I prefer to use BuildSystem macro, because it seems more convenient and because BuildModel is deprecated. However I don't find any examples that uses the BuildSystem with cross links and EM restrains. Specifically, how can I extract the representation from BuildSystemso can I pass it to the restrains? Thanks
On Tue, Oct 24, 2017 at 3:38 AM, Ben Webb ben@salilab.org wrote:
> On 10/23/17 12:43 AM, מירב בריטברד wrote: > >> *I have attached my topology file. I have one PDB that contains 3 >> proteins and should be one rigid body (ARP7, ARP9, RT102). I also have one >> protein with 3 subunits that should be 3 rigid bodies (RCS2_1, RCS2_2, >> RCS2_3) and should belong to the super rigid body. >> What would be the right way to specify that in the topology file? or >> should it be done in the script like in rnapolii example (which is not >> clear either)? >> > > It depends on whether you are using PMI 1 or PMI 2. > > For PMI 1 (using the BuildModel macro) specify the components you want in > each rigid body and super rigid body in your Python script. > > For PMI 2 (using the BuildSystem macro) use the relevant columns in the > topology file. In order for two components to be in the same rigid body, > you should use the same number in the rigid body column. Looks like you > have that right for rigid bodies already. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >