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

[Nathaniel Echols]

Can you please send us the .hhr file so we can reproduce the problem?
(Feel free to send to me directly instead of the list, and I'll make
sure it gets to the right people.)

thanks,
Nat

On Sat, Sep 1, 2012 at 9:39 PM, Dmitry Rodionov
<dmitry.rodionov at mail.mcgill.ca> wrote:
> 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             HhhHHHHHH!
>  hccccccccchhHHHHHHHHhhccccccceeeeeccCcHHHHHHHHHHH'
>
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