Re: [PyMOL] on PDB

[Smith L. <smi...@16...>]

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" <spe...@gm...> 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 <smi...@16...> 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" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> 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" <sha...@gm...> 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 <smi...@16...> 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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