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December 2001

8 participants
12 discussions

Regarding including of heteroatoms in dimer molecule
by R Senthil Kumar 06 Dec '01

06 Dec '01

Dear modeller users, I am having a template molecule and it is of homodimer.one chain is of 267aa and other chain has 267aa and has two molecule of heteroatoms.Each heteroatoms in each subunit. I want to include this heteroatoms in my model.I am having trouble in representing the following line in template molecule so that it will take heteroatoms also. structureX:xxxx: 1 :A: 267 :B: 1 : 267 : 2.10:99.90. please help me in this regard.Advance thanks. from Senthil kumar.R R.Senthil Kumar, Junior Research Fellow(JRF), c/o Dr.Akash Ranjan, Computational & Functional Genomics Group, Center For DNA Fingerprinting(CDFD), Hyderabad-500 076 Ph:040-7151344-Extn(Lab:1304) (Hostel:2300) E-mail:skumar@www.cdfd.org.in

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regarding modeller usage
by R Senthil Kumar 04 Dec '01

04 Dec '01

Dear friends, The bottom is my ali file.The template has 267 residues in A-chain and 267 residues in B-chain.After 267th residue in the template .atm file two heteroatoms are there. I want to include that heteroatoms in my target protein(omp). say that heteroatoms start with 601 and 602 after 267th residue of B-chain how can i include in this line: >P1;xxx structureX:1dqx: 1 :A: 267 :B: 1 : 267 : 2.10:99.90 So, that it takes that heteroatoms and include that in target protein. If i try to do like this >P1;xxx structureX:1dqx: 1 :A: 267 :B: 1 : 267 : : 601 : 602 : 2.10:99.90 it says residue index out of bounds. please suggest me solution for this. >P1;xxx structureX:xxx: 1 :A: 267 :B: 1 : 267 : 2.10:99.90 MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKT HVDILTDFSMEGTVKPLKALSAK--YNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADI TNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDF VIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLF AKGRDAKVEGERYRKAG-WEAYLRRCGQQD----/MHKATYKERAATHPSPVAAKLFNIM HEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAK-- YNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKE PRGLLMLAELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPG VGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAG-WEAYLRR CGQQD----/..* >P1;omp MTGFGLRLAEAKARRGPLCLGIDPHPELLRGWDLATTADGLAAFCDICVRAFADFAVVKP QVAFFESYGAAGFAVLERTIAELRAADVLVLADAKRGDIGATMSAYATAWVGDSPLAADA VTASPYLGFGSLRPLLEVAAAHGRGVFVLAATSNPEGAAVQNAAADGRSVAQLVVDQVGA ANEAAGPGPGSIGVVVGATAPQAPDLSAFTGPVLVPGVGVQGGRPEALGGLGGAASSQLL PAVAREVLRAGPGVPELRAAGERMRDAVAYLAAV/MTGFGLRLAEAKARRGPLCLGIDPH PELLRGWDLATTADGLAAFCDICVRAFADFAVVKPQVAFFESYGAAGFAVLERTIAELRA ADVLVLADAKRGDIGATMSAYATAWVGDSPLAADAVTASPYLGFGSLRPLLEVAAAHGRG VFVLAATSNPEGAAVQNAAADGRSVAQLVVDQVGAANEAAGPGPGSIGVVVGATAPQAPD LSAFTGPVLVPGVGVQGGRPEALGGLGGAASSQLLPAVAREVLRAGPGVPELRAAGERMR DAVAYLAAV/..*

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