Re: [PyMOL] FInd the number of residues within a selection

2012-05-02 Thread Thomas Holder
Hi Anasuya, what you need is: count_atoms byca (sele) Cheers, Thomas Anasuya Dighe wrote, On 05/02/12 19:27: > Hello, > > I wanted to know what is the command-line syntax for finding out the number of > residues which fall within a selection made in PyMOL. > > Once the selection is made, t

[PyMOL] FInd the number of residues within a selection

2012-05-02 Thread Anasuya Dighe
Hello, I wanted to know what is the command-line syntax for finding out the number of residues which fall within a selection made in PyMOL. Once the selection is made, the command line shows the number of atoms selected, but I wanted to know the number of residues present in such subsequent selec

Re: [PyMOL] Intel Video - Please Respond

2012-05-02 Thread Michael Banck
Hi, On Mon, Apr 09, 2012 at 11:01:35AM -0400, Jason Vertrees wrote: > The latest commit (3995) should fix this for the Intel card. Try > pulling the latest (3996) from the open source branch. That worked splendidly, I am uploading pymol-1.5.0.1 with some subversion changesets to Debian now. Are

Re: [PyMOL] Improved Plugin Manager

2012-05-02 Thread Michael Banck
Hi, On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote: > Thanks for this feedback. Since the inception the Script Library on > the PyMOLWiki the policy is that all deposited scripts are > open-source: > http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy. > This link i

Re: [PyMOL] Attachment of two proteins via disulfide

2012-05-02 Thread Thomas Holder
Hi Julianne, put the two molecules into one object, preferably with different chain identifiers. Example: alter molecule1, chain="A" alter molecule2, chain="B" create combined, molecule1 molecule2 delete molecule1 molecule2 Now you can bond the two atoms. You can also use the "fuse" command wh

Re: [PyMOL] Improved Plugin Manager

2012-05-02 Thread Jason Vertrees
Hi Michael, Thanks for this feedback. Since the inception the Script Library on the PyMOLWiki the policy is that all deposited scripts are open-source: http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy. This link is "Policy" from the PyMOLWiki Scripts page. Cheers, -- Jason On

Re: [PyMOL] Improved Plugin Manager

2012-05-02 Thread Thomas Holder
Hi Michael, meta information is implemented in the new plugin system. The syntax is very simple, just put it at the beginning of the python file like this: # License: BSD-2-Clause # Author: Your Name # Version: 1.0 ''' Plugin XYZ for PyMOL Here some more general description, link to PyMOLWiki p

Re: [PyMOL] Improved Plugin Manager

2012-05-02 Thread Michael Banck
On Mon, Apr 30, 2012 at 01:14:39PM -0400, Jason Vertrees wrote: > This is just a quick note to let you know that as of revision 3997 > PyMOL has an improved plugin/script manager. This system was written > by Thomas Holder as part of his PyMOL Open Source Fellowship. Some new > features include: >

[PyMOL] Attachment of two proteins via disulfide

2012-05-02 Thread Julianne Kitevski
I would like to attach two proteins with a disulfide linkage via two cysteine residues I introduce using the mutation wizard. I know the 'bond' command can be used for intramolecular disufides, but is there a way to introduce intermolecular disulfides? Thanks JK

Re: [PyMOL] Dont resequence atoms when saving

2012-05-02 Thread Jason Vertrees
Hi Martin, I don't think there's a fix for this. Please file a bug report on the open-source tracker. Cheers, -- Jason On Mon, Apr 30, 2012 at 10:09 AM, Martin Hediger wrote: > Dear Pymol users > We are trying to generate a number of mutated structures using the > mutagenesis wizard. However,