Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system files for pymol, which will depend on your operating system and
architecture.
Shane
Shane Caldwell
McGill University
On Fri, No
Dear All,
Osvaldo is new here for this question, so I repeat it a little. By pymol I open
a pdb and orient it and I want to save the oriented pdb. First I input command
"orient" after load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newp
try running
find ~/ -name “newpdb.pdb”
> On Nov 27, 2015, at 9:08 PM, Smith Liu wrote:
>
>
> Dear All,
>
> Osvaldo is new here for this question, so I repeat it a little. By pymol I
> open a pdb and orient it and I want to save the oriented pdb. First I input
> command "orient" after lo
By Jordan,
by
find ~/ -name “newpdb.pdb” or by
find / -name “newpdb.pdb”
still does not work. Is any possibility the original "save_transformed.py" does
not work?
Smith
At 2015-11-28 13:11:25, "Jordan Willis" wrote:
try running
find ~/ -name “newpdb.pdb”
On Nov 27, 20
very possible, can you send me the script?
> On Nov 27, 2015, at 10:58 PM, Smith Liu wrote:
>
> By Jordan,
>
> by
>
> find ~/ -name “newpdb.pdb” or by
>
> find / -name “newpdb.pdb”
>
> still does not work. Is any possibility the original "save_transformed.py"
> does not work?
>
>
> Smith
>
Dear Jordan,
My purpose is, once you move a molecule in pymol, I want to save a new pdb,
when we open the new pdb, pymol will display the new position as default.
The script is
"# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
get view takes in camera coordinates. You can’t open a PDB and it have know
anything about the camera view. You will have to grab the view, save it
somewhere, and then load it. You can’t code a view change within the PDB.
> On Nov 27, 2015, at 11:27 PM, Smith Liu wrote:
>
> Dear Jordan,
>
>
Dear Jordan,
To save a new view is not my purpose, my purpose is to save a new set of PDB.
For example， if the original PDB does not orient well by pymol by default,
first I input "orient", and I want to save a set of new pdb, when I display by
pymol the new pdb, it will display as "oriented“.
Yes, but what you are describing, saving a new view is your purpose. All orient
does is move the camera. It does not do anything to the x,y,z coordinates of
the PDB.
> On Nov 27, 2015, at 11:49 PM, Smith Liu wrote:
>
> Dear Jordan,
>
> To save a new view is not my purpose, my purpose is to s
