[modeller_usage] Re: Homodimer modelling
* on the number of residues On Tuesday, July 25, 2023, Joel Subach wrote: > Hi Alphafold Multimer may be able to predict the entire oligomer depending > on the residues, thanks:) >> On...
View Article[modeller_usage] Regarding licensing registration
I want to install modeller on my device. But couldn’t complete licensing registration. I dont know what glitch is happening right now. Please advise and help regarding this. I have a Bioinformatics...
View Article[modeller_usage] Re: Homodimer modelling
On 7/25/23 6:52 AM, g.m.tuveri--- via modeller_usage wrote: > Hello, I'm trying to add some missing domains to a big homodimeric > protein, pdb 8em4. I predicted the missing structures with...
View Article[modeller_usage] generate a psf file
Dear all, I have used modeller to generate a pdb file. unfortunately, the pdb file is not regular as the columns 10 and 11 interfere. What can I do? I can not use the pdb file to generate a psf file.
View Article[modeller_usage] Re: generate a psf file
On 8/8/23 9:43 AM, sedmo.info--- via modeller_usage wrote: > I have used modeller to generate a pdb file. unfortunately, the pdb > file is not regular as the columns 10 and 11 interfere. What can...
View Article[modeller_usage] to model heterodimer protein of mossing residue
i tried a build a homology model of a heterodimer protein,since it contains missing residue i have to model that. But i am only familiar with single chain homology modelling and fro multi chain i am...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
I think the only trick is not forgetting the chain break in the ali file: https://salilab.org/modeller/manual/node29.html Best, Ajasja PS: It's a very broad question, so I can only give a broad reply....
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
Hi Arun how many residues in each chain total and how many residues are missing in each chain that need to be modeled? Best, Joel On Thursday, August 31, 2023, Ajasja Ljubetič via modeller_usage wrote:...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
...and below is a link to the Modeller UsageHelp Forum indicating a methodology that I had used successfully to loop missing residue model via constraining the rest of the heptamer given residues...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
https://salilab.org/mm/hyperkitty/list/modeller_usage＠salilab.org/thread/H56FDNOAUM4S6YWUYYVRHLFSQH3NO4GO/ On Thursday, August 31, 2023, Joel Subach wrote: > ...and below is a link to the Modeller...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
Hi Arun thank you for your kind update and sure anytime:). Please let me know where these missing residues are located i.e. are they in highly dynamic loop regions? are they located in parts of the...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
and your welcome:) On Fri, Sep 1, 2023 at 9:58 AM Joel Subach wrote: > Hi Arun thank you for your kind update and sure anytime:). >> Please let me know where these missing residues are located...
View Article[modeller_usage] Re: to model heterodimer protein of mossing residue
On 8/31/23 11:25 PM, Arun Dhanasekaran via modeller_usage wrote:> My reference pdb contains two chains of different protein, one with 306 > residues in which 39 residues are missing and another...
View Article[modeller_usage] CONECT records writing mutated PDB
Hello there, I use Modeller to induce point mutations on a PDB. This part works very well (see code below). My problem is the protein has several disulfides defined by CONECT records in the template...
View Article[modeller_usage] Re: CONECT records writing mutated PDB
On 9/13/23 8:51 AM, Pedro Guillem via modeller_usage wrote:> I use Modeller to induce point mutations on a PDB. This part works very > well (see code below).>> My problem is the protein has...
View Article[modeller_usage] Add Modeller to Spack
Hi, I am a French System. administrator and I just wanted to know it you would consider adding Modeller to the Spack package manager ? It is a very useful and flexible package managers that is used...
View Article[modeller_usage] Re: Add Modeller to Spack
On 10/10/23 12:35 PM, Gabriel CRETIN via modeller_usage wrote:> I am a French System. administrator and I just wanted to know it you > would consider adding Modeller to the Spack package manager...
View Article[modeller_usage] Missing residues - restrain crystal coordinates
Good afternoon, I am trying to model missing residues into my crystal structure following the method on the website: https://salilab.org/modeller/wiki/Missing_residues. I am also trying to restrain the...
View Article[modeller_usage] Re: Missing residues - restrain crystal coordinates
Hi Isabel thank you for your inquiry, if you restrain certain residues they should not move, maybe double-check to be sure that you properly coded these residues to be restrained, thanks On Mon, Oct...
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