ssPine - Gap in Sequence

[Christopher Williams]

Hello,

I'd like to run ssPine on a sequence with a gap in it. For example, the sequence has residues 1-10 and then 20-30, but nothing from 11-19. Is there a way to do run just ONE ssPine job to get this done? Or must I run two? Thanks.

-Chris

[Lee, Woonghee]

Chris,

 

ssPINE tries to overlook global assignment quality, so you try to get the assignments in one shot, I guess over probabilities won’t be very high. If you divide into two jobs, you will want to only include peaks involved in the specific job. Hopefully it helps.

 

Best,

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <pinenmr-u...@googlegroups.com> on behalf of Christopher Williams <cwil...@ucr.edu>
Date: Tuesday, September 13, 2022 at 11:13 AM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: ssPine - Gap in Sequence

 

[External Email - Use Caution]

Hello,

 

I'd like to run ssPine on a sequence with a gap in it. For example, the sequence has residues 1-10 and then 20-30, but nothing from 11-19. Is there a way to do run just ONE ssPine job to get this done? Or must I run two? Thanks.

 

-Chris

--
You received this message because you are subscribed to the Google Groups "I-PINE/PINE and ssPINE user group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pinenmr-user-gr...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/pinenmr-user-group/c076b3f7-28ff-46af-9263-28bd44763d99n%40googlegroups.com.

[Christopher Williams]

Alright, how would I input a seq file that has a gap in it? How do I indicate the gap so Residue 20 doesn't try connecting to Residue 10, for example?

[Lee, Woonghee]

Actually, it is cumbersome. You should provide a sequence file starting from 1 for both jobs. ssPINE will be improved and accept pre-assignment for the fix in the future like I-PINE. One by one. But until then, that’s what we have now.

To view this discussion on the web visit https://groups.google.com/d/msgid/pinenmr-user-group/1bcdd800-b09a-4f21-a929-f790bca9dec5n%40googlegroups.com.