[PyMOL] ZM-M220W and TRIMON ZM-M220W
Hi PyMOL users: I am looking into stereo 3D on LCD monitors. What is the difference between ZM-M220W and TRIMON ZM-M220W? http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?c=usl=ens=hiedcs=RC956904sku=A2550610 and http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?c=usl=ens=hiedcs=RC956904sku=A1997135 Thanks! -- ___ 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] ZM-M220W and TRIMON ZM-M220W
The difference? $769.99 - $354.99 = $415 exactly. But seriously, this is a question for Dell, not pymol-users. For what it is worth, mid $300's is the current per-unit pricing for the ZM-M220W display - but they originally hit the market at a 2-3X higher price, so one of those links is probably old. Cheers, Warren From: Lihua Wang [mailto:mole...@gmail.com] Sent: Tuesday, June 30, 2009 11:44 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ZM-M220W and TRIMON ZM-M220W Hi PyMOL users: I am looking into stereo 3D on LCD monitors. What is the difference between ZM-M220W and TRIMON ZM-M220W? http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx? c=usl=ens=hiedcs=RC956904sku=A2550610 http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx ?c=usl=ens=hiedcs=RC956904sku=A2550610 and http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx? c=usl=ens=hiedcs=RC956904sku=A1997135 http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx ?c=usl=ens=hiedcs=RC956904sku=A1997135 Thanks! -- ___ 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
[PyMOL] Homology Modeling in Pymol
Hi All, I have a very large library (almost 1000) of similar genetic sequences, for which I would like to generate homology models. Does anyone know of a way to automate requests to a homology modeling server, such as SWISS-Model through pymol, or alternatively through python? Thanks! and all the best, --Buz -- ___ 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] Homology Modeling in Pymol
On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow b...@mac.com wrote: I have a very large library (almost 1000) of similar genetic sequences, for which I would like to generate homology models. Does anyone know of a way to automate requests to a homology modeling server, such as SWISS-Model through pymol, or alternatively through python? I believe Modeller uses Python - never tried it myself, though. There is a server for Modeller but academic users can download the program itself. There is in fact an API for using SWISS-Model from a Perl script (which could probably be converted to Python, or wrapped by a Python script), which I used years ago for a similar project. As far as I know this is unpublished, probably because they don't want people to trash their server, but they were happy to supply it when I contacted the site maintainer. They asked that I limit the frequency of my requests, however. I would recommend emailing them. (I have no idea how Modeller compares to SWISS-Model, but I suspect it's more rigorous, especially when sequence homology is remote.) There are other ways to go about this - bioinformaticists have been abusing online databases and servers like this for years - but it's considered bad etiquette to do this without permission (and some groups explicitly forbid this use). -Nat -- ___ 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
[PyMOL] Caver 2.0.003 plugin
Has anyone got the Caver 2.0.003 plugin working in Ubuntu 9.04? I can install the plugin in pymol, load the example pdb (1MJ5) and open the dialog box, which seems to have the correct paths to the plugin .jar and lib directory. I can even select the correct starting point and have it displayed in pymol. However, when I click on compute tunnel, I get the error dialog box with: Error: 1 type 'exceptions.RuntimeError' Exception in Tk callback Function: function lambda at 0xb024c6c (type: type 'function') Args: () Traceback (innermost last): File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /home/rrowlett/pymol/modules/pmg_tk/startup/Caver2_0_003.py, line 429, in execute self.CreateDirectory(outdir) File /home/rrowlett/pymol/modules/pmg_tk/startup/Caver2_0_003.py, line 504, in CreateDirectory . . . etc. Same result in pymol 1.2r0 or 1.2b5 The Windows version works OK, but it would be nice to have my Linux workstations work, too. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -- ___ 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] homology modeling in python
Hi Buz (and everyone) The biopython package together with Bizkit (http://biskit.pasteur.fr/) claim to be able to do this sort of thing (see: http://biskit.pasteur.fr/use/workflows/homology-modelling) , and will chew up your processor rather than someone else's! Marcus Collins - Marcus D. Collins NIH NRSA Postdoctoral Fellow Departments of Physics and Chemistry University of Washington -- ___ 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
