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,