Hi There,
I am looking to automate the calculation of centre of mass and placing a
pseudo atom on the COM and save it as a pdb file . Going through the forum [
https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some
useful scripts for this, but, I am having trouble getting it don
Hi Subha,
Probably this will get close:
for pdb in open('./out').readlines():
pdb = pdb.strip()
cmd.load(pdb,'tmp')
cmd.pseudoatom('tmp',name='pseudo')
cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
cmd.delete('tmp')
cmd.delete('pseudo')
... Just a bit too much for a oneliner
Every time you loop through the list of files, you set X=1 ; you do your X=X+1
in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going
to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2,
then back to X=1 before you process the next entry. That is wh
Thanks David and Tsjerk for the kind reply and suggestion.
I Figured a solution by combining both of your suggestions
def center(selection, com=True):
model = cmd.get_model(selection)
xyz = np.array(model.get_coord_list())
mass = [i.get_mass() for i in model.atom]
xyz_m = xyz
Hi Subha,
Sorry, my bad. It should've been object='pseudo' and not name='pseudo'.
Should've tested it first.
Cheers,
Tsjerk
On Wed, Oct 12, 2016 at 9:56 PM, Subha K wrote:
> Thanks David and Tsjerk for the kind reply and suggestion.
>
> I Figured a solution by combining both of your suggestio
Oh yes, I am not familiar with the pymol options yet. So, couldn't figure
that out.
Thanks anyways for the quick help.
Cheers,
Subha
On Wed, Oct 12, 2016 at 2:02 PM, Tsjerk Wassenaar wrote:
> Hi Subha,
>
> Sorry, my bad. It should've been object='pseudo' and not name='pseudo'.
> Should've test
