- modeller_usage - salilab.org

struggling to make structure predictions
by Adhikari, Badri (MU-Student) 06 Aug '12

06 Aug '12

Hello all, I am struggling to write a python program that takes protein sequence as input and produces some conformations as the output (with no any other input data). With the help of previous replies, I tried merging the examples: "structure_from_sequence.py", "charm_forcefield.py" and "basic_optimization.py" and wrote a script that is attached. This script runs and produces chimera python files that I can visualize through chimera. 1. Will the script that I have prepared work as an example to produce 3D structures with just sequence as input? OR have I made any fundamental/conceptual mistakes while merging them? 2. I can produce chimera python files for each of the predicted conformations. But I want pdb files. Is it possible to do that? Are there any examples? 3. Is it possible to add contacts restrain (distance between atoms as a restrain) moving forward with this approach? 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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Modelling of GFP
by James Starlight 06 Aug '12

06 Aug '12

Dear Modeller Users! I'm using lattest version of Modeller with the Easy Modeller GUI. I'm modelling Green fluorescent protein (GFP) which consist of chromophore heterogroup which is covalently lincked in the middle of the sequence of that protein ( so this HET group is missing in the fasta sequence of that protein- and during sequence-template alignment I obtained GAP in the place where Chromophore group should be). How I could model this protein with inclusion of the Heterogroup in the final model ? If I try to make my model based on my template ( with missing some regions) ussing of its sequence ( where Chromophore group is absent) I've obtained error like class_modeller'_sequenceMissmatchError' On other hand in some case I've used template without chromphore groups ( with the mutations for instance where this region replaced with standart amino acids ). In that case I have no problems but my final model lack for chromophore group ( as in the template). Thanks for help James

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[Fwd: Re: doubt on selecting condition]
by vmahesh＠ibab.ac.in 30 Jul '12

30 Jul '12

Respected sir Could you please clarify my doubt that among these four values which one we have to more preference (RMSD(Å),Seq.Id.%)'Eq.Pos.P-value) for selecting these four Structure's(2mdh:A,2mdh:B.1b8p:A,1dbm:A) for given example of advance modelling in modeller tutorial. Really sorry for asking this same question again and again because i could not convince with your last messages and i hope this time you will clear my doubt. thanks you somuch for your reply's -----------------------------------------------------------------------------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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Biological unit
by Po-Lin Chiu 30 Jul '12

30 Jul '12

Hi, Sorry for the question not related to homology modeling! I would like to create a PDB file of my protein in 500x500 unit cells (in 2D crystal) based upon the crystal symmetry, and I believe MODELLER has certain functions or commands to build it. Could anyone give me a hint of how to do it? Thanks a million for the help! Best, Po-Lin

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(no subject)
by Othman Houcemeddine 27 Jul '12

27 Jul '12

http://www.studiothink.net/communicare/orders/anaoler.html?yu=eretuam

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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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