Saxier Forum

Hi Alex,

the array is dynamic and I think you can feed GAJOE as many models as you can generate

Let me know if you manage to hit a wall, very keen to find out!

Cheers,

Hayds

Hi Alex, long time no hear :) So, pool generation in RANCH/EOM is effectively unlimited in model size, and although I have only tested up to 20,000 input model intensities for GAJOE/EOM myself, I think the array size is not fixed. Let me know how you go and how many model intensities worked :) Best ...

Hi, the trick to do this is to add the GLYCANS (using the GLYCOSYLATION ATSAS toll for example), but to then split the PDB files of the protein and the attached glycan. Then when EOM asks if there is 'bound DNA' for each rigid body you then provide the glycan PDB file. Let us know how this works for...

Dear vas2201, can you explain a little more what you mean by the "global orientation of the domains from the EOM structures" ? I assume you don't mean the orientation of the domains relative to each other in each model as that is pretty straight forward. I'm not sure what you're after exactly. Cheer...

Dear Kermani, the issue could be the system itself. The data looks like it comes from a membrane protein in detergent, is this the case? If so, one thing you can do is extract only the "shape" scattering by using the data up to the first minimum in the curve as input for DAMMIN/DAMMIF. You need to c...

Hi James, the most straight forward thing to do is extract the representative model (usually MODEL 1) from the PDB file. Check the PDB entry to make sure the first model is considered to be the representative one of the ensemble. Then just use this as your input rigid body. Although I have not teste...

Hi Julie, I just removed all the extra characters and EOM runs fine with the modified sequence file (EOM run without using any rigid bodies, just random coil from sequence). In your case I assume you have corresponding rigid bodies. Do you have anything in the PDB files that is unusual? Cheers, Haydyn

Hi Julie, try removing all the non-alphabetical characters from the sequence files, you should only have something like this: MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQG ELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLI YTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYL...

Hi Julie,

can you please pm me your sequence file? Is the EOM run using any PDB files or just random structure?

Structural and biophysical methods for biological macromolecules in solution Singapore • 06 – 14 December 2017 poster.png [/url] About the course: Structural methods applicable to solutions facilitate structural and functional studies on biological macromolecules under close to native conditions. F...

Hi, one typically sees this problem if you have no "flexible" sequence for EOM to generate. There must be some sequence missing between the n-terminal and c-terminal domain PDB files. So for example, if the sequence is: AAAAAAAAAABBBBBBBBBBCCCCCCCCCC and PDB file 1 contains the residues: AAAAAAAAAA ...

Dear vb, it will take a bit of time to reimplement a best_curve001.txt output file from EOM 2.1. In the meantime you can use the -w flag to write out all the work files used by the genetic algorithm. The GA_CYCLE files list the selected curves for each ensemble, from these files you could estimate t...

Dear vb,

We did indeed remove this file at some point and as you noted it is no longer part of the output in EOM 2.0. I was not sure people actually used it. I will see what can be done to recreate it (or reintroduce it into EOM again).

Cheers,

Haydyn

Hi thd1,

I'm a bit interested in why the Rflex is higher for the selected ensemble than the pool. Does it make sense in this particular case? I assume you are using rigid bodies and a flexible region between?

Haydyn

Hi Abhi, the output files include for example: CaCa_distr_001_1.dat --> distribution of end to end distances Size_distr_001_1.dat --> ensemble size (Dmax) distribution pdbs --> conformations in the selected ensemble statistics_flexibility.svg --> a vector graphic summarising the flexibility metrics ...