Automatic assignment

Analysis Version 3
#1

Hi,
I am rather new to CCPN. I have a new project where I need to assign a protein and I would like to use CCPN together with an automatic assignment software. I know MARS was integrated into the CCPN version v2, but is not part of v3. How would you suggest to proceed? Shall I run it using NMRbox? Can I use the data from CCPN v3 directly?

I am open to alternative ways, if there is any better one than MARS. Just I would like to use my CCPN data.

Thank you!
Francesca

#2

Hi Francesca,

I’m afraid I don’t really see an easy way for you to use MARS with V3 at the moment. However, you can to some extent move data between V2 and V3. So if you have a project in V3, you can save it as a NEF file with CCPN tags and get most of it into V2. You can then run MARS there and then once you are done with that, you can open the V2 project in V3 again.

The program that is likely to work better in combination with V3 than MARS is FLYA, as I think that can read and write NEF files. @ElizaP might be able to offer some insight into how easy it would be do to that. But I think you probably need to pay for a licence for that one (as it is part of the CYANA family).

Best wishes,
Vicky

#3

Hi Vicky,
thank you very much for your reply and for all the suggestions.

Another option would be the UNIO NMR App. Do you have any experience with it using CCPN data? I read that it uses XEASY format: I guess that in this case I should probably save the CCPN v3 project, open it into v2, convert it to xeasy and then use it into UNIO. Sounds correct?

Thank you again.
Francesca

#4

Hi Francesca,
Yes, that should be possible, though I don’t think anyone on the CCPN team has ever tried this.
Vicky

#5

Ok, thanks: than probably it is not advisable to be the first one to try…!

Thank you, I think I now have all the options, I will figure out which one might work best for me.

Best wishes,
Francesca

#6

Sorry, I forgot one more thing: will it be possible in the future to use MARS also from v3 of CCPN?

Thanks!
Francesca

#7

Yes, we are very much planning that! How long it will take, I can’t say, though I would hope that we will get it done within the next year.
Vicky

#8

Thank you very much, Vicky!

Best wishes,
Francesca