Hi Miguel, The trouble with your code was you needed to use needle(a.xformCoord()) instead of needle(a.coord()) The a.coord() gives the coordinates in the molecule's local coordinates while a.xformCoord() gives the coordinates in global Chimera coordinates which is what the place_marker() routine wants. Tom Miguel Ortiz Lombardia wrote:

Dear Tom,

I'm naively trying to modify your molecular voodoo script to have needles pointing to selected residues (specifically to their CA atoms) I would really appreciate if you can help me with two probably simple questions. Firstly, this is my current code

8<----------------------------- def needle(center):

xyz_in = center xyz_out = center[0]+5,center[1]+5,center[2]+5

from chimera import selection selection.clearCurrent() from VolumePath import place_marker place_marker(xyz_in) place_marker(xyz_out)

from chimera import selection, UserError atoms = [a for a in selection.currentAtoms() if a.name == 'CA'] if not atoms: raise UserError("No CA atoms selected")

for a in atoms: needle(a.coord()) ------------------------------>8

And these are the questions:

1. Why the positions of the m1 markers don't correspond to those of the CA atoms? 2. How could I modify the code to make every marker go to a different set, so I can then rotate them one by one appropriately so the figure shows the 'needles' in different directions, so that I can label them later on without overlap?

I hope it isn't too silly...

Cheers,

-- Miguel Ortiz Lombardía !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! NEW ADDRESS !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Architecture et Fonction des Macromolécules Biologiques UMR6098, CNRS, Université Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2