Re: [PyMOL] on PDB

[Jordan Willis]

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 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"  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  > 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"  > 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_Scripting 
>  Running_Scripts 
> 
> 
> The script defines a new command which can be run e.g. `save_transformed 
> , `. 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 
> _backup, `
> 
> -Spencer
> 
> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  > wrote:
> Dear All,
> 
> For get view, we get something like
> 
>  set_view (\
>0.999876618,   -0.000452542,   -0.015699286,\
>0.000446742,0.99821,   -0.000372844,\
>0.015699454,0.000365782,0.999876678,\
>0.0,0.0, -150.258514404,\
>11.842411041,   20.648729324,8.775371552,\
>118.464958191,  182.052062988,0.0 )
>  
> 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"  > wrote:
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures 
> 
> 
> 
> Andreas
> 
> 
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  > 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"  > 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  > 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
> 
> 
>  
> 
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 
> 
> 

Re: [PyMOL] on PDB

[Smith Liu]

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"  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  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"  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 
, `. 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 _backup, 
`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  wrote:

Dear All,


For get view, we get something like


 set_view (\
   0.999876618,   -0.000452542,   -0.015699286,\
   0.000446742,0.99821,   -0.000372844,\
   0.015699454,0.000365782,0.999876678,\
   0.0,0.0, -150.258514404,\
   11.842411041,   20.648729324,8.775371552,\
   118.464958191,  182.052062988,0.0 )
 
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"  wrote:

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





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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"  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  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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Re: [PyMOL] on PDB

[Shane Caldwell]

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  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"  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_Scripting
>  Running_Scripts
> 
>
> The script defines a new command which can be run e.g. `save_transformed
> , `. 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
> _backup, `
>
> -Spencer
>
> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  wrote:
>
>> Dear All,
>>
>> For get view, we get something like
>>
>>  set_view (\
>>0.999876618,   -0.000452542,   -0.015699286,\
>>0.000446742,0.99821,   -0.000372844,\
>>0.015699454,0.000365782,0.999876678,\
>>0.0,0.0, -150.258514404,\
>>11.842411041,   20.648729324,8.775371552,\
>>118.464958191,  182.052062988,0.0 )
>>
>> 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"  wrote:
>>
>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>
>>
>> Andreas
>>
>>
>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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" 
>>> 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  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





 --
 Go from Idea to Many App Stores Faster with Intel(R) XDK
 Give your users amazing mobile app experiences with Intel(R) XDK.
 Use one codebase in this all-in-one HTML5 development environment.
 Design, debug & build mobile apps & 2D/3D high-impact games for
 multiple OSs.
 http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>>
>>
>>
>> --
>> Go 

Re: [PyMOL] on PDB

[Smith Liu]

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"  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 
, `. 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 _backup, 
`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  wrote:

Dear All,


For get view, we get something like


 set_view (\
   0.999876618,   -0.000452542,   -0.015699286,\
   0.000446742,0.99821,   -0.000372844,\
   0.015699454,0.000365782,0.999876678,\
   0.0,0.0, -150.258514404,\
   11.842411041,   20.648729324,8.775371552,\
   118.464958191,  182.052062988,0.0 )
 
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"  wrote:

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





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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"  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  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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Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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Archives: h

Re: [PyMOL] on PDB

[Spencer Bliven]

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_Scripting
 Running_Scripts


The script defines a new command which can be run e.g. `save_transformed
, `. 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
_backup, `

-Spencer

On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  wrote:

> Dear All,
>
> For get view, we get something like
>
>  set_view (\
>0.999876618,   -0.000452542,   -0.015699286,\
>0.000446742,0.99821,   -0.000372844,\
>0.015699454,0.000365782,0.999876678,\
>0.0,0.0, -150.258514404,\
>11.842411041,   20.648729324,8.775371552,\
>118.464958191,  182.052062988,0.0 )
>
> 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"  wrote:
>
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>
>
> Andreas
>
>
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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" 
>> 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  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
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>>
>>
>>
>> --
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
>
>
>
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
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Re: [PyMOL] on PDB

[Smith Liu]

Dear All,


For get view, we get something like


 set_view (\
   0.999876618,   -0.000452542,   -0.015699286,\
   0.000446742,0.99821,   -0.000372844,\
   0.015699454,0.000365782,0.999876678,\
   0.0,0.0, -150.258514404,\
   11.842411041,   20.648729324,8.775371552,\
   118.464958191,  182.052062988,0.0 )
 
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"  wrote:

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





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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"  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  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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Re: [PyMOL] on PDB

[Andreas Forster]

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


Andreas


On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  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" 
> 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  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
>>
>>
>>
>>
>>
>> --
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
>
>
>
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
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Re: [PyMOL] on PDB

[Smith Liu]

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"  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  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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Re: [PyMOL] on PDB

[David Hall]

http://pymolwiki.org/index.php/Save ??

-David

> On Nov 24, 2015, at 9:45 PM, Smith Liu  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
> 
> 
>  
> 
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
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Re: [PyMOL] on PDB

[Shane Caldwell]

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  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
>
>
>
>
>
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
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> OSs.
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[PyMOL] on PDB

[Smith Liu]

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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Re: [PyMOL] on PDB display and calculation

[Jared Sampson]

Hi Smith - Check out the `orient` and `clip` commands.  

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

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


Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

> On Nov 23, 2015, at 12:15 AM, Smith Liu  wrote:
> 
> Dear All,
> 
> Once I have displayed a tetramer PDB by pymol, is any way I can get the 
> central axis of the tetramer and display it? Is any way I can get the 
> cross-section of the tetramer (perpendicular to the central axis) and display 
> it? If the tetramer is asymmetric, then how to get the central axis and 
> cross-section？
> 
> Smith
> 
> 
> 
> 
>  
> --
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Re: [PyMOL] on PDB display and calculation

[Julian Heinrich]

Hi Smith,

are you looking to visualize symmetrie axes? Then this might be a starting
point:
http://www.pymolwiki.org/index.php/SuperSym

Cheers,
Julian

On Mon, Nov 23, 2015 at 4:15 PM, Smith Liu  wrote:

> Dear All,
>
> Once I have displayed a tetramer PDB by pymol, is any way I can get the
> central axis of the tetramer and display it? Is any way I can get the
> cross-section of the tetramer (perpendicular to the central axis) and
> display it? If the tetramer is asymmetric, then how to get the central axis
> and cross-section？
>
> Smith
>
>
>
>
>
>
>
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
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[PyMOL] on PDB display and calculation

[Smith Liu]

Dear All,


Once I have displayed a tetramer PDB by pymol, is any way I can get the central 
axis of the tetramer and display it? Is any way I can get the cross-section of 
the tetramer (perpendicular to the central axis) and display it? If the 
tetramer is asymmetric, then how to get the central axis and cross-section？


Smith



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