From: <re...@wu...> - 2003-12-02 21:08:26
|
Hi everyone, I am quite new to PyMol and structural biology as well, since I am=20 still a student. I installed PyMol via Fink on my iBook running Panther=20= 10.3.1. I want to view the homotetramer of the TTR-protein. I got it=20 from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the=20 assumed biological molecule is the tetramer. One can download the=20 coordinates of this molecule. But when I try to load it in Pymol, only=20= the dimer shows up. I am quite sure that this file should contain the=20 right coordinates, because the "origin of rotation" differs between the=20= tetramer file and the dimer file. How can display the other dimer? This=20= is necessary in particular, because i am supposed to examine the loops=20= which mediates the dimer-dimer-interaction. Do you want me to send the=20= coordinates file to the list? Thanks in advance and please apologize my bad english, Ren=E9 Wuttke= |
From: Warren L. D. <wa...@de...> - 2003-12-02 22:07:52
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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=3D1, target_state=3D1 create 1f41_tetra_2, 1f41_tetra, source_state=3D2, target_state=3D1 dele 1f41_tetra=20 Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154=20 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] On Behalf Of Ren=E9 Wuttke > Sent: Tuesday, December 02, 2003 1:08 PM > To: pym...@li... > Subject: [PyMOL] Viewing homotetramers with PyMol >=20 > Hi everyone, >=20 > 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? >=20 > Thanks in advance and please apologize my bad english, > Ren=E9 Wuttke >=20 >=20 > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |