[modeller_usage] structure not read in

["Nicolas Fusseder" <>]

Hello,

I have an application which models protein sequences based on template
structures which are found by blasting the query sequence against all
sequences from pdbaa. The entire modeling process works fine, only when
one of the templates structures found via blast was solved with Cryo-EM
the modelling process fails with the following error (sorry for the nasty
formatting):

C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks>mod8v2
C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks.py
C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File
"C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks.
py", line 8, in ?
    a.make()
  File "C:\Program
Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in
make
    self.homcsr(exit_stage)
  File "C:\Program
Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 331, in
homcsr
   aln.check()
  File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line
153, in check
   io=io.modpt, libs=libs.modpt, **vars)
  File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line
37, in check_alignment
   return _modeller.check_alignment(aln, io, libs, *args)
_modeller.error: check_a_337E> Structure not read in (please consult the
log file for more details):        1  1D3E1
ExitValue: 0
Status(3): Loading file...
Status(1): Load failed!



alignment file looks like this:

C; Produced by MODELLER

>P1;1D3E1
structureE:1D3E:1    :1:285  :1:MOL_ID  1;  MOLECULE  INTERCELLULAR
ADHESION MOLECULE-1;  CHAIN  I;  FRAGMENT:MOL_ID  1;  FRAGMENT  1 - 185; 
ORGANISM_SCIENTIFIC  HOMO SAPIENS;  ORGANISM_CO:28.00:-1.00
APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSG
CIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAP
IPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSE
QLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV*

>P1;FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks
sequence:FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks:1    : :113  : :::-1.00:-1.00
----VGHD------------SGGFSTTVSTGQSVPDPQVGITTM---KDLKANR-----GKMDVSGVQAPVG---
----AITTIED---------------------------------------PVLAKK-------------------
VPET---------------------FPELK-----------------PGE---SRH----------------TSD
HM-------SIYKFMGRSHFLC---------TFTFNSNNK---EKEYTFPI---TL----*


I also noticed that unlike sucessful modelling attemps, when I attempt to
model with 1D3E (Cryo-EM structure) as a template structure the .RSR as
well as a .D00000001 file are never created.

All help would be greatly appreciated,

Sincerely,

-- 
Nicolas Fusseder