AttributeError: Segment has no attribute name about kinconform HOT 7 CLOSED

On Tue, Jul 25, 2017 at 11:20 AM, fabricecarles ***@***.***> wrote: Hi, I am interested by your tools, but unfortunately when a want to use it against the structure 1atp (rename here test1atp.pdb) I get the following error: kinconform test1atp.pdb Traceback (most recent call last): File "/bin/kinconform", line 169, in <module> results = do_one(args) File "/bin/kinconform", line 133, in do_one temp,posn = get_sequence(x) File "/bin/kinconform", line 55, in get_sequence chains = [x.name for x in prot.segments] File "/usr/lib64/python2.7/site-packages/MDAnalysis/core/groups.py", line 2709, in __getattr__ "".format(cls=self.__class__.__name__, attr=attr)) AttributeError: Segment has no attribute name Any idea ? could you provide the exact version of each dependencies ? I suspect an issue with version of MDAnalysis. For your intention I have install the last MDAnalysis version using pip pip install --upgrade MDAnalysis Collecting MDAnalysis Downloading MDAnalysis-0.16.2.tar.gz (2.6MB) 100% |████████████████████████████████| 2.6MB 285kB/s Sincerely — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB1HovephKsw8Sgydnw-0E9CW_1ICJFiks5sRgepgaJpZM4Oith0> .

On Wed, Jul 26, 2017 at 10:02 AM, fabricecarles ***@***.***> wrote: Hi Daniel, Thank a lot for this quick patch. Now I have a mistake with an other fonction... I have add in my bashrc the mapgaps1.0.1 bin executable after extraction of the tar.gz export PATH=$PATH:/home/carles/Documents/sources/mapgaps1_0_1/bin Then I run a test from mapgaps1_0_1/example/run_example shell script and everything seem to be ok. Unfortunately when I try to run kinconform from my /home I get the following error. kinconform struct1atp.pdb struct1atp.pdb Traceback (most recent call last): File "/bin/kinconform", line 179, in <module> results = do_one(args) File "/bin/kinconform", line 150, in do_one mapping = align_and_map_fasta('pdbs.fasta', positions, basedir) File "/bin/kinconform", line 83, in align_and_map_fasta mapping = make_mapfile(fasta+'_aln.cma',positions) File "/bin/kinconform", line 25, in make_mapfile block = cma.read(aligned_seq) File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 12, in read File "build/bdist.linux-x86_64/egg/biocma/cma.py", line 16, in parse File "/usr/lib64/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "build/bdist.linux-x86_64/egg/biocma/sugar.py", line 34, in maybe_open IOError: [Errno 2] No such file or directory: 'pdbs.fasta_aln.cma' Did I miss something on the configuration of my environnement ? where is supposed to be the pdbs.fasta_aln.cma file ? Fabrice — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB1HoqW6JiVcwzGzsDYn_DUw41I0R3Ysks5sR0cRgaJpZM4Oith0> .