Re: [PyMOL] distances

Hi Krisztina, > [...] The only nag is how to convert atom IDs in i1 and i2 into > atom names? I usually first prepare an id-to-something map where I later on can look up the desired atom properties (like the name). from pymol import cmd, stored stored.i2n = dict() cmd.iterate('hcpl1 or hcpl2',

[PyMOL] distances

x27;hcpl1 near_to 5 of hcpl2') inoe21=cmd.select('inoe21', 'hcpl2 near_to 5 of hcpl1') cmd.distance('tmp', 'inoe12' ,'inoe21', 5, mode=0) #for (i1, i2, dst) in get_raw_distances.get_raw_distances('tmp'): dist= get_raw_distances('

Re: [PyMOL] distances

Hi Krisztina, the syntax for the "around" operator is wrong, there is no "of" keyword. One of these would be correct: hcpl1 within 5 of hcpl2 hcpl2 around 5 and hcpl1 See also: http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators To iterate over atoms of a selection

[PyMOL] distances

Hi Everyone, I would like to write a script, which writes out intermolecular distances shorter than 5A between hydrogens into a text file. Here is what I made so far on the basis of the Measure distance script in the respository: from pymol import cmd # open dist.txt for writing f=open('dist.t

Re: [PyMOL] distances between rotated molecules

Hi Louise, In PyMOL v1.4 you can now do: set dynamic_measures, on before rotating. PyMOL should update the distance in real time. Cheers, -- Jason On Thu, Apr 7, 2011 at 3:43 AM, Louise Carøe Vohlander Rasmussen wrote: > I loaded two forms A and B of the same molecule and aligned domain 1 >

[PyMOL] distances between rotated molecules

I loaded two forms A and B of the same molecule and aligned domain 1 of A to domain 1 of B. Then I used the rotation command to rotate A, until I was satisfied with the alignment. Now I want to measure distances between A and B, but the distance lines go out into 'space'! Pymol seems to cal

Re: [PyMOL] Distances and Python scripts

Hi Xavier, here is a naive approach to solve problem 2), which should include your first problem. # from pymol import cmd, stored ## setup myProt = "2gsm" mySegm = "" myChain = "B" cmd.fetch(myProt) outfile = open("/tmp/n_

[PyMOL] Distances and Python scripts

Hi all, I have 2 problems regarding the distance command and python scripting: 1/ I would like to use a script in order to print in a file the results of this following command:        distance dist6, (/MyProt/MyProt/A/181/N), (/MyProt/MyProt/A/*/N), 6.0 This command displays distances and d

Re: [PyMOL] distances and selections within states?

to:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Michael Lerner > Sent: Tuesday, April 17, 2007 12:29 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] distances and selections within states? > > Hi, > > I feel like I'm missing something obviou

[PyMOL] distances and selections within states?

Hi, I feel like I'm missing something obvious here. How do I say "Find me the distance between atom1 and atom2 in state 4" or "select all waters that are within 5.0 angstroms of residue 15 during state 7" I'm trying to analyze various properties throughout the course of a trajectory. I made

[PyMOL] distances and list of atoms

Hallo, "'m using the distance command to show hydrogen bonds between two proteins. Is there a way to list the atoms and distances chosen with "distance"? Thanks Sabine

[PyMOL] distances and list of atoms

Hallo, "'m using the distance command to show hydrogen bonds between two proteins. Is there a way to list the atoms and distances chosen with "distance"? Thanks Sabine