July 2020 - modeller_usage

Re: [modeller_usage] Treading onto known PDB template
by Modeller Caretaker 20 Jul '20

20 Jul '20

On 7/6/20 2:49 PM, Geoffrey Woollard wrote: > Can I do the modelling in the context of the tetramer? Otherwise I would > have to just do it with the protomer, and then delete out parts that > were clashing. > > Are there options for applying symmetry during modelling? Sure, this is also covered in the manual: https://salilab.org/modeller/9.24/manual/node29.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Re: [modeller_usage] reg: modeling against docked protein-ligand complex
by Anwesha Mohapatra 16 Jul '20

16 Jul '20

Hello Sir, Could you tell me where am going wrong? On Wed, Jul 15, 2020, 2:10 PM Anwesha Mohapatra < anwesha.mohapatra11(a)gmail.com> wrote: > > > <https://mail.google.com/mail/u/0?ui=2&ik=2650c6341a&attid=0.1&permmsgid=msg…> > Hello Sir, > > I have a protein (6eqe.pdb) which I have docked to a ligand using autodock > vina. I want to model my query gene taking this receptor-ligand complex as > the template. The ligand is identified as UNK in the pdb file. On modeling > I am not getting all the atoms of the ligand in the modelled output (Only 1 > carbon and 1 oxygen).Attached to this mail are the template file which has > been docked to the ligand *(6eqe_bhet.pdb) , *the modelled protein with > incomplete/erroneous ligand > *(ARN19002.1_Rhizobacter_gummiphilus_NS21.B99990001.pdb)* and the > alignment file for the same* > (ARN19002.1_Rhizobacter_gummiphilus_NS21.ali) . * > Could you please look into the files? > > Kindly let me know where I am going wrong. > > Thanks and regards > Anwesha >

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Multiple CPUs
by Casey Becker 06 Jul '20

06 Jul '20

Hello again, I'm trying to use modeller directly through python's IDLE interface to run a parallel job. I've attached my script and also the python core file that's created up to a point, because it stops before it actually makes the models. Three files with .slave0, .slave1, and .slave2 are created, but when edited with notepad, show an error. I've attached one of them as well. Thanks.

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Treading onto known PDB template
by Geoffrey Woollard 06 Jul '20

06 Jul '20

I'm studying a transmembrane ion channel (protein 1). There are structures of protein 1 in a closed conformation, and I am interested in the open conformation. There is a very similar protein in an open conformation (protein 2). So I am trying to thread the sequence of protein 1 onto the atomic model of protein 2. I know the template. I tried robetta and swiss prot for this. How should I do things with modeller? Could someone point me to a tutorial? The sequences are quite similar, except for some insertions. I know my protein very well and am looking for a protein modelling approach where I can have low level control, and manual manipulation at the sequence alignment and structure level. I don't need something that does everything automagically. -- Geoffrey Woollard, MSc PhD student Department of Medical Biophysics, University of Toronto Princess Margaret Cancer Centre, University Health Network

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