Re: Regarding NMRFAM Ponderosa Web Server

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WOONGHEE LEE

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Oct 16, 2019, 11:07:29 PM10/16/19
to Dahal, Salik, ponderosa-...@googlegroups.com, I-PINE/PINE and ssPINE user group
Dear Salik,

I wonder if your resonance assignments agree well with your NOESY data.
Also, peak picking is based on your contour-level as well. 

To confirm your assignments are valid ones, 

  1. Make 2D projections of NOESY data which look like N-HSQC and C-HSQC using easy_ucsfdata program. https://www.youtube.com/watch?v=KyfyS5inLwI
    2. and share it all with friends, family, and the world on YouTube.

  2. Copy and paste your assignments from N-HSQC and C-HSQC to 2D projections.
  3. If they are shifted, 
    1. make them corrected in 2D projections and drop all the experiments other than 2D projections and NOESY data, or
    2. Align NOESY data to HSQCs (al or st)
  4. Then, run "c3" calculation.
About whitelists and blacklists, you already know your disulfide bond pairs. For the initial runs, you can promote neighboring residues around them while demoting residues they cannot be never be close (e.g. in same helix apart farther than 8 a.a., in different helix but other part of the helix is interacting with the other robustly, etc)

Cheers,
Woonghee

================================================

Woonghee Lee, M.S., Ph.D.

Assistant Scientist
        and
Principal Investigator

National Magnetic Resonance Facility at Madison (NMRFAM)
and Biochemistry Department
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive Rm B160E
Madison, WI USA 53706-1544



From: Dahal, Salik <sal...@ostatemail.okstate.edu>
Sent: Wednesday, October 16, 2019 9:45 PM
To: WOONGHEE LEE <wle...@wisc.edu>
Subject: Re: Regarding NMRFAM Ponderosa Web Server
 
Dr,

 I have upgraded the latest version.  And followed as you said. But, it started picking  7/8 thousand noises (automatic pick peaking)  

Also, how can we conclude whitelist and blacklist pairs? 

Is there any possible ways you can assist me further. 

 Sincerely, 

Salik Dahal

On Wed, Oct 16, 2019 at 10:46 AM WOONGHEE LEE <wle...@wisc.edu> wrote:
I wonder if you are using the latest NMRFAM-SPARKY program. If you are using "c3" plug-in of recent versions, you will see disulfide bond and blacklist/whitelist columns that you can fill in.
If you do not see these columns, I suggest upgrading it (two-letter-code "dN").

Woonghee

================================================

Woonghee Lee, M.S., Ph.D.

Assistant Scientist
        and
Principal Investigator

National Magnetic Resonance Facility at Madison (NMRFAM)
and Biochemistry Department
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive Rm B160E
Madison, WI USA 53706-1544


From: Dahal, Salik <sal...@ostatemail.okstate.edu>
Sent: Tuesday, October 15, 2019 8:33 PM
To: wh...@nmrfam.wisc.edu <wh...@nmrfam.wisc.edu>
Subject: Re: Regarding NMRFAM Ponderosa Web Server
 
Dr. Woonghee Lee,

I fixed that disulfide bond pair.
I uploaded raw .ucsf files  and .list files. I am kind lost to how to make whitelist and blacklist in ponderosa. 

My protein is a helical protein. 

 Is there any possible things I can proceed ahead to improve my input?

Thank you for your response , your time and your suggestion.
  Sincerely,
Salik

--
================================================

Woonghee Lee, M.S., Ph.D.

Assistant Scientist
        and
Principal Investigator

National Magnetic Resonance Facility at Madison (NMRFAM)
and Biochemistry Department
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive Rm B160E
Madison, WI USA 53706-1544

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