PONDEROSA/ssPONDEROSA user group

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1–26 of 26

Welcome.

This group is to communicate among POKY (new) / PONDEROSA(-C/S) / ssPONDEROSA users. The PONDEROSA is a program automates protein 3D structure determination by NMR spectroscopy and hybrid approaches (small X-ray scattering / cryo-electron microscopy) and also provides visual verification tools to investigate its outcomes for structural studies.

Software packages can be found from here: https://poky.clas.ucdenver.edu.

The POKY suite includes POKY-Analyzer (two-letter-code "Pa") and POKY-Builder (two-letter-code "Pb") programs alongside the simple PONDEROSA plugin (two-letter-code "c3").

Enjoy!

Woonghee Lee

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5/13/22

Re: Ponderosa NMRFAM-SPARKY Issue with Structure Calculations

Dear Elanor, PONDEROSA Server is not running on NMRFAM servers ATM. To get around, use the latest

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Re: Ponderosa NMRFAM-SPARKY Issue with Structure Calculations

Dear Elanor, PONDEROSA Server is not running on NMRFAM servers ATM. To get around, use the latest

5/13/22

Lee, Woonghee, Mukesh Mahajan6

5/1/22

Re: Ponderosa Server

Thanks for understanding. Use two-letter-code “ep” and the “Submit” button from there to submit not

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Re: Ponderosa Server

Thanks for understanding. Use two-letter-code “ep” and the “Submit” button from there to submit not

5/1/22

4/26/22

PONDEROSA-C/S on POKY Servers is running.

Dear all, We made PONDEROSA-C/S running on POKY Servers. Use the latest POKY suite for the structure

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PONDEROSA-C/S on POKY Servers is running.

Dear all, We made PONDEROSA-C/S running on POKY Servers. Use the latest POKY suite for the structure

4/26/22

4/24/22

Current server issues

Dear POKY/SPARKY/I-PINE/PONDEROSA users, Many of you experience some features that utilizes NMRFAM

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Current server issues

Dear POKY/SPARKY/I-PINE/PONDEROSA users, Many of you experience some features that utilizes NMRFAM

4/24/22

Lee, Woonghee, Yiting Paung2

1/28/22

Re: RDC value prediction using Poky?

Thank you so much for the clarification! On Fri, Jan 28, 2022 at 12:25 PM Lee, Woonghee <WOONGHEE.

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Re: RDC value prediction using Poky?

Thank you so much for the clarification! On Fri, Jan 28, 2022 at 12:25 PM Lee, Woonghee <WOONGHEE.

1/28/22

Christopher Williams, Lee, Woonghee3

12/13/21

"Clean_1.pdb" Output

Thank you very much. That explains why those structures matched up so perfectly. -Chris On Monday,

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"Clean_1.pdb" Output

Thank you very much. That explains why those structures matched up so perfectly. -Chris On Monday,

12/13/21

8/17/21

Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

Hi Jun, I guess it is driver related issue. But you don't need to use the pymol included in the

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Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

Hi Jun, I guess it is driver related issue. But you don't need to use the pymol included in the

8/17/21

大木JAIST, Lee, Woonghee2

7/28/21

Hi Shinya, You should stick with standard sequence until you collect enough restraints to fold the

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Hi Shinya, You should stick with standard sequence until you collect enough restraints to fold the

7/28/21

7/21/21

Re: Question about NMR complex

Dear Margaret, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861749/ See the figure 14. You can

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Re: Question about NMR complex

Dear Margaret, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861749/ See the figure 14. You can

7/21/21

margaret phillips, Lee, Woonghee3

5/4/21

Username for PONDEROSA web server

Dear Margaret, If you click “Show in Space” button, it automatically sets. If not, the file is in “

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Username for PONDEROSA web server

Dear Margaret, If you click “Show in Space” button, it automatically sets. If not, the file is in “

5/4/21

4/20/21

Re: Structure refinement

Dear Thilini, If you haven't added by Add New button during constraints-only x phase, you may

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Re: Structure refinement

Dear Thilini, If you haven't added by Add New button during constraints-only x phase, you may

4/20/21

4/8/21

Re: Set to imit does not work

Hi Thilini, The violation is subject to the calculated structure of that job not the previous one.

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Re: Set to imit does not work

Hi Thilini, The violation is subject to the calculated structure of that job not the previous one.

4/8/21

Lee, Woonghee, Soumendu Boral5

3/7/21

Re: Backbone & Heavy-atom RMSD

Yes. Agreed with you. --------------------- Soumendu Boral Ph.D. Research Scholar Structural and

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Re: Backbone & Heavy-atom RMSD

Yes. Agreed with you. --------------------- Soumendu Boral Ph.D. Research Scholar Structural and

3/7/21

2/2/21

Re: Ponderosa file structure not found?

Dear Yiting, The “structure” is not the structure structure of the protein. It means file

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Re: Ponderosa file structure not found?

Dear Yiting, The “structure” is not the structure structure of the protein. It means file

2/2/21

1/27/21

Re: Torsion angle Constraints

Dear Rama, You can just add in the restraint section in Ponderosa Client. It accepts DYANA .aco

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Re: Torsion angle Constraints

Dear Rama, You can just add in the restraint section in Ponderosa Client. It accepts DYANA .aco

1/27/21

1/23/21

Dear Thilini, Those VMs are configured to identify PyMOL path automatically and it is surprising.

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Dear Thilini, Those VMs are configured to identify PyMOL path automatically and it is surprising.

1/23/21

11/10/20

FW: Connect PONDEROSA analyzer

Hi, you should open your NOESY data and type “up”. Your upper and lower bounds are final.upl and

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FW: Connect PONDEROSA analyzer

Hi, you should open your NOESY data and type “up”. Your upper and lower bounds are final.upl and

11/10/20

Woonghee Lee, Lee, Woonghee2

9/2/20

Fwd: Sparky NOE integration volume problem

Dear Indrani, “But there are many peaks which are not integrated due to 'bounding contour too

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Fwd: Sparky NOE integration volume problem

Dear Indrani, “But there are many peaks which are not integrated due to 'bounding contour too

9/2/20

Leah Roe, Lee, Woonghee3

8/26/20

Non-converging Runs

Leah, first thing is to make sure you have full, reliable assignments and peak list files contain

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Non-converging Runs

Leah, first thing is to make sure you have full, reliable assignments and peak list files contain

8/26/20

miqueladrov...@gmail.com, Lee, Woonghee2

8/5/20

NOE peak list from Cara/Xeasy

Dear Miquel, PONDEROSA-C/S is designed to make a complete framework along with NMRFAM-SPARKY and

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NOE peak list from Cara/Xeasy

Dear Miquel, PONDEROSA-C/S is designed to make a complete framework along with NMRFAM-SPARKY and

8/5/20

5/14/20

Using a model structure to accelerate NOESY data interpretation and structure calculation

Dear Anon, You can use your PDB file from CS-Rosetta as a restraint in the restraint section in

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Using a model structure to accelerate NOESY data interpretation and structure calculation

Dear Anon, You can use your PDB file from CS-Rosetta as a restraint in the restraint section in

5/14/20

3/2/20

Re: Running ponderosa

Dear Thilini, If HCCH-TOCSY aligns significantly better with your C-NOESY than C-HSQC and C(CO)NH/H(

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Re: Running ponderosa

Dear Thilini, If HCCH-TOCSY aligns significantly better with your C-NOESY than C-HSQC and C(CO)NH/H(

3/2/20

1/8/20

Re: Ponderosa Analyzer Questions

Dear Jacob, Those numbers are all arbitrary. You can some number to another runs with same option and

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Re: Ponderosa Analyzer Questions

Dear Jacob, Those numbers are all arbitrary. You can some number to another runs with same option and

1/8/20

11/14/19

Where is assigned NOESY peak lists in I-PINE web report page?

This is an answered question came in my email: NOESY will be assigned by AUDANA algorithm not I-PINE

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Where is assigned NOESY peak lists in I-PINE web report page?

This is an answered question came in my email: NOESY will be assigned by AUDANA algorithm not I-PINE

11/14/19

10/16/19

Re: Regarding NMRFAM Ponderosa Web Server

Dear Salik, I wonder if your resonance assignments agree well with your NOESY data. Also, peak

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Re: Regarding NMRFAM Ponderosa Web Server

Dear Salik, I wonder if your resonance assignments agree well with your NOESY data. Also, peak

10/16/19

9/4/19

NMRbox workshop and Chicago Area Discussion Group (Nov. 1-2, 2019)

NMRbox @ CANMRDG PROGRAM Syllabus is posted here. WHERE > University of Wisconsin-Madison >

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NMRbox workshop and Chicago Area Discussion Group (Nov. 1-2, 2019)

NMRbox @ CANMRDG PROGRAM Syllabus is posted here. WHERE > University of Wisconsin-Madison >

9/4/19

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