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