RE: [PyMOL] multi distance object to single distance objects

Hi Daniel, This problem has been tackled several times, maybe have a look at the following URLs, it might help you getting started: http://www.rubor.de/bioinf/tips_python.html#msdist http://sourceforge.net/mailarchive/message.php?msg_id=2914266 And also don’t forget the ‘search’ feature

RE: [PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO

The question is: how can I then delete the created MyColor object? I tried the cmd.delete command, it does not generate an error but apparently the color is still defined... Any idea?! Colors can't be undefined, and that would especially be true if an object is still using a given color,

[PyMOL] Creating PDB files from Primary Sequence

Hello, This may be slightly off-topic, but I was wondering whether PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used for structural refinements (minimizations, etc.) elsewhere. If PyMol cannot do this, is

RE: [PyMOL] Creating PDB files from Primary Sequence

James, PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used Just hold down ALT/OPTION and type in the peptide sequence. The numbering will be arbitrary, but at least you'll have something to work with.

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi James, Sounds like you want a homology model type set up, ie generate coordinates based on a template. Modeller can do this and an easier way is via the swissmodel http://swissmodel.expasy.org//SWISS-MODEL.html If however you want a relatively random structure then pymol _can_ do this.

Re: [PyMOL] Creating PDB files from Primary Sequence

Thanks for the prompt responses, Warren and Joe! Works like a charm! Now, I just wish that my Kensington Expert Mouse could function as a true three button mouse...is there a keystroke that mimics the third mouse button? Thanks again, james