- modeller_usage - salilab.org

help regarding some problems related to modelling
by DHWANI DHOLAKIA 12 Nov '13

12 Nov '13

Dear sir/mam I am Dhwani Dholakia Doing M.Tech from Delhi Technological University. I am Using advanced homology modelling for my project work but while doing pdb search i could not find much good E value or % identity or query coverage.. I am confused that should i use a invivo modelling software like I-TASSER or advanced modelling . And also if can help me with the threshold values of various parameters to be used for advanced homology modelling.. Thanking You -- Dhwani Dholakia M.Tech bioinformatics Delhi Technological University

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questions about multichains modeller
by Yi Kong 12 Nov '13

12 Nov '13

Dear colleagues, I have a problem in multichain modeller. according the template file in automodel folder, I created the input file and script file. however when I　run this script, I recieved warnings listed below. Who knows how to reslove the problem? Thanks a lot! You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod9.12' to run them instead. d:\Program Files (x86)\Modeller9.12> d:\Program Files (x86)\Modeller9.12>cd examples d:\Program Files (x86)\Modeller9.12\examples>cd automodel d:\Program Files (x86)\Modeller9.12\examples\automodel>python model-multichain-d ec1.py > model-multichain-dec1.log Traceback (most recent call last): File "model-multichain-dec1.py", line 37, in <module> a.make() # do homology modeling File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 96, in make self.homcsr(exit_stage) File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 410, in homcsr aln = self.read_alignment() File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 400, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was n ot found in the alignment file; ALIGN_CODES( 1) = 4h10 d:\Program Files (x86)\Modeller9.12\examples\automodel>

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multiple templates - loop modelling
by Simone Fulle 08 Nov '13

08 Nov '13

Dear all, I would like to model a protein using two templates and (!) define which parts of the structure are modeled by which template. I.e. the core of the structure by template_1 and a specific loop by template_2. The template structures are already aligned. Any suggestions and comments will be highly appreciated. I am aware that I could generate a "Fused_template_structure" manually but it would be really nice if I could do it in an automatic fashion. Kind regards, Simone

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homology modelling
by pr＠tibh＠ 07 Nov '13

07 Nov '13

How can i build a homology model using template,my template is a crystal structure of a chimeric protein. though it has a 94% query coverage and 48% identity with my target sequence. sequence alignment of non chimeric protein as a whole is very much identical.Can i use the chimeric crystal structure for modelling?

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Hardware?
by Istvan Jonyer 06 Nov '13

06 Nov '13

What hardware is everyone using for Modeller? What do you think would be the ideal configuration? Anyone using any cloud providers? ᐧ

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Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11
by listek_wfrp＠interia.pl 30 Oct '13

30 Oct '13

Hello everybody ! I am new to modeller, so please excuse me if my question seems trivial. I have a problem building a model from multiple templates. When i try to run build model script I get an error: "Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11" I followed all the previous steps from advanced modeling tutorial and all of them worked fine. Now I am stuck, and all solutions I`ve tried dont work. I attatch my script and alignment file. Thank you for your help in advance !

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Fwd: Extract Chain ID
by Amjad Farooq 28 Oct '13

28 Oct '13

I am not scanning against PDB95 but rather working on multi-chain PDBs locally. For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested in extracting the chain ID of the second segment (D) that best aligns with my query sequence, I do not believe you can extract that from PIR alignment file, which only provides chain IDs of the first (A) and the last chain (P). Also, how would I know if my query sequence aligned up against chain D unless I look at the alignment file manually. I want to automate this procedure. In other words, have a python script extract the chain ID of the aligned segment in a multi-chain PDB and automatically proceed to next step for homology modeling--that is I only want to use segment D as a template during homology modeling rather than the whole multi-chain PDB, which compromises the quality of the alignment and hence the model. Thanks! On Mon, Oct 28, 2013 at 2:36 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 10/27/2013 11:08 AM, Amjad Farooq wrote: > >> Is it possible to perform an automatic search of a multi-chain PDB >> template with a known protein sequence that is to be modeled (say >> 100-200 residues in length) and then extract the chain ID of the segment >> of the PDB template that best matches with the query sequence. >> > > If I understand you correctly, this is straightforward. If you're scanning > against our PDB95 database, for example, all the templates are single > chain, and the chain ID is simply the last character in the align code. > > If you're trying to align against a multi-chain template (presumably a > local alignment) you could extract the chain ID trivially from the > alignment object. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/**modeller/<http://www.salilab.org/modeller/> > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usage<https://salilab.org/mailman/listinfo/modeller_usage> >

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Extract Chain ID
by Amjad Farooq 28 Oct '13

28 Oct '13

Hi everyone, Is it possible to perform an automatic search of a multi-chain PDB template with a known protein sequence that is to be modeled (say 100-200 residues in length) and then extract the chain ID of the segment of the PDB template that best matches with the query sequence. As far as I understand, if you align a protein sequence against a multi-chain PDB template in MODELLER, it generates an alignment file (PIR/PAP) that does not automatically give you the chain ID of the PDB segment against which the alignment has been performed. Of course, this is a non-issue if you work manually but I would like to automate modeling for a large number of sequences. Any insights would be greatly appreciated. Thank you! Amjad *************************************************************************************************************************************************** *AMJAD FAROOQ PhD DIC | Associate Professor* Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad(a)farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net ***************************************************************************************************************************************************

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Check out my profile on LinkedIn
by Sako Mirzaie 28 Oct '13

28 Oct '13

LinkedIn ------------ I'd like to include you in my network to share updates and stay in touch. - Sako Sako Mirzaie assistant professor at university Iran Confirm that you know Sako Mirzaie: https://www.linkedin.com/e/-xaf1me-hnbd4jjr-2e/isd/17610846466/X2KwjCWW/?hs… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-xaf1me-hnbd4jjr-2e/3GpqQCFu9Ujj9Gys3027RLVJQStjD… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Re: [modeller_usage] missing sc atoms and rotamers
by micheal j twin 25 Oct '13

25 Oct '13

Dear Ben, thank you very much for your quick reply, I will try your suggestions. Regards Micheal > 1. Use complete_pdb() to make a complete structure for the second PDB (just with "wrong" sidechains). > > 2. Make an alignment using the two PDB structures as templates (presumably this a simple 1:1:1 100% identical alignment). Use the output structure from step 1 as the initial model. > > 3. Override automodel's select_atoms() to select only the missing sidechains, and then build ?> comparative models as per usual. Those sidechains should inherit the dihedral preferences from the first PDB. Dear Lalith, As I said, I'm really new to modeller but I will help you with this when I figure out how to perform Ben's suggestions. Regards Micheal > Dear Michael. > I am also working and facing with the same kind of issue through Modeller. I mean I have to copy residues selectively from two different templates for my homology model and have to follow exactly the same steps as Ben suggested to you in the last reply. Here, I am unable to use the initial model for my second strep model generation. I am facing the usual error (saying 'No atoms are specified from input file) as reported earlier by others. Please let me know if you could successfully execute this step. > Thank you in Advance > > Regards, > Lalith

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