modeller_usage

modeller_usage@salilab.org

3147 discussions

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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DNA nucleotide protein modeling
by Rana Rehan Khalid 26 Apr '21

26 Apr '21

Dear Modeller Users I want to model my receptor protein with single nucleotide probes. For exp: receptor ARG residue has interaction with adenine e, So I want to keep adenine in close proximity to receptor ARG. We have done the same thing for receptor against single residue probe (mean single aa residues e.i ALA LYS or ARG residues) But now we want to do this with a single nucleotide probe. In the case of protein, we tried this to generate a PIR file. here is the files >P1;PROBE_PLUS_RECEPTOR sequence:none::.::.:::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMRKQE/RKP* #RKP mean arginine lysine proline etc nut we choose only middle one K >P1;REC # here we have receptor structure sequence structureX:rec.reformat.pdb:FIRST: :LAST: :::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMRKQE/---* #here we have receptor with blank probes --- (for three residues) >P1;CENTER_RES #here we choose middle residue structure while our receptor is -------------- structureX:temp_centerRes_full.pdb:FIRST: :LAST: :::: --------------------------------------/-K-* __________________________________Modeller script___________________________________________ # Comparative modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class from modeller.scripts import complete_pdb log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.'] env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') mdl=complete_pdb(env,'temp_centerRes_reduced.pdb') # fill rest of residue from 2 given atoms mdl.write('temp_centerRes_full.pdb', model_format='PDB') # selected atoms do not feel the neighborhood #env.edat.nonbonded_sel_atoms = 2 env.io.hetatm = True a = automodel(env, alnfile = 'temp_alignment.ali', # alignment filename knowns = ('CENTER_RES', 'REC'), # codes of the templates sequence = 'PROBE_PLUS_RECEPTOR') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.make(exit_stage=2) # do the actual comparative modeling, exit w/o optimization # output: pdbfile PROBE_PLUS_RECEPTOR.ini ____________________________________________________________________________ This same script also work fine for RNA nucleotides here are the results >P1;PROBE_PLUS_RECEPTOR sequence:none::.::.:::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/g* >P1;REC structureX:rec.reformat.pdb:FIRST: :LAST: :::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/-* >P1;CENTER_RES structureX:temp_centerRes_full.pdb:FIRST: :LAST: :::: ----------------------------------------------------------/g* script is this # Comparative modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class from modeller.scripts import complete_pdb log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.'] env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') mdl=complete_pdb(env,'temp_centerRes_reduced.pdb') # fill rest of residue from 2 given atoms mdl.write('temp_centerRes_full.pdb', model_format='PDB') # selected atoms do not feel the neighborhood #env.edat.nonbonded_sel_atoms = 2 a = automodel(env, alnfile = 'temp_alignment.ali', # alignment filename knowns = ('CENTER_RES', 'REC'), # codes of the templates sequence = 'PROBE_PLUS_RECEPTOR') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.make(exit_stage=2) # do the actual comparative modeling, exit w/o optimization # output: pdbfile PROBE_PLUS_RECEPTOR.ini I used naming for RNA nucleotides are GUA CYT THY ADE see the final model in attachment this works fine for RNA nucleotides ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// I apply same thing again with DNA Nucleotides its gives me error, I used following names for DNA Resi DADE DGUA DCYT DTHY # I also want to ask is this right to use DADE DCYT etc or modeller recognise these namings DT, DA, DG, DC here is alignment >P1;PROBE_PLUS_RECEPTOR sequence:none::.::.:::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/l* >P1;REC structureX:rec.reformat.pdb:FIRST: :LAST: :::: RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/-* >P1;CENTER_RES structureX:temp_centerRes_full.pdb:FIRST: :LAST: :::: ----------------------------------------------------------/l* modeller script is same as i pasted above error is this Read the alignment from file : temp_alignment.ali Total number of alignment positions: 59 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 CENTER_RE 1 1 temp_center 2 REC 58 1 rec.reforma 3 PROBE_PLU 59 2 none check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open temp_centerRes_full.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495379 483.769 0.472 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 495379 483.769 0.472 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment l PDB . Match Alignment residue type 50 (l, DGUA) does not match pdb residue type 67 (., DGU), for align code CENTER_RES (atom file temp_centerRes_full.pdb), pdb residue number "1", chain "" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 CENTER_RES Please guide thanks RNA nucleotide model is attached. Best ray

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modeller_usage