- modeller_usage - salilab.org

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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SequenceMismatchError when adding missing residues in LoopModel()
by Steven Truong 07 Apr '21

07 Apr '21

Dear Ben and Modeller Mailing List, Hello, I was hoping to get some help on an error I get when trying to add missing residues to a structure using the AutoModel/LoopModel classes. The error looks like: x (mismatch at alignment position 9) Alignment NSFTRVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTKSNIIRGWI PDB NSFTRGVYYPDKVFRSSVL.STQDLFLPFFSNVTWF.AI.VSGTNGTKRFDNPVLPFNDG Match ***** * * * Alignment residue type 18 (V, VAL) does not match pdb residue type 6 (G, GLY), for align code 6z43 (atom file structure_aligned), pdb residue number " 35", chain "A" When I check my alignment file, I can begin to see what’s going on. Here is the first entry of the alignment file: >P1;6z43 structureM:structure_aligned:27:A:+3600:C:::-1.00:-1.00 --------------------------AYTNSFTR-VYYPDKVFRSSVLHSTQDLFLPFFS NVTWFH--------------NPVLPFNDGVYFAST >P1;6z43_fill sequence:6z43_fill:.:.:.:.:::: MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST It appears that Modeller does not recognize the dashes “-“ as actual missing residues. Instead, it appears to read the alignment as NSFTR()V…, rather than NSFTRG. However, isn’t the dash supposed to signal AutoModel/LoopModel to treat that as a missing residue to fill? Thank you for your help! Best wishes, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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Adding glycans in AutoModel?
by Steven Truong 19 Mar '21

19 Mar '21

Dear Modeller Mailing List, I was hoping to ask if there is a way to automate glycan-building in Modeller. I’ve been able to get all residues/atoms built using AutoModel. However, I lose the glycan information when using AutoModel. Is there another program that interfaces well with Modeller, or is there a class in Modeller that can add glycans at known positions (e.g. if I know NAG is attached to residue 6, can I add that to the PDB output somehow?). Thank you! Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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Modeller 10.1 release
by Modeller Caretaker 18 Mar '21

18 Mar '21

A new version of Modeller, 10.1, 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 10.1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.1 is a minor update that adds support for Apple Silicon. The Mac installer (dmg file) is now universal and will work on both Intel Macs and the new Apple Silicon (M1 or ARM64) Macs. The Homebrew Modeller package also works on both Intel and Apple Silicon Macs. If you encounter bugs in Modeller 10.1, please see https://salilab.org/modeller/10.1/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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query regarding alignment
by anuricha sharma 15 Mar '21

15 Mar '21

Hello sir, I have a query regarding the alignment, that how can I align my two pdb structures and one query sequence(xyz.ali) together using basic modelling, I am unable to to do alignment using two models and one query sequence in basic modelling as it aligns only one model and one query sequence, can you suggest any changes that I need to do in my align2d.py file. ReplyForward Sent from Mail for Windows 10

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