Carsten,

What about http://www.pymolwiki.org/index.php/List_Selection and http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar script for retrieving object names: http://www.pymolwiki.org/index.php/GetNamesInSel.

Cheers,

-- Jason


On Fri, Jan 31, 2014 at 10:30 AM, Schubert, Carsten [JRDUS] <CSCHUBER@its.jnj.com> wrote:

Hi All,

 

probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not flexible enough. For large molecules the performance is not great either.

 

 

#### start script

def list_resi(obj=""):

    """

DESCRIPTION

 

    "list_resi" prints and returns the unique residue IDs from the input

                object. The object must be present in the object list

                on the GUI. Selections are currently not implemented.

                Chain or Segments are also not taken into account

USAGE

 

                list_resi obj

 

EXAMPLES

 

    list_resi my_prot

 

    l = list_resi(my_prot)

    """

 

    if ( obj == "" ):

        obj="(all)"

 

    ol = cmd.get_object_list()

    if (obj in ol):

        pass

    else:

        print "Error: Object (%s) not found" % obj

        return

 

    stored.resi_list = []

    cmd.iterate(obj,"stored.resi_list.append(int(resi))")

    stored.resi_list=list(set(stored.resi_list))          # make list unique

    stored.resi_list.sort()

   

    for i in range(0,len(stored.resi_list)):

        print "%s," % stored.resi_list[i],

        if ((i+1) % 10 == 0):

            print ""

   

    return stored.resi_list

 

##### End Script

 

Thanks for any input

 

 

                Carsten


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&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.Vertrees@schrodinger.com
(o) +1 (603) 374-7120