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Re: [modeller_usage] Automatically find gaps in the alignment



This is what I get:

_modeller.ModellerError: chk_aln_340E> Number of residues in model ( 248) does not match that in alignment ( 221).

Please, see the attached files. The alignment file and the structure files work fine with other inputs.


On 02/04/2015 05:40 PM, Modeller Caretaker wrote:
On 2/4/15 8:35 AM, Edelmiro Moman wrote:
Great!

But can I insert that directly within the selection like this?

class MyModel(automodel):
     def select_atoms(self):
         return selection(self.get_insertions(aln, minlength=1,
maxlength=30, extension=0, include_termini=True))

Yes - although you'll need to read the alignment first. There's a method
read_alignment() which returns it. (Note that this is basically what the
default loopmodel.select_loop_atoms() method does, except that it
includes deletions too.)

     Ben Webb, Modeller Caretaker


--
Edelmiro Moman, PhD
ProSciens, computer-aided drug design
2-4 rue du Palais de Justice
L-1841 Luxembourg

Phone  : +352 2728-2588
E-mail : 
http://prosciens.com

Attachment: 4WLBA.aln
Description: x-application-x/aln

                         MODELLER 9.14, 2014/07/30, r10190

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2014 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
              B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
          M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
             A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
                     F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux aeolux 3.16.0-4-amd64 x86_64
Date and time of compilation         : 2014/07/30 10:40:58
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2015/02/04 17:47:38

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v14}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v14}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       191566     187.076     0.183

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       192094     187.592     0.183
openf___224_> Open           ${MODINSTALL9v14}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       240694     235.053     0.230
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
openf___224_> Open           ${MODINSTALL9v14}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       253994     248.041     0.242
openf___224_> Open           ${MODINSTALL9v14}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v14}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v14}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           4WLBA.aln

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       256172     250.168     0.244

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       257622     251.584     0.246

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       260522     254.416     0.248

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       266322     260.080     0.254

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       383378     374.393     0.366

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       384366     375.357     0.367

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       385246     376.217     0.367

Read the alignment from file       : 4WLBA.aln
Total number of alignment positions:   248

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1      4WLBA     248      1        4WLB
  2  4WLB_flex     221      1 4WLB_flexpr
openf___224_> Open           4WLBA.aln

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       400861     391.466     0.382

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       415953     406.204     0.397

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       431353     421.243     0.411

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       462153     451.321     0.441

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       523753     511.478     0.499

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       524633     512.337     0.500

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       525621     513.302     0.501

Read the alignment from file       : 4WLBA.aln
Total number of alignment positions:   248

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1  4WLB_flex     221      1 4WLB_flexpr
  2      4WLBA     248      1        4WLB
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open           ./4WLB_flexprot.pdb

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       593646     579.732     0.566

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       593646     579.732     0.566

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       593817     579.899     0.566

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       594667     580.729     0.567

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       595925     581.958     0.568

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       597829     583.817     0.570

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       597829     583.817     0.570

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       597919     583.905     0.570

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       600775     586.694     0.573

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       600775     586.694     0.573

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       600910     586.826     0.573

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       605194     591.010     0.577

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       605194     591.010     0.577

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       605392     591.203     0.577

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       611818     597.479     0.583

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       621440     606.875     0.593

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       621440     606.875     0.593

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       621737     607.165     0.593

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       621737     607.165     0.593

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       622187     607.604     0.593

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       636637     621.716     0.607

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:       636637     621.716     0.607

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       637312     622.375     0.608

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]:       658970     643.525     0.628

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:       658934     643.490     0.628

check_ali___> Checking the sequence-structure alignment. 

Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
     28     1  287   288      L     R    8.699
     52     1  311   312      K     S   18.632
END OF TABLE
check_a_344_> << END OF COMMAND
openf___224_> Open           ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file:        3
openf___224_> Open           ${LIB}/par.lib

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       798186     779.479     0.761

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       799786     781.041     0.763

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       803766     784.928     0.767

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       805766     786.881     0.768

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       808766     789.811     0.771

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       813266     794.205     0.776

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       818838     799.646     0.781

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       821638     802.381     0.784

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       825838     806.482     0.788

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       832138     812.635     0.794

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       834910     815.342     0.796

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:       836310     816.709     0.798
read_pa_232_> parameters    BONDS   ANGLS  DIHEDS IMPROPS    MODE
                              227     561     661     112       0

Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:       875089     854.579     0.835

Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:      1074911    1049.718     1.025

Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:      1105607    1079.694     1.054

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    16   248
              atom names           : C     +N
              atom indices         :  2019     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    16   248
              atom names           : C     CA    +N    O
              atom indices         :  2019  2016     0  2020

mkilst______> segment topology constructed from sequence and RTF:
              segments residues atoms bonds angles dihedrals impropers:
                     1      248  2020  2065      0         0       886

Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:      1191199    1163.280     1.136

patch_______> segment topology patched using RTF:     1  ;  GLY  ;  GLYP
              segments residues atoms bonds angles dihedrals impropers:
                     1      248  2020  2065   2783      3264       886


Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:      1283295    1253.218     1.224
patch_______> segment topology patched using RTF:   248  ;  SER  ;  CTER
              segments residues atoms bonds angles dihedrals impropers:
                     1      248  2021  2066   2785      3266       887

genseg______> segment topology constructed from sequence and RTF:
              segments residues atoms bonds angles dihedrals impropers:
                     1      248  2021  2066   2785      3266       887
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer:        1
              After transferring coordinates of the equivalent template atoms,
              there are defined, undefined atoms in MODEL:     1808      213
openf___224_> Open           4WLBA.ini
wrpdb___568_> Residues, atoms, selected atoms:      248     2021     2021
make_re_417_> Restraint type to be calculated:  stereo

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1390340    1357.754     1.326

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1398532    1365.754     1.334

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1414916    1381.754     1.349

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1447684    1413.754     1.381

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1480452    1445.754     1.412

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1545988    1509.754     1.474

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1578756    1541.754     1.506

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1611524    1573.754     1.537

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1677060    1637.754     1.599

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1808132    1765.754     1.724

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1873668    1829.754     1.787

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      1939204    1893.754     1.849

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      2070276    2021.754     1.974
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
              Added bond,angle,dihedral,improper restraints  :     2066    2785    3080     880
              Total number of restraints before, now         :        0     8811
make_re_422_> Number of previous, current restraints         :        0     8811
make_re_423_> Number of previous, current selected restraints:        0     8811
make_re_417_> Restraint type to be calculated:  phi-psi_binormal

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2215061    2163.146     2.112
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch1.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/mnch1.mdt
errdih__638_> Missing atoms in a dihedral, residue index, residue type:        5      159  ARG
errdih__638_> Missing atoms in a dihedral, residue index, residue type:        6      159  ARG
errdih__638_> Missing atoms in a dihedral, residue index, residue type:        7      159  ARG
errdih__638_> Missing atoms in a dihedral, residue index, residue type:        8      159  ARG
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1
make_re_422_> Number of previous, current restraints         :     8811     9057
make_re_423_> Number of previous, current selected restraints:     8811     9057
make_re_417_> Restraint type to be calculated:  omega_dihedral

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2215077    2163.161     2.112
openf___224_> Open           ${MODINSTALL9v14}/modlib/omega.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/omega.mdt
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1
omgdel__425_> Unselected all O C +N +CA dihedrals:      254
              (This is to avoid clashes between STEREO
              and OMEGA_DIHEDRAL restraints)

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      2477221    2419.161     2.362
make_re_422_> Number of previous, current restraints         :     9057     9304
make_re_423_> Number of previous, current selected restraints:     9057     9050
make_re_417_> Restraint type to be calculated:  chi1_dihedral

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2477221    2419.161     2.362
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi1234.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi1.mdt
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1
make_re_422_> Number of previous, current restraints         :     9304     9524
make_re_423_> Number of previous, current selected restraints:     9050     9270
make_re_417_> Restraint type to be calculated:  chi2_dihedral

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2477221    2419.161     2.362
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi1234.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi2.mdt
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      2608293    2547.161     2.487

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      2739365    2675.161     2.612
make_re_422_> Number of previous, current restraints         :     9524     9695
make_re_423_> Number of previous, current selected restraints:     9270     9441
make_re_417_> Restraint type to be calculated:  chi3_dihedral

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2739365    2675.161     2.612
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi1234.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi3.mdt
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1
make_re_422_> Number of previous, current restraints         :     9695     9774
make_re_423_> Number of previous, current selected restraints:     9441     9520
make_re_417_> Restraint type to be calculated:  chi4_dihedral

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      2739365    2675.161     2.612
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi1234.bin
openf___224_> Open           ${MODINSTALL9v14}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted:  4WLB_flexprotA
getdata_289_> Proteins (all/accepted):        1        1
make_re_422_> Number of previous, current restraints         :     9774     9803
make_re_423_> Number of previous, current selected restraints:     9520     9549
make_re_417_> Restraint type to be calculated:  DISTANCE

Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]:      3321377    3243.532     3.168
make_re_422_> Number of previous, current restraints         :     9803    13765
make_re_423_> Number of previous, current selected restraints:     9549    13511
make_re_417_> Restraint type to be calculated:  DISTANCE

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      3583521    3499.532     3.418
make_re_422_> Number of previous, current restraints         :    13765    17688
make_re_423_> Number of previous, current selected restraints:    13511    17434
make_re_417_> Restraint type to be calculated:  DISTANCE

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      4107809    4011.532     3.918

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      4369953    4267.532     4.168
make_re_422_> Number of previous, current restraints         :    17688    20859
make_re_423_> Number of previous, current selected restraints:    17434    20605
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    20859    22976
make_re_423_> Number of previous, current selected restraints:    20605    22722
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    22976    22976
make_re_423_> Number of previous, current selected restraints:    22722    22722
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    22976    22976
make_re_423_> Number of previous, current selected restraints:    22722    22722
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    22976    22976
make_re_423_> Number of previous, current selected restraints:    22722    22722
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    22976    22976
make_re_423_> Number of previous, current selected restraints:    22722    22722
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated:  DISTANCE
make_re_422_> Number of previous, current restraints         :    22976    22976
make_re_423_> Number of previous, current selected restraints:    22722    22722
rmdupl__427_>     1522 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    22976    21200
openf___224_> Open           4WLBA.rsr
openf___224_> Open           4WLBA.rsr

Dynamically allocated memory at  amaxrestraints [B,KiB,MiB]:      4484478    4379.373     4.277
rdcsr2__307_> Number of restraints read    :    21200
              Number of excluded pairs read:        0
              Number of pseudo atoms read  :        0
rdcsrs__304_> Restraints in memory, selected restraints:    21200    21200
              Explicitly excluded atom pairs in memory :        0
              Pseudo atoms in memory                   :        0
chk_aln_340E> Number of residues in model (     248) does not match
              that in alignment (     221).

Attachment: refine_gaps_only.py
Description: application/chimera