I would like to add a protein-RNA cross-link restraint to my representation. Is this possible at all in IMP?
I tried to use a csv file similar to polii_juri.csv which is given in the IMP tutorial (https://integrativemodeling.org/2.6.2/doc/manual/rnapolii_stalk.html):
prot1,res1,prot2,res2 RNA_component,345,protein_component,49
But this failes when I read it with IMP.pmi.restraints.crosslinking.ISDCrossLinkMS
ISDCrossLinkMS: WARNING> residue 345 of chain RNA_component is not there
Nevertheless, if I run:
list_of_residues=[(345,"RNA_component")] for res in list_of_residues: particles=IMP.pmi.tools.select(representation,resolution=10,name=res[1],residue=res[0]) if len(particles)>1 : print(res[0],res[1],"more that one particle selected"); continue if len(particles)==0 : print (res[0],res[1],"no particle was selected"); continue print(res[0],res[1],IMP.core.XYZR(particles[0]).get_radius())
I get:
345 RNA_component 10.307014164455413
Thanks in advance!
Genis