- modeller_usage - salilab.org

Reg: Ligand HETATM atoms missing in model
by Samdani A 04 Jan '22

04 Jan '22

Hi all, I am trying to model an ion, water and ligand from a template and below is my alignment file. >P1;SAM_docked structureX:SAM_docked.pdb:3:A:+1048:B:::-1.00:-1.00 -S-QVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEG HVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETN FITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCF-----IAYNIVKIPPLQADKEDPISKSEI VVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSS----GANYMDCFESNETMGVWLHIADKKRKKYI NNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNID KADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKL NVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVT FHGLFKKS.w./S--QVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDG QALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYP VGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCF-----IAYNIVKIPPLQ ADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLG------ANYMDCFESNETMGVW LHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQP EVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLG LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEV ARAEVEINIPVTFHGLFKKS.w.* >P1;EGR sequence:EGR:: :: ::: 0.00: 0.00 MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEG HVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNVYPVGEDYYACTETN FITKINPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEI VVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYL NNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNID KADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYCGKPYTYAYGLGLNHFVPDRLCKL NVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVT FHGLFKKS.w./MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDG QALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNVYP VGEDYYACTETNFITKINPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQ ADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVW LHIADKKRKKYLNNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQP EVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYCGKPYTYAYGLG LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEV ARAEVEINIPVTFHGLFKKS.w.* and I tried a model using the below specified script. from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = Environ() env.io.hetatm = True env.io.water = True class MyModel(AutoModel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: rsr.add(secondary_structure.Alpha(self.residue_range('111:A', '123:A'))) rsr.add(secondary_structure.Alpha(self.residue_range('646:B', '658:B'))) a = MyModel(env, alnfile='alignment.ali', knowns='SAM_docked', sequence='EGR', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() The modelled structure generated without any error containing ion and water. But only two atoms were observed in the modelled structure but the ligand in the template contains 38 atoms. The atoms in ligand were not retained in the model from the template. Please provide me with suggestions to solve this error? Samdani

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Modelling missing residues
by Karki, Sudeep 15 Dec '21

15 Dec '21

Hi, I have a structure with a small molecule bound in the active site. There are missing residues in the structure, how can I model it? I tried without the small molecule but it forces the neighbor loop to go in the active site and definitely I don´t want that. Sudeep

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Mutate Model -reg.
by Swapnil Bhujbal 07 Dec '21

07 Dec '21

Hello, I want to use this script (*https://salilab.org/modeller/wiki/Mutate%20model <https://salilab.org/modeller/wiki/Mutate%20model>*) for mutating a single amino acid residue from aspartic acid to tyrosine. How and where do I need to modify the script? Thank you in advance. Sincerely, Dr. Swapnil.

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Modeller 10.2 release
by Modeller Caretaker 30 Nov '21

30 Nov '21

A new version of Modeller, 10.2, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 10.2 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.2 is a minor update that adds support for Python 3.10. The Mac .dmg installer should now also work with Apple's Python 3 (although we generally recommend Homebrew or Anaconda for Python 3 users on Mac). If you encounter bugs in Modeller 10.2, please see https://salilab.org/modeller/10.2/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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commercial license fee
by 礒崎達大 06 Oct '21

06 Oct '21

Dear modeller administrators I would like to know how much the commercial license fee per year. As the MODELLER's installation page described, I contacted Biovia. However, I could not get any reply from them. Then, I am asking this question here although this may be different from the scope of the mail list. If anyone knows about the price, I'm happy to hear any clue of the information. Best regards, Tatasuhiro Isozaki –––––––––––––– 株式会社digzyme 事業開発部礒崎達大/Tatsuhiro Isozaki 〒113-0033 東京都文京区本郷５丁目２５−１８ハイテク本郷ビル１F isozaki.tatsuhiro(a)digzyme.com 070-5024-5116

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DNA nucleotide modeling
by Rana Rehan Khalid 04 Oct '21

04 Oct '21

Dear Modeller Users I have a nucleotide Adenine (please see figure) I want to model it on the particular atomic position of DNA, can I do it in the modeler. I mean can the modeler generate the model in which I have both input files. Please guide me if any ideas thanks. input files = dna.pdb input = DA Thanks best Rehan

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can we keep track of the modeller optimization process
by Li Xue 29 Jul '21

29 Jul '21

Hello, Is it possible that we could track all the details of the modeller conjugate gradients optimization process? For example, ask modeller at each optimization step to output the PDB coordinates, modeller molpdf energy terms and so on? Best, Li

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Sequence alignment with missing residues
by He, Amy 26 Jul '21

26 Jul '21

Dear Modeller experts, My apologies for the multiple posts. I’m using Modeller to align sequences, find missing residues in pdb and then perform loop modeling for the missing regions. And I have a small issue with sequence alignment when there’re missing residues. Here’s my .ali file: >P1;6cqx_a_unmod structureX:6cqx_a_unmod:3:A:+532:A:::-1.00:-1.00 -REDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTL YPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNY RVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGE.AGAASVGMHLLSPPSRGLFHRAV LQSGAPNGPWATVGMGEARRRATQLAHLVGCPPGG---NDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVP VVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAE AVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEI EFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNE-----APQWPPYTAGAQQYVSLDLRPLEVRRGLRA QACAFWNRFLPKLLSA-* >P1;6cqx_A sequence::: :: :::-1.00:-1.00 GREDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTL YPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNY RVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGESAGAASVGMHLLSPPSRGLFHRAV LQSGAPNGPWATVGMGEARRRATQLAHLVGCPPGGTGGNDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVP VVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAE AVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEI EFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNEPRDPKAPQWPPYTAGAQQYVSLDLRPLEVRRGLRA QACAFWNRFLPKLLSAT* And here’re the alignment commands I’m using: e = Environ() aln = Alignment(e) aln.append(file='two_seq.seq', align_codes=('all')) aln.align(gap_penalties_1d=(-600, -400)) aln.write(file='two_seq.ali') quit() The first sequence is read from a pdb file, with some residues (“-”). And the second sequence is the full sequence. However, because of the peculiar pattern, the alignment is not correct in this region: GCPPGG---NDTEL (from the pdb file) PPGGTGGNDTEL (the full sequence) I checked the structure file and then I found that the alignment should be as follows: GCPP---GGNDTEL (from the pdb file) PPGGTGGNDTEL (the full sequence) Is there any way to avoid this type of “mismatch” in the sequence alignment? Thank you very much for your kind advice in advance. Massive Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu

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Modeller objective function in the modeling of missing residues
by He, Amy 26 Jul '21

26 Jul '21

Dear Modeller experts, I’m a new user of Modeller and I’m using the x86_64 type of executable on Linux platform. I wanted to model some loop regions which are the missing residues in PDB structure, and basically I follow the “Missing residues” tutorial from the modeler website: https://salilab.org/modeller/wiki/Missing%20residues I have two questions: 1. About the "Modeller objective function" as an output score for each model: Could you help me understand what exactly the function is for the modelling of the missing residues? Is it a score for just the modelled loop region, or does it include the pair potential between the loop and the existent structure? 1. About the “md_level” of the loop refinement in “a.loop.md_level = refine.<option>”: Comparing the “fast” and the “large_slow” options, the “fast” option gave me models with better (lower) values of the “Modeller objective function”. Is this normal for the modeling of missing residues? Should I rather choose the “fast” option not the “large_slow”? Thank you for your time and kind advice in advance! Thanks, Amy

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Refining part of a model using another structure as reference
by Rafael Lemos 02 Jul '21

02 Jul '21

Hi, I have two questions/problems: 1. I need some help refining part of a model using another structure as reference. I tried the 'model-segment.py' script (https://salilab.org/modeller/manual/node23.html) but I'm unable to add the second structure (.pdb) to be used as the reference for the atoms that will be refined. 2. Is there a way to generate a model using only parts of two different structures? Like some residues from 'model1', and some from 'model2'. They are highly different sequences, so I tried modelling with multiple templates and got bad results. Thanks in advance.

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