Hi,
* Lisa Craig [2005-01-27 20:43] wrote:
>
> How do I select side chains without selecting the backbone atoms?
>
Add "&! n. n+ca+c+o" or in long form "and not name n+ca+c+o" to your
selection. So to colour all arginine and lysine side chains blue:
color blue, r. arg+lys &! n. n+ca+c+o
Ch
Dear PyMOL community,
I am trying to use the align command (from within python)
and want to evaluate the pairwise matches.
the command
cmd.align(sel1, sel2, object="alignment")
should do. Sorry for this stupid question,
but how do I get hold of the "alignment" object, and what is its
function
Andreas,
It's not a stupid question -- its just a year or more ahead of its time.
Right now "aligment" objects currently don't do anything other than show you
which atoms were aligned in the 3D viewer. In time however, those objects
will integrate with the sequence-viewer...
Cheers,
Warren
>
Eiza,
This isn't possible yet -- first someone needs to chemical recognition
patterns, atom names, atom types, formal charges, partial charges and radii
for nucliec acids to the dictionaries in the files:
PyMOL/modules/chempy/champ/amber99.py
and
PyMOL/modules/chempy/champ/formal_charges.py
hi,
i want to combine the models in a biounit file. for example,
ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.gz
has two models. so, i
- load it
- split_states on it
- save everything into a pdb file
but .. the pdb file ends up empty (it's just an END line).
Thanx Warren, perfect! But when entering:
"> load map1.dsn6
> slice_new slice1,map1
I get the message:
Syntax Error: invalid syntax with a ^ pointing to the "1" in slice1
I have tried several permutations of the syntax, but always receive an
error message!
On 27 Jan 2005 at 22:51, Warren DeLan
