- modeller_usage - salilab.org

changes in MODELLER9 optimization & DNA denaturation
by RYAN PAVLOVICZ 22 Mar '07

22 Mar '07

Hi. I just upgraded from MODELLER8v2 to 9v1 and am experiencing problems when modelling a protein-DNA complex in that the DNA is denaturing after optimization. When I use the same modelling script in 8v2, the DNA stays in its double-helical form, even when i use md_level= refine.very_slow. Can anyone explain to me what changes in the optimizers were made that cause this denaturation? I am using the MODELLER residue types ADE, GUA, CYT, and THY for the modelling. Thanks! ryan

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secondary structure assignment and patching
by Ryan 22 Mar '07

22 Mar '07

The template for one of my models has a large region in the middle of its sequence that shares no homology to my target sequence. Fortunately this region does not interact with the catalytic region in which I am interested, so I am able to remove this segment from the model. This means than my final model is composed of two chains. The problem I am having is with the secondary structure assignment to the second chain of the model. Without any explicit special secondary structure assignment the first chain of my model faithfully replicates the secondary structures of the template, while the second chain is lacking most if not all secondary structure. I know I could fix this problem by adding special restraints, but would rather have the model pick up secondary structure from the template. I am doing this modelling with default patching off. After a lot of testing, it seems that the N and C terminal patches are the cause of this loss in secondary structure to only the second chain of my model. If I comment out the patches to the protein termini but keep the patches I'm making to the DNA in my model, then I get the results I am looking for. Anyone have an idea why this is happening? Here is my input file: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.patch_default = False env.io.hydrogen = env.io.hetatm = True env.io.atom_files_directory = './:~/homology' class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='5MC2', residues=(self.residues['253:C'])) self.patch(residue_type='DEO1', residues=(self.residues['248:C'])) ... self.patch(residue_type='5PHO', residues=(self.residues['248:C'])) self.patch(residue_type='5PHO', residues=(self.residues['260:D'])) # adjust 3' hydroxyl terminals of DNA strands self.patch(residue_type='3TER', residues=(self.residues['259:C'])) self.patch(residue_type='3TER', residues=(self.residues['271:D'])) # manually patch N termini self.patch(residue_type='NTER', residues=(self.residues['1:A'])) self.patch(residue_type='ACE ', residues=(self.residues['166:B'])) # manually patch C termini self.patch(residue_type='CTER', residues=(self.residues['165:A'])) self.patch(residue_type='CTER', residues=(self.residues['247:B'])) a = mymodel(env, alnfile = 'alignment.ali', knowns = ('template1','template2'), sequence = 'model3') a.starting_model= 1 a.ending_model = 1 a.make() I'd appreciate any help. Thanks! ryan

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HYP and alignment from other than modeller
by yuemin liu 21 Mar '07

21 Mar '07

Hi everyone, Is that possible to model HYP(Hydroxylproline) containing protein with PRO? I found HYP in the modeller lib, but no one-letter code for HYP. Another question is that how feasible is we use alignment from other program like blast when do modeling. Thanks, Liu, Yuemin ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front

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how to select the best template?
by deepti 19 Mar '07

19 Mar '07

Dear modeller caretakers, please explain me the output of compare.py file,how to select the best template and what is Weighted pair-group average clustering based distance method? thanks and regards. --------------------------------------------------------------- Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1uluA @11jw7A @12fhsA @1 1uluA @1 246 106 101 1jw7A @1 43 274 108 2fhsA @1 41 42 258 Weighted pair-group average clustering based on a distance matrix: .--- 1uluA @1.0 57.0000 | .---------------------------------------------------------- 1jw7A @1.0 58.5000 | .------------------------------------------------------------ 2fhsA @1.0 +----+----+----+----+----+----+----+----+----+----+----+----+ 58.5600 58.2900 58.0200 57.7500 57.4800 57.2100 56.9400 58.4250 58.1550 57.8850 57.6150 57.3450 57.0750

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how to select the best template?
by deepti 19 Mar '07

19 Mar '07

Dear modeller caretakers, please explain me the output of compare.py file,how to select the best template and what is Weighted pair-group average clustering based distance method? thanks and regards. --------------------------------------------------------------- Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1uluA @11jw7A @12fhsA @1 1uluA @1 246 106 101 1jw7A @1 43 274 108 2fhsA @1 41 42 258 Weighted pair-group average clustering based on a distance matrix: .--- 1uluA @1.0 57.0000 | .---------------------------------------------------------- 1jw7A @1.0 58.5000 | .------------------------------------------------------------ 2fhsA @1.0 +----+----+----+----+----+----+----+----+----+----+----+----+ 58.5600 58.2900 58.0200 57.7500 57.4800 57.2100 56.9400 58.4250 58.1550 57.8850 57.6150 57.3450 57.0750

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How to incorporate NAD and water in my model
by deepti 16 Mar '07

16 Mar '07

Dear Modeller caretakers, I am trying to construct a model for a protein having a known structure for the purpose of learning Modeller. The pdb structureis in form of protein-NAD adduct. My aim is to build a similar model. Using the templates I have built a model, please tell me how to incorporate NAD and water in my model. I have read the manual 'faq' , but am confused how to change my alignment (including '.' for BLK residues and 'w' ). How do I change the template pdb files for this? How do I make my own restraint file? My alignment file is(generated by align2d.py):- >P1;1qsgA structureX:1QSG.pdb: 2 :A: 259 :A:undefined:undefined:-1.00:-1.00 GFLS-GKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQND--KLKGRVEEFAAQLGSDIVLQCDVAEDASIDT MFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLG AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIK--------DFRKMLAHCEAVTP IRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL* >P1;1eny sequence:1eny: : : : ::: 0.00: 0.00 AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAG RVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP S-RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQR APIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL* I got a lesser objective function while using the alignment generated by clustalw. Which would be a better option? Also please suggest me ways to further refine my model so as to make it almost like the pdb structure. Thanks and Regards, Deepti

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Re: [modeller_usage] How can modeller build the structure of antibodies ?
by Modeller Caretaker 12 Mar '07

12 Mar '07

jitrayut jitonnom wrote: > I want to know that can modeller build some kind of antibodies structure > in which they have two chains (Vl and Vh). Actually, I have searched for > some similar problems but I am still in doubt. Besides, I also found the > literatures that use the modeller program to build the antibody model. > Most of them did not tell more details on how they performed to obtain > the antibody model. All I know from those papers are that there are two > ways to performs: first, model two chains from a single template; > second, model those two chains separately. Therefore, I was wondering > that which one is the best method and how to do modeling by using > modeller. Especially, after modeling the two chains (in case of the > second method) how can I concatenate these chains? See http://salilab.org/modeller/9v1/manual/node27.html For the second method, you will need to add additional constraints or do some additional modeling or docking simulations with the generated models, since Modeller will not know the relative orientation of the two chains. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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query
by deepti 09 Mar '07

09 Mar '07

Hi, i wish to model a protein having known pdb structure. After getting a model from modeller and evaluating it I found the Dope scores from template_evaluation.py (-279092.718750)and from model_evaluation.py (-26497.847656). How do I refine the model further so that it becomes comparable with the known pdb structure? Why do I get a violatins file,Does this mean that my model is incorrect? The pdb structure is in form of the protein-NAD adduct, how do I insert NAD in my model. Can I separately model the active site and incorporate a ligand(not biological)in my model? Thanks and regards, Deepti

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Re: [modeller_usage] Errors during generate alignment file for two chains
by Modeller Caretaker 09 Mar '07

09 Mar '07

jitrayut jitonnom wrote: > and the PIR file of scfv is > >P1;scfv > sequence:scfv:1:L:123:H:::0.00: 0.00 > vmtqtpalmaaspgekvtitcsvsssisssnlhwyqqksetspkpwiygtsnlasgvpvrfsgsgsgtsysltis > smeaedaatyycqqwsnypltfgagtklelkssggggsggggggssrssl/evkllesggglvkpggslklscaas > gftfssyamswvrqtpekrlewvatissggtytyypdsvkgrftisrdnakntlylqmsslrsedtamyycarfr > ngaywgqgtlvtvsaatttapsv* > > After i run the script above i found some errros like this; > > read_al_373E> Protein specified in ALIGN_CODES(i) was not found > in the alignment file; ALIGN_CODES( 2) = scfv > > So, if anyone can help me for this problem i will be appreciated. You have two problems: 1. Alignment files are case-sensitive. The 20 standard amino acids are all in upper case, not lower case. 2. Save your alignment file in plain text. While the file here looks OK, the attachment you sent separately is formatted as Rich Text Format. If you make the file in a text editor in Windows, make sure when you save the file, you select "plain text" format. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Creating a dimer using model generated by modeller
by Charlie Allerston 08 Mar '07

08 Mar '07

I have created a model using a template from a dimer. I was wondering if I could incorporate this model back into the dimer in any way as I am interested in the monofacial contact between the 2 molecules? cheers charlie _________________________________________________________________ Match.com - Click Here To Find Singles In Your Area Today! http://match.engb.msn.com/

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