Re: [PyMOL] A structural superimposition and further post-processing

[James S. <jms...@gm...>]

Hi Thomas,

could you also send the same script but just with the Super command
for the superimposition without PSICO?

it's strange I have a problems of PSICO installation on MAC with python 3

Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
README        psico        setup.py
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
  File "setup.py", line 10
    print 'Warning: could not import version'
                                            ^

2017-07-18 19:37 GMT+02:00 James Starlight <jms...@gm...>:
> Hi Thomas,
>
> could you also send the same script but just with the Super command
> for the superimposition without PSICO?
>
> it's strange I have a problems of PSICO installation on MAC with python 3
>
> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>>
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
> README        psico        setup.py
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>   File "setup.py", line 10
>     print 'Warning: could not import version'
>                                             ^
> SyntaxError: Missing parentheses in call to 'print'
>
> 2017-07-18 19:05 GMT+02:00 Thomas Holder <tho...@sc...>:
>> Hi Gleb,
>>
>> If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient:
>>
>> loadall *.pdb
>> import psico.fitting
>> extra_fit *, reference, method=tmalign, object=aln
>> remove not (byres aln)
>>
>> https://pymolwiki.org/index.php/Psico
>>
>> Cheers,
>>   Thomas
>>
>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jms...@gm...> wrote:
>>>
>>> Dear Pymol Users!
>>>
>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>> reference.pdb (it consist of only one GPCR monomer - seven
>>> transmbembrane scaffold).
>>>
>>> I need to write a simple script which will do the following things:
>>>
>>> 1 - allign (in loop) each structure against reference.pdb using
>>> "super" or "TMalign" (is better!)
>>>
>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>> (assuming that each pdb has several chains, some insertions like
>>> lyzocyme which were not aligned against reference), thus keeping only
>>> seven-transmembrane scaffold present in reference.pdb.
>>>
>>> I thanks so much for the help!
>>>
>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>