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 …
[View More]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
[View Less]
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 …
[View More]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.
[View Less]
