[PyMOL] Missing parts in cartoon mode

Hi everybody I am getting quite desperate! For some strange reason PyMol do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon display mode. When I display the structure in "lines" or "sticks" everything is ok. Other pdb-viewers dont have this problem with the same .pd

[PyMOL] [colors frozen for rendering modes defined in .pymolrc]

Hello, I defined some default colors in the $HOME/.pymolrc file. E.g.: set cartoon_color, slate It works fine but in PyMOL viewer (version 0.98) I cannot change the color for rendering modes I defined. The one I defined is always kept. Is this a normal behavior ? Thanks -- Sébastien Morett

Re: [PyMOL] Missing parts in cartoon mode

Which parts are missing? Looks fine to me... Although the pdb file has some horrible features. Some residues are multiply defined (eg 170 in chain H) and there is some kind of poly- calcium binding tail in chain L. gilleain torrance On 14 Oct 2005, at 10:43, wrote: Hi everybody I am

[PyMOL] Need testers for new MacPyMOL on Tiger

For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its own copy (in part this is necessary preparation for Intel...). http://delsci.com/beta Please let me know how it works for you! Cheers, Warren

Re: [PyMOL] Need testers for new MacPyMOL on Tiger

Hi, Works great for me! Very nice to have access to the system python. gilleain torrance On 14 Oct 2005, at 16:50, Warren DeLano wrote: For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its ow

[PyMOL] script feedback: how print out distance and not average

Hi all, this script below runs well in pymol. It loads pdb files and calculates the distance of some atoms contained in the fileAmb whose format is: 26,O11:HN 28,*:HE1 ... With * I select whole ligand (segi B) and pymol returns only one value, the average distance for all atoms to the H

[PyMOL] Pharmacophore visualizations

Has anyone done anything with with making PyMol able to display pharmacophores as CGOs? Being able to align molecules in pymol with a defined pharmacophore would be nice too, but I realize that doing that would require much more effort from some developer. For the time being, it would be good t

Re: [PyMOL] ugly font in GUI, FAQ wrong

Thanks Renato. My distribution is Ubuntu. But, what I want is independent of distribution. There's a default font being used by Pymol and I want to change it, like you do in nedit, for instance. Cheers, Alan On 14/10/05, Joao Renato Carvalho Muniz wrote: > Hey Alan > > What's your linux distro