Re: error: Structure not read in

Hi,

thanks for spotting my typo error! now the files read in, but I'm having trouble getting modeller to choose the right chain as the template for each part of the structural alignment.....using the chain identifiers in the PIR second lines, in the fields after the residue numbers doesn't seem to be working. see bleow for how I specify the chain to use in the ali

Even weirder........., when I edit the pdb template files so each one only contains the one chain (A B C or D) which I specify in the alignment, the model generated still has most of the structure superimposed on one of the chains (looks like ther are at least 3 chains in the same place in many parts of the model generated)

now I think there is something very odd happening, as the templates are being read in ok, but the positions of the modelled residues are not in the same place as the template chain they are being modelled on......??????????

>P1,t2avi1 structureX:t2avi1:3 :A:123 :A :::: blah

>P1,t2avi1 structureX:t2avi1:3 :B:123 :B :::: blah

>P1,t2avi1 structureX:t2avi1:3 :C:123 :C :::: blah

>P1,t2avi1 structureX:t2avi1:3 :D:123 :D :::: blah

Cheers

Dan

On Monday, November 11, 2002, at 08:21 , Raghurama P. Hegde wrote:

> Hi > > I assume from your message that none of the structure coordinates > are read > in. Well the problems seems to be with the "known" codes you have > used in > the TOP script and the ones you hace used in the alignment. The TOP > script > says that the knowns are 't2avi1' 't2avi2' 't2avi3' .... but in the > .ali > file the first entry has the code as 2avi1 instead of t2avi1 (after > structureX), so MODELLER would be looking for 2avi1.atm instead of > t2avi1.atm and hence gving the error 'Structure not read in'. If you > change your alignment file there should be no problems. If you still > have > the same problem try changing the codes in the comment line too (the > one > after >P1). Also if you aren't using the entire sequence of the > structure > in your alignment your .atm file should contain only those residues > which > you are using in the alignment and you have to specify the residue > numbers > appropriately in the alignment. > > Hope this helps. > regards > Raghu > >> Hi All, >> >> I am a newbie to Modeller, and am having a problem reading in my >> template files >> in the log I get the error message: >> >> 3 lines just before the end bit..... >> check_a_343_> >> BEGINNING OF COMMAND >> check_a_347E> Structure not read in: 1 >> recover____E> ERROR_STATUS >=STOP_ON_ERROR: 1 1 >> >> All my files (.ali .top .atm .log) are shown below >> >> The 8 template files are in fact all the same (so I just show 1) , >> just with different filenames, to model different bits of the query >> sequence. >> They are called t2avi1.atm t2avi2.atm ..... t2avi8.atm >> >> I specify which of the 4 chains in the template files to use in the >> PIR alignment file >> in the 4th and 6th fields of the 2nd lines. >> >> >> My .top script file, .atm template files, and .ali PIR alignment file >> are all in /home/model/henri/ >> >> # Homology modelling by the MODELLER TOP routine 'model'. >> >> INCLUDE # Include the predefined TOP >> routines >> >> SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large >> log file >> SET ALNFILE = 'avi4.ali' # alignment filename >> SET ALIGNMENT_FORMAT = 'PIR' #sets alignment format >> SET KNOWNS = 't2avi1' 't2avi2' 't2avi3' 't2avi4' 't2avi5' 't2avi6' >> 't2avi7' 't2avi8' # codes of the templates >> SET SEQUENCE = 'avi4' # code of the target >> SET ATOM_FILES_DIRECTORY = '/home/model/henri' # directories for input >> atom >> files >> SET STARTING_MODEL= 1 # index of the first model >> SET ENDING_MODEL = 1 # index of the last model >> # (determines how many models to >> calculate) >> >> CALL ROUTINE = 'model' # do homology modelling >> >> >>> P1;2avi1 >> structureX:2avi1:3 :A:123 :A:::: >> -----------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIK >> ESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND >> IGDDWKATRVGINIFTRL------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------------------------------* >>> P1;2avi2 >> structureX:t2avi2:3 :A:123 :A:::: >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> -------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTG >> TYTTAVTATSNEIKESPLHGTENTINK--------------------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ----------------------------------------------------RTQPTFGF >> TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >>> P1;2avi3 >> structureX:t2avi3:3 :D:123 :D:::: >> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK---- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------RTQPTFGFTVNWKFSESTTVFTGQCFI >> DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL---------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------------------------------* >>> P1;2avi4 >> structureX:t2avi4:3 :D:123 :D:::: >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------------------------KCSLTGKWT >> NDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWK >> FSE--------------------------------------------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> --------STTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >>> P1;2avi5 >> structureX:t2avi5:3 :C:123 :C:::: >> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK---- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV >> NDIGDDWKATRVGINIFTRL---------------------------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------------------------------* >>> P1;2avi6 >> structureX:t2avi6:3 :C:123 :C:::: >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEF >> TGTYTTAVTATSNEIKESPLHGTENTINK------------------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ----------------------------------------------------RTQPTFGF >> TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL* >>> P1;2avi7 >> structureX:t2avi7:3 :B:123 :B:::: >> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQP >> TFGFTVNWKFSES----------------------------------------------- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL--- >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ---------------------------------------------------------* >>> P1;2avi8 >> structureX:t2avi8:3 :B:123 :B:::: >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> ------------------------------------------------------------ >> -----------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHG >> TENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWK >> ATRVGINIFTRL---------------------------------------------* >>> P1;avi4 >> sequence:avi4:1 : :554 : :::: >> ------------------------------------------------------------ >> -------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND >> IGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEFTG >> TYTTAVTATSNEIKESPLHGTQNTINK-SGGS------------------TTVFTGQCFI >> DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWD >> NDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWK >> FSEGGSGSGSGSGSGRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV >> NDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEF >> TGTYTTAVTATSNEIKESPLHGTQNTINKSGGS--------------------------- >> ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQ >> KEGGSGGSAR-KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHG >> TQNTINKRTQPTFGFTVNWKFSE------------------------------------- >> ---------------------------------------------------------* >> > > dan@chalkie.org.uk http://www.chalkie.org.uk

Daniel James White PhD. Cell Biology Department of Biological and Environmental Science University of Jyväskylä FIN-40351 Jyväskylä Finland

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