Re: [PyMOL] storing 3d vectors in python

2013-05-07 Thread Tsjerk Wassenaar
Hi Bharat, Not exactly a Pymol question, is it? But in case you're using a list of simple vectors as tuples or lists you can easily add them the Python way, provided that the list is not too long (or it'll be slow): vecs = [(a,b,c),(d,e,f),...] v = [sum(i) for i in zip(vecs)] Alternatively, you

[PyMOL] repair the missing loop in crystal structure

2013-05-07 Thread yp sun
Dear pymol users,     Are there anyone know how to modeling the missing fragment in a crystal structure? This missing fragment may be a flexible loop and so its disordered the electron density is invisible.Thanks. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF

Re: [PyMOL] Pymol error

2013-05-07 Thread David Hall
by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas,

Re: [PyMOL] Pymol error

2013-05-07 Thread Rhitankar Pal
Hi David, I installed tcl without the corefoundation and now while trying to install pymol I am getting the following error message: Error: org.macports.archivefetch for port pymol returned: tk must be installed without +quartz. How can I install tk without +quartz? Are these issues happening

Re: [PyMOL] Pymol error

2013-05-07 Thread David Hall
sudo port install tk -quartz It has nothing to do with what OS X ships with, it has to do with current macports defaults, which changed around 18 months ago. You can dig around the macports bug reports to see discussion of the change. -David On Tue, May 7, 2013 at 1:32 PM, Rhitankar Pal