Smith,
Let's take this off-list. I will reply to you directly. We can send a summary
to the list once it's working for you.
Cheers,
Thomas
On 29 Nov 2015, at 22:13, Smith Liu wrote:
> Dear Thomas,
>
> I do not know I still do something wrong.
>
> First I load a PDB in pymol, then I input
Dear Thomas,
I do not know I still do something wrong.
First I load a PDB in pymol, then I input orient (with orient input the
molecule really moved significantly in display), then I input
transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb,
the withneworientation.pdb
Hi Smith, and everybody who tried to help you so far,
Short answer: copy and paste this into the PyMOL command line, it will save the
view-transformed object to "transformed.pdb" in your home folder.
cv=list(cmd.get_view())
cmd.transform_selection("all", \
cv[0:3]+[0.0]+ \
cv[3:6]+[0.0]+ \
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
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“.
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,
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):
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
>
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
