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):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)
cmd.extend('save_transformed',save_transformed)"
shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
Here I notice that once load a pdb, you move it a little, then you input
"get_view", you will get the matrix like
0.448818117, 0.886667669, -0.111277729
-0.889764965, 0.454960942, 0.036454394
which should be the m[0] to m[5] in the above script.
In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also
a transcript. For matrix it uses *.odb file. Is this *.odb same as the
get_view matrix, if not, can we convert get_view matrix to *.odb?
Besides, in http://www.pymolwiki.org/index.php/Transform_selection there is
another script.
I do not know how to use this scripts to realize my purpose.
Smith
At 2015-11-28 15:07:18, "Jordan Willis" <[email protected]> wrote:
very possible, can you send me the script?
On Nov 27, 2015, at 10:58 PM, Smith Liu <[email protected]> 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
At 2015-11-28 13:11:25, "Jordan Willis" <[email protected]> wrote:
try running
find ~/ -name “newpdb.pdb”
On Nov 27, 2015, at 9:08 PM, Smith Liu <[email protected]> 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 load the pdb, then I input command "run save_trannsforme.py all,
newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find
newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My
pymol is Linux Open-Source PyMOL 1.6.X.
I am looking forward to getting a reply from you on how to get the oriented
pdb, which should be different from the original PDB I load.
Smith
At 2015-11-28 00:44:07, "Shane Caldwell" <[email protected]> wrote:
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, Nov 27, 2015 at 12:59 AM, Smith Liu <[email protected]> wrote:
Dear All，
Once a molecule displayed in pymol, first I input command "orient", then I
input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
oriented newpdb.pdb.
Will you please show me how to get the oriented newpdb.pdb?
Smith
At 2015-11-26 18:58:48, "Spencer Bliven" <[email protected]> wrote:
Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_ScriptingRunning_Scripts
The script defines a new command which can be run e.g. `save_transformed
<object>, <file>`. You don't have to replace anything in the script yourself.
Note that the save_transformed command modifies the object it's run on, so you
might want to run it on a backup copy by first calling `create <object>_backup,
<object>`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <[email protected]> wrote:
Dear All,
For get view, we get something like
set_view (\
0.999876618, -0.000452542, -0.015699286,\
0.000446742, 0.999999821, -0.000372844,\
0.015699454, 0.000365782, 0.999876678,\
0.000000000, 0.000000000, -150.258514404,\
11.842411041, 20.648729324, 8.775371552,\
118.464958191, 182.052062988, 0.000000000 )
For save trasformed pdb file, we need sonething like
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by
get_view? Which item is which item?
In addition, for the save_transformed.py, the last sentence is
"cmd.extend('save_transformed',save_transformed)". Should we replace the second
save_transformed with something, for example *.pdb? Ortherwise how to get the
output modified PDB?
I am looking forward to getting a reply from you.
Smith
At 2015-11-26 14:24:15, "Andreas Forster" <[email protected]> wrote:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Andreas
On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <[email protected]> wrote:
Dear Shane,
get_view is a nice command. Is any way to change the original PDB based on what
we get by set_view to get the new pdb?
Smith
At 2015-11-26 03:54:32, "Shane Caldwell" <[email protected]> wrote:
Hi Smith,
You can type
>get_view
and copy the output into a txt file for later use. The output set_view command
will return the window to the same camera settings
Shane
Shane Caldwell
McGill University
On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <[email protected]> wrote:
Dear All,
Suppose the original PDB was not oriented. Once we have it oriented by pymol,
is any way we can save the new PDB oriented?
Smith
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