[PyMOL] moving molecules separately

2005-03-16 Thread Joel Tyndall
Hi again, I found it! Fore those who have the same question, In 3 button edititing mode (click in the bottom right to toggle), if you click and hold on the molecule with shift down it moves on its own! Sorry to clog up the box but its always the way ...as soon as you ask, you remember! Che

[PyMOL] moving molecules separately

2005-03-16 Thread Joel Tyndall
Hi folks, I know the mouse command is out there but I can't seem to find it. I want to move one molecule and not the other (with at least two molecules read in). So I can use it with manual alignment. How do I do it? Cheers J -- Joel Tyndall, PhD Lecturer National School of Pharmacy Unive

RE: [PyMOL] surfaces and transparency

2005-03-16 Thread Garcia, Tzintzuni I.
To smooth your surface representation try: set surface_quality, 1 or higher if you wish, though it will take longer and might look odd. The easiest way to do the other things would be to create separate objects for each type of display. Example: Show solid surface over most of a protein, with

Re: [PyMOL] surfaces and transparency

2005-03-16 Thread Virgile ADAM
Dear Paula, for smoothen rendering, you can use the "smooth", "set ribbon_smooth"... commands or try to raytrace your molecule thanks to the "ray" command. Concerning transparency, there is no simple way to my knowledge to render transparency on some of the residues of a single loaded protein. Yo

[PyMOL] surfaces and transparency

2005-03-16 Thread Paula Salgado
Hi, I'm a new pymol user and have been trying to generate an image of a solvent-accessible surface in pymol. How can I smooth the surface representation? Another questions relates to transparency: is it possible to have bits of a protein transparent and others coloured? If so, how can you do it?