Re: [PyMOL] sequence file extraction

[Thomas H. <sp...@us...>]

Hi Stefano,

this is a known bug and it has not been fixed yet. A workaround is to 
only save one object at a time to fasta format.

See bug report:
http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546

Cheers,
   Thomas

On 07/24/2012 12:08 PM, Stefano Marzi wrote:
> I have got the same problem with pymol 1.5.0.4 and restarting the
> computer is not fixing it.
>
> Any help please?
>
> Thanks
>
> Stefano
>
> Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit :
>> Never mind. After restarting the computer fasta file is being written.
>>
>>        Vaheh
>>
>>
>> -----Original Message-----
>> From: Oganesyan, Vaheh [mailto:Oga...@Me...]
>> Sent: Tuesday, December 27, 2011 11:16 AM
>> To: pym...@li...
>> Subject: [PyMOL] sequence file extraction
>>
>> I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
>> I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
>> =========================
>> Traceback (most recent call last):
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
>>       self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
>>       st = _self.get_fastastr(selection)
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
>>       if seq.has_key(obj):
>> AttributeError: 'str' object has no attribute 'has_key'
>> =========================
>>
>> Is there now a different way of extracting sequence info in PyMOL?
>>
>> Thank you.
>>
>>        Vaheh

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen