Re: [PyMOL] Help

Hi Babban,

regarding your questions on peptide building:

> My last doubt is about creating polymers out a given PDB ?
> I am studying the fibrils of some proteins and although the structure of 
> fibril is not know but through some analysis I have come to understand 
> the region in peptide which is leading to fibrillation.

PyMOL has a builder where you can create a peptide with given secondary 
structure. In the external GUI click on "Builder" on the right and then 
"Protein" on the left side.

You may also check this PyMOLWiki page:
http://www.pymolwiki.org/index.php/Peptide_Sequence

> I want to be able to create a PDB which has like 4/8/16 monomeric 
> peptide combined through some BETA PLEATED region(i.e the peptides will 
> join/aggregate around that region (beta region) of the peptide ) and all 
> I have is the PDB of the monomeric peptide.

As far as I know there's no build-in PyMOL function that sticks together 
two beta-strands.

In editing mode you can freely drag around objects: Right-click, "drag 
object coords", SHIFT+Middle-Mouse-Drag.

More precide movements can be achived with translate and rotate commands:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures#Translate_or_rotate_individual_objects

If this is not precise enough for you and you want real beta-sheet 
modeling, you should use something like modeller.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen