Dear O users, We use O version 5.10.3 on a R4400 SGi Indigo Machine. We are having problems in inserting residues and following it with the lego_loop command. I have enclosed the error output in this mail to make the situation clear. Can anyone suggest what may be going wrong with our strategy of inserting amino acids inbetween a protein chain..? With regards Jawahar O > zone 40 55 end O > mutate_ins Mut> Mutate a molecule by inserting residues. Mut> Molecule ([FIT2 ]) : Mut> After which residue: 45 Mut> New residue name and type (<cr> to end) : 45a val Mut> New residue name and type (<cr> to end) : Mut> There are 1 mutations O > sel_on fit2 Sel> Residue range [all molecule]: O > sel_off fit2 45 47 O > lego_loop fit2 43 49 Lego> FIT2 43 49 FIT2 Lego> Number of selected atoms in zone is 4 Lego> The DB is now being loaded. Lego> DGNL> Top matches Lego> Protein Start Res. Score Sequence Lego> TLN_3 103 0.234 SVHYSQGY Lego> PA 122 0.312 KVLDAVRG Lego> PA 6 0.365 KVLDAVRG Lego> FDX_1 28 0.373 YAIDADSC Lego> CYT_4 31 0.388 NLWGLFGR Lego> APP_2 308 0.411 VVFDSDGP Lego> HCAC 101 0.419 GSEHTVDK Lego> HCAC 143 0.543 FLKVGSAK Lego> PA 86 0.548 FTANDSGP Lego> PCY_1 81 0.551 SFYCSPHQ Lego> C2C_3 31 0.574 NLFGVFEN Lego> APP_2 88 0.582 DSVTVGGV Lego> APP_2 163 0.595 GVYDFGFI Lego> PA 202 0.608 FTANDSGP Lego> APP_2 274 0.610 YGPSGDGS Lego> DFR_3 120 0.623 GSFEGDTK Lego> RHD_1 56 0.643 SFFDIEEC Lego> FDX_1 7 0.662 SCIACGAC Lego> APP_2 19 0.694 TPVTIGGT Lego> FB4_1 197 0.700 CQVTHEGS O > yes Lego> Centre of gravity updated for 22 27 O > zone 40 55 end O > refi_zo fit2 43 49 Refi > FIT2 43 49 FIT2 Refi > R.m.s.d. in bond lengths, angles, fixed diherals Refi > NaN 0.20NaN Refi > Centre of gravity updated for 21 28 Refi > Accept new coordinates? Hit *Yes/*No O > yes O > pep_flip fit2 43 49 Util> FIT2 43 49 FIT2 Util> Calculating zone 43 to 49 in molecule FIT2 , object FIT2 Util> Atmxyz, setzon error. Util> Atmxyz, setzon error. Util> Atmxyz, setzon error. Util> Atmxyz, setzon error. Util> 20 fragments used for residue 43 pep_flip value= NaN And so on for each residue in the range !! --------------------------------------------------------------------------- Jawahar Swaminathan \ / Phone: 91-11-618 9622 Ext.309 Structural Biology Unit | Phone(R) 91-11-467 7312 National Inst. of Immunology \ / \ / Facsimile: 91-11-616 2125 New Delhi - 110 067 INDIA | | Email: jawahar@nii.ernet.in ---------------------------------------------------------------------------
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