i am new to pymol. i dont know how the coordinates are made in pdb file.
cold someone tell me? how do we arrive at the coordinates from crystal
cold we change the coordinated of the existing pdb file?
also cold any one tell me how to introduce a substrate? eg when i am viewing
the structure of a lipase how could i introduce the substrate in to pymol.
thanking you in advance.
Novozymes south asia pvt ltd
Hi Mohan Raj,
> i am new to pymol. i dont know how the coordinates are made in pdb file.
This is not really related to Pymol. Maybe you should go to
http://www.rcsb.org/pdb and have a look around.
> cold someone tell me? how do we arrive at the coordinates from crystal
Do you mean from a crystal structure, or from a crystal? Structure
implies that the coordinates have been solved already from the
crystal. Solving them from a crystal is is a field by itself (if you
neglect the obtaining/growing of the crystals :)).
> cold we change the coordinated of the existing pdb file?
Coordinates are just numbers, so of course they can be changed. Just
have a look at a pdb file. For some reason I presume you're using
Windows, don't blame me if I'm wrong, but in that case you might want
to use wordpad or so (notepad may not be suited when the files were
written under linux). If you happen to work under linux anyway, then
you should know how to view files.
> also cold any one tell me how to introduce a substrate? eg when i am viewing
> the structure of a lipase how could i introduce the substrate in to pymol.
> thanking you in advance.
Pymol is also not really the tool of choice for that. If you want to
do docking, find a docking program. I think you might want to do some
more general background reading in structural biology.
Tsjerk A. Wassenaar, Ph.D.