Ah, I'm sorry for not being clear. When using the GUI and loading the example PDB file in the demo R2 directory, the spin viewer would generate 2 molecules, both of which are identical. It might be because I am not specifying something about the PDB file.
I redid the spin states this time specifying the name of the molecule to be Ap4Aase and it only generated one spin state this time. So I'm guessing I need to be specify the name of the molecule to be read from the PDB file? Cheers, Kapil On Fri, May 31, 2024 at 12:41 PM Kapil Modi <[email protected]> wrote: > I'm unsure if screenshots work but I'll explain in case they don't. When > using the GUI and loading the example PDB file in the demo R2 directory, > the file spin viewer would generate 2 molecules, both of which are > identical. It might be because I am not specifying something about the PDB > file. I redid the spin states this time specifying the name of the molecule > to be Ap4Aase and it only generated one spin state this time. So I'm > guessing I need to be specify the name of the molecule to be read from the > PDB file? > > Cheers, > Kapil > > On Fri, May 31, 2024 at 11:25 AM Edward d'Auvergne <[email protected]> > wrote: > >> On Fri, 31 May 2024 at 16:54, Kapil Modi <[email protected]> wrote: >> > Thank you for the response and the guidance! Also, I apologize if I am >> once again sending this message incorrectly because I am also new to >> SourceForge. >> >> Not a problem. The messages are working correctly now. >> >> > While running test data using the Ap4Ase for the R2 demo, I noticed >> that there would be two molecules loaded in the spin states that had the >> exact same residues and spins. >> >> In the demo repository, there is a single NMR model with a single >> polypeptide in the PDB file: >> >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_nmr-2Drelax_relax-2Ddemo_ci_master_tree_R2_Ap4Aase_Ap4Aase-5Fnew-5F3.pdb&d=DwIBaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=7ULZ3RgKGAAE_RtB3PHsQg&m=tedO9SRMV_M2Nu5ehUoXH03y6XSd0AHM-55ZJXjvM9SCOuO4raUoUlgEyaprD0GA&s=iLWSBQTb1V5kVWW7BmnsXsl1HrpCi8H8fxUUnzvNf7I&e= >> >> In which file within the demo do you see two molecules? You should >> use this PDB file with the R2 demo data. As a hint, in the analysis/ >> directory, you can find the relax_fit.py script which shows you >> exactly how to perform the analysis. >> >> >> > I deleted one of the molecules for the execution of my data because I >> assumed that the PDB file only contains one molecule. Is there an error I'm >> making in my setup that causes this to occur? >> >> Are you talking about your measured data and a real PDB structure? If >> so, is the PDB a set of NMR models or an X-ray PDB with multiple >> structures? I'm a little confused as to what is going on. >> >> Regards, >> >> Edward >> >
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