Rene,
The problem is that each biological unit copy in the PDB is
handled as a separate molecular state (i.e. a movie), which then become
distinct states in PyMOL. Hit play to see what I mean.
To solve this, the most recent versions of PyMOL can split multi-state
objects into multiple single-state objects automatically:
load 1f41_tetra.pdb
split_states 1f41_tetra
dele 1f41_tetra
With older versions, you'll need to create the new objects manually
load 1f41_tetra.pdb
create 1f41_tetra_1, 1f41_tetra, source_state=1, target_state=1
create 1f41_tetra_2, 1f41_tetra, source_state=2, target_state=1
dele 1f41_tetra
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of René Wuttke
> Sent: Tuesday, December 02, 2003 1:08 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Viewing homotetramers with PyMol
>
> Hi everyone,
>
> I am quite new to PyMol and structural biology as well, since I am
> still a student. I installed PyMol via Fink on my iBook running
Panther
> 10.3.1. I want to view the homotetramer of the TTR-protein. I got it
> from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the
> assumed biological molecule is the tetramer. One can download the
> coordinates of this molecule. But when I try to load it in Pymol, only
> the dimer shows up. I am quite sure that this file should contain the
> right coordinates, because the "origin of rotation" differs between
the
> tetramer file and the dimer file. How can display the other dimer?
This
> is necessary in particular, because i am supposed to examine the
loops
> which mediates the dimer-dimer-interaction. Do you want me to send the
> coordinates file to the list?
>
> Thanks in advance and please apologize my bad english,
> René Wuttke
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
