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" <spencer.bli...@gmail.com> 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 <smith_liu...@163.com> 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" <docandr...@gmail.com> wrote:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Andreas
On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smith_liu...@163.com> 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" <shane.caldwel...@gmail.com> 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 <smith_liu...@163.com> 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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