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:oganesy...@medimmune.com] >> Sent: Tuesday, December 27, 2011 11:16 AM >> To: pymol-users@lists.sourceforge.net >> 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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
