Dear all, thanks a lot for your answers. I seem to have a problem though. When running the script, one way or another I always ends up with something like: a.residue.removeAtom(a) AttributeError: 'NoneType' object has no attribute 'removeAtom' AttributeError: 'NoneType' object has no attribute 'removeAtom' File "M:\REUNIONS\dibuixos\Manipulate_structure\newres.py", line 20, in <module> a.residue.removeAtom(a) See reply log for Python traceback. I think I got the origin of the problem but can't figure out how to solve it. What I observed is that, before running the script if I do the following after selecting my atoms:

...

...

for a in at: print a.residue I have the following list printed

UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 but doing the same AFTER having run the script gives : None UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 ... It seems like the residue type of the first atom disappeared. Any clue? all the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: Eric Pettersen <pett@cgl.ucsf.edu> Data: Divendres, Març 11, 2011 8:29 pm Assumpte: Re: [Chimera-users] Selection through bond and fragment naming

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