when the png file has been written ? Thanks, Jerome Pansanel
[PyMOL] New PyMOL plugin
Hi, I've develop a new plugin. It offers the ability to do a PDB advance search. You can search directly keywords into the PDB entries file. For this, the PDB entries file is downloaded (the file is stored into the home directory). The results are diplayed into a spreadsheet. By a double click on a result line, the structure is open into the PyMOL visualization window. You can find the plugin at this address: http://www.pansanel.net/chemistry/resources/pymol_pdbsearch.tar.gz I'm waiting for your comments ! Thanks Jerome Pansanel Mail sent through IMP: http://horde.org/imp/
Re: [PyMOL] Plugins
Le Mardi 25 Octobre 2005 08:15, Tjaart de Beer a écrit : Hi We are looking at possibly writing some plugins to extend the functionality of PyMOL. How would we go about this? Is there some documentation on the general process? Any help would be greatly appreciated!! Hi, Here is a usefull resource : http://www.pymolwiki.org/index.php/Category:Plugins_Tutorial Jerome Pansanel
[PyMOL] New plugin
Hi, I've develop a new extension (plug in) for PyMOL : dbSearch. It enable PyMOL to search a molecular structure (MDL mol format) by her name into a database (MySQL) and display it in PyMOL. You can find the archive there: http://pansanel.adlp.org/chemistry/resources/pymol_dbsearch.tgz Cheers, Jerome Pansanel
Re: [PyMOL] PyMol training
Hi, I've planned to write a french training document for PyMOL. I would enjoy that some people help me by reading my draft, before I release it. This document will be released under a Creative Common License (cc). Thanks, Jerome Pansanel Le Lundi 10 Octobre 2005 09:29, Kristian Rother a écrit : 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 --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] [OT] alternative python module
Hello, You can find modules inside some software package, like: PyQuante (http://pyquante.sourceforge.net/) FROWNS (http://frowns.sourceforge.net/) MMTK (http://starship.python.net/crew/hinsen/MMTK/) All these software are free software. Regards, Jerome PANSANEL -- Jerome PANSANEL http://www.alchem.org Le Lundi 25 Juillet 2005 15:42, andrea spitaleri a écrit : Hi all, I am using pymol also for python scripting and perlmol for perl scripting. They are both very nice. I am just wondering if there are some other useful python modules around for chemistry. Sorry for the OT. Regards, andrea --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
