modeller_usage

modeller_usage@salilab.org

2 participants
3148 discussions

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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Is occupancy value in the PDB considered for MODELLER?
by ZHANG Cheng 17 May '21

17 May '21

Dear MODELLER, The occupancy value is the 57th-60th columns in the PDB file. Is this considered by MODELLER? For example, will a value of "0.00" or "1.00" have different effect (e.g. weights) for the modelling? I ask this because the Rosetta will ignore the lines with occupancy values of 0. I wonder if MODELLER does the same. Thank you! Yours sincerely Cheng

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Use $SGE_TASK_ID in the python script
by ZHANG Cheng 13 May '21

13 May '21

This thread told me to use $SGE_TASK_ID to generate random integer https://salilab.org/archives/modeller_usage/2020/msg00077.html I tried: random_integer = int(-1*str($SGE_TASK_ID)[-4:])  # so that the number is within the range of (-50000, -2) But I was told the $ sign is invalid: random_integer = int(-1*str($SGE_TASK_ID)[-4:])                                            ^ SyntaxError: invalid syntax So is that possible to use the job ID (e.g. 7172646) as an variable in the python environment? Thank you!

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ligand is not generated
by MARIANA BRANDI MENDONÇA PINHEIRO 12 May '21

12 May '21

I am having a problem with ligand generation. Alignment file: >P1;2q3z structureX:2q3z:1:A:+929:X:MOL_ID 1; MOLECULE TRANSGLUTAMINASE 2; CHAIN A; SYNONYM TISSUE TRANSGLUTAMINASE, TGASE C, TGC, TGC, TRANSGLUTAMINASE-2, TGASE- H; EC 2.3.2.13; ENGINEERED YES; MOL_ID 2; MOLECULE POLYPEPTIDE; CHAIN X; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE TGM2; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; MOL_ID 2; SYNTHETIC YES; OTHER_DETAILS CHEMICALLY SYNTHESIZED.: 2.00: 0.23 MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYQASVDSLTFS VVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLE ASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPW NFGQFQDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVGSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDS--NLLIEYFRN---------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRAN----------HGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLTLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLVPLHMGLHKLVVNFESDKLKAVKGFRNVI----/.P.LPF./.....wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* >P1;3s3j_L structureX:3s3j_L:2:A:+782:B:MOL_ID 1; MOLECULE PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 2; CHAIN A; FRAGMENT UNP RESIDUES 2-687; SYNONYM TISSUE TRANSGLUTAMINASE, TRANSGLUTAMINASE C, TG(C) TGASE C, TRANSGLUTAMINASE H, TGASE H, TRANSGLUTAMINASE-2, T EC 2.3.2.13; ENGINEERED YES; MOL_ID 2; MOLECULE PEPTIDE INHIBITOR; CHAIN B; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE TGM2; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; MOL_ID 2; SYNTHETIC YES; ORGANISM_SCIENTIFIC SYNTHETIC CONSTRUCT; ORGANISM_TAXID 32630: 2.25: 0.22 -AEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAH----NLLIEYFRN---------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTP-----GTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANH---------TGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIG--/-------/.......wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww/w* >P1;P21980 sequence:P21980: FIRST :A:LAST :B:::0.00:0.00 MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPA/-------* The ligand is chain X at 2q3z = /.P.LPF./ The models are created but without chain B/X or any ligand/polypeptide. The script: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() #Considering heteroatoms and waters molecules env.io.hetatm = env.io.water = True # Directories with input atom files: #env.io.atom_files_directory = './:../atom_files' env.io.atom_files_directory = ['./', '../atom_files'] a = MyModel(env, alnfile = 'aln-all.ali' , # alignment filename knowns =('2q3z', #sequences '3s3j_L' ), # codes of the templates sequence = 'P21980', # code of the target assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341) #assess model with DOPE ) a.starting_model= 1 # index of the first model a.ending_model = 3 # index of the last model Regards, Mariana.

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Do a loop refinment in order to mimic loop in a template
by Miguel Lacerda 06 May '21

06 May '21

Hello all. Is it possible to do a loop refinment of a model by giving the residue range plus the template (which will hold the desired spatial location)? The orientation of the loop in my model its different to my template’s. I’m trying to refine a model in hope to switch the position/orientation of the loop, but im having dificulties… Regards. Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

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modeller_usage