Re: [PyMOL] Viewing cavities?

ns Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 "You have opened a new door, and I share this with you, for I have been where you are now." **

[PyMOL] Bfactor

How can I the Bfactor for each residue in pymol script? Bingding

[PyMOL] conformation change

Hi, I want to generate a figure that shows clearly the conformation change upon ligand-binding in 3tga(unbound) and 1mtw (ligand bound). The ligand-binding site is a small pocket in the 3tga and is bigger pocket in bound structure. The loops of resi 190-195 strech to allow ligand binds. I want

[PyMOL] corresponding residue pairs after alignment

Dear all, After use "align" command to align two protein structures in pymol, how can I get the corresponding residue paire or atom pairs which are used to calculate the RMSD value in pymol? Thanks a lot! Bingding

[PyMOL] How can I the coordinates of the mesh representation of a protein in PyMol?

In PyMol, we can visualize the protein surface as mesh representation ("show mesh"). Now I want to print out the coordinates of every point in the mesh representation. How can I do that? Thanks Bingding

[PyMOL] orient the molecule

Hi, When I try "orient" command to orient the molecule, the camera changes but the coodinates don't change. I wonder whether it is possible that when I orient the molecule the coodinates also change. Thanks Bingding

Re: [PyMOL] orient the molecule

after orient it. Regards Bingding Hi, I think that you should use translate[x,y,z] to change the coordinates of your molecule bye andrea 2005/4/21, Bingding Huang : Hi, When I try "orient" command to orient the molecule, the camera changes but the coodinates don't change. I

[PyMOL] gradient color scheme in pymol

Is there any gradient color scheme in pymol? i.e, different residues have different values and I want to color them in a gradient color scheme in pymol. For example, green for a value of 1, blue for a value of 2, red for a value of 5 and so on! Thanks! -- Bingding Huang PhD student

Re: [PyMOL] gradient color scheme in pymol

. For example, green for a value of 1, blue for a value of 2, red for a value of 5 and so on! Thanks! -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (

[Fwd: Re: [PyMOL] orient the molecule]

-- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049 351 46340061 Mobile: 01772981375 E-mail: bhu...@biotec.tu-dresden.de --- Begin Mes

[PyMOL] discontiguous surface patches

I want to get surface patches using expand like select res, resi 14 select patch, res expand 6.0 But I got some discontiguous surface patches which are not what I want. How can I get rid of the discontiguous part of surface patches? Thanks Bingding -- Bingding Huang PhD student

[PyMOL] vdw volume

Hi, How to get the vdw volume of a selection in pymol and how to set different radii for atoms? Thanks Bingding -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 440

[PyMOL] mesh represenation of surface

I am wondering where I can find mesh represenation of protein surface in PyMol API. -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049

Re: [PyMOL] "show surface" and the "get_view" cmd

e.net/lists/listinfo/pymol-users -- Bingding Huang PhD student Bioinformatics group Biotec & Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049 351 46340061 Mobile: 01772981375 E-mail: bhu...@biotec.tu-dresden.de