minimum number of nstruct to build at 65% homolgy

Member Site Forums Rosetta 3 Rosetta 3 – General minimum number of nstruct to build at 65% homolgy

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    • #1699

        Hi everyone, I am trying to model one protein using template which is ~65% homologue, i used comparative modeling protocol given along with the software, my question is how many “nstructures” we have to make , what is the standard number, i used 1000 but it seemed never ending in my lap top, so i stopped that, what is the minimum number of nstructures i can apply? and after getting structure what other applications i have to use in-order to make it final? i used 100, i gor result but not in PDB formate, but its threaded model.out, i am very new to Rosetta, suggestions would be very helpful for me, thank you.

      • #9222

          The number of models you need highly depends on the length of the loops. Longer loops need more samples. It’s hard to tell a priori.

          Talking with an expert, he recommended a progressive approach. Generate a small number of models and examine them. If you get convergence (all the structures look pretty much the same), you don’t need to do more sampling. If not, you need to increase the number of models. Keep running more models until all the new models you generate look pretty much like models you’ve already encountered.

          Regarding the output, it’s in the space-saving, Rosetta-specific “silent file” format. Most Rosetta programs are able to read in silent files, even if they’re typically used with PDBs. You can always convert silent files to PDB with the extract_pdbs application. “extract_pdbs.linuxgccrelease -database $ROSETTADB -in:file:silent silent.out -in:file:tags TAG1 TAG2 TAG3 …” where the TAG* is the list of which structures you wish to extract. Leave off the “-in:file:tags” designation to extract everything. (You can also use -in:file:tagfile with the name of a file with a list of which tags you wish to pass.)

        • #9225

            Thank you, i will try it.

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