TransWikia.com

Loop Pymol command get_area

Bioinformatics Asked by shome on August 16, 2021

I want to select multiple residues from different PDB files loaded on the same pymol session.

select resi LIG
get_area sele

How do I loop the above command to enable the command below:

select ligands,resn LIG

One Answer

from https://www.blopig.com/blog/2019/08/how-to-iterate-in-pymol/

Example 1: Print the names of all the selected objects

You’ve selected several objects in PyMOL, and you want to see their names. By default, a new selection object called “(sele)” is created. We can create a Python variable called seleobjs, say, and then loop over them:

seleobjs = cmd.get_object_list('(sele)')
    for obj in seleobjs: print obj

Example 2: Disable all the selected objects

If you still have your selection, “(sele)”, you can disable them (effectively turn them off on the right-hand sidebar):

seleobjs = cmd.get_object_list('(sele)')
    for obj in seleobjs: cmd.disable(obj)

Example 3: Delete all the selected objects

You’re done with the objects in your selection, “(sele)”: you might be able to delete them using “delete ”, but if you can’t write a wildcard that covers all the names of the objects, you can iterate over a selection and delete them:

seleobjs = cmd.get_object_list('(sele)')
    for obj in seleobjs: cmd.delete(obj)

from https://pymolwiki.org/index.php/Get_Area

get_area calculates the surface area in square Angstroms of the selection given. Note that the accessibility is assessed in the context of the object(s) that the selection is part of. So, to get the surface areas of e.g. a component of a complex, you should make a new object containing a copy of just that component and calculate its area.

please let us know if it worked

Answered by pippo1980 on August 16, 2021

Add your own answers!

Ask a Question

Get help from others!

© 2024 TransWikia.com. All rights reserved. Sites we Love: PCI Database, UKBizDB, Menu Kuliner, Sharing RPP