Hi,
My name is Merav and I am working with the modeling with EM and cross links. I started from the example with rnapolii
*. *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)?
thanks, Merav
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
We ran the script with the topology file that we attached, but all the domains don't move at all. Furthermore, we didn't understand the syntax of the 'super rigid bodies' coulmn, in the tutorial they use 2 numbers separated with a comma, but what do they refer to? Thanks again, Merav
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 >
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 >
On 10/23/17 11:53 PM, מירב בריטברד wrote: > Furthermore, we didn't understand the syntax of the 'super rigid bodies' > coulmn, in the tutorial they use 2 numbers separated with a comma, but > what do they refer to?
All domains that have the same number in that column will be grouped into the same super rigid body.
Ben
On 10/26/17 2:16 AM, מירב בריטברד wrote: > 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?
BuildSystem returns the root hierarchy, which you then pass to each of your restraints. See https://github.com/salilab/imp_tutorial/blob/develop/rnapolii/modeling/model... for an example.
Ben
Yes, in fact note that Ben pointed you to the develop version of the tutorial (not the master branch, which is not yet updated)
Riccardo Pellarin, PhD =================== Institut Pasteur CNRS UMR 3528 25, rue du Docteur Roux 75724 Paris Cedex 15, France riccardo.pellarin@pasteur.fr +33 (0)1 44 38 93 63
On Thu, Oct 26, 2017 at 8:44 PM, Ben Webb ben@salilab.org wrote:
> On 10/26/17 2:16 AM, מירב בריטברד wrote: > >> 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? >> > > BuildSystem returns the root hierarchy, which you then pass to each of > your restraints. See https://github.com/salilab/imp > _tutorial/blob/develop/rnapolii/modeling/modeling.py for an example. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
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מירב בריטברד