[PyMOL] H-bonds too thick
I am drawing hydrogen bonds using command dist, but the "rayied" image has a too thick line to these interactions. I was not able to find the command to set the thickness of it, but I hope someone (DeLano?) will be able to help me. Thank you indeed. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] Cell
I would like to know if anyone knows how to set up cell thickness and color. I am trying to generate a picture of a packing and I would like to show the unit cell in a white background. Thanks. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] Cell
I would like to know if anyone knows how to set up cell thickness and color. I am trying to generate a picture of a packing and I would like to show the unit cell in a white background. Thanks. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] e-density around atoms
Hi all I am trying to draw an eletronic density around some specific atoms only, but pymol always draw a box in the region. I am using the following comand: ## isomesh den, map21, 1.0, (c;A & i;12 & !n;n,o,ca,cb | c;A & i;89 & !n;n,o,ca,cb | c;E & i;327), 0.4 ## The problem is that the e-density for aa E327, for exemple, is cutted due the box. Is there a way to draw the density only around the selected atoms without defining this box? Thanks. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] 2D scketch
Sorry 'couse it is not a directly related question. I am trying to find some program like Chemdraw or ACD chemscketch to Linux. I already find some, but all not so good like these. Can anyone give me some tip? Thank you in advance. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] Colors and labels.
I have some questions using pymol and I wonder if someone can give me some help. At first I would like to know if there are any way to define more colors than that appearing in the menu. Is there some kind of "rgb" definition, for exemple? I also tried to change the colors of the sticks only, without success. When I chance the colors of the atoms in side chains it works, but changing color of carbon alpha causes change in cartoon too. Is there a way to do it? Finally I didn't find a way to put labels in residues -- like Tyr-25 beside a tyrosine -- and to make "ray" of it. I will appreciate very much any suggestion. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
