[ccp4bb] South American Macromolecular Crystallography School

Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School 2021 "Structural Biology to enhance high impact research in health and disease” to be held from Sep 20 to Oct 1, 2021 Please find the application form and further information at

Re: [ccp4bb] Analysis of NMR ensembles

You are much more knowledgeable than me about the details of structure determination via resonance spectroscopy. I was attempting to come up with a toy example that showed that there are reasons for the absence of cross-peaks other than flexibility. I accept that the misinterpretation I

Re: [ccp4bb] Analysis of NMR ensembles

Dear Dale, Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the lucky situation though that they should have noticed the absence of terminal residues during the assignment phase though? I.e. they would usually have peaks for the protons of those residues in the 1D, TOCSY,

Re: [ccp4bb] Analysis of NMR ensembles

Dear Boaz, We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) arise from their flexibility, ..." This makes it sound like you agree that these deficiencies in other regions may be caused by properties other than flexibility. As an extreme example, the

Re: [ccp4bb] Analysis of NMR ensembles

Hi Dale and Cecil, This is quite a circular argument, isn't it? Deficient NOE's for some regions (e.g. loops) arise from their flexibility, hence they are not as well resolved as other (e.g. internal ) regions for which the number of NOE is large. So they are flexible by all accounts and, not

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

https://pubmed.ncbi.nlm.nih.gov/8744573/ Old but worked... Best br On Wed, May 26, 2021, 19:43 Tristan Croll wrote: > (sending properly this time, rather than just to Rasmus) > > I don't believe a "color by RMS" option is in ChimeraX right now (I'll > suggest it to the developers), but this

Re: [ccp4bb] Analysis of NMR ensembles

(sending properly this time, rather than just to Rasmus) I don't believe a "color by RMS" option is in ChimeraX right now (I'll suggest it to the developers), but this will align all models then set B-factors for each residue to the RMS CA deviation from the mean position. Could be extended

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? >

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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

Re: [ccp4bb] Unmodeled density

Public If the large “blob” sits on a 2-fold crystallographic axis then its occupancy is ½. So one possible interpretation is: * A cation present on the 2-fold axis, occupancy 0.5 * Waters next to the cation position, also with occupancy 0.5, even if they are not on the 2-fold: the

Re: [ccp4bb] Unmodeled density

oh, 1.45 Å is a very short distance for metal coordination. perchlorate has a Cl to O distance of that length https://en.wikipedia.org/wiki/Perchlorate Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor

Re: [ccp4bb] External: Re: [ccp4bb] Unmodeled density

That looks like a magnessium hexahydrate. From: CCP4 bulletin board On Behalf Of Pearce, N.M. (Nick) Sent: May 26, 2021 7:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: External: Re: [ccp4bb] Unmodeled density Is it on a symmetry axis? If so it could be the superposition of two molecules (a

Re: [ccp4bb] Unmodeled density

PS I’d model a metal and 4 waters and then measure the distances after refinement. And then look at M Harding's ActaD papers and try to work out which coordination configuration and distances work best. And, when you get the chance, run an emission spectrum at the beamline to help identify the

Re: [ccp4bb] Unmodeled density

the central blob looks too big for B or even for P or S. Perhaps Zn, Cd? (although you didn’t add it, it might have been in the protein buffer or dragged through the purification by the protein?) Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle

Re: [ccp4bb] Unmodeled density

How about [B(OH) 4]− From: CCP4 bulletin board on behalf of Dale Tronrud Sent: Wednesday, May 26, 2021 3:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Unmodeled density Something to give context and scale would be helpful. Two views would also be

Re: [ccp4bb] Unmodeled density

Something to give context and scale would be helpful. Two views would also be good. Dale Tronrud On 5/26/2021 6:08 AM, leo john wrote: Hi Group Can you please suggest what this unmodeled blob can be (see appended picture)? I have Malonate, Boric Acid and Peg in my condition, and crystals

Re: [ccp4bb] Unmodeled density

Hi All: Thank You very much for the response and yes it is at symmetry axis. Distance between the bigger blob and smaller ones is approx 1.45 Ang. I have tried fitting BO3, BO4, but no luck? Thanks John On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) wrote: > Is it on a symmetry axis? If

Re: [ccp4bb] Unmodeled density

Is it on a symmetry axis? If so it could be the superposition of two molecules (a molecule and a copy of itself). On 26 May 2021, at 15:08, leo john mailto:ljohn16012...@gmail.com>> wrote: Hi Group Can you please suggest what this unmodeled blob can be (see appended picture)? I have Malonate,

[ccp4bb] Fwd: Abstract submission deadline extended to 2 June - PSB Symposium "Frontiers in Bioimaging", 1-2 July 2021

Dear all, Please note that the abstract submission deadline for the PSB Symposium "Frontiers in Bioimaging" (1-2 July 2021) has been extended to *Wednesday 2 June*. For further information:

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

If you have PyMOL installed, you can paste the bash function below into your .bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'. All that you have to remember a month from now is 'bu'. Otherwise, you can replace the pymol command with one of the other commands that have been

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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

another one: gemmi convert --assembly=N input.pdb output.pdb On Wed, 26 May 2021 at 07:30, Frank von Delft wrote: > > Thanks for the quick responses! I was looking for a command-line tool > (should have said). Here's the list: > > 1. phenix.pdb.biomt_reconstruction > 2. Makemultimer.py: