May 2021 - modeller_usage

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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