[phenixbb] phenix.mr_model_preparation_1.8-1069 can't parse hhr

Dmitry Rodionov dmitry.rodionov at mail.mcgill.ca
Sat Sep 1 21:39:58 PDT 2012


Dear all,

I was trying to run MR_rosetta, but encountered a problem: my hhr files can't be parsed. GUI does not recognize files as HHR and phenix.mr_model_preparation_1.8-1069 exits with the error below. I can't figure out what does it want from me. Any help will be greatly appreciated.

Best regards,
	Dmitry

Reading homology search file: local.hhr
Sorry: Uninterpretable: 'Q ss_pred             CC-CCCeEEEEECCCCcccccCHHHHHHHHHHHHHhCCCcEEEEechHHH------------------------------\nQ Sht1-d52         42 AP-IPQRVWQTWKVGADDKNFPSSFRTYQKTWSGSYSPDYQYSLISDDSI------------------------------   90 (428)\nQ Consensus        42 ~~-IPk~IwQtW~~~~~~~~lP~~~~~~i~sW~~~~nP~~~~~l~~D~~~------------------------------   90 (428)\n                      .+ |||+||.+|.++    .+|+..+.|+.+| ++.+|||++.+|+|.++                              \nT Consensus        93 ~~~IPKiIHyIWiGg----~~P~~~~~yI~sW-kk~~PDYei~lW~Dsna~lA~~LKk~i~e~A~~~~~~~~~~~~~d~~  167 (551)\nT 2vk9_A           93 STIASKNLSFIWIGG----PISDQSLEYYNMW-KMFNKDYNIRLFYDKNSLLVNTLKTAIIQESSKVIIEQNQSNILDGT  167 (551)\nT ss_dssp             SCBCCSEEEEECCSS----CCCHHHHHHHHHH-HHHCTTSEEEEEECTTCCCHHHHHHHHHHHHHHHHHHTTSGGGTTTS\nT ss_pred             CCCCCcceEEEEcCC----CCCHHHHHHHHHH-HHHCcCCEEEEEeccchHHHHHHHHHHHHHHHHHHHHHHhhccCccc\n\n\nQ ss_pred             --------------------------------------HHHHHHhcccChHHHHHHHh----------------------\nQ Sht1-d52         91 --------------------------------------IPFLENLYAPVPIVIQAFKL----------------------  110 (428)\nQ Consensus        91 --------------------------------------~~~V~~~~~~~Pdv~eay~~----------------------  110 (428)\n                                                            .+|+...++...+.++.|..                      \nT Consensus       168 ~~~~~fy~~~l~~i~~~Q~~f~Nyy~~~~~~~s~D~~ri~yL~~~~~~d~eeLe~~k~~n~~ki~~~~g~DIr~l~~f~~  247 (551)\nT 2vk9_A          168 YGHNKFYSDRMKLIYRYKRELKMLYENMKQNNSVDDIIINFLSNYFKYDIGKLNNQKENNNNKMIAIGATDINTENILTN  247 (551)\nT ss_dssp             CCSCTHHHHHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHTCEEGGGTTCSCH\nT ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcCCCchhHHHhhh\n\n\nQ ss_pred             -----------cC-chHHHHHHHHHHHHHHcCCEEEecCceee--ccHHHhhccchh-----------------------\nQ Sht1-d52        111 -----------MP-GNILKADFLRYLLLFARGGIYSDMDTMLL--KPIDSWPSQNKS-----------------------  153 (428)\nQ Consensus       111 -----------lp-~~i~kAD~lRyllL~~~GGIY~DiDt~~l--kPi~~wi~~~~~-----------------------  153 (428)\n                                 ++ +.+..||++|+.+|+.+||||+|+|++|-  ..+-.-|.....                       \nT Consensus       248 ~~~~~Y~~e~~~r~N~aaASDi~R~~il~~~GGiY~D~D~lP~~s~~v~k~I~~~~~~~~~~~e~~~Le~I~k~~~li~~  327 (551)\nT 2vk9_A          248 KLKSYYYQELIQTNNLAAASDILRIAILKKYGGVYCDLDFLPGVNLSLFNDISKPNGMDSNYWEAAIFEAIANEKKLMNN  327 (551)\nT ss_dssp             HHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHCEEEECTTCBSCBCGGGGGGSCCCTTCCHHHHHHHHHHHHHHHTTCCSS\nT ss_pred             hHHHHHHHHHHhccchHHHHHHHHHHHHHHhCCEEEeccccccccHHHHHHhcCCCcchhhHHHHhHHHHHHHhHhhccC\n\n\nQ ss_pred             ----------------------------hhhcccccccccccccccccccccccccCCCceEEEeecCC---Cccccccc\nQ Sht1-d52        154 ----------------------------WLNNIIDLNKPIPYKNSKPSLLSSDEISHQPGLVIGIEADP---DRDDWSEW  202 (428)\nQ Consensus       154 ----------------------------~l~~~~d~~~p~~y~~~~~~~~s~~~~~~~~~lvvGiE~D~---~~~~W~~~  202 (428)\n                                                  .|.                          +.+-.+-.+..+   -.. |..+\nT Consensus       328 ~~s~~~d~L~~e~k~~L~~i~~~~~~~~iF~--------------------------pl~d~~Vrd~~~il~R~~-~~~G  380 (551)\nT 2vk9_A          328 YPYKYMEQVPSEIKERILSFVRNHDINDLIL--------------------------PLGDIKISQLEILLSRLK-AATG  380 (551)\nT ss_dssp             CCCSSSSSSCHHHHHHHHHHHHTSCHHHHBC--------------------------CCCCCBCCTTCCEEEEEE-CTTS\nT ss_pred             CcchhhccCCHHHHHHHHHHHhhccchhhcc--------------------------CccccccCchHHHHHHHH-Hhcc\n\n\nQ ss_pred             ccccceEEEEEEEecCCCHHHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccccc-----------cccc\nQ Sht1-d52        203 YARRIQFCQWTIQAKPGHPILRELILNITATTLASVQNPGVPVSEMIDPRFEEDYNVNYRHKRRH-----------DETY  271 (428)\nQ Consensus       203 ~~r~~qf~qw~iaA~PgHPvL~~~I~~I~~~~~~~~~~~~~~~~~~~d~~~~~~~n~~~~~~~~~-----------~~~~  271 (428)\n                      |   +.+.|.+|+|.+|++++..+|..+..+                           |+--++.           +..|\nT Consensus       381 w---~~~~N~~m~shkgS~~v~~VI~~~~~~---------------------------Y~~l~~~~r~~v~~~~t~~~~f  430 (551)\nT 2vk9_A          381 K---KTFSNAFIISNNDSLTLNNLISQLENR---------------------------YEILNSIIQEKFKICETYDSYI  430 (551)\nT ss_dssp             C---EEEEEEEEEECTTCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHHCSSHHHHH\nT ss_pred             c---cchhhhhHhhCCCCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHhhccccHHH\n\n\nQ ss_pred             c-------------------------cchhhccccccCCCcccccCcHHHHHHHHHHH\nQ Sht1-d52        272 K-------------------------HSELKNNKNVDGSDIMNWTGPGIFSDIIFEYM  304 (428)\nQ Consensus       272 ~-------------------------~~~~~~~~~~~~~dv~~~TGP~~~Tdai~~yL  304 (428)\n                      .                         .+-.+..-..+....+.+|||++++++..++|\nT Consensus       431 ~s~~~~~~e~~~~~~~~~~~~f~~~i~~Y~~Dg~~pe~~~Ti~LtGP~~~~~~~~dl~  488 (551)\nT 2vk9_A          431 NSVSELVLETTPKNLSMDGSSFYQQIIGYLSSGFKPEVNSTVFFSGPNIYSSATCDTY  488 (551)\nT ss_dssp             HHHHHHHHHHSCSSCCHHHHHHHTTGGGSTTBTTBTTCCGGGTTTSHHHHHHHHHHHH\nT ss_pred             HhhHHHHHHhccccccccchhHHHHHHHHhhccccccceeeeeccCcHHHHHHHHHHH'



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