parameters.csv file for RNA modeling

[Deepak kumar]

Thanks Sam.

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

cheers!
Deepak

[Samuel Flores]

I will look forward to that.

Sam

[Deepak kumar]

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.com/s/uya2nlwvf29k8 ... chainA.pdb

template-chainB:
https://www.dropbox.com/s/trif5t2sjnmf4 ... chainB.pdb

model-crystal-structure-chainA:
https://www.dropbox.com/s/u6y3jxwuhh2ay ... chainA.pdb


Please have a look and let me know about your suggestions.

Also, I would like to ask your comments on this model below:

This is the model for chain B using chain A as the template (opposite of above case)

so :

target : chain B

template : chain A

The model chain B is modeld fine for all regions except for the region 12-119 . In this region secondary structure constraints are satisfied as per literature but the region seems to have a high energy orientation.

the structures are :

model-chainB:
https://www.dropbox.com/s/mt5tcf3vncvwq ... chainB.pdb

template-chainA:
https://www.dropbox.com/s/b7lbvdpy8f0kf ... chainA.pdb

model-crystal-structure-chainB:
https://www.dropbox.com/s/rqne3irmfobwh ... chainB.pdb

It would be nice of you to give your comments on how this issue can be resolved.

Thanks.
cheers!
Deepak

[Deepak kumar]

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!

[Samuel Flores]

With regard to your first message of yesterday, first modeling run:

I think your model looks nice. There are some close contacts around model residue 20, which you can perhaps relax a bit.

The structure doesn't agree everywhere with the crystal, but then again if you think you've done all you can with the NON-crystallographic information, this may be the best that can be done. In general I think it is quite good.


I didn't understand your second question about switching template and target.

Your second message of yesterday was also confusing -- I think you are misusing the terms "model" and "target" again. Please be very careful with vocabulary.

Thanks

[Deepak kumar]

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 all regions except for the region 12-119 . In this region secondary structure constraints are satisfied as per literature but the region seems to have a high energy orientation.

the structures are :

model-chainB: model of chain B
https://www.dropbox.com/s/mt5tcf3vncvwq ... chainB.pdb

template-chainA: template chain A
https://www.dropbox.com/s/b7lbvdpy8f0kf ... chainA.pdb

model-crystal-structure-chainB: crystal structure of chain B
https://www.dropbox.com/s/rqne3irmfobwh ... chainB.pdb

It would be nice of you to give your comments on how this issue can be resolved.

Thanks.
cheers!
Deepak

[Samuel Flores]

Hi Deepak,

good to hear that you're satisfied with your modeling. I also think you converged to a point, beyond which one could perhaps argue the non-crystallographic data can't take you. That's coming from someone who has just been providing tech support -- I don't even know which species this structure is from -- so you should perhaps run it by another scientist to see if they find it credible.

It's good that you're minimizing it with (presumably) and MD package. Minimization can be tricky though. I would like you to be aware that you can turn on the Amber99 force field in a limited region, e.g.:

setDefaultMDParameters
includeResidues A 139 143
includeResidues A 23 34

In this example, we are including chain A residues 139 to 143 and 23 to 34 in the "physics zone." This means other atoms are not interacting. This can help you equilibrate a limited region at very low cost. Of course, you have to make sure you have just the right sort of flexibility. Maybe flexibilize a hinge some ways from the problem area.

I'm not sure that I can provide guidance on further structures, though. That seems less like tech support and more like me being a second author without the benefits!

Best of luck!

Sam

[Deepak kumar]

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


cheers!
Deepak