There were some errors in the executing pymol script with your commands using
@ script.pml
or
run script.pml
probably because of my MAC Pymol which is v 1.74 mb outdated, no?
BTW on the same MAC I just have tried to install updated setup.py and
it was the following error:
Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
File "setup.py", line 7
<!DOCTYPE html>
^
SyntaxError: invalid syntax
2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> With super instead of tmalign:
>
> loadall *.pdb
> extra_fit *, reference, method=super, object=aln
> remove not (byres aln)
>
> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>
> Cheers,
> Thomas
>
>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> 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 <jmsstarli...@gmail.com>:
>>> 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 <thomas.hol...@schrodinger.com>:
>>>> 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 <jmsstarli...@gmail.com>
>>>>> 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.
>
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