Hi,

I'm trying to model a complex of 3 components: a peptide including 2 phosphotyrosines, and 2 signal protein recognizing each one phosphotyrosine. I have 2 templates, one for each complex protein-phosphopeptide. I've put each PTR as BLK. But one of the PTR is changed in ASP in my results, because Modeller change the alignment I gave in my .ali file.

This is the alignment file:

> P1;2iuh #Pi3k structureX:2iuh:4:A:208:B:::: -------------------------------------------------------------------------------- --------------------------NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKE-/ TNE.MDMK-------------*

> P1;2pld #PLC structureX:2pld:1:A:12:B:::: GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL ISYYEKHPLYRKMKLRYPINEENSS/------------------------------------------------------- --------------------------------------------------------------/ ---------DNDYIIPLPDPK*

> P1;comp sequence:comp:1:A:21:C:::: GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL ISYYEKHPLYRKMKLRYPINEENSS/NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKED/ TNE.MDMKPGVSYVVPTKADK*

and this is part of the .out:

read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 120) Alignment ETNE.MDMK PDB ETNEMDMK Match ***** Alignment residue type 11 (M, MET) does not match pdb residue type 3 (D, ASP), for align code 2iuh (atom file 2iuh), pdb residue number "206", chain "B"

This is the PTR of the template 2iuh: ATOM 967 CD GLU B 203 28.500 18.086 19.085 1.00 23.93 C ATOM 968 OE1 GLU B 203 28.474 16.841 18.975 1.00 25.60 O ATOM 969 OE2 GLU B 203 29.534 18.753 18.901 1.00 25.56 O1- HETATM 970 N BLK B 204 23.987 20.311 19.503 1.00 17.56 N HETATM 971 CA BLK B 204 23.170 20.645 18.345 1.00 17.48 C HETATM 972 C BLK B 204 23.958 20.440 17.054 1.00 17.87 C HETATM 973 O BLK B 204 25.071 20.949 16.905 1.00 17.97 O HETATM 974 CB BLK B 204 22.668 22.083 18.435 1.00 16.51 C HETATM 975 CG BLK B 204 21.236 22.165 18.925 1.00 16.28 C HETATM 976 CD1 BLK B 204 20.236 21.731 18.070 1.00 16.08 C HETATM 977 CD2 BLK B 204 20.937 22.626 20.204 1.00 15.99 C HETATM 978 CE1 BLK B 204 18.914 21.746 18.468 1.00 15.70 C HETATM 979 CE2 BLK B 204 19.616 22.637 20.615 1.00 15.90 C HETATM 980 CZ BLK B 204 18.643 22.197 19.729 1.00 16.36 C HETATM 981 OH BLK B 204 17.254 22.157 20.018 1.00 16.93 O HETATM 982 P BLK B 204 16.513 22.838 21.260 1.00 16.40 P HETATM 983 O1P BLK B 204 15.064 22.662 21.118 1.00 15.57 O HETATM 984 O2P BLK B 204 16.982 22.261 22.527 1.00 16.50 O1- HETATM 985 O3P BLK B 204 16.829 24.260 21.166 1.00 17.35 O ATOM 986 N MET B 205 23.429 19.583 16.187 1.00 17.64 N ATOM 987 CA MET B 205 24.111 19.203 14.953 1.00 17.33 C ATOM 988 C MET B 205 23.824 20.152 13.795 1.00 17.59

Do you have an idea of why Modeller switch the PTR of my template? Many thanks in advance,

Isaure