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[modeller_usage] CORRECT SECOND LINE with CHAIN ID




Hello,

Thank you for previous advice - it helped.

I have another problem

1) I aligned structures with one sequence - alignmnent below

>P1;1ALU
structureX:1ALU:19  : :184 : : : : :
-------------------LTSSERIDKQIRYILDGISALRKETCN---KSNMCE---------NLNLPKMAEK--DGC---F-------QSGFNEETCLVKIITGLLEFEVYL-EYLQNRFE------SSEEQA-------RAVQMSTKVLIQFLQKKAKNLDA-----ITTPDPTTNASLLT--KLQAQNQW-LQDMTTHLILRSFKEFLQSSLRALRQM--------------------------------------------------------------------------------------------------*

>P1;1CNT
structureX:1CNT:12  : :187 : : : : :
---------------------------------------HRRDLCS---RS------IWLARKIRSDLTALTESYVKHQ---G-------LL--TEAERLQENLQAYRTFHVLLARLLEGDFH------QAI----------HTLLLQVAAFAYQIEELMILL-------EYKIPRNFEKKLWGLKVLQELSQWTVRSIHDLRFISSHQT----------GI----------------------------------------------------------------------------------P---------------*

>P1;1I1R
structureX:1I1RB:'6:B 172:B' : : : :
-------------------EFEKDLLIQRLNWMLWVIDECFRDLCY---RTGICKGILEPAAIFHLKLPAINDT--DHC---G-------LIGFNETSCLKKLADGFFEFEVL-FKFLTTEFG------KSVINV-------DVMELLTKTLGWDIQEELNKLTK-----THYSPPKFDRGLLG--RLQGLKYW-VRHFASFYVLSAMEKFAGQAVRVLDSI----------------------------------------------------------------------------------P---------------*

>P1;1AX8
structureX:1AX8:3  : :146  : :LEPTIN:HUMAN: 2.4: 0.215
------------------IQKVQDDTKTLIKTIVTRINDI----------------------------------------LDF-------IPGLHPILTLSKMDQTLAVYQQIL-TSMPS---------RNVIQI---SNDLENLRDLLHVLAFSK--------------SCHLPEAS-----GLETLDSLGG-VLEASGYSTEVVALSRLQGSLQDMLWQLD------------------------------------------------------------------------LSPGC--------------------*

>P1;spP41160
sequence:spP41160:1  : :146 : : : : : 
----------------VPIQKVQDDTKTLIKTIVTRINDI--------------------------SHTQSVSAKQRVTGLDF-------IPGLHPILSLSKMDQTLAVYQQVL-TSLPS---------QNVLQI---ANDLENLRDLLHLLAFSK--------------SCSLPQTS-----GLQKPESLDG-VLEASLYSTEVVALSRLQGSLQDILQQLD------------------------------------------------------------------------VSPEC--------------------*

>P1;1EVS
structureX:1EVS:4  : :187 : : : : :
------------GSCSKEYRVLLGQLQKQTDLMQD-TSRLLDPYIRI-------QGLDVPKLREH-CRERPGAFPSE-E---T-------LRGLGRRGFLQTLNATLGCVLHRL-ADLEQRLPKAQDLERSGLNIEDLEK-LQMARPNILGLRNNIYCMA-QLLD-----------------------NASDA-FQRKLEGCRFLHGYHRFMHSVGRVFSKW--------------------------------------------------------------------------------------------------*

>P1;1LKI
structureX:1LKI:9  : :180 : : : : :
NATCAIR-----HPCHGN---LMNQIKNQLAQLNGSANALFISYYTA-------QGEPFPNNVEKLCAPNMTDFPSF-------------HGNGTEKTKLVELYRMVAYLSASL-TNITRDQ---KVLNPTAV--SLQVK-LNATIDVMRGLLSNVLCRLCNKYRVGHVDVPPVPDH-----------SDKEA-FQRKKLGCQLLGTYKQVISVVVQAF-----------------------------------------------------------------------------------------------------*

>P1;1PVH
structureX:1PVH:12  : :180 : : : : : 
---CAIR-----HPCHNN---LMNQIRSQLAQLNGSANALFILYYTA-------QGEPFPNNLDKLCGPNVTDFPPF-------------HANGTEKAKLVELYRIVVYLGTSL-GNITRDQ---KILNPSAL--SLHSK-LNATADILRGLLSNVLCRLCSKYHVGHVDVTYGPDT-----------SGKDV-FQKKKLGCQLLGKYKQIIAVLAQAF-----------------------------------------------------------------------------------------------------*

>P1;1F6F
structureX:1F6F:1  : :197 : : : : :
A-QHPPYCRNQPGKCQIPLQSLFDRATTVANYNSKLAGEMVNRFDEQYV--------------I-NCHTSSITTPNSKA---E-------AINTEDKILFKLVISLLHSWDEPL-HHAVTEL---A-----NP--ALLTK-AQEIKEKAKVLVDGVEVIQKRIH-PGEK-NEPYPVWS-----EQSSLTSQDE-NVRRVAFYRLFHCLHRDSSKIYTYLRIL----------------------------------------------------------------------------------KCRLT---SC------*

>P1;1N9D
structureM:1N9D:1  : :199 : : : : :
----LPICPGGAARCQVTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYT---HGRGF-ITKAIN-SCHTSSLATPEDKE---Q-------AQQMNQKDFLSLIVSILRSWNEPL-YHLVTEV---RGMQEAPE--AILSK-AVEIEEQTKRLLEGMELIVSQVH-PETKENEIYPVWS-----GLPSLQMADE-ESRLSAYYNLLHCLRRDSHKIDNYLKLL----------------------------------------------------------------------------------KCRIIHNNNC------*

>P1;1HWG
structureX:1HWG:1  : :190 : : : : :
-------------FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSF-LQNPQTSLCFSESIPTPSNRE---E-------TQQKSNLELLRISLLLIQSWLEPV-QFLRSVF---A-----NS--LVYGASDSNVYDLLKDLEEGIQTLMGRLE-DGS------PRTG-----QIFKQTYSKF-DDALLKNYGLLYCFRKDMDKVETFLRIV----------------------------------------------------------------------------------QCRSVEGSCG------*

>P1;1BGC
structureX:1BGC:9  : :173 : : : : :
----------------SLPQSFLLKCLEQVRKIQADGAELQERLCA---AH-------------KLCHPEELMLLRHSLGIPQAPLSSCSSQSLQLRGCLNQLHGGLFLYQGLL-QALAGISP---ELAPTL----------DTLQLDVTDFATNIWLQMEDLGA-----APAMPTF-------------TSA-FQRRAGGVLVASQLHRFLELAYRGLRYLA-------------------------------------------------------------------------------------------------*

>P1;1RHG
structureX:1RHG:9  : :172 : : : : :
-----------------LPQSFLLKCLEQVRKIQGDGAALQEKLCA---TY-------------KLCHPEELVLLGHSLGIPWAPL---------LAGCLSQLHSGLFLYQGLL-QALEGISP---ELGPTL----------DTLQLDVADFATTIWQQMEELGM--------MPAF-------------ASA-FQRRAGGVLVASHLQSFLEVSYRVLRHLA-------------------------------------------------------------------------------------------------*

2) I obtained an error

openf5__224_> Open       11  OLD  SEQUENTIAL  $(LIB)/restyp.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/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  ${MODINSTALL8v2}/modlib/radii.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/radii14.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/mnch1.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/mnch2.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/mnch3.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v2}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
runcmd______> alignment.append(align_codes=['1AX8', '1ALU', '1CNT', '1I1R', '1EVS', '1LKI', '1PVH', '1F6F', '1N9D', '1HWG', '1BGC', '1RHG', 'spP41160'], atom_files=[], file='MSA-CYTOKIN-T-COFFEE.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)

openf___224_> Open           MSA-CYTOKIN-T-COFFEE.ali

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2270569    2217.353     2.165

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2293501    2239.747     2.187

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2316901    2262.599     2.210

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2363701    2308.302     2.254

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2457301    2399.708     2.343

Read the alignment from file       : MSA-CYTOKIN-T-COFFEE.ali
Total number of alignment positions:   238

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       1AX8     130      1        1AX8 LEPTIN
  2       1ALU     157      1        1ALU 
  3       1CNT     130      1        1CNT 
  4       1I1R     167      1        1I1R 
  5       1EVS     163      1        1EVS 
  6       1LKI     172      1        1LKI 
  7       1PVH     169      1        1PVH 
  8       1F6F     183      1        1F6F 
  9       1N9D     199      1        1N9D 
 10       1HWG     184      1        1HWG 
 11       1BGC     158      1        1BGC 
 12       1RHG     145      1        1RHG 
 13   spP41160     146      1    spP41160 
runcmd______> alignment.check()

check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1AX8.pdb

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2531305    2471.978     2.414
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1AX8.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1ALU.pdb

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2621619    2560.175     2.500
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1ALU.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1CNT.pdb
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: residue number " 12", chain " "
rdabrk__288W> Protein not accepted:        3  1CNT
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1I1R.pdb
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: residue number " 6", chain " "
rdabrk__288W> Protein not accepted:        4  1I1R
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1EVS.pdb
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: residue number " 4", chain " "
rdabrk__288W> Protein not accepted:        5  1EVS
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1LKI.pdb

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2719647    2655.905     2.594
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1LKI.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1PVH.pdb
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: residue number " 12", chain " "
rdabrk__288W> Protein not accepted:        7  1PVH
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1F6F.pdb
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: residue number " 1", chain " "
rdabrk__288W> Protein not accepted:        8  1F6F
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1N9D.pdb
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: residue number " 1", chain " "
rdabrk__288W> Protein not accepted:        9  1N9D
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1HWG.pdb
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: residue number " 1", chain " "
rdabrk__288W> Protein not accepted:       10  1HWG
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1BGC.pdb

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2808743    2742.913     2.679
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1BGC.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\1RHG.pdb
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: residue number " 9", chain " "
rdabrk__288W> Protein not accepted:       12  1RHG
check_a_337E> Structure not read in (please consult the log file
              for more details):        3  1CNT



3) Residue position is corect so I think that I have to specify 
CHAIN ID and tried it - for example:

>P1;1I1RB  
structureX:1I1RB:'6:B 172:B' : : : : 
                    or
structureX:1I1RB:6    :A:172  :A: : : :

- it didn't help - so my question is

 A)how looks a correct second line when I have to use chain ID
 B)In one of my PDB files I have a chain ID which exists as number - 2 
   this same question as above

4) Script below

# Homology modelling by the automodel class

from modeller.automodel import *    # Load the automodel class

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 = './:../atom_files'

a = automodel(env,
              alnfile  = 'MSA-CYTOKIN-T-COFFEE.ali',		            
              knowns   = ('1AX8','1ALU','1CNT','1I1R','1EVS','1LKI','1PVH','1F6F','1N9D','1HWG','1BGC','1RHG'),              			         # codes of the templates
              sequence = 'spP41160',				      
              assess_methods=assess.DOPE)                     
              	                   	 
a.starting_model = 1                 # index of the first model 
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.md_level = refine.slow_large                                    
a.make()                            # do the actual homology modelling



Yours sincerely,

Karol Kaszuba