RE: [PyMOL] Radii in Angstrom

Yusuf, alter selection, vdw=radius eg. alter elem c, vdw=3.2 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872

[PyMOL] Radii in Angstrom

Hi, if I show up a sphere around an picked atom, and want to change its radius, I always use the set sphere_scale method. But, to which value am I scaling to? Isn't it possible to change the radius of a sphere with something like 'set sphere_radius' in Angstroms? I could not find any information

Re: [PyMOL] run script

Hi, yes it worked. that mistake is so shameful ... :P thanks andrea 2005/6/30, lie...@ultr.vub.ac.be : > On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > > from pymol import cmd > > file=open("file.nam") > > for i in file.readlines(): > > cmd.load(i) > > You may have to strip the tr

Re: [PyMOL] run script

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > from pymol import cmd > file=open("file.nam") > for i in file.readlines(): > cmd.load(i) You may have to strip the trailing newline ("\n") from each file name by using "cmd.load(i.strip())". Hope this helps, -- Lieven Buts Vrije Univ

Re: [PyMOL] run script

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > from pymol import cmd > file=open("file.nam") > for i in file.readlines(): > cmd.load(i) You may have to strip the trailing newline ("\n") from each file name by using "cmd.load(i.strip())". Hope this helps, -- Lieven Buts Vrije Univ

[PyMOL] run script

Hi this is my "unsuccessful" first script for pymol. I have a series of files: prot1.pdb prot4.pdb prot55.pdb and so on I'd like to open them using a loop (instead to open one by one) I cat them to a file and then I tried to open all of them in pymol: from pymol import cmd file=open("file.nam") fo

RE: [PyMOL] Sum distances in loop via python script

Hello, thanks for the prompt reply, it works great! Cheers Yusuf Quoting Warren DeLano : Yusuf, see http://sourceforge.net/mailarchive/forum.php?thread_id=7495694&forum_id=60 Close! Actually I like you're usage expectation even better than how PyMOL currently works -- but at the present t

Re: [PyMOL] Renumber protein segid

Hi Joel, thanks a lot for the tip! excellent stuff using my loved editor! andr 2005/6/29, Joel Tyndall : > Hi andrea, > > I have found an excellent add on tool for emacs which does a lot of > renumbering stuff (on unix/linux) > > http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html >