[PyMOL] problem saving the transformed coordinate after alignment

[Subha K]

Hi there,

I am trying to save the transformed coordinates of an object after
performing an alignment. I came across the save_transformed.py [
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this
seems to give a completely different coordinate of the object and not the
one that is aligned.

Is there any other way of saving the coordinates of an object after
performing an alignment?

Thanks,
Subha
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Re: [PyMOL] problem saving the transformed coordinate after alignment

[Gabriel Marques]

Subha K,

You can just call cmd.save or save on the object name as so:

fetch 1oky 1t46, async=0
align 1oky, 1t46
save /tmp/1oky_transformed.pdb, 1oky

PyMOL will write out the transformed coordinates of 1oky into the pdb file. The 
structure of the alignment command is such that pymol transforms the first 
object onto the second.

align mobile, target

mobile will have it’s coordinates changed, target will be unchanged.

Regards,
Gabriel Marques
PyMOL


> On Oct 19, 2016, at 1:47 PM, Subha K  wrote:
> 
> Hi there,
> 
> I am trying to save the transformed coordinates of an object after performing 
> an alignment. I came across the save_transformed.py 
> [https://pymolwiki.org/index.php/Modeling_and_Editing_Structures 
> ], but, this 
> seems to give a completely different coordinate of the object and not the one 
> that is aligned.
> 
> Is there any other way of saving the coordinates of an object after 
> performing an alignment?
> 
> Thanks,
> Subha
> --
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! 
> http://sdm.link/slashdot___
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Re: [PyMOL] problem saving the transformed coordinate after alignment

[David Hall]

I think the answer is to just use save, not that save_transformed function.

-David

> On Oct 19, 2016, at 1:47 PM, Subha K  wrote:
> 
> Hi there,
> 
> I am trying to save the transformed coordinates of an object after performing 
> an alignment. I came across the save_transformed.py 
> [https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this 
> seems to give a completely different coordinate of the object and not the one 
> that is aligned.
> 
> Is there any other way of saving the coordinates of an object after 
> performing an alignment?
> 
> Thanks,
> Subha
> --
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Re: [PyMOL] Adding a new internal GUI to Pymol for Leap motion support

[Thomas Holder]

Hi Johan and Casper,

You can create a menu above the mouse mode panel by writing a wizard. There is 
no API documentation for wizards, so you have to learn from existing wizards as 
examples.

You can create an external menu or panel with Tkinter and/or Pmw. See for 
example eMovie as an example for a button panel, or BNI Tools for a multi-level 
menu.

Cheers,
  Thomas

On 10 Oct 2016, at 11:47, Schneiders J, Johan  wrote:

> Dear Pymol community, 
> We are students at the Hanze University of Applied Sciences, the Netherlands.
> Together with our teachers, Tsjerk Wassenaar and Jasper Bosman, we are 
> working on integrating
> the leap motion sensor (hand gesture sensor) into Pymol for moving, and 
> altering the display of, molecules in Pymol.
> 
> We want to create a menu within the GUI of Pymol that will be operated by 
> hand gestures (the amount of extended fingers)
> and display what gestures you can make to manipulate the program.
> 
> Is there a built in way to add/create a menu within Pymol? We have looked on 
> the Pymol wiki, tried googling 
> (keywords: 'pymol edit mouse viewing menu', 'Pymol external GUI', 'pymol 
> adding GUI', 'pymol viewing menu', and so on...), 
> read some of the source code and searched the Pymol user mailing list archive,
> but haven't found a suitable solution.
> 
> In short:
> How do we go about adding an internal menu above the 'mouse mode' menu or 
> adding
> an external window that will run alongside Pymol representing a menu, 
> and adding in our own attributes?
> 
> Thanks in advance,
> 
> Casper Peters and Johan Shcneiders.
> 
> P.S.
> Here are our e-mail addresses for contacting us:
> Casper Peters: c.c.pet...@st.hanze.nl
> Johan Schneiders: j.schneid...@st.hanze.nl

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] problem saving the transformed coordinate after alignment

[Subha K]

Thanks Gabriel and David for the useful suggestion.

Best Regards,
Subha

On Wed, Oct 19, 2016 at 12:11 PM, David Hall  wrote:

> I think the answer is to just use save, not that save_transformed function.
>
> -David
>
> On Oct 19, 2016, at 1:47 PM, Subha K  wrote:
>
> Hi there,
>
> I am trying to save the transformed coordinates of an object after
> performing an alignment. I came across the save_transformed.py [
> https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but,
> this seems to give a completely different coordinate of the object and not
> the one that is aligned.
>
> Is there any other way of saving the coordinates of an object after
> performing an alignment?
>
> Thanks,
> Subha
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
> ___
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>
>
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[PyMOL] Using 'python' and 'python end' in pymol scripts

[#YEO JINGJIE#]

Dear Users,

I am trying to implement a script which uses a mix of pymol and python 
scripting. I enclosed the main portion within the 'python' and 'python end' 
commands. This runs perfectly fine in Pymol GUI mode, however when I tried it 
with 'pymol -cg my_script.py', it generates an error:

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 452, in 
run_file
execfile(file,global_ns,local_ns)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 447, in 
execfile
b.execfile(filename, global_ns, local_ns)
  File "bondH.py", line 122
python end
 ^
SyntaxError: invalid syntax

How do I overcome this problem?

Best Regards,
Jingjie
**Disclaimer** The sender of this email does not represent Nanyang 
Technological University and this email does not express the views or opinions 
of the University.

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Re: [PyMOL] Using 'python' and 'python end' in pymol scripts

[Gabriel Marques]

Rename the script from .py to .pml

Regards,
Gabriel Marques
PyMOL

> On Oct 19, 2016, at 4:39 PM, #YEO JINGJIE#  wrote:
> 
> Dear Users,
> 
> I am trying to implement a script which uses a mix of pymol and python 
> scripting. I enclosed the main portion within the 'python' and 'python end' 
> commands. This runs perfectly fine in Pymol GUI mode, however when I tried it 
> with 'pymol -cg my_script.py', it generates an error:
> 
> Traceback (most recent call last):
>  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 338, in parse
>parsing.run_file(path,self.pymol_names,self.pymol_names)
>  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 452, in 
> run_file
>execfile(file,global_ns,local_ns)
>  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 447, in 
> execfile
>b.execfile(filename, global_ns, local_ns)
>  File "bondH.py", line 122
>python end
> ^
> SyntaxError: invalid syntax
> 
> How do I overcome this problem?
> 
> Best Regards,
> Jingjie
> **Disclaimer** The sender of this email does not represent Nanyang 
> Technological University and this email does not express the views or 
> opinions of the University.
> 
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Re: [PyMOL] Compile error svn 4162

[QT]

Dear Thomas,

Yes, confirmed fixed in rev 4163.  Thank you.

Best,
Quyen

On Tue, Oct 18, 2016 at 5:41 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Quyen,
>
> This should be fixed in svn rev 4163.
>
> Cheers,
>   Thomas
>
> On 18 Oct 2016, at 01:05, QT  wrote:
>
> > Dear all,
> >
> > I'm having a compile error that I've never had before on the current svn
> revision 4162.  Compile broke on file CifDataValueFormatter.cpp
> >
> > g++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE
> -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS
> -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4
> -Ilayer5 -Imodules/cealign/src -Ibuild/generated
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
> -I/home/quyen/lib64/python2.7/site-packages/numpy/core/include
> -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2
> -I/usr/include/python2.7 -c layer3/CifDataValueFormatter.cpp -o
> build/temp.linux-x86_64-2.7/layer3/CifDataValueFormatter.o
> -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math
> -funroll-loops -fcommon -O3
> > In file included from layer3/CifDataValueFormatter.cpp:8:0:
> > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids
> initialization of member 'm_i'
> > layer3/CifDataValueFormatter.h:20:13: error: making 'm_i' static
> > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids in-class
> initialization of non-const static member 'm_i'
> >
> > g++ version 4.5.1
> >
> > Do you have any advise on how to get past this blocker?
> >
> > Best,
> > Quyen
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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