Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan

Date: Fri, 14 Dec 2007 19:55:39 -0500 From: Ryan <pavlovicz.7@osu.edu> Subject: Re: [Chimera-users] printing "zone" search To: chimera-users@cgl.ucsf.edu Message-ID: <17bf4817f850.17f85017bf48@osu.edu> Content-Type: text/plain; charset=us-ascii

Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like.

So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try:

print chimera.selection.currentResidues()

i get a list like this:

...

[<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ]

but if i try:

for x in chimera.selection.currentResidues(): print x

i get output that is much closer to what i'm looking for:

...

#0:499 #0:496 ...

What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]?

Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again,

ryan