April 2021 - modeller_usage

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;… [View More]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 [View Less]

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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) … [View More]

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