Hey, having an issue modelling inorganic ligands in a large dimer protein.  My pdb file is a vmd cut-up of a larger pdb that looks as follows..

ATOM      1  N   ALA A   3     -60.617 -12.474 -31.114  1.00 43.43           N
ATOM      2  CA  ALA A   3     -59.796 -11.349 -30.513  1.00 46.97           C
ATOM      3  C   ALA A   3     -59.651 -11.332 -28.938  1.00 48.20           C
ATOM      4  O   ALA A   3     -60.595 -11.655 -28.205  1.00 47.64           O
ATOM      5  CB  ALA A   3     -60.235  -9.947 -31.052  1.00 48.47           C
ATOM      6  N   ARG A   4     -58.445 -10.979 -28.485  1.00 44.79           N
...
TER   2039
ATOM   2040  N   GLU B1003     -60.710 -26.975 -64.326  1.00 44.60           N  
...
ATOM   6402  OXT HIS B1561     -32.057 -14.269 -58.556  1.00 23.80           O  
ANISOU 6402  OXT HIS B1561     3054   3146   2843   -160     47    -56       O  
TER    6403      HIS B1561                                                      
HETATM25650 FE1  SF4 A2001     -31.581  -9.338 -45.929  1.00 15.82          FE  
HETATM25651 FE2  SF4 A2001     -34.045  -9.711 -44.672  0.50 17.11          FE  
...
HETATM25689  O4  NFV B2005     -32.416 -23.476 -49.460  1.00 19.96           O  
END

There are three inorganic residues in the first chain and one in the second placed as "." in my ali file.  

>P1;TrHyd
sequence:TrHyd:::::::0.00: 0.00
AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGSIPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPIPMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTYNACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQAYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHVMHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLPPEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQVYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAHSWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQTKELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGAGYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPCIACAVH.*

Using this structure and the template ali file to do the alignment (w/ salign) I get poor alignment in the PAP file, but not in the PIR file??? (P/---XXXX instead of P---/XXX in PAP).  I figured this wasn't a huge issue since modeller doesn't use the PAP file but it is odd.  Anyway my alignment looks like this...

>P1;Avfull
structureX:Avfull.pdb:   3 :A:+827 :B:::-1.00:-1.00
ARRPSVIWLSFQECTGCTESLTRAHAPTLEDLILDFISLDYHHTLQAASGEAAEAARLQAMDENRGQYLVIVDGS
IPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPI
PMVITGVIAHYLVFGRLPELDGYGRPLAFYGQSIHDRCYRRPFYDKGLFAESFDDEGAKQGWCLYRLGCKGPTTY
NACATMKWNDGTSWPVEAGHPCLGCSEPQFWDAGGFYEPVSVP---/ERIVVDPITRIEGHLRIEAQMDGATIAQ
AYSSGTMVRGIETILKGRDPRDAWAFVQRICGVCTLVHGIASVRAVEDALRIELPLNAQLIRNLMIGAQYIHDHV
MHFYHLHALDWVDVVSALSADPRATSELAQSISAWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYRLP
PEANLMAVAHYLEALAWQRDTAKFHAIFGGKNPHPNFVVGGVPSPIDLDSDSALNAKRLAEVRNLIQSMRTFVDQ
VYVPDTLAIAGFYKDWGERGEGLGNFLCYGDLPTGASLDPATFLFPRGAILDRDLSTIHEVDLEATGEIQEFVNH
SWYEYSVGNDRGLHPYEGQTNLEYDRRGGVAPPYKQLDVSDGYSWLKAPRWKGRSVEVGPLARVLMLYATGHDQA
RELVDSTLSRLDLPVDALYSTLGRTAARALESKILVDAMQGWYDGLIANVKSGDTKTFNETLWEPSSWPSRAQGV
GIMEAPRGALGHWIVIEDGRIANYQAVVPSTWNAGPRDGRGQAGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC
IACAVH-*

>P1;TrHyd
sequence:TrHyd:     : :     : ::: 0.00: 0.00
AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGS
IPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPI
PMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTY
NACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQ
AYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHV
MHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLP
PEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQ
VYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAH
SWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQT
KELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGA
GYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC
IACAVH.*

Using the template code in advanced modeling with similar for loops for all constraints of the inorganic ligand connections to the protein backbone through side chains modeller begins to compute the model and quickly returns this error...

"No aligned template residues for BLK residue; number of templates:          1 Make sure that each BLK residue in your target sequence is aligned with your templates..."

So my question is, is there a problem with my alignment that I am not seeing or is it some formating issue in the pdb that needs to be resolved?  Any ideas would be much appreciated!



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