Re: [Chimera-users] Selection through bond and fragment naming

11 Mar 2011

      On Mar 11, 2011, at 7:42 AM, Jean Didier Pie Marechal wrote:
...
Hi,
I have a system from which I only have xyz coordinates. What I would  
like to do is to define myself residue attribute on different  
fragments of the molecules. Could you tell me how (or if there is a  
way to ):
1. expand a selection to bonding atoms (i.e. I click on one atom and  
expand selection through one bond after each actions) This would be  
of the easiest way for me to select the fragments I want to.
Hi JD,
	My only idea as to how to do this is with a short Python script:

from chimera.selection import currentAtoms, addCurrent
addAtoms = set()
for a in currentAtoms():
	addAtoms.update(a.neighbors)
addCurrent(addAtoms)

	You could then use the open command to run it:

open <script folder location (e.g. ~marechal/scripts)>/expand.py

which you could short to "xp" with the alias command:

alias ^xp open blah-blah/expand.py
...
2. set a residue attribute to the given selected fragment. I think I  
remember how to do so in scripting, but what is the command line to  
do so?
So, do you really want to set a residue-level attribute, or do you  
want to organize the selected atoms into a residue?  Setting a residue- 
level attribute for the atoms is easy:

	setattr r myAttrName my-attr-val sel

Organizing the atoms into a residue again requires Python, and not as  
simple a script as for your first question, e.g.:

# script designed to run under "runscript" command, therefore has an  
"arguments" variable available...
try:
	rname, rnum = arguments
except ValueError:
	raise chimera.UserError("must supply residue name and number  
arguments")

try:
	rnum = int(rnum)
except ValueError:
	raise chimera.UserError("residue number (second arg) must be an  
integer")

atoms = chimera.selection.currentAtoms()
if not atoms:
	raise chimera.UserError("No atoms selected")

# make a new residue
newRes = atoms[0].molecule.newResidue(rname, "A", rnum, ' ')

# withdraw atoms from their current residues
for a in atoms:
	a.residue.removeAtom(a)
	if len(a.residue.atoms) == 0:
		a.molecule.deleteResidue(a.residue)

# add atoms to new residue
for a in atoms:
	newRes.addAtom(a)

	So you would run this script with the command "runscript blah-blah/ 
newres.py TYR 1", which could again be shorted using aliasing:

	alias ^nr runscript blah-blah/newres.py $1 $2

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu