[modeller_usage] MODELLER behaviour with non-standard residues / HETATM

[Thomas Juettemann <>]

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--