question about unusual bond length, bond angle, Chirality deviations
Dear Modeller users
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%.
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 "
I am a beginner, so I don't what should I do to correct above warning message. Please help me, Any suggestions or comments are welcomed. Thanks.
Hyun.
---align2d.py---- from modeller import *
env = environ() aln = alignment(env) mdl = model(env, file='****', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='******', atom_files='*****') aln.append(file='******.ali', align_codes='*****') aln.align2d() aln.write(file='**************.ali', alignment_format='PIR') aln.write(file='**************.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 = '***************.ali', # alignment filename knowns = '*******', # codes of the templates sequence = '******') # 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() # do homology modeling
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
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 [modeller-care@salilab.org] Sent: Monday, March 29, 2010 2:26 PM To: Song, Hyundeok (songhk) Cc: modeller_usage@salilab.org 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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
On 04/14/2010 08:08 PM, Song, Hyundeok (songhk) wrote: > After alignment, I used loop patch to generate the model. I thought > using loop modelling gives more accurate structure for homology > modelling.
No, loop modeling will probably give better structures for the loop regions than regular homology modeling, since homology modeling doesn't do any refinement of the loops. But it won't affect the aligned regions at all.
> 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.
Your original question suggested you had a single 70-residue long loop. Looking at your alignment, I now see that that's not the case - you have several shorter loops. Thus there aren't really any parts of the template you can remove.
> My question: In order to generate best model from Modeller, which > residues of template should I delete?
It depends on what you want to use the model for. It may be that the warning you're getting can be ignored. Or you have several loops in your structure, so you should concentrate your loop refinement on just the loops that you are most interested in (for example, loops that are close to a ligand binding site or an interface region). Just doing default loop modeling will try to simultaneously refine all of the loops.
Ben Webb, Modeller Caretaker
participants (2)
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Modeller Caretaker -
Song, Hyundeok (songhk)