Re: Structure refinement
Lee, Woonghee
Hi Thilini,
1,2) In the BestEvalated folder, you have files named “XXXXX.list.assigned.list”. If you load those files using “rp”, you will see how many peaks are assigned and unassigned.
3) Show NOE bar button will visualize restraints per residue. You can simply inspect visually. In the Ponderosa Analyzer, you can right-click on the main window’s grid area and select “Count NOE used for this calculation”.
4) In the Ponderosa Analyzer’s main window’s grid area, right-click and select “Show ordered residues (cyrange)”.
Best,
Woonghee
--
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
Denver, CO 80217-3364, USA
Office: +1-303-315-7672
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 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
From: Thilini O Ukwaththage <tuk...@lsu.edu>
Date: Tuesday, April 20, 2021 at 6:22 PM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Re: Structure refinement
Dear Dr. Lee,
I was managed to find scores for some of the criteria you mentioned. But I am not sure how to find these criteria. Can you help me with them? I am very sorry for asking lot of questions.
1) Are your NOESY spectra assigned enough?
I am not sure how to check that I have enough NOESY assigned. I have not manually assigned the NOESY peaks. I used ponderosa c/s with raw NOESY spectra. Does ponderosa assign the NOESY peaks? Can we see those assignments on NOESY spectra?
2) Are you leaving a large number NOE peaks unassigned?
How can I know which NOESY peaks are assigned, and which peaks does not? If I have lot of unassigned peaks, how should I assign them?
3) How many distance restraints per residue?
Is there a way to get this number? or just divide the total NOEs by assigned amino acids number in the sequence? (I only have 1700 total NOEs for 114 assigned residues from 133 total residues. is it enough?)
4) Is RMSD low enough for “ordered” regions?
How can we know the RMSD for ordered regions. I only can see the numbers for backbone and heavy atoms.
Thank you!
Regards
Thilini
Thilini Ukwaththage
Ph.D. Candidate
Macnaughtan Research Group
Choppin Hall 427
Department of Chemistry
Louisiana State University
Baton Rouge, LA 70803
Lee, Woonghee
Dear Thilini,
If you haven’t added by Add New button during constraints-only x phase, you may look into the ponderosa-x refinement option one.
If you have a lot of unassigned peaks, what you can do is to use the best structure that should be very close to the final one (optional though) and distance restraints as additional inputs while running audana or ponderosa-x refinement option. It will assign more based on the structure and existing restraints. You will have a lot of violations but that is necessary if your structure is floppy.
Best,
Woonghee
--
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
Denver, CO 80217-3364, USA
Office: +1-303-315-7672
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 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
From: Thilini O Ukwaththage <tuk...@lsu.edu>
Date: Tuesday, April 20, 2021 at 7:22 PM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Re: Structure refinement
Dear Dr. Lee,
Thank you for your help. I have few more questions regarding the previous answers you gave me.
1,2) In the recent cycles, I used Constraints only option. Those results do not have XXXXX.list.assigned.list file in the best evaluated folder. XXXXX.list.assigned.list file is only in the very first cycles I did with ponderosa X refinements. Should I look at that file? If I have lot of unassigned peaks, should I assign them? Is there a way to manually/or automated way to assign those unassigned NOE peaks? If I assigned more, how can I use these newly added assignments in my future calculations?
4) Show ordered residues (cyrange) only showed me the ordered residue regions. How can I know the RMSD of those regions?
Regards
Thilini
Thilini Ukwaththage
Ph.D. Candidate
Macnaughtan Research Group
Choppin Hall 427
Department of Chemistry
Louisiana State University
Baton Rouge, LA 70803