On Tue, 2021-07-27 at 15:20 +0100, Helge Paternoga wrote: > Dear all, > > I have what feels like a trivial question about modelling in coot, but > unfortunately I have not managed to solve it > myself. > > I would like to create a bond between a P-tRNA and nascent chain and then > subsequently use RSR in Coot for modelling. > > What I gathered so far is that I should use acedrg to create the restraints > of the linked unit (in my case "A" to > "VAL"). Therefore, I first followed the tutorial in the Coot development blog > which worked well. > > But when I try to do the "real world" example with my model, acedrg crashes > (and I could not find a useful error > message). > > What I could figure out is that it has something to do with the > RNA-nucleotide being referred to as "A", because > linking an imported "AMP" molecule to valine as well as my whole nascent > chain works as it should. > > Therefore, I wanted to ask if you could briefly tell me what is the correct > way to achieve this type of linkage in > Coot? > > Many thanks for reading and best wishes, > > Helge > > > P. S. I have modified Oli Clarke's trimmings to automatically load the > "Restraints" menu with > "add_module_restraints()", but this is only partially working as the menu is > not showing all entries upon starting > coot. I have to still manually load "Calculate -> Modules -> Restraints" to > get the rest of the entries to show. Is > there something I could do to have the full menu from the get go? > >
Hello Helge, It is not a trivial question. I suggest that you use CCP4i2 interface for now - it is more featureful than the Coot interface. You can see Rob demoing the interface here: https://www.youtube.com/watch?v=p4oTJ0bjD3M https://onlinelibrary.wiley.com/iucr/doi/10.1107/S2059798321001753 But IIRC, your problem is more tricky yet, because one of the chains is "backwards" relative to the other. I don't think that I ever solved that. As for auto-loading the module, this is what I have in my ~/.coot-preferences/modules.scm (if (defined? 'coot-main-menubar) (begin (add-module-prosmart) (add-module-restraints) (add-module-cryo-em))) Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
