Hi Carsten,
Is there an (un)documented way of merging multiple molecular objects in
Pymol into one molecule, which then can be written in a nicely formatted PDB
file? I cobbled something cludgy together with ‘multisave’ and a couple
read-sort-save cycles, but this is ugly and probably quite fragile. An API
function might be much more robust. Is there a provision like this in
ChemPy? I’ve already taken care of adjusting each molecule to be unique with
respect to chain IDs and IDs, so that would not be an issue.
It's documented:
* help create
* http://www.pymolwiki.org/index.php/Create
Create can be used to create a single single-state object or a single
multi-state object. The former will just 'do what you say' but may
create biologically unrealistic molecules (it just combines the
objects). The latter is better as it saves to biologically realistic
multi-state pdbs. Try these examples:
# method 1
# create a single state (possibly biologically infeasible) molecule
# from two objects
frag ala
frag cys
save test.pdb, ala or cys
Now load test.pdb.
# method 2
# create a single multi-state object from two molecules
frag ala
frag cys
create test, ala, 1, 1
create test, cys, 1, 2
save test.pdb, test, state=0
Cheers,
-- Jason
On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
Hi,
Is there an (un)documented way of merging multiple molecular objects in
Pymol into one molecule, which then can be written in a nicely formatted PDB
file? I cobbled something cludgy together with ‘multisave’ and a couple
read-sort-save cycles, but this is ugly and probably quite fragile. An API
function might be much more robust. Is there a provision like this in
ChemPy? I’ve already taken care of adjusting each molecule to be unique with
respect to chain IDs and IDs, so that would not be an issue.
Any pointers would be appreciated.
Cheers,
Carsten
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