Hi Pascal, PyMOL treats .pml and .py files differently. The "cluster_count" script was written as a .py file as needs to be used as such.
run cluster_count.py cluster_count PO4 worked just fine when run as a Python file. Cheers, -- Jason On Tue, Jul 9, 2013 at 6:06 AM, Pascal Auffinger <p.auffin...@ibmc-cnrs.unistra.fr> wrote: > Hi, > > I tried to use the "cluster_count" script > (http://www.pymolwiki.org/index.php/Cluster_Count) > in a pymol.pml file. Unfortunately I get the following message: > --- > PyMOL>cluster_count PO4 > Traceback (most recent call last): > File "/home/sws2/Desktop/pymol/modules/pymol/parser.py", line 464, in > parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "<string>", line 1 > cluster_count PO4 > ^ > SyntaxError: invalid syntax > --- > (PO4) is a selection of five atoms > > When I use the same script as a pymol plugin, it works fine > when I type in the command "cluster_count PO4" > > Any idea ??? > > Thanks for helping, > > Pascal > > > > ----- > Pascal Auffinger > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex > > p.auffin...@ibmc-cnrs.unistra.fr > ----- > > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ 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
