[PyMOL] center of mass and distances

Hi all! Two questions: Does anyone know how to read the coordinates (x,y,z) of a selected atom in a protein? Or even better Does anyone know how to visualize the center of mass of the protein, reset the axis (x,y,z) using the centroid as origin and then calculate the distance of a resi or an atom

Re: [PyMOL] center of mass and distances

Am Freitag, 2. März 2007 schrieb Filippo Marchioni: Hi all! Two questions: Does anyone know how to read the coordinates (x,y,z) of a selected atom in a protein? Or even better Does anyone know how to visualize the center of mass of the protein, reset the axis (x,y,z) using the centroid as

[PyMOL] WRL Output

Dear all, I wondered whether there is a possibility in PyMol to export the rendered polygon data in any kind of 3D format such as wrl or inventor? Best, Markus -- PD Markus Wahl, Ph.D. Max-Planck-Institut fuer Biophysikalische Chemie Abteilung Zellulaere Biochemie/Roentgenkristallographie Am

Re: [PyMOL] center of mass and distances

Hi Filippo, Here is a python script that calculates the Center of mass for a given selection and creates a CGO sphere there. It is is not 100% exact as it only weighs C-Alpha atoms. This is exactly how pymol centers selections: when you run the script, the domain is centered and if you rotate

Re: [PyMOL] contour levels in pymol

a mystery to me. Why is there a difference bewteen contour levels of FFT electron density maps displayed in Xfit vs pymol? When using the command for example :isomesh mesh1, fo-fc, 1.0, etc..., in pymol what does 1.0 in terms of sigma level really mean. I was under the assumption that 1.0

Re: [PyMOL] WRL Output

Hi Markus, You can export the scene to pov-ray format, for which you should be able to find a converter for vrml. Best, Tsjerk On 3/2/07, Markus Wahl mw...@gwdg.de wrote: Dear all, I wondered whether there is a possibility in PyMol to export the rendered polygon data in any kind of 3D format

Re: [PyMOL] contour levels in pymol

Peter Gabrielle, Though I can't say for certain what Gabrielle is seeing, generally speaking there is some ambiguity with visualization tools as to how map data is to treated: Some map file formats are normalized by convention (in the file data itself) and others do not. Some visualization

[PyMOL] Sequence Viewer Details

Hello, Where can I find information about the sequence viewer? I would like to know more about the red zeros, etc. --Kevin -- Kevin Neff Mayo College of Medicine Registered Linux User #432952