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] 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] Deadline today -- IUCr SARS-CoV-2 special symposia.

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural

[ccp4bb] Abstracts for IUCr SARS-CoV-2 methods session

Dear BB, Sorry for any cross-posting with the phenixBB. Jane Richardson & I are co-chairing a late-breaking session added to the lineup of microsymposia at the IUCr congress in August. Its title is "New Methods in Structural Biology to help with the COVID-19 Pandemic” and it will take place

Re: [ccp4bb] unknown density

This doesn’t surprise me in the slightest, given what how the two maps are calculated. The polder map is essentially the same as your "simple omit map” without the bulk solvent contribution that is present in the omit-refine map. Since this is an approximately constant contribution, if you

Re: [ccp4bb] Open position - data management in biophysics

has stated, they should absolutely be applauded for that. After all, as Frank said, we do this for the science, and it shouldn’t need to include personal sacrifice. Nick On 22 Jan 2021, at 11:18, Pearce, N.M. (Nick) mailto:n.m.pea...@uu.nl>> wrote: Meant to write “perpetual impending unempl

Re: [ccp4bb] Open position - data management in biophysics

Meant to write “perpetual impending unemployment”. Thanks, Nick On 22 Jan 2021, at 11:02, Jan Dohnalek wrote:  On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) mailto:n.m.pea...@uu.nl>> wrote: Academia, one of the only careers where _success_ is rewarded with perpetual imp

Re: [ccp4bb] Open position - data management in biophysics

Academia, one of the only careers where _success_ is rewarded with perpetual impending employment every two+ years. Nick On 22 Jan 2021, at 08:25, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: It is a long time

[ccp4bb] protein web viewer that shows ADPs

Hi all, I’m looking for a web applet (preferably javascript) that can be used to show anisotropic displacement parameters (thermal ellipsoids) for atoms. Does anyone know of one that supports this? I’ve looked through the usual suspects but none of them seem to go beyond cartoon/sticks/etc.

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Hi, I agree with Melanie and I think we should also go further... We could require reviewers to tick a box on a PDB reviewer page to confirm they have “checked” the structure. Whether this box has been ticked could then be displayed on the PDB page (of course the reviewer would remain

Re: [ccp4bb] fix b-factors/coordinates during refinement

ouched by using the 'refi bonly' keywords. You can also preset an average (e.g. Wilson B) and have refmac do coordinate refinement (http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#refi). Cheers, Jon On Wed, 20 Feb 2019 at 11:29, Pearce, N.M. (Nick) mailto:n.m.pea...@uu.nl>> w

[ccp4bb] fix b-factors/coordinates during refinement

Hi all, Is it possible to fix the B-factors/coordinates of a model in refinement with REFMAC? It’s trivial to do so in phenix.refine (strategy=…), but I can’t find an equivalent command line flag in refmac… Thanks, Nick Post-doctoral Fellow, Crystal and Structural Chemistry, Utrecht

Re: [ccp4bb] visualising anis B factors

in pymol you can just type “as ellipsoids”. On 23 Jan 2019, at 16:17, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Is there any easy way to do this? Coot? ccp4mg? Eleanor Dodson

Re: [ccp4bb] unmodeled blobs

Hi, I think it's unlikely to be “just one” molecule — It’s much more likely an average over multiple states in the crystal (i.e. that site is disordered). Therefore, IMHO, modelling anything more than a couple of waters is highly misleading to anyone interpreting your model afterwards. If you

Re: [ccp4bb] PanDDA error revisiting old run

Hi, Yes, it is the case that newer pandda version may not be compatible with old pandda analyses. You’ll have to downgrade to the version you used originally. Thanks, Nick > On 20 Jun 2018, at 12:17, Chris Richardson wrote: > > One of our group has been using the newly updated PanDDA

Re: [ccp4bb] AW: [ccp4bb] Pandda problems

could also have been caused by old .pyc files and gave instructions how to remove these. If the alignment is to get a superposition, you could consider aligning on sequence numbers, which is trivial and which should be identical for all data sets. Best regards and have a nice weekend! Herman

Re: [ccp4bb] Pandda problems

Hi, Yes, that’s not a very useful error message — sorry. I am still in the process of intermittently rewriting the pandda code to be …better. I don’t think you’ve necessarily done anything wrong — pandda has not been extensively tested on running on series of structures that are not identical

[ccp4bb] Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS

Dear BB, Tomorrow is the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral

[ccp4bb] Abstract deadline is 28th April for Diffraction Methods in Structural Biology GRS

Dear BB, There are five more days until the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

d "resolution range" boundaries. Sometimes even round-off error can be enough. So, if low-resolution is important it is always a good idea to replace the low-angle resolution limit with A. Just be sure your beamstop was properly masked off. -James Holton MAD Scientist On 4/5/2018 10:5

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Could you expand a bit on what you mean by a “putative” systematic absence? (e.g. why only the lowest order hkl?) On 5 Apr 2018, at 19:39, James Holton > wrote: You need to be careful with the exact space group at the particular

Re: [ccp4bb] Overlapping ligand electron density

It’s definitely possible to have a superposition of states: https://www.ncbi.nlm.nih.gov/m/pubmed/28291761/ You need to use alternate conformers to generate the different states of the crystal. Thanks, Nick On 13 Dec 2017, at 20:12, Matthew Bratkowski