Re: Backbone & Heavy-atom RMSD
Lee, Woonghee
Soumendu, you will want to calculate your own RMSD because they are influenced by determined ordered residues. When you right-click on the grid table in the POKY Analyzer, you see Cyrange’s ordered residues. In PyMOL, you can use that range to align against the first model. In PyMOL, type @p to split the models, and repeat
align i. 1-100 & n. N+CA+C+O & final_water_refined_0002, final_water_refined_0001, cutoff=0
align i. 1-100 & n. N+CA+C+O & final_water_refined_0003, final_water_refined_0001, cutoff=0
align i. 1-100 & n. N+CA+C+O & final_water_refined_0004, final_water_refined_0001, cutoff=0
.
.
.
To get backbone RMSDs and use Excel or etc to calculate mean and dev.
Replace n. N+CA+C+O to n. N*+C*+O*+S* for all heavy atoms.
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://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: Soumendu Boral <soumen...@gmail.com>
Date: Saturday, March 6, 2021 at 5:42 AM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Backbone & Heavy-atom RMSD
Dear Dr. Lee,
In the POKY analyzer (or the result zip folder), can you tell me where backbone and heavy-atom RMSD of the calculated structure can be found? In the result summary (in the mail), the backbone and heavy-atom RMSD were given already. Should I follow that?
Regards,
Soumendu
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Soumendu Boral
Ph.D. Research Scholar
Structural and Molecular Biology Lab
School of Bioscience
Indian Institute of Technology Kharagpur
Post-Graduate Department of Biotechnology
Indian Institute of Technology Roorkee
Phone: +91-9735145817 / +91-8979999619
Alternate Email: sbor...@iitkgp.ac.in
Lee, Woonghee
Correction:
@s is splitting not @p.
You can just
> split_models final_water_refined
If it isn’t explicit water refinement, it can be just
> split_models final
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://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
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Lee, Woonghee
Dear Soumendu,
I have written a script that calculates the BB and HA RMSDs.
https://github.com/pokynmr/POKY/blob/master/User_Modules/ponderosa_rmsd_script.py
Just copy the code and paste into the Poky Notepad (two-letter-code “Pn”) and File -> Run Python Module.
It will be more convenient for you to save the code somewhere in your computer and use it by drag’n drop into the “Pn” window when you need to calculate. FYI, dropping into the text area of Poky Notepad will get you only the file path when dropping into non-text area of Poky Notepad will read the file and fill the text area.
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://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: Soumendu Boral <soumen...@gmail.com>
Date: Saturday, March 6, 2021 at 11:09 AM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Re: [NMR POKY/SPARKY] Re: Backbone & Heavy-atom RMSD
Dear Dr. Lee,
Thank you very much. It worked.
Lee, Woonghee
Great to know. Now you don’t have to do repetitive tedious tasks every time you get new results.
--
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://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: Soumendu Boral <soumen...@gmail.com>
Date: Sunday, March 7, 2021 at 9:02 AM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Re: [NMR POKY/SPARKY] Re: Backbone & Heavy-atom RMSD
Dear Dr. Lee,
This is Excellent!! The output python shell (in POKY) showing the RMSD with its std. dev. (of all models with the first model) matches exactly with my calculations (I did in Excel) as you guided me to follow.
Thank you very much. It has WORKED!!
Soumendu Boral
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