- modeller_usage - salilab.org

Incorrect Number or residues/Starting position
by Kevin Galens (RIT Student) 21 Nov '05

21 Nov '05

To Whom It May Concern: I'm attempting to use modeller to use two templates to model on short sequence. I'm also creating the alignment file (PIR format) on my own and I'm having some troubles with one of my sequences. My alignment file is as follows: >P1;15c8 structure:15c8:1:H:217:H:::: EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQI DPANGNTKYDPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYY-----CA ADPPYYG--------------HGDYWGQGTTLTVSSAKTTPPSVYPLAPGS AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS SVTVPSSTWPSETVTCNVAHPASSTKVDKKIV-----* >P1;1fns structure:1fns:1:H:225:H:::: QVQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVDWVRQPPGKGLEWLGMI WGD-GSTDYNSALKSRLSITKDNSKSQVFLKMNSLQTDDTARYYCVRDP-- -------ADYGNYDYALDYWG------QGTSVTVSSAKTTPPSVYPLAPGS AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS SVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG* >P1;1f11 sequence:1f11:1::15::::: --------------------------------------------------- --------------------------------------------CANDY-- ---GSTY--------GFAYWG------------------------------ --------------------------------------------------- -------------------------------------* The script that was run (quite simple): from modeller.automodel import * log.verbose() env = environ() a = automodel(env, alnfile='modAln.ali', knowns=('15c8','1fns'), sequence='1f11') a.starting_model = 1 a.ending_model = 5 a.make() And then the log file with the error: openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['15c8', '1fns', '1f11'], atom_files=[], file='modAln.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open modAln.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2457301 2399.708 2.343 Read the alignment from file : modAln.ali Total number of alignment positions: 241 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 15c8 217 1 15c8 2 1fns 225 1 pdb1fns.ent 3 1f11 15 1 1f11 runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL pdb15c8.ent Dynamically allocated memory at amaxstructure [B,kB,MB]: 2579199 2518.749 2.460 openf5__224_> Open 11 OLD SEQUENTIAL pdb15c8.ent openf5__224_> Open 11 OLD SEQUENTIAL pdb1fns.ent rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: 1: H rdabrk__288W> Protein not accepted: 2 check_a_337E> Structure not read in: 2 I'm running version 8v1 on Fedora core 3. The best that I can decipher is that modeller can't understand the starting position. Or perhaps it can't find the chain. The pdb file has the same exact sequence (minus the gaps of course) and chain id H. Interestingly (or confusingly) I also tried replacing the residue start and end with the words 'FIRST' and 'LAST' leaving the chain H, thinking that Modeller could grab the chain without me telling it where to start and end explicitly. The end of the error file was as follows: Total number of alignment positions: 241 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 15c8 217 1 15c8 2 1fns 225 1 1fns 3 1f11 15 1 1f11 runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL pdb15c8.ent Dynamically allocated memory at amaxstructure [B,kB,MB]: 2579199 2518.749 2.460 openf5__224_> Open 11 OLD SEQUENTIAL pdb15c8.ent openf5__224_> Open 11 OLD SEQUENTIAL pdb1fns.ent Dynamically allocated memory at amaxstructure [B,kB,MB]: 2703099 2639.745 2.578 openf5__224_> Open 11 OLD SEQUENTIAL pdb1fns.ent rdabrk__290E> Number of residues in the alignment and pdb files are different: 225 220 For alignment entry: 2 rdabrk__288W> Protein not accepted: 2 check_a_337E> Structure not read in: 2 Okay, so modeller thinks there are 220 residues in the pdb file? Is it looking at the right chain? The other chains in that file are length 217 and 195 (which isn't 220). It's looking at the correct file, who knows what chain it's going for. Anything I try here ends up giving me different results in the log file (like FIRST and 225, modeller tells me it found 11 residues in the pdb file). Perhaps I'm way off in my thinking and I have some huge error in my alignment file. I've tried modelling with three proteins (in the very same way, just a different protein for this problem one) and I was getting very similar errors. I can't make the second protein be able to be read in. Any help would be appreciated. Kevin

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The assessment of protein model with the function in modeller 8.1
by 서주현 21 Nov '05

21 Nov '05

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import site failed error
by S.Sundar Raman 21 Nov '05

21 Nov '05

dear modeller users, i am new to this software. i try to run the model-default.py it shows the error as "import site" failed . i am using mod8v1 version in windows XP operating system. i don't know how to solve this problem kindly help me in this regard. thank you -- S.Sundar Raman Chemical Lab, CLRI Chennai-20 ph: 044-24411830

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modeller
by Renée Vancraenenbroeck 18 Nov '05

18 Nov '05

dear modeller, I wanted to restrain secondary structure in the target sequenc and I've used the following command (see bottom). The outcoming structure included the wanted alpha-helices but the structure didn't contain the anti-parallel sheet. What did I do wrong? renée vancraenenbroeck renée.vancraenenbroeck(a)student.kuleuven.ac.be from modeller.automodel import * # Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('133', '146'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('69', '83'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids= ('164', '177'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids= ('96', '113'), spline_on_site=False) # Two strands: rsr.make(aln, restraint_type='STRAND', residue_ids= ('44', '54'), spline_on_site=False) rsr.make(aln, restraint_type='STRAND', residue_ids= ('56', '66'), spline_on_site=False) # An anti-parallel sheet: rsr.make(aln, restraint_type='SHEET', atom_ids= ('N:44', 'O:66'), sheet_h_bonds=-5, spline_on_site=False) log.verbose() env = environ() a = mymodel(env, alnfile='Lrrk2-mult5.ali', knowns=('2aedA','1byuA'), sequence='Lrrk2roc') a.make()

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Problems w/ rand_seed for Mod8v1
by zkatsim＠nimr.mrc.ac.uk 16 Nov '05

16 Nov '05

Hello all, I'm having problems changing the rand_seed in my script files. The changes I make don't have any effect, and I end up with the same models. I've tried setting it in various positions within the script but to no success. I've also looked through the previous posts on this topic, but they all refer to previous modeller versions that use the SET command to do this. Can someone tell me exactly where/how to insert the change rand_seed = 'my own number' line? Thanks, Zoe

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Builing models with big distances
by Fabio Passetti 09 Nov '05

09 Nov '05

Dear all, I am working on trying to build models of a protein that is shorter than the template. The gap between the model and the template is spatially big (~30 angstroms) and I could not configure modeller properly to deal with this. Up to now, modeller built models just deleting the part that I wanted, but it was unable to join the CAs of the remained boundaries of the deleted region. The models done by modeller always have two parts separated spatially: the before and the after the deletion. Does anybody have a guess how to solve this problem? Best regards, Fabio Passetti

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Modeling multiple domains
by randalla＠uci.edu 03 Nov '05

03 Nov '05

Hello- Is there a way to force/encourage Modeller to join domains in a manner with few or no clashes/atom overlaps between domains? My first test modeling a multiple domain protein, just as in the example from FAQ #1, resulted in a model with many clashes between the CAs and other atoms of the domains. I realize that Modeller cannot correctly predict domain orientation, but I hope there is a way to strongly discourage inter-domain clashes. Thanks, Arlo Randall University of California, Irvine

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error
by sankari thirumal 03 Nov '05

03 Nov '05

Dear all, I'm not able to solve the following error. i get the same error even when i tired with the known pdbs. how to rectify this problem.please do suggest me. ERROR msg C:\mod\sanmod>mod8v1 model-default.py Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v1\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Program Files\Modeller8v1\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args)_modeller.error: check_a_337E> Structure not read in: 1 with regards sankari --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click.

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Refinement of part of model
by Matt wagner 02 Nov '05

02 Nov '05

I was curious to know if I could refine only part of my model. I want to make a 12 amino acid segment from a loop into an alpha helix without changing the rest of the model. What I am trying to do is only make certain parts of the model less solvent accessible. Thanks for any help, Matt Wagner Cleveland State University

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add new residue type
by Hai-long Wang 02 Nov '05

02 Nov '05

Hi, Modeller I am trying to add a ligand as new residue type. My ligand is acetylcholine. I found its topology in CHARMM /toppar/top_all27_port_lipid.rtf as ACHO. This is how I did: I copy the part from CHARMM file for ACHO to the end of $MODLIB/top_heav.lib. Then add a line at the end of $MODLIB/restyp.lib 142 | ACH | # | ACHO | acetylcholine I use # in the alignment file I have the following in my top file: SET TOPLIB = '$(LIB)/top_heav.lib' SET PARLIB = '$(LIB)/par.lib' SET HETATM_IO = 'ON' However, mod7v7 still indicate that I have unknown residue type. Where I was wrong? Thank you Hailong

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