Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: RNA Structures  (Read 2070 times)

Offline jdbrown444

  • regular
  • *
  • Posts: 1
    • View Profile
RNA Structures
« on: September 02, 2014, 09:35:13 am »
Hi Xiang-Jun,

I tried running the program on RNA structures with protein interactions and it seems to not be able to recognize the interactions. Is this program only meant for DNA complexes? I saw in the description that this is focused on DNA-protein structures but later on you mention it can characterize DNA/RNA-protein interactions. I apologize if i misunderstood. My computer programing background is very limited. Thank you in advance.

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1215
    • View Profile
    • 3DNA homepage
Re: RNA Structures
« Reply #1 on: September 02, 2014, 03:57:22 pm »
Hi,

Thanks for your question regarding SNAP's applicability to RNA-protein structures. Yes, SNAP can be used for RNA-protein complexes as well as DNA-protein complexes, by specifying explicitly the --rna option. Given the complexities of nucleic-acids/proteins interactions, I've intended to start SNAP with DNA-protein structures. Since this question has been brought up several times (both in the Forum and privately), here is the response. Note that in the future, the --rna option may be removed from SNAP when the functionality becomes default.

Move functionality is being added to SNAP, and a new release is coming out soon. As always, please do not hesitate to ask any SNAP-related questions on the Forum.

Xiang-Jun
« Last Edit: September 02, 2014, 08:44:07 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.