Dear all,
could someone enlighten me how MODELLER treats non-standard residues. I am using Dunbrack's S2C as a source for ATOM sequences. In the PDB file 1M2W, I have several selenomethionine (MSE) residues, marked as HETATM. Running MODELLER, it seems to convert them to methionine (which I appreciate) and successfully produces a model.
My question is: How does MODELLER check / replace HETATM that have a residue identifier that is in the permitted range (not 'X', '.' or '-')? I did not not set env.io.hetatm to true.
My apologies if I missed this information in the manual or my question is not clear enough.
Many thanks, Thomas
Template: http://www.pdb.org/pdb/files/1M2W.pdb (e.g. residue 1,50 & 105)
Alignment
>P1;1M2W structureX:1M2W:FIRST:@ END:::::: MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP / MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP *
>P1;P09424-P77260 sequence:P09424-P77260:::::::: MK---------------------ALHFGAGNIGRG----FIGKLL-ADAGIQLTFADV-----NQVVLDALNAR-HSYQVHVVGETEQ-----VDTVSGVNAVSSIGDDVVDLIAQ-----VDLVTTAVGPVV----------LERIAPAIAK------------GQVKRKEQGNESPLNIIACENMVR-GTTQLKGHVMNALPEDAK--AWVEEHVGFVDSAVDRIVPPSASA----------TNDPLEVTVETFSEWIVDKTQFKG--ALPNIPGMELTDNLMAFVERKLFTLNTGHAITAYLGKLAGHQTIRDAILDEKIRAVVKGAME-ESGAVLIKRYGFDADKHAAYIQKILGRFENPYLKDDVERV---GRQPLRKLSAG--DRLIKP-----------------LLGTLEYGL------PHKNLIEGIAAAMHFRSEDDPQAQELAALIADKGPQ--AALAQISGLDANSEVVSEAVTAYKAMQ / ---NLLSAKATLPVYDLNNLAPRIVHLGFGAFHRAHQGVYAD-ILATEHFSDWGYYEVNLIGGEQQI-ADLQQQDNLYTVAEMS-ADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIVSLTITEKGYFHSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVMSCDNMPENGHVMRDVVTSYAQAVDVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDPAGVACEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFLAYLGYLAGYQHINDCMEDEHYRYAAYGLMLQEQAPTL-KVQGVDLQDYANRLIARYSNPALRHRTWQIAMDGSQKLPQRMLDSVRWHLAHDSKFDLLALGVAGWMRYVGGVDEQGNPIEISDPLLPVIQKAVQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAKATVAKYSVK--