Does anyone have an experience in extracting average structure from multiple PDB structures? I know that in MD simulations there is something like averaging structures but here I have original PDB crystal structures sharing some structural features and on that basis I want to extract an average structure which could serve as a representative of all PDB structures.
Any help would be appreciated. Thanks.
Dear Lee
Thank you for your input. I am reading about XPLOR. Hopefully it will resolve my issue. I might write in to you if I find any difficulties in that. Thanks
Yeah. If you prefer modern python code, Dr. Charles Schwieters did excellent job for that.
https://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/simulationTools.html
Please read "class StructureLoop".
Mailing list for Xplor-NIH is very active and everyone including Charles may be willing to answer.
Dear Lee
Sorry for late response. Thank you for introducing me to Xplor-NIH. Yes, I'd rather prefer modern codes, I will have to look into it in detail to see how it works.
Regards
Hi dear Lee
Hope you are doing good. I installed xplor-nih package and was going through tutorials and examples. I found there should be a script named aveStruct.py for generating non-regularized average structure, which is missing. However the input file aveStruct.inp is present. Could you please elaborate a little how to use xplor for my purpose. As per tutorial python script for calculating average structure should be there which is not. Am I supposed to write one? or am I missing out something?
I will be grateful for any help
Regards
Hi Sara,
There are many ways you can get around. However, I would still suggest asking Charles and some one by using Xplor-NIH mailing list.
If you want to align structures first before using averaging them, then you can use targetRMSD.py
Cheers,
Woonghee
- Badges
- Science topic