[PyMOL] Fwd: Apply a transformation matrix to a selection

create a, resi cmd.transform_selection(a, [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]], homogenous=1) Thanks (is better late than never)! But I want to apply a set of selective transformations with a time between them (using the time.sleep() function of python), making the efect to

[PyMOL] Animations between two pdb files

Hi! I wish to show a smart animation between two pdb files, or between two loaded objects. Something like a transform_selection[1], but doing the transformation like a movie. I don't know if exists such a feature in Pymol, and obviously I can make some intermediate transformation matrix and apply

Re: [PyMOL] Distance labels

An object whose name begins with an underscore will not appear in the menu. Perfect! But how can I change the name of one name in the Names Panel? -- Two of the most famous products of Berkeley are LSD and Unix. I don't think that this is a coincidence. http://servomac.blogspot.com

[PyMOL] Distance labels

Hi! When I create a distance in a pymol session, an object called dist n is created, and a label with there name is shown at the right of the screen, with the other objects loadeds. Can I create a dist, and render the dotted line at the screen, without having the label in the right menú? Thanks

[PyMOL] Apply a transformation matrix to a selection

Hi people! I'm trying to apply a transformation matrix to a few atoms in a representation. By now I'm using a python script that modify the position vector directly in the pdb, and then load the new pdb, but I think that should exist some other way to apply the matrix direct with the pymol.

[PyMOL] Transparency in cartoons

Hello! I'm trying to show some aminoacids transparent in a cartoon view. I use the command cmd.set(transparency, 0.8 ,(resi + values[0] + : + values[1] + )). When i see the cartoon view, happens nothing, but if I use show surface the transparency is shown. Do you know how to do it in the

[PyMOL] Distance and scripts

Hi guys! I hope you enjoy your time with Pymol, it's so nice ;) I have a few doubts; anybody know if it's possible to change the color of the dotted line drawn by the distance command? How can I pass an argument to a python script run with run script.py? Thank you!

Re: [PyMOL] Distance and scripts

I'm not sure this is what you're asking, but I use scripts by typing: @script.pml Thanks for your response, but I'm asking how to pass arguments to pymol's scripts written in Python. I type run nameOfScript.py within pymol for this, but I would pass some arguments, such as run script.py arg0