Ilaria, ConnectedCloud was created to connect different objects, not atoms within a single object. Try changing(*)
cmd.select( cName, "bo. " + subSel + " within 1 of " + cName ) to cmd.select( cName, subSel + " within " + radius + " of " + cName ) which should do the trick, actually. Your call to ConnectedCloud will now look like: connectedCloud yourObj and resi XYZ, yourObj, yourRadius Lastly, I haven't tested any of this, but it should work. :-) (*) -- This also corrects a bug I just found (an correspondingly updated on the wiki; I was ignoring the radius parameter). Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Thu, Jan 7, 2010 at 7:16 AM, ilaria carlone <ilariacarl...@hotmail.com> wrote: > Hi everyone! > > I am using PyMOL for creating molecular surfaces (SAS), starting form a pdb > file. I have some problems with "large" proteins like the head of a protein > kinase, because the program creates some internal surfaces, disconnected > from the larger one. > I have found the ConnecetdCloud tool and I would use it for selecting all > the connected surface atoms taking part to the calculus of the surface. I > don't know if it is a good way. Anyway, I tried to do this and the program > returned an invalid syntax error while specifing the origSel (I tried both > with atom name and aminoacid...). Can anyone help me? > > Thank you very much in advance, > > Ila > > ________________________________ > Foto delle vacanze? Crea il tuo album online e condividile con gli amici! > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
