Re: [PyMOL] distance between atoms
Try with the command hide labels -- "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] 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 the user that the molecule is animated. Therefore I can't use
the create function, because it centers and zoom the new object
created, and I doesn't want this.
Anybody know how to apply a transform to a selection, without crating
a new object? Or create a new object without zooming them?
Another subject... why this command outputs me an error?
cmd.transform_selection("all",
[[0.99,-0.116,-0.081,0.391],[0.119,0.993,0.027,0.321],[0.077,-0.037,0.996,0.233],[0.0,0.0,0.0,0.0]],
homogenous=1)
The result is
PyMOL>cmd.transform_selection("all",
[[0.99,-0.116,-0.081,0.391],[0.119,0.993,0.027,0.321],[0.077,-0.037,0.996,0.233],[0.0,0.0,0.0,0.0]],
homogenous=1)
CmdTransformSelection-DEBUG: bad matrix
--
"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] 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 them sequentially, waiting some time between "frames", but is a lot of work, and I don't want to reinvent the wheel. Thanks for your time! [1] http://www.pymolwiki.org/index.php/Transform_selection -- "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
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 a lot, and sorry for my poor english! -- "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] 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. Something like create a,resi 10 apply_transformation_matrix a, [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]] Or I'm just dreaming? Thanks! -- "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] 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
cartoon view?
Thanks!
Toni
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 arg1". It's this possible? -- Unconditional Proenza Fan http://servomac.blogspot.com
[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!
