From: Margaret Luk-P. <ma...@ph...> - 2006-10-15 18:08:23
|
Hello -- Can someone please advise me? I'm a new user of PyMol trying to get the kabsch alignment script to work. I only installed the main pymol installer (v 0.99r6), and I have copied the kabsch.py script as the wiki said. However, I can't find this Numeric.py you are referring to in the wiki... The wiki infers that the Numeric.py script is a native part of the installer, but I don't seem to have it in my folders anywhere. Obviously, kabsch doesn't want to run either. I am running PyMol v0.99r6 on RHE4 (intel32). I'm a bit of a newbie when it comes to the more advanced tools with PyMol, so maybe I forget to install something? Does it require the APBS plugin to work? Any help would be appreciated. Thanks! Sincerely yours, Maggie L.-P. SUNY Stony Brook |
From: Shiven S. <shi...@gm...> - 2006-10-16 04:12:17
|
On 10/15/06, Margaret Luk-Paszyc <ma...@ph...> wrote: > > Hello -- > > Can someone please advise me? > I'm a new user of PyMol trying to get the kabsch alignment > script to work. I only installed the main pymol installer > (v 0.99r6), and I have copied the kabsch.py script as the > wiki said. However, I can't find this Numeric.py you are > referring to in the wiki... The wiki infers that the > Numeric.py script is a native part of the installer, but I > don't seem to have it in my folders anywhere. Obviously, > kabsch doesn't want to run either. I am running PyMol > v0.99r6 on RHE4 (intel32). > > I'm a bit of a newbie when it comes to the more advanced > tools with PyMol, so maybe I forget to install something? > Does it require the APBS plugin to work? > > Any help would be appreciated. > > Thanks! > > Sincerely yours, > Maggie L.-P. > SUNY Stony Brook Hi Maggie, Numeric.py is usually located (on Windows platforms) under "C:\Program Files\DeLano Scientific\PyMOL\modules\Numeric" If you see the wiki, this is also listed under the "Notes" section of the Kabsch wikipage. The changes you need to make to Numeric.py are also listed in the same section. Here is a direct link: http://pymolwiki.org/index.php/Kabsch Best, Shiven |
From: Margaret J. Luk-P. <ma...@ph...> - 2006-10-16 18:40:44
|
Shiven Shandilya wrote: > > > On 10/15/06, *Margaret Luk-Paszyc* <ma...@ph... > <mailto:ma...@ph...>> wrote: > > Hello -- > > Can someone please advise me? > I'm a new user of PyMol trying to get the kabsch alignment > script to work. I only installed the main pymol installer > (v 0.99r6), and I have copied the kabsch.py script as the > wiki said. However, I can't find this Numeric.py you are > referring to in the wiki... The wiki infers that the > Numeric.py script is a native part of the installer, but I > don't seem to have it in my folders anywhere. Obviously, > kabsch doesn't want to run either. I am running PyMol > v0.99r6 on RHE4 (intel32). > > > Hi Maggie, > > Numeric.py is usually located (on Windows platforms) under > "C:\Program Files\DeLano Scientific\PyMOL\modules\Numeric" <snip> Thank you for your help, but I think you misunderstood my post. As I said, I am using Linux (red hat enterprise edn v4), not Windows. And at least in the Linux distro of PyMol, there is no numeric.py in any of the subfolders. My guess is that the numeric.py is required for the window install, but I just don't know. The wiki also says that this works for all installs of PyMol 0.97 and greater, but it looks like the page was written a while ago and something may have changed in v0.99. Any more suggestions from the lot? :) Your desperate-to-align-in-PyMol-user, Maggie L.-P. |
From: David B. <db...@ny...> - 2006-10-17 01:37:50
|
Maggie, I found that I need to install the python-scientific package for my distro (Ubuntu Dapper) in order to get the LinearAlgebra and Matrix python modules required by the script. Can you forward the error message you're getting when you try to run kabsch.py in pymol? Best, David |
From: Robert C. <rob...@qu...> - 2006-10-16 14:39:41
|
Hello Margaret, * Margaret Luk-Paszyc <ma...@ph...> [2006-10-15 14:07] wrote: > Hello -- > > Can someone please advise me? > I'm a new user of PyMol trying to get the kabsch alignment > script to work. I only installed the main pymol installer > (v 0.99r6), and I have copied the kabsch.py script as the > wiki said. However, I can't find this Numeric.py you are > referring to in the wiki... The wiki infers that the > Numeric.py script is a native part of the installer, but I > don't seem to have it in my folders anywhere. Obviously, > kabsch doesn't want to run either. I am running PyMol > v0.99r6 on RHE4 (intel32). > > I'm a bit of a newbie when it comes to the more advanced > tools with PyMol, so maybe I forget to install something? > Does it require the APBS plugin to work? Numeric is a python module (independent of PyMOL) that you need to install. If you do a google search for "python-numeric rpm rhel4" you would find something like this: http://rpm.pbone.net/index.php3/stat/4/idpl/1953241/com/python-numeric-23.7-2.i386.rpm.html There you will find a number of links to the python-numeric-23.7-2.i386.rpm file that you need to install (I'm assuming that version 23.7.2 works here). Perhaps another RHEL4 user can offer better advice. I use Debian GNU/Linux myself. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://adelie.biochem.queensu.ca/~rlc |