Re: [ccp4bb] Analysis of NMR ensembles

eers, >>> >>> Boaz >>> >>> >>> /Boaz Shaanan, Ph.D. >>> Dept. of Life Sciences >>> Ben-Gurion University of the Negev >>> Beer-Sheva 84105 >>> Israel >>> >>> E-mail: bshaa...@bgu.ac.il >>> Phone: 972-8-647-2220 &

Re: [ccp4bb] Analysis of NMR ensembles

This even seems to have a”batch” mode (similar to the well-known homology modelling server Phyre2) that might accept a zip file containing multiple PDBs. If it does, and if it will take my ~700 PDBs, then that would save me a little bit of scripting. Harry > On 27 May 2021, at 22:03, Jon

Re: [ccp4bb] Analysis of NMR ensembles

A bit late, I know, but a bit more googling gave me this site which I don't think has been mentioned so far: http://old.protein.bio.unipd.it/mobi/ Given the pdb code, it is a one click job to get a pdb file with the "B-factors changed to averaged Scaled Distance x 100" and the resulting

Re: [ccp4bb] Analysis of NMR ensembles

If you want something comparable to B-factors don’t forget to put the MSF in the B-factor column, not the RMSF. Will change the scaling of the tube radius considerably! Nick On 27 May 2021, at 11:16, Harry Powell - CCP4BB

Re: [ccp4bb] Analysis of NMR ensembles

bject:* Re: [ccp4bb] Analysis of NMR ensembles I agree with Dr Breyton. The variability in an NMR ensemble does not reflect "mobility" but simply "uncertainty" in conformation.  The spread in coordinates in some regions simply reflects the lack of experimental data which coul

Re: [ccp4bb] Analysis of NMR ensembles

Cool… Purely for visualisation this does look like the approved CCP4 way - Harry > On 27 May 2021, at 10:01, Stuart McNicholas > <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote: > > Drawing style (right menu in display table) -> Worm scaled by -> Worm > scaled by NMR variability > >

Re: [ccp4bb] Analysis of NMR ensembles

Drawing style (right menu in display table) -> Worm scaled by -> Worm scaled by NMR variability in ccp4mg? This changes the size of the worm but not the colour. On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Anyway, thanks to all

Re: [ccp4bb] Analysis of NMR ensembles

Anyway, thanks to all those who answered my original question - especially Tristan: Chimerax (+ his attached script) Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/) Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ ) Rasmus CYRANGE

Re: [ccp4bb] Analysis of NMR ensembles

y of the Negev >> Beer-Sheva 84105 >> Israel >> E-mail: bshaa...@bgu.ac.il >> Phone: 972-8-647-2220 >> Fax: 972-8-647-2992 or 972-8-646-1710 / >> // >> // >> / >> / >> ------------ >> *From:* CCP4 bulletin board on behalf

Re: [ccp4bb] Analysis of NMR ensembles

2-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board on behalf of Dale Tronrud *Sent:* Wednesday, May 26, 2021 10:46 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Analysis of NMR ensembles I agree with Dr Breyton. The variability in an NMR ensemble does not reflect &quo

Re: [ccp4bb] Analysis of NMR ensembles

gt;> Fax: 972-8-647-2992 or 972-8-646-1710 / >> // >> // >> / >> / >> ------------ >> *From:* CCP4 bulletin board on behalf of Dale >> Tronrud >> *Sent:* Wednesday, May 26,

Re: [ccp4bb] Analysis of NMR ensembles

on behalf of Dale Tronrud *Sent:* Wednesday, May 26, 2021 10:46 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Analysis of NMR ensembles     I agree with Dr Breyton. The variability in an NMR ensemble does not reflect "mobility" but simply "uncertainty" in conformati

Re: [ccp4bb] Analysis of NMR ensembles

: Re: [ccp4bb] Analysis of NMR ensembles I agree with Dr Breyton. The variability in an NMR ensemble does not reflect "mobility" but simply "uncertainty" in conformation. The spread in coordinates in some regions simply reflects the lack of experimental data which c

Re: [ccp4bb] Analysis of NMR ensembles

I agree with Dr Breyton. The variability in an NMR ensemble does not reflect "mobility" but simply "uncertainty" in conformation. The spread in coordinates in some regions simply reflects the lack of experimental data which could define a single conformation. There are many reasons why

Re: [ccp4bb] Analysis of NMR ensembles

Dnia 2021-05-26, o godz. 16:04:59 Harry Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> napisał(a): > is there a tool available that will > give me some idea about the bits of the structure that do not vary > much (“rigid”) and the bits that are all over the place (“flexible”)?

Re: [ccp4bb] Analysis of NMR ensembles

dues, it should do the trick. > Example image for 2kv5 attached. > > Have fun! > > -- Tristan > -- > *From:* CCP4 bulletin board on behalf of Harry > Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> > *Sent:* 26 May 2021 16:04

Re: [ccp4bb] Analysis of NMR ensembles

ll - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> Sent: 26 May 2021 16:04 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Analysis of NMR ensembles Hi Given that there are plenty of people on this BB who are structural biologists rather than “just” crystallographers, I thought someon

Re: [ccp4bb] Analysis of NMR ensembles

Hi, It has been a bit since I was in NMR, but I would propose CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html), based on the recommendation of the PDB NMR Validation Task Force (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884077/). You can do both superposition and per-residue RMSD

Re: [ccp4bb] Analysis of NMR ensembles

Hello Harry, Looking at: http://www.mcgnmr.mcgill.ca/ProtSkin/ It says: "If your input is a plain file containing your scalar data to map, such as heteronuclear NOE or chemical shift differences, ensure the first column in your file contains residue numbers and the second column contains the

Re: [ccp4bb] Analysis of NMR ensembles

Hello, In my understanding of NMR, the loops and terminii that adopt very different conformations in the structure ensemble rather reflect the fact that for those residues, the number of constraints is lower, thus the number of structures that fulfil the constraints is larger A dynamics

Re: [ccp4bb] Analysis of NMR ensembles

Hi Smita Yes, that’s the kind of analysis I had in mind. I have > 700 structures to “look” at so something that would say “these residues overlay with a small RMSD so this bit is rigid, but these residues don’t, so that part is flexible” ~700 times. Using an MG program of any kind would just

Re: [ccp4bb] Analysis of NMR ensembles

Hi Harry, (Oooh - after lurking on this list for probably 20 years, I can actually comment on something...) If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures that fit the NOEs, is there a tool available that will give me some idea about the bits of the structure

Re: [ccp4bb] Analysis of NMR ensembles

I vaguely recall that using MUSTANG you will get the distance between residues reflected in the b-value column and then you can color by B-value. https://lcb.infotech.monash.edu/mustang/mustang_psfb-final.pdf Jürgen > On May

Re: [ccp4bb] Analysis of NMR ensembles

The hard bit is to get the rmsd's into the B-factor column, but it shouldn't stretch you too much, Harry ;- There is ProtSkin on the web which does something similar with sequence alignments. Sent from ProtonMail mobile Original Message On 26 May 2021, 16:28, Harry Powell -

Re: [ccp4bb] Analysis of NMR ensembles

Hi Harry, The superpose/overlay of all the structures in PyMol should inform you the rigid part of the protein as well as the flexible part. The rigid part would have very low backbone RMSD or overlay tightly and the flexible part (loops, N-term and C-term etc.) would not superpose tightly. If

Re: [ccp4bb] Analysis of NMR ensembles

Hi Jurgen NMR structures don’t appear to have B_factors, or at least not meaningful ones (e.g. in 2kv5 they’re all 0.00…). thanks for the response, though Harry > On 26 May 2021, at 16:21, Jurgen Bosch wrote: > > How about color by B-factor and look for the cold areas and hot areas? >

Re: [ccp4bb] Analysis of NMR ensembles

How about color by B-factor and look for the cold areas and hot areas? Jürgen > On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Given that there are plenty of people on this BB who are structural > biologists rather than

[ccp4bb] Analysis of NMR ensembles

Hi Given that there are plenty of people on this BB who are structural biologists rather than “just” crystallographers, I thought someone here might be able to help. If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures that fit the NOEs, is there a tool available