Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations
To: "" <>
Subject: Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations
From: "Song, Hyundeok (songhk)" <>
Date: Thu, 15 Apr 2010 03:08:37 +0000
Accept-language: en-US
First of all, thanks for reply. I don't know many things about homology modeling.
I did homology modelling for dimer.
Modeller found the template for MJ0305(model) as 1ots.pdb. The fasta sequence length of template(1ots.pdb) is 466, and the fasta sequence length of model (MJ0305) is 396. According to the Modeller, the sequence identity between model and template is 24%.
After alignment, I used loop patch to generate the model. I thought using loop modelling gives more accurate structure for homology modelling. When I checked model pdb structure, it gave the warning message "unusual bond length, bond angle, Chirality deviations".
I think this error comes from 70 fasta sequence length difference between model and template as suggested from Modeller Caretaker.
My question:
In order to generate best model from Modeller, which residues of template should I delete?
(I heard that the limit of Modeller is about 15 residues from last email). My current sequence difference is 70, so I should delete some residues.
My attached my code, outputs to explain my situation...
1. align2d.py ---> output: MJ0305-1otsAB.ali, MJ0305-1otsAB.pap // alignment
2. model-loop.py // loop modeling
after loop modeling, I got pdb structure for model.
Thanks so much...
Sincerely
Hyun.
************************** Fasta sequence *********************************************
Template: (1ots.pdb)
MKTDTPSLETPQAARLRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLSDAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGGGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEAEQLARSK
Model: (Y305_METJA, Uncharacterized protein MJ0305 )
MPMNIVNMFGKYIKIIKWIGIASLIGIVGGLSSVIIAIIIEYFPEKHNVLLIPIVFFIAGLFVDYIYELKGSGIDRVLKALNTNEKLTWIRGLLKVLLAGAVIAVGGSAGKEGPCVQSSASFADELYRLLKLKNRELVIITGIAGGLGGAFSAPLGTAILACEIIEHENFNYINLIPPIIASVVGYLIFYLITGRKHLFNITLSYTINIHDFLLFILGAFFCSLIAHCYIKTYRKISSTFDNLKIPYCIKTLIGGILVAVISYFIPEVMGMGLTLTKELFIMEFSLVFLVLLLIGKILATSFTVGSGTPGGLVFPSMCIGAISGIIFGSLIGDCSAPYIVLGIATTLSATTNAPLGGAVLCTEIFGFDFAVPASIGAVIGYQMTKLETIFKYIRF
**************************************align2d.py*********************************************************
from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1ots', model_segment=('FIRST:A','LAST:B'))
aln.append_model(mdl, align_codes='1otsAB', atom_files='1ots.pdb')
aln.append(file='MJ0305.ali', align_codes='MJ0305')
aln.align2d()
aln.write(file='MJ0305-1otsAB.ali', alignment_format='PIR')
aln.write(file='MJ0305-1otsAB.pap', alignment_format='PAP')
*****************************model-loop.py***************************************************************
# Homology modeling by the automodel class
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
a = loopmodel(env,
alnfile = 'MJ0305-1otsAB.ali', # alignment filename
knowns = '1otsAB', # codes of the templates
sequence = 'MJ0305') # code of the target
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 = None # No refinement of model
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 50 # Last loop model
a.loop.md_level = refine.fast # Loop model refinement level
a.make()
************************** MJ0305-1otsAB.ali **********************************************
>P1;MJ0305
sequence:MJ0305: : : : :::-1.00:-1.00
--------------MPMNIVNMFGKYIKIIKWIGIASLIGIVGGLSSVIIAII--IEYFPEKHNVLLI-PIVFFI
AGLFV--DYIYELKGSGIDRVLKALNTNEKLTWIRGLLKVLLAGAVIAVGG-SAGKEGPCVQSSASFADELYRLL
KLK---NRELVIITGIAGGLGGAFSAPLGTAILACEIIEHENFNYINL-IPPIIASVVGYLIFYLITGRK-HLFN
I-TLSYTINIHDFLLFILGAFFCSLIAHCYIKTYRKISSTFDNLKIPYCIK-TLIGGI---LVAVISYFIPEVMG
MGLTLTKELFIMEFSLVFLVLLLIGKILATSFTVGSGTPGGLVFPSMCIGAISGIIFGSLIG-------DCSAPY
IVLGIATTLSATTNAPLGGAVLCTEIFG-FDFAVP---ASIGAVIGYQMTKLETIFKYIRF/MPMN---------
--IVNMFGKYIKIIKWIGIASLIGIVGGLSSVIIAIIIEYF-PEKHNVL---------LIPIVFF---IA---GL
FV--DYIYELKGSGIDRVLKALNTNEKLTWIRGLLKVLLAGAVIAVGG-SAGKEGPCVQSSASFADELYRLLKLK
---NRELVIITGIAGGLGGAFSAPLGTAILACEIIEHENFNYINL-IPPIIASVVGYLIFYLITGRK-HLFNI-T
LSYTINIHDFLLFILGAFFCSLIAHCYIKTYRKISSTFDNLKIPYCIK-TLIGGI---LVAVISYFIPEVMGMGL
TLTKELFIMEFSLVFLVLLLIGKILATSFTVGSGTPGGLVFPSMCIGAISGIIFGSLIG-------DCSAPYIVL
GIATTLSATTNAPLGGAVLCTEIFG-FDFAVP---ASIGAVIGYQMTKLETIFKYIRF--------*
>P1;1otsAB
structureX:1ots.pdb: 17 :A:+885 :B:MOL_ID 1; MOLECULE VOLTAGE-GATED CLC-TYPE CHLORIDE CHANNEL ERIC; CHAIN A, B; ENGINEERED YES; MOL_ID 2; MOLECULE FAB FRAGMENT (HEAVY CHAIN); CHAIN C, E; MOL_ID 3; MOLECULE FAB FRAGMENT (LIGHT CHAIN); CHAIN D, F:MOL_ID 1; ORGANISM_SCIENTIFIC ESCHERICHIA COLI; ORGANISM_COMMON BACTERIA; GENE ERIC OR B0155; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_COMMON BACTERIA; EXPRESSION_SYSTEM_STRAIN BL21DE3; EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PET28B+; MOL_ID 2; ORGANISM_SCIENTIFIC MUS MUSCULUS; ORGANISM_COMMON MOUSE; CELL_LINE HYBRIDOMA CELL LINE; MOL_ID 3; ORGANISM_SCIENTIFIC MUS MUSCULUS; ORGANISM_COMMON MOUSE; CELL_LINE HYBRIDOMA CELL LINE: 2.51:-1.00
RRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAM
FGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIF
RLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQ-FRYTLISIKAVFIGVIMSTIMYRIFNHEVALID
VGKLS-DAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSG
GGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTF
AIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILA-RTLAKQEAEQ/RR
QLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGY
FLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLK
GDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQ-FRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGK
LS-DAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGGGF
NLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIA
GMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEA*
************************** MJ0305-1otsAB.pap **********************************************
_aln.pos 10 20 30 40 50 60
1otsAB RRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFL
MJ0305 --------------MPMNIVNMFGKYIKIIKWIGIASLIGIVGGLSSVIIAII--IEYFPEKHNVLLI
_consrvd * * * * * * * *
_aln.p 70 80 90 100 110 120 130
1otsAB CSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTV
MJ0305 -PIVFFIAGLFV--DYIYELKGSGIDRVLKALNTNEKLTWIRGLLKVLLAGAVIAVGG-SAGKEGPCV
_consrvd * * * * * **** ** * * * * ** * *** *
_aln.pos 140 150 160 170 180 190 200
1otsAB QIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQ-FRYTLISIKAVF
MJ0305 QSSASFADELYRLLKLK---NRELVIITGIAGGLGGAFSAPLGTAILACEIIEHENFNYINL-IPPII
_consrvd * ** * ** * ** ** *** * * * *
_aln.pos 210 220 230 240 250 260 270
1otsAB IGVIMSTIMYRIFNHEVALIDVGKLS-DAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGG
MJ0305 ASVVGYLIFYLITGRK-HLFNI-TLSYTINIHDFLLFILGAFFCSLIAHCYIKTYRKISSTFDNLKIP
_consrvd * * * * * ** * *
_aln.pos 280 290 300 310 320 330 340
1otsAB NITKWVLMGGAIGGLCGLLGFVAPATSGGGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPG
MJ0305 YCIK-TLIGGI---LVAVISYFIPEVMGMGLTLTKELFIMEFSLVFLVLLLIGKILATSFTVGSGTPG
_consrvd * * ** * * * * * ** ** * ** **
_aln.pos 350 360 370 380 390 400
1otsAB GIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLI
MJ0305 GLVFPSMCIGAISGIIFGSLIG-------DCSAPYIVLGIATTLSATTNAPLGGAVLCTEIFG-FDFA
_consrvd * * * * ** * * * *** * * *
_aln.p 410 420 430 440 450 460 470
1otsAB LPMIITGLGATLLAQFTGGKPLYSAILA-RTLAKQEAEQ/RRQLIRQLLERDKTPLAILFMAAVVGTL
MJ0305 VP---ASIGAVIGYQMTKLETIFKYIRF/MPMN-----------IVNMFGKYIKIIKWIGIASLIGIV
_consrvd * ** * * * * * *
_aln.pos 480 490 500 510 520 530 540
1otsAB VGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIE
MJ0305 GGLSSVIIAIIIEYF-PEKHNVL---------LIPIVFF---IA---GLFV--DYIYELKGSGIDRVL
_consrvd ** * * * * * * * * ****
_aln.pos 550 560 570 580 590 600 610
1otsAB GALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATG
MJ0305 KALNTNEKLTWIRGLLKVLLAGAVIAVGG-SAGKEGPCVQSSASFADELYRLLKLK---NRELVIITG
_consrvd ** * * * * ** * *** ** ** * **
_aln.pos 620 630 640 650 660 670 680
1otsAB AAAGLAAAFNAPLAGILFIIEEMRPQ-FRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLS-DA
MJ0305 IAGGLGGAFSAPLGTAILACEIIEHENFNYINL-IPPIIASVVGYLIFYLITGRK-HLFNI-TLSYTI
_consrvd * ** ** *** * * * * * * * * * **
_aln.pos 690 700 710 720 730 740
1otsAB PLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGG
MJ0305 NIHDFLLFILGAFFCSLIAHCYIKTYRKISSTFDNLKIPYCIK-TLIGGI---LVAVISYFIPEVMGM
_consrvd * * * * ** * * *
_aln.p 750 760 770 780 790 800 810
1otsAB GFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYH
MJ0305 GLTLTKELFIMEFSLVFLVLLLIGKILATSFTVGSGTPGGLVFPSMCIGAISGIIFGSLIG-------
_consrvd * * ** ** * ** *** * * * **
_aln.pos 820 830 840 850 860 870 880
1otsAB LEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILAR
MJ0305 DCSAPYIVLGIATTLSATTNAPLGGAVLCTEIFG-FDFAVP---ASIGAVIGYQMTKLETIFKYIRF-
_consrvd * * * *** * * * * ** * * *
_aln.pos 890
1otsAB TLAKQEA
MJ0305 -------
_consrvd
________________________________________
From: Modeller Caretaker []
Sent: Monday, March 29, 2010 2:26 PM
To: Song, Hyundeok (songhk)
Cc:
Subject: Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations
On 03/27/2010 07:26 PM, Song, Hyundeok (songhk) wrote:
> I generated the dimer by Modeller.
> Fasta sequence number of model(400) is 70 less than Fasta sequence
> number of template(470).
> Sequence identity between template and model is 24%.
If I understand you correctly, you have a loop that is about 70 residues
long. There's no way Modeller will be able to accurately model that (the
limit is about 15 residues). I can't tell for sure without seeing your
alignment file though.
> after selecting the template, I aligned them, and then I did loop
> modeling. (I attached the code at the bottom.) Finally I got final pdb
> structure, but when I checked my model, I found the below warning message.
>
> "Unusual bond length, unusual bond angle, Chirality deviations "
Looks from your script like you built 50 loops, so you can check the
other 49 PDB files to see if another loop looks better. But if your
loops are really 70 residues long, Modeller won't be able to help you.
Your best bet there is simply to remove those 70 residues from your
model sequence, and build a model of part of the protein.
Ben Webb, Modeller Caretaker
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