Hi, I am trying to run rnadb.py but i get this error: Traceback (most recent call last): File "rnaDB.py", line 509, in <module> class RNA_DB_Entry: File "rnaDB.py", line 512, in RNA_DB_Entry rcsb_pdb = Bio.config.DBRegistry.CGIDB( AttributeError: 'module' object has no attribute 'config' I thought i...

Thanks Sam for all valuable suggestions. I will let you know when I accomplish this project.


cheers!
Deepak

Hi Sam, Thanks for your comments . Finally, the modeling for the first case of chain A is done. I am minimizing the structure to relax it. The second modeling case I wanted to ask your suggestion is this : In this case : model is : chain B template is : chain A The model chain B is modeled fine for ...

in continuation to last message :

The RMSD's for the first case (model chain A and template chain B) are :

template and model (model is chain A) : 0.55

template and target : 5.42

and

model and crystal-structure : 5.45

Please let me know about your comments.

thanks.
cheers!

Hi Sam, I am back with the result. I have been modeling other models too for which I took a while. The model of chain A as per me is well modeled now with correct secondary structure constraints and tertiary interactions. The model along with the template is here : model-chainA: https://www.dropbox....

Thanks Sam.

I am on to it and close to have an accurate model. Will send you the result for your comments.

cheers!
Deepak

Hi Sam I am at present working on other models along with the model whose result i sent you in my last message. Since the result of chain A model obtained from ranbuilder is very close to good I have taken this model to do simulation. I have a program that does the rna simulation based on secondary ...

Hi Sam, thank you for giving me right guidance on this issue too: I have the correct RMSD calculations following this commands in vmd : a) set sel1 [atomselect template "backbone and resid 1 to 50"] b) set sel2 [atomselect model "backbone and resid 1 to 50"] c) set tmat [measure fit $sel1 $sel2] d) ...

Thanks again Sam for the valuable information. The tertiary structure contacts available in the crystal structure for the region 103-137 and 188-219 are : for the region 103-137 : most of the tertiary structure contacts are not as per the reference (crystal structure) for the region 188-219 : some o...

hi Sam, I repaired the residue 30 and other geometric problems with the residues. last.2.pdb: https://www.dropbox.com/s/e2zqqq0ecrelzxu/last.2.pdb This model looks fine now. Please let me know about your comments. Also, I would like to ask some basic queries about this model (could be generalized to...