Re: [PyMOL] save_transformed.py

[Thomas Holder]

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 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 was really saved, but the newly saved 
> withneworientation.pdb has the all atom orientations (x,y,z) exactly same as 
> those of the original PDB I initially input to the pymol for the process I 
> obtained the withneworientation.pdb.
> 
> Smith

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] save_transformed.py

[Thomas Holder]

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]+ \
  cv[6:9]+[0.0]+ \
  cv[12:15]+[1.0], transpose=1)
cmd.save('~/transformed.pdb')

To comment on the many emails that have been posted so far:

1) I think you haven't used the script correct. Instead of "run 
save_trannsforme.py all, newpdb.pdb", you have to do "run save_transformed.py", 
followed by "save_transformed all, newpdb.pdb"
2) The script is actually wrong (missing transpose=1)
3) A correct solution has been posted for example here:
https://sourceforge.net/p/pymol/mailman/message/27824450/

Hope that helps.

Cheers,
  Thomas

On 28 Nov 2015, at 02:52, Jordan Willis  wrote:

> 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 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“. Is any way we 
>> can get this oriented pdb?
>> 
>> Smith
>> 
>> 
>> At 2015-11-28 15:37:10, "Jordan Willis"  wrote:
>> 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,
>>> 
>>> 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"  wrote:
>>> 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
 
 
 At 2015-11-28 13:11:25, "Jordan Willis"  wrote:
 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 

Re: [PyMOL] save_transformed.py

[Smith Liu]

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 was really saved, but the newly saved 
withneworientation.pdb has the all atom orientations (x,y,z) exactly same as 
those of the original PDB I initially input to the pymol for the process I 
obtained the withneworientation.pdb.




Smith







At 2015-11-30 08:08:52, "Thomas Holder"  wrote:
>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]+ \
>  cv[6:9]+[0.0]+ \
>  cv[12:15]+[1.0], transpose=1)
>cmd.save('~/transformed.pdb')
>
>To comment on the many emails that have been posted so far:
>
>1) I think you haven't used the script correct. Instead of "run 
>save_trannsforme.py all, newpdb.pdb", you have to do "run 
>save_transformed.py", followed by "save_transformed all, newpdb.pdb"
>2) The script is actually wrong (missing transpose=1)
>3) A correct solution has been posted for example here:
>https://sourceforge.net/p/pymol/mailman/message/27824450/
>
>Hope that helps.
>
>Cheers,
>  Thomas
>
>On 28 Nov 2015, at 02:52, Jordan Willis  wrote:
>
>> 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 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“. Is any way 
>>> we can get this oriented pdb?
>>> 
>>> Smith
>>> 
>>> 
>>> At 2015-11-28 15:37:10, "Jordan Willis"  wrote:
>>> 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,
 
 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"  wrote:
 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
> 
> 
> At 2015-11-28 13:11:25, "Jordan Willis"  wrote:
> 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 

Re: [PyMOL] save_transformed.py

[Jordan Willis]

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
> 
> 
> 
> 
> 
> At 2015-11-28 13:11:25, "Jordan Willis"  wrote:
> 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 

Re: [PyMOL] save_transformed.py

[Jordan Willis]

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 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“. Is any way we can get 
> this oriented pdb?
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-11-28 15:37:10, "Jordan Willis"  wrote:
> 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,
>> 
>> 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" > > wrote:
>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-28 13:11:25, "Jordan Willis" >> > wrote:
>>> 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.
 
 

Re: [PyMOL] save_transformed.py

[Smith Liu]

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“. Is any way we can get this 
oriented pdb?


Smith







At 2015-11-28 15:37:10, "Jordan Willis"  wrote:
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,


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"  wrote:
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







At 2015-11-28 13:11:25, "Jordan Willis"  wrote:
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_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 

Re: [PyMOL] save_transformed.py

[Smith Liu]

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"  wrote:
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







At 2015-11-28 13:11:25, "Jordan Willis"  wrote:
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_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:

Re: [PyMOL] save_transformed.py

[Jordan Willis]

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,
> 
> 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"  wrote:
> 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
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-28 13:11:25, "Jordan Willis" > > wrote:
>> 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, `
>>> 

[PyMOL] save_transformed.py

[Smith Liu]

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, 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_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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