[PyMOL] dss & ribbon representation

Hi pymol community. Two questions. - The dss algorithm is great, a very quick way to assign secondary structure. Is there a way of conserving the information when saving the pdb? Sometimes it's nice to edit the assignment. - In contrast to versions 0.9 and earlier, version 0.93 connects the CA wi

Re: [PyMOL] Spheres and backbone coloring

slo...@mail.med.upenn.edu: > does anyone know how to color only the ribbon of a polypeptide, while > not coloring the CA atoms when using spheres? > duplicate your polypeptide, show the ribbon of one instance and atoms of another one -igor

[PyMOL] you know what would be cool?

When making a movie It would be cool if you could set way-points to create a sophisticated "tour" of your molecule. Each way-point would be a different view of your molecule. Then you could specify the number of frames between any two way-points (views). Each frame would be a specified amount

[PyMOL] Spheres and backbone coloring

Hi, does anyone know how to color only the ribbon of a polypeptide, while not coloring the CA atoms when using spheres? If I say "color grey, name ca", then the CA atoms of my spheres representations are also colored grey. thanks Avram -- Avram M. Slovic Biochemistry and Molecular Biophys

[PyMOL] RE: surface area calculation

Warren L. DeLano wrote: >> 1) "get_area selection" command will return the effective surface area >> of the dots that you would see from "show dots, selection". This is a >> discrete approximation -- not an exact calculation. >> >> 2) you can use the "dot_solvent" setting to control whether you

RE: [PyMOL] Reference

http://pymol.sourceforge.net/faq.html#CITE -- 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.so

[PyMOL] RE: Stereo parameters, again

> I still do not understand your stereo parameters: the > stereo_angle should > define the rotation (around the y-axis) between the pictures > for the left and > right eye, whereas the stereo_shift should define whether the > origin or > midpoint of the picture is within the plane of the scre

[PyMOL] stereo inversion?

Dear PyMol users, I've got an annoying effect under RedHat 9.0 with a Nvidia Quadro4 980 XGL graphics card, the most recent Nvidia driver and Stereographics glasses & emitter: occasionally, the hardware stereo is inverted (back appears in front and vice versa) and doesn't come back to normal mo