- modeller_usage - salilab.org

A question about using multiple template
by Xiongzhuo Gao 25 Jul '12

25 Jul '12

Dear Modellers, Our lab is studying the structure of the rod and cone photoreceptor phosphodiesterase that is central to the visual signaling pathway. The rod enzyme contains a regulatory tandem GAF domain (GAFa-GAFb) and a catalytic domain, and exists as a heterodimer (PDE6A and PDE6B). There are currently no full length crystal structures for this catalytic heterodimer, only a structure for the GAFa regulatory domain of cone PDE6C, the GAF domain that binds cGMP noncatalytically. The most homologous protein to PDE6 is the PDE that is abundant in vascular smooth muscle and is the target for Viagra, PDE5 (a catalytic homodimer). There is a dimeric structure for the PDE5 tandem GAF domains (GAFa-GAFb) and for the isolated, monomeric catalytic domain, but no full-length structures. cGMP binds to the GAFa domain of PDE5, the same as PDE6. A more distantly related PDE, PDE2, has a crystal structure of the nearly full-length, dimeric protein, but unfortunately the GAF domains of PDE2 occur in an opposite order compared to PDE5 and PDE6 (i.e., the cGMP binding site is in GAFb). See the attached diagram for a visual description of the domain organization of the three PDEs. We are trying to build a homology model for PDE6 heterodimer. The homology model when PDE6 is threaded onto the PDE2 structure is poor. In contrast, structural homology modeling of PDE6 GAF and catalytic domains using PDE5 as a template gives excellent results. Unfortunately, it is only in the PDE2 structure that the molecular architecture of the nearly full-length dimer has been determined, namely the region between the GAF and catalytic domains and the relationship of the two catalytic domains. Is there some way to rearrange (cut-and-past) the individual domains in the sequence alignment to allow PDE5 to serve for the template for those domains that have been determined, while still using the PDE2 template to thread the PDE6 linker region and to define the relationship of the two catalytic domains with each other? Could you kindly give us some advice on how to do the alignment and build the model? I would greatly appreciate your help. Best, Xiongzhuo Gao Molecular, Cellular and Biomedical Sciences Department University of New Hampshire Durham, New Hampshire 03824 Phone: 603-862-3829

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Re: [modeller_usage] what based we have to select structure from DBali and how ?
by vmahesh＠ibab.ac.in 19 Jul '12

19 Jul '12

Respected sir Hi dear friend Rene you are absolutely correct because when i was clustered 1bdmA i got nearly 2782 similar structures including these four (2mdh:A, 2mdh:B,1b8p:A and 1dbm:A) but i didnt get 1b8p:A in this series that's why i got confused. one more confusion is for selecting these structures which one we have to give more preference among these four values (RMSD (Å),Seq. Id.(%),Eq.Pos,P-value) ----------------------------------------------------------------------------> Hello Ben, > > I talked to someone that has experience with inputting data into this > system and he had told me that I submitted it wrong. I do apologize for > the inconvenience. > > Rene > > On Tue, Jul 17, 2012 at 12:29 PM, <vmahesh(a)ibab.ac.in> wrote: > >> Respected sir >> >> when i am practising example of advance modelling in modeller tutorial >> .... i got little confusion that in what based we have to select >> structure >> from DBali and how and why you choosed specifically these four >> structures >> >> Doubted line: >> >> "The structure of the Malate Dehydrogenase 1bdm has been clustered in >> the >> DBAli database within the family fm00495 of 4 members (2mdh:A, 2mdh:B. >> 1b8p:Aand 1dbm:A). " >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage

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Re: [modeller_usage] what based we have to select structure from DBali and how ?
by vmahesh＠ibab.ac.in 18 Jul '12

18 Jul '12

Respected sir when i am practising example of advance modelling in modeller tutorial .... i got little confusion that in what based we have to select structure from DBali and how and why you choosed specifically these four structures Doubted line: "The structure of the Malate Dehydrogenase 1bdm has been clustered in the DBAli database within the family fm00495 of 4 members (2mdh:A, 2mdh:B. 1b8p:Aand 1dbm:A). "

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Re: [modeller_usage] doubt on selecting condition
by vmahesh＠ibab.ac.in 18 Jul '12

18 Jul '12

Respected sir could you please clarify my doubt that what based we have to select these four structure's(2mdh:A,2mdh:B.1b8p:A,1dbm:A) for given example of advance modelling in modeller tutorial -----------------------------------------------------------------------------Multiple templates The structure of the Malate Dehydrogenase 1bdm has been clustered in the DBAli database within the family fm00495 of 4 members (2mdh:A, 2mdh:B. 1b8p:Aand 1dbm:A). The multiple alignment generated by the command salign() in MODELLER is used in DBAli to generate a multiple structure alignment of the family. The alignment can be downloaded from the DBAli database or you can use the file `salign.py' to calculate it on your computer. -----------------------------------------------------------------------------

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Re: [modeller_usage] doubt on input for DBAli and selecting conditions
by vmahesh＠ibab.ac.in 18 Jul '12

18 Jul '12

Respected sir could you please clarify my doubt that what is the input for DBAli database? and what based we have to select similar structure's? with respectfully Mahesh velusamy

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ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different
by Jonathan Crane 16 Jul '12

16 Jul '12

Hi, I am trying to model a 2-chain Ab sequence, but I keep getting the same error. I think it is not reading the chain break '/' correctly, but not sure. Here's the ali text: >P1;1U6A structure:1U6A:2:H:215:L:antiGP120:human:2.81:-1.00 -VQLQESGPGLVKPSETLSLTCTVSGGSISSHYWSWIRQSPGKGLQWIGYIYYSGSTNYSPSLKSRVTISVETAKNQFSLKLTSMTAADTAVYYCAR--GPVPAVFYGDYRLDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP/EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE* >P1;rAb53 sequence:rAb53:2:H:215:L:rAb53mod:human:-1.00:-1.00 QVQLQESGAGLVKPSETLSLTCTVSGGSISGHYWNWIRQPPGKGLEWIGYIHYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARAEGRGWSAFY-YYYMEVWGKGSTVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP/EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE* and the log result: read_te_290E> Number of residues in the alignment and pdb files are different: 436 222 For alignment entry: 1 1U6A x (mismatch at alignment position 223) Alignment YICNVNHKPSNTKVDKKVEPEIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKP PDB YICNVNHKPSNTKVDKKVEP Match ******************** It looks like the PDB ends after the heavy chain instead of reading after the chain break and including the light chain, but I can't figure out why. Any ideas? Thanks Jon

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help required in preparing .ali file
by Sumra Wajid Abbasi 30-FBAS/MSBI/F09 16 Jul '12

16 Jul '12

Dear Sir/Madam In my case there are to starting residue positions first residues start from 2nd position and continuous upto 39th position than from 40 to 45th positions residues are missing, thn from 46th onwards residues are present now while preparing ali file i am confused how to mention the 2 starting positions of residues? kindly tell me how can i specify residues from 2nd upto 39th position and than from 46th till end ? Sincerely Sumra Abbasi

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Problem with model-segment.py (same model obtained)
by Lipi Thukral 16 Jul '12

16 Jul '12

Dear Modeller users, I would like to model only a segment of my protein, precisely res 76 - 94. I am using model-segment.py script for this purpose. I have looked at the existing example on web (http://salilab.org/modeller/9v1/manual/node22.html) I created alignment file with the same protein. I have no problems running the script but the model obtained is exactly the same as the template which is expected but even the residue range 76-94 is exactly the same. I am pasting my script here, please let me know where am I going wrong? ------------------------------------------------------------------------------ from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() class MyModel(automodel): def select_atoms(self): # Select residues 1 and 2 (PDB numbering) return selection(self.residue_range('76:', '94:')) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = '5tmg-5tmg.ali', # alignment filename knowns = '5tmgA', # codes of the templates sequence = '5tmg') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling ------------------------------------------------------------------------------ Many Thanks, Lipi

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Question about compressing Uniprot90
by Dimitrije Jevremovic 11 Jul '12

11 Jul '12

I am trying to compress the Uniprot90 FASTA file database into a binary file using convert() function as provided in examples for the MODELLER. However, my compressed file ends up being even larger than the uncompressed original one. What may be the problem here? Here is the Python code which I a using with MODELLER v9.7. from modeller import * log.verbose() env = environ() sdb = sequence_db(env) sdb.convert(seq_database_file='/gne/research/data/bioinfo/modeller/db/uniprot90', seq_database_format='FASTA', chains_list='ALL', minmax_db_seq_len=[30, 4000], clean_sequences=True, outfile='/gne/research/data/bioinfo/modeller/db/uniprot90_pruned.bin') Kind regards and thank you, Dimitrije Jevremovic -- ----------------- Dimitrije Jevremovic intern at Bioinformatics & Computational Biology Department

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Is the function - forms.upper_bound(..) - supposed to restrain precisely?
by Adhikari, Badri (MU-Student) 11 Jul '12

11 Jul '12

Hello modeller users and experts, I am trying to impose distance restrains in structure prediction python script as explained in the example at http://salilab.org/modeller/manual/node27.html. Following the example I used the forms.gaussian(group, feature, mean, stdev) function. But my predicted model does exactly satisfy the distance restrain. I can observe that adding the distance restrain, HAS added some distance restrain but it looks like modeller is not giving 100% weightage to the distance restrain. I also tried forms.upper_bound(group, feature, mean, stdev) as explained at http://salilab.org/modeller/9v5/manual/node97.html. With this function, I verified that modeller gives more weightage to the distance restrain, but STILL does not precisely satisfy the restrain. Is this what these functions are supposed to do? OR is there any other technique to instruct modeller to absolutely satisfy the distance restrain? Case I: Restrain used: rsr.add(forms.gaussian(group = physical.xy_distance, feature = features.distance(at['CA:2'], at['CA:4']), mean = 7.0, stdev = 0.1)); Distance between CA:2 and CA:4 in the final model: 8.5 Case II: Restrain used: rsr.add(forms.upper_bound(group = physical.xy_distance, feature = features.distance(at['CA:2'], at['CA:4']), mean = 7.0, stdev = 0.1)); Distance between CA:2 and CA:4 in the final model: 8.2 Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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