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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On 7/18/11 7:22 AM, Greene, Brandon Lee wrote: > There are three inorganic residues in the first chain and one in the > second placed as "." in my ali file.
Your alignment file does not match the PDB. Modeller reads the residues sequentially, so what it will see is
- A chain amino acids - B chain amino acids - A chain ligands - B chain ligands
So your sequence should also be in this order (XXXXXX/XXXXXX/.../.).
Alternatively, you can edit the PDB file to place the A chain ligands immediately after the A chain amino acids and leave your alignment unchanged.
> 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).
Those two alignments are identical. Since neither gaps nor chain breaks are "real" residues, their relative ordering is irrelevant - it only matters which "real" residues (amino acids or ligands) they come between.
> "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..."
Just like it says, a BLK (".") residue in the target sequence must be aligned with a residue in the template. Usually this means you need a "." residue in the template in the same place as the "." in the target. You can't align a "." with a chain break or gap, because "." means to copy the aligned residue directly from the template to the target, so it needs a "real" residue to copy from.
Ben Webb, Modeller Caretaker
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Greene, Brandon Lee -
Modeller Caretaker