RE: [PyMOL] residues deviate from protein secondary catoon representation

(becoming an FAQ) For starters, set cartoon_smooth_loops, off set cartoon_flat_sheets, off If that doesn't meet your needs, then you'll need to split your object into separate objects to get the desired effect of mixing smoothed and non-smoothed cartoons. Thankfully, the next version will prov

RE: [PyMOL] Viewing homotetramers with PyMol

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 si

[PyMOL] residues deviate from protein secondary catoon representation

Dear pymol users, I am trying to show some residues in sticks while the whole protein is in cartton representation. However I find that some residues do not attach to the cartoon at all. I understand that the secondary cartoon is an approximation along the backbone. Is there a way that I can show

[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 ass

[PyMOL] Clarification on "A Few Good MacPyMOL OS X Beta Testers"

Sorry, a bit of confusion seems to have arisen over the MacPyMOL beta test. What is MacPyMOL? See below. > Subject: [PyMOL] A Few Good Mac PyMOL OS X Beta Testers > Mac Users: > > I have something new in the works for OS X/Aqua and need some beta > testers for the next couple of months. > > Sp

RE: [PyMOL] cannot 'fit' a particular pdb file

Michael, Try align... Fit only works when all of the atom identifiers match. Align matches atoms through a 1D alignment and then performs some optimization: align TtHisRSca, EcHRSadeca align SaHRSca, EcHRSadeca Cheers, Warren -- mailto:war...@delanoscientific.

[PyMOL] cannot 'fit' a particular pdb file

Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then Sh

FW: [PyMOL] detecting the existence of a selection

(repost: the mailing list was down yesterday afternoon and this message never made it onto the list) -Original Message- From: Warren L. DeLano [mailto:war...@delanoscientific.com] Sent: Monday, December 01, 2003 3:21 PM To: 'Tina Li'; 'pymol-users@lists.sourceforge.net' Subject: RE: [PyMO

RE: [PyMOL] detecting the existence of a selection

>if no atoms were picked, I would see the alarming error messages: >Selector-Error: Unknown keyword or selection. >Selector-Error: Malformed selection. >( ( lb<-- >Is it possible to suppress them and still get the result? Some kind of preliminary existence check might help. Something similar to f

RE: [PyMOL] Object orientation matrices

Laurence, Sort of. Right now PyMOL doesn't fully support translations of individual objects by independent matrices, but you can translate their representations by a matrix for animation purposes using "translate" and "rotate" with the object argument. However, you can cleanly

[PyMOL] More on "A Few Good MacPyMOL OS X Beta Testers"

Sorry, a bit of confusion seems to have arisen over the MacPyMOL beta test. What is MacPyMOL? See below. > Subject: [PyMOL] A Few Good Mac PyMOL OS X Beta Testers > Mac Users: > > I have something new in the works for OS X/Aqua and need some beta > testers for the next couple of months. > > S

[PyMOL] Object orientation matrices

Is there any way of accessing the matrices that define the orientation and position of an individual object relative to the world in PyMol in the same way that get_view and set_view do for the overall view matrix ? --