I see, that makes a lot of sense, thank you! On Mon, Jun 3, 2024 at 5:52 AM Edward d'Auvergne <[email protected]> wrote:
> On Sat, 1 Jun 2024 at 17:23, Kapil Modi <[email protected]> wrote: > > 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? > > Hi, > > I think one of the above messages didn't make it to the mailing list. > I guess there was a problem with attaching a file. This is disabled > by default to avoid too much strain on the open source infrastructure. > > I've just tested running the analysis through the GUI and I think > there might be an issue with the way you worked through the wizard. > On the page to load the PDB file, you have both an 'Apply' and 'Next' > button. Both of these will cause the PDB file to be loaded by > executing the structure.read_pdf user function. This is deliberate, > as there are cases where you want to load models or structures > one-by-one out of a PDB file and change their numbering or for > converting between individual structures to models or reverse. So if > you accidentally load the molecule twice using the 'Apply' button, it > is safe to delete all but the first. This is also why there is a > 'Skip' button, so you can avoid loading it a second time. > > Regards, > > Edward >
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