modeller_usage

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modeller_usage@salilab.org

June 2024

3 participants
2 discussions

Issues with incorporating ligands in multichain protein
by Kyle- richard Dawson 17 Jun '24

17 Jun '24

Hi there, I am trying to model a multichain protein (homodimer) using 2 templates. I have two issues, Currently my .pir file looks like this >P1;seq1 sequence:seq1:1:A:1224:A:::: xxxx/ xxxx* >P1;template1.pdb structureX:template1.pdb:40:A:651:B:41:B:648:xxxx/xxxx* >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx/-------/ >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:-------/xxxx* Firstly, my template 1 I am using both chain A and chain B, they have slightly different missing residues in the template but thats fine.For template 2 I cant put them under the same header, modeller doesn't seem to understand that I want to use chain B of template 2 for both chain A and B of my target so I specified it separately - it seems to work fine though with this setup. Unfortunately when I try add HETATM information ".." at the end of my target and template 1 and 2 gaps "--" for template 2 modeller says the whole sequence is out of alignment suddenly. I have specific HETATM=true in my script so it reads that part fine. My alignment looks like this but does not work? Am I missing some obvious? >P1;seq1 sequence:seq1:1:A:1224:A:::: xxxx../ xxxx..* >P1;template1.pdb structureX:template1.pdb:40:A:651:B:41:B:648:xxxx../xxxx..* >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx--/---------/ >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:---------/xxxx--* RegardsKyle

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Building multi-chain models
by alina.s123567＠gmail.com 06 Jun '24

06 Jun '24

Good day, I would like to build a GABA A receptor with (two alpha2 subunits chain A, D), (two beta2 subunits chain B, E) and (one gamma subunit chain C). I create an .ali file with template (6HUG) and with target sequences. I have received the error: 'There should be 10 fields separated by colons, : This line actually contains 15 fields.' I don't understand how I should correctly change it, if I have 5 chains. Could you please advise, how I should correctly write this 10 field line. I have already read the manual https://salilab.org/modeller/manual/node501.html#alignmentformat, but there is information about 2 chains. I still can not understand how correctly I should write it for 5 chains. The alignment for my template is look like: >P1;6HUG structureX:6HUG:FIRST:A 437:A 473:B 495:C 437:D 473:E:::3.5:-1.00 ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------/ MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK VPEGDVTVILNNLLEGYDNKL---------------RPD----IGVKPTLIHTD-MYVNS IGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADA HWITTPNRMLRIWNDGRVLYTLRLTI----DAECQLQLHNFPMDEHSCPLEFSSYGYPRE EIVYQWKRSSVEV--GDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGY FTIQTYIPC---------------TLIVVLSWVSFWINKD-AVPARTS-LGITTVLTMTT LSTIA----RKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNRKPS------K DKDKKKKNPLLRMFS---FK--------------APTI--------D-I----------- -----------------------------------R------------------------ ---------------PRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFEDCRTGA ---------WRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVS-----YLYLGGSGGSG GSGKTETSQVAPA-/ ------------------------------DYKDDD----DKQPSLQDEL---------K DNTTVFTRILDRLLDGYDNRL---------------RPG----LGERVTEVKTD-IFVTS FGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVA HNMTMPNKLLRITEDGTLLYTMRLTV----RAECPMHLEDFPMDAHACPLKFGSYAYTRA EVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGY FVIQTYLPC---------------IMTVILSQVSFWLNRE-SVPARTV-FGVTTVLTMTT LSISA----RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVP EKPKKVKDPLIKKNN---TY--------------APTA--------TSYT---------- -----------------------------PNLARGD------------------------ ---------------PGLATIAKSATIEPKEVK----------------------PETKP ---------PEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWAT-----YLNREPQLKAP TPHQ----------/ -----MCSGLLEL-------------LLPIWLSWTLGTRGSEPRSV-----------NDP GNMSFVKETVDKLLKGYDIRL---------------RPD----FGGPPVCVGMN-IDIAS IDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFV HGVTVKNRMIRLHPDGTVLYGLRITT----TAACMMDLRRYPLDEQNCTLEIESYGYTTD DIEFYWRGGDKAV--TGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGY FILQTYMPS---------------ILITILSWVSFWINYD-ASAARVA-LGITTVLTMTT INTHL----RETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAE KTAK-AKNDRSKSES--------------------------------------NRVDAHG NILLTSL--E-VHNE---------MNE--VSGGIGD------------------------ ---------------TRNSAISFDNSGI-QYRK-----QSMPREGHGRFLGDRSLPHKKT HLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLY-----YVN-------- --------------* Thank you for your help.

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