Re: [ccp4bb] CCP4BB Digest - 7 Jun 2024 to 8 Jun 2024 (#2024-142)

Paul and Lucrezia, Restarting Coot seems to be the magic bullet to restore atom fixing. This works for the tutorials and the DNA model I'm working on. Thanks for your help, Simon > > Date:Sat, 8 Jun 2024 18:47:22 +0100 > From:Paul Emsley > Subject: Re: Coot 1.1 General Tools > > > Re

Re: [ccp4bb] Coot 1.1 General Tools

Lucrezia, Thanks for your help! 1) This works very well -- thanks for pointing me in the right direction. 2) Thanks 3) When I do this, no anchor appears. There's a "no intermediate atoms" error, with a 0x0 matrix of fixed atoms. Maybe it's a DNA refinement error? Cheers On Mon, Jun 3, 2024

Re: [ccp4bb] help with wwPDB validation warning

Hi Aline, I see nothing wrong with / being 0.83 Mean((I)/sd(I)) is , which is not the same as / so you cannot expect the numerical values to be the same (even in case the resolution shell definition is identical), although the two values usually do not differ much. Take for example two

[ccp4bb] PostDoc position in VU Amsterdam

Dear all, There is a postdoctoral position available in my group (VU Amsterdam) in the field of serial crystallography: https://workingat.vu.nl/vacancies/postdoc-using-advanced-crystallographic-approaches-to-study-photoreactions-amsterdam-1078907 Please spread the word to any suitable

Re: [ccp4bb] help with wwPDB validation warning

Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2 Eleanor On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação < d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > > I am currently validating a structure for deposition in the wwPDB and > encountered the following

[ccp4bb] Attn: UK Based research groups - UK CryoEM community Meeting - 19th July @Royal Society London

Dear all UK based researchers, Just a reminder that the deadline for submitting an expression of interest to join in the meeting is today! See below for full details and how to register if you are interested in attending On behalf of the UK cellular structural biology community, with

[ccp4bb] help with wwPDB validation warning

Dear all, I am currently validating a structure for deposition in the wwPDB and encountered the following warning in the validation system: Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in SF file). The Mean((I)/sd(I)) in the aimless log is 1.7 in the

[ccp4bb] Opening in crystallography at ISTA

Dear colleagues, We have an opening in chemical crystallography at the Institute of Science and Technology Austria near Vienna. We are looking for a colleague to handle our SC-XRD service (harvesting-collection-solution-refinement). We are looking for someone with experience in traditional

Re: [ccp4bb] Key bindings WinCoot 0.9

This (.coot-preferences) is where the key bindings script should be installed to (*). Not sure why it didnt happen in your case. I assume some permission issue. Difficult to say from your description. Anyway, good that it works now. B (*) which actually resides in %COOT_HOME% which by

[ccp4bb] PDRA positions available for CCP4 methods and software development

Please do not reply directly to this message CCP4 collaboratively develops and supports cutting edge methods for the experimental determination and analysis of protein structure, principally by X-ray crystallography. New developments are released through the CCP4 suite of programs, which

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

Well, REFMAC output a (mislabelled) F SIGF which was detwinned so if you deposited the REFMAC output I guess that is detwinned.. Do you have the original REFMAC input still? Eleanor On Thu, 6 Jun 2024 at 15:18, Ben Bax wrote: > Hi, > I am just re-refining an old twinned dataset - which I

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

Dear Jon, We will continue to serve the maps and are looking into updating the process to use the map coefficients now available in the wwPDB FTP data to make the maps compatible with the validation process. Kind regards, Deborah Harrus PDBe On 01/06/2024 14:28, Jon Cooper wrote: It

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

Hi, I am just re-refining an old twinned dataset - which I will redeposit (refinement is never finished). The pdb seem to have automagically detwinned my data. Where do I find my original twinned data (F and SIGF)? (or will I have to redeposit my original un-detwinned structure factors).

[ccp4bb] Key bindings WinCoot 0.9

Dear all, We are experiencing issues with installing key bindings in WinCoot 0.9.8.93 EL. There are simply no buttons displayed for this option. [image: image.png] The key binding buttons were at least visible once and could be installed when executing WinCoot from a Windows admin account, but we

[ccp4bb] Extension of the deadline for abstract submission | XI AUSE Conference and ALBA Users Meeting: 2-6 September 2024 at the University of Oviedo

Dear CCP4bb members, The joint *XI AUSE - Asociación de Usuarios de Sincrotrón de España - Conference, and the VI ALBA Users Meeting* will be held *from **the 2nd to the 6th of September 2024* in *Oviedo, *a beautiful town in the Asturias region, in the north of Spain at the *Faculty of Geology

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Paul, Thank you Regards Devbrat On Thu, Jun 6, 2024, 8:53 AM Paul Emsley wrote: > > On 06/06/2024 04:00, Devbrat Kumar wrote: > > > -- > Dear Paul, > > Thank you for your response. I wanted to compare a Coulomb potential map > to an electron density map. Before aligning these maps, I

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

On 06/06/2024 04:00, Devbrat Kumar wrote: -- Dear Paul, Thank you for your response. I wanted to compare a Coulomb potential map to an electron density map. Before aligning these maps, I need to bring them to similar parameters, which requires rescaling one map to match the other. After

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Paul, Thank you for your response. I wanted to compare a Coulomb potential map to an electron density map. Before aligning these maps, I need to bring them to similar parameters, which requires rescaling one map to match the other. After that, I can proceed with density subtraction. I hope

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Jon I will keep this in mind while working on it. Thank you. Regards Devbrat On Wed, Jun 5, 2024, 7:11 PM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Another factor might be that ccpem uses a different axis order to gemmi > and ccp4 ;-0 > > Best wishes, Jon

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Guillaume I will keep that in mind while trying. Thank you Regards Devbrat On Wed, Jun 5, 2024, 5:21 PM Guillaume Gaullier < guillaume.gaull...@kemi.uu.se> wrote: > With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in > real space (this is trivial to do interactively

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Hello Eleanor, Thank you for your consistent response to my inquiry. I will follow your suggestions and willl tell you the updates. Regards Devbrat On Wed, Jun 5, 2024, 5:10 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Hmm - rather tricky! I would do an MR

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Hello Martin, Thank you for your email and I will look into it. Regards Devbrat On Wed, Jun 5, 2024, 4:16 PM Martin Malý wrote: > Dear Devbrat, > > I am now playing with a similar problem but I don't have a simple solution > for you as I'm also quite stuck. You can check these software tools

[ccp4bb] CBMS MX LECTURES - Thursday June 6, 2024 @ 8:30 am - 17:00 pm

Dear Colleagues You are cordially invited to join the Center for Biomolecular Structure for an exceptional Day of Lectures and Tutorials on MX DATA ANALYSIS THURSDAY, JUNE 6, 8:30 to 17:00 (EDT) https://bnl.zoomgov.com/meeting/register/vJIsc--srTsqHvgMPLQHSte_WZcH61J8hDw Time

[ccp4bb] Two Job Positions available at Helix BioStructures

Dear colleagues, Helix currently has two open job positions that we are looking to fill. We are seeking both a talented Senior Scientist and a Lab Operations Manager to join our growing team in Indianapolis, IN. Both positions require industrial experience and will help with project and people

Re: [ccp4bb] Ligand identification in X-ray density

At this resolution you should be able to infer differences between C and O based on the map levels at each location. Another dead giveaway is the bond lengths and the asymmetry of the top region - that is not a carboxylic acid to me. This looks lime MPD to me, very classic shape. Artem On Wed,

Re: [ccp4bb] Ligand identification in X-ray density

Oooops, correct, got my reasoning turned around too…. But it could still be a betain if the water is more distant… We need a different view! Best J. __. Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting

Re: [ccp4bb] Ligand identification in X-ray density

I sent my last response too soon…. The ‘top’ end of the molecule in the image looks more like a carboxylic acid accepting H-bonds from two backbone amides (supporting the betaine assignment, and not MPD), but the ‘bottom’ end of the molecule looks like it is forming an H-bond with a

Re: [ccp4bb] Ligand identification in X-ray density

Yes! That is why I excluded MPD as there is the water molecule close-by…. But we need a different view…. Best J. __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics South

Re: [ccp4bb] Ligand identification in X-ray density

It is pretty well-ordered, so I would expect the H-bonding pattern to distinguish between betaine and MPD. Best regards, Z *** Zachary A. Wood, Ph.D. (He/Him) Professor and Graduate Coordinator Josiah Meigs Distinguished Teaching Professor

Re: [ccp4bb] Ligand identification in X-ray density

Or, it could be MPD ;-? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 05/06/2024 17:54, Jeroen Mesters wrote: > Thank you for this intriguing information! > > At the same time, this also implies that not all entities

Re: [ccp4bb] Ligand identification in X-ray density

Thank you for this intriguing information! At the same time, this also implies that not all entities that have been modelled as MPD are actually MDP but could also be a betain, right!?….. Best, Jeroen __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer,

Re: [ccp4bb] Ligand identification in X-ray density

"but another view might help." I second that. I would specifically like to be assured that it is not sitting on a special symmetry position. === All Things Serve the Beam

Re: [ccp4bb] Ligand identification in X-ray density

Hello Everyone, It does look like trimethylglycine (betaine), but another view might help. If it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in the microbial and animal kingdom…useful for balancing osmotic stress and stabilizing protein structure (it is a strong

Re: [ccp4bb] Ligand identification in X-ray density

Hi, proteins my pick up ligands from the „source" from which they were isolated…. Looks to me like trimethylglycine, an amino-acid derivative found in plants… Regards, Jeroen __ https://orcid.org/-0001-8532-6699 Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan : Dear All, I am a

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

On 05/06/2024 07:00, Devbrat Kumar wrote: -- Hello Everyone, Hello Devbrat, I have a query regarding the resampling of cryoEM density to match crystal density to obtain a density difference map. Specifically, I am trying to determine if it is feasible to resample a cryoEM map with an

Re: [ccp4bb] E. coli strain M15 or SG13009 - muchas gracias to all who replied

Many thanks to all who took out some time to reply. Summary: you can also use https://www.neb.com/en/products/c3037-nebexpress-iq-competent-e-coli-high-efficiency this has LacIq, we use it with all our pQE bassed vectors. Gentauer may still sell those…

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Another factor might be that ccpem uses a different axis order to gemmi and ccp4 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 05/06/2024 12:51, Guillaume Gaullier wrote: > With a cryoEM map, it's easier to do the

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in real space (this is trivial to do interactively in ChimeraX) rather than by MR. From: CCP4 bulletin board on behalf of Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent:

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Hmm - rather tricky! I would do an MR search with the crystal model v the EM density, Steps would be: 1) convert EM density to "structure factors". - there are tools which do this .. 1a) You need to go back to ccp4i - program sfall to read map to generate SFs from map - then cad or sftools to

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Devbrat, I am now playing with a similar problem but I don't have a simple solution for you as I'm also quite stuck. You can check these software tools which involve some scripting in Python (NumPy, SciPy) and C++: EMDA (for cryoEM maps, included in CCP-EM) https://gitlab.com/ccpem/emda

[ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Hello Everyone, Greetings! I have a query regarding the resampling of cryoEM density to match crystal density to obtain a density difference map. Specifically, I am trying to determine if it is feasible to resample a cryoEM map with an XRD density map. However, each time I attempt this, the

Re: [ccp4bb] Crystal optimization

Hi, these crystals look large enough for VMXm at Diamond Light Source. We have collected excellent data out of smaller crystals. Get in touch with me (or any other members of the team) and we can discuss a possible visit. Kind regards, Jose

Re: [ccp4bb] Coot 1.1 General Tools

Dear Simon, 1. The new clipping keybindings are ‘1’ and ‘2’ for clipping front and ‘3’ and ‘4’ for clipping back (like in Moorhen as well). You can find them in ‘About’- ’Shortcuts' (page 2 to be precise). 2. We need to fix this (about a week) 3. You center on an atom, then click on ‘Fixed

[ccp4bb] Coot 1.1 General Tools

Paul and CCP4 Community, Emailing the larger listserv because some of these might be useful to all. Thanks for the updates to the latest build. 1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to clip the view for figure building. In old Coot, there was a "d" and "f" keyset

Re: [ccp4bb] Topology diagram

Dear community, Thanks for your helpful answers. @Xavier: Obviously, I knew TopDraw, but as mentioned by Andy “TOPDRAW doesn't interpret a pdb file, it just allows you to draw your own topology diagram.” And I wanted it to be as simple as possible for my biochemist colleague with no access

[ccp4bb] Advancing Drug Discovery Webinar Series - Stephen Burley speaking tomorrow 6/4/2024

Hello colleagues, The next webinar in the Advancing Drug Discovery: A Webinar Series of the National Academies of Sciences, Engineering and Medicine will feature Professor Stephen K. Burley. His talk is entitled Protein Data Bank: From two epidemics & the global pandemic to mRNA vaccines &

[ccp4bb] CCPBioSim Industry talk - MDAnalysis 19 June

Hi all, Our next online Industry Talk is by Richard Gowers, a core developer of MDAnalysis. The talk will take place on Wednesday 19 June 2024 at 2pm UK time. Free registration can be found at https://www.ccpbiosim.ac.uk/mda-talk2024. Title: MDAnalysis and Alchemical Simulations Abstract:

[ccp4bb] RES: [ccp4bb] Crystal optimization

Hi, It seems to my eyes that you have multiple nucleation events happening simultaneously. I would recommend you to try crystallization under 10 or 4 ºC Best of luck Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de

[ccp4bb] Fwd: [ccp4bb] Crystal optimization

Apologies, my response was directly to the OP and not to the BB. I have forwarded the response to maintain the chain. -- Forwarded message - From: Nicholas Clark Date: Fri, May 31, 2024 at 7:23 AM Subject: Re: [ccp4bb] Crystal optimization To: 白雪慧 I had a protein that no

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

RCSB PDB is independent of PDBe with regards to this.  The  PDB archive does not distribute electron density maps.  Each site can provide "feature added" data content from their websites. As you mentioned, PDBe runs a service that uses urls like

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

On 01/06/2024 14:28, Jon Cooper wrote: It would be interesting to know if this will affect the the electron density maps which are downloadable from the EBI: PDBe is to RCSB as DVLA is to HMRC (surely?) To unsubscribe

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

It would be interesting to know if this will affect the the electron density maps which are downloadable from the EBI: www.ebi.ac.uk/pdbe They don't currently serve the older dsn6 format, only ccp4, I think. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android

Re: [ccp4bb] Crystal optimization

Hi, In addition, you might want to test additives. I would suggest the additive screen from Hampton Research. We made best experiences with neutral solvents like: ethylacetate (doi.org/10.1021/ic010790t and doi.org/10.1021/acs.inorgchem.6b00672), dioxane (doi.org/10.1021/acs.inorgchem.6b00672)

[ccp4bb] microseed matrix screening (MMS)

Is there a specific operation instruction for microseed matrix screening (MMS), according to the hampton research manual? To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] E. coli strain M15 or SG13009

Hi Mark, Gentauer may still sell those… https://maxanim.com/strains/m15-prep4-escherichia-coli-strains/ Cheers, Jeroen __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics South

[ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

In fall of 2024, electron density map coefficients will be available in the public PDB archive for all X-ray structures. These map coefficients will be the same as used in wwPDB Validation Reports. The new map coefficients files will replace the electron density maps and combined map

Re: [ccp4bb] E. coli strain M15 or SG13009

We got an aliquot of SG13009 once from https://labs.utsouthwestern.edu/jiang-youxing-lab back when I was a postdoc at UT Southwestern. I don't have any now. Doeke = Doeke Hekstra Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS), Director of Undergraduate

[ccp4bb] E. coli strain M15 or SG13009

Dear All. we are looking for E. coli strain M15 or SG13009 to use for expressing a protein from the vector pQE30. Are these strains still availabe commercially? If not, we'd be open for another way to obtain an aliquot. Wbw, Mark Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B

[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

Hi All, The deadline for applications is rapidly approaching – please apply by 10th June. Dave - Hi All, The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA Protein Crystallography Summer School. Please follow this link for more details and to

Re: [ccp4bb] Topology diagram

Dear Lionel, If you want a programme that takes a PDB file and automatically generates a topology diagram, then Pro-origami may be the software you need (https://sites.google.com/site/alexdstivala/home/pro-origami) - it generates prettier diagrams than PDBsum, and the diagrams are output as

Re: [ccp4bb] CCP4i2 COOT no showing model or map?

Dear Marco, Please don't you mind to export your refmac5 job and send it to me so I can have a look? I will keep it confidential. In the following coot job, do you open the structure model in PDB or mmCIF format? You can also export a PDB or a mmCIF file from the refmac5 job - similarly as

Re: [ccp4bb] valine difference map interpretation

Your pictures 1 3 & 4 don't seem to show multiple occupancy? Maybe the difference map 2 is saying - too much complexity ?? Eleanor On Thu, 30 May 2024 at 23:29, Michael Colaneri wrote: > Dear All, > We have alternate conformations for a number of residues in a structure > and one is a Val that

Re: [ccp4bb] CCP4i2 COOT no showing model or map?

On 31/05/2024 07:44, Marco Bravo wrote: Has anyone had the issue where they run coot from ccp4i2 on say a refmac5 job and when coot opens the model or even the map do not show up? its just empty? Does anyone know how to fix this and display the model and map? I like ccp4i2 so far more than

[ccp4bb] CCP4i2 COOT no showing model or map?

Has anyone had the issue where they run coot from ccp4i2 on say a refmac5 job and when coot opens the model or even the map do not show up? its just empty? Does anyone know how to fix this and display the model and map? I like ccp4i2 so far more than ccp4 and I did not have this issue with ccp4

Re: [ccp4bb] Crystal optimization

Usually, you should try to push up the protein concentration, often quite a lot (30, 50, even 100 mg/ml), and decrease precipitant (might have to be really low, eg <3% PEG is not unthinkable). To get the protein up, you may need to find a new buffer solution - there are screens for this, and

Re: [ccp4bb] Crystal optimization

I believe someone has already mentioned matrix seeding- taking the crystals you currently have, making microseeds and then using this in a new screen (whatever your favourite initial screens may be). This can give you different conditions that will give you better crystals as you already have

Re: [ccp4bb] Topology diagram

Dear Lionel, I would say it depends what do you intend to use the topology diagram for? I personally like Overprot (https://overprot.ncbr.muni.cz/) as you can also see topological diagram for the CATH protein family. Kind regards, Deborah On 30/05/2024 16:32, Lionel wrote: Dear

Re: [ccp4bb] Skimming crystal

Hi 白雪慧 There's another solution, which I have never known to fail. Set up your conditions with everything in the drop except for the butanol in one of our "Vapor Batch" plates. Cover the drops with oil - we use light mineral oil - although I'm sure heavy would be just as good. Then put the same

Re: [ccp4bb] Topology diagram

Dear Lionel and Xavier, Unfortunately TOPDRAW doesn't interpret a pdb file, it just allows you to draw your own topology diagram. PDBSUM (available from https://www.ebi.ac.uk/thornton-srv/software/PDBsum1/) has a topology diagram as part of the output. You can also access a database of

[ccp4bb] Scientific Officer for the Electron Microscopy Imaging Centre at Sussex University

Dear Colleagues, The University of Sussex are seeking to appoint a Scientific Officer responsible for the operation of electron and cryo electron microscopes ( JEOL JEM1400+, JEOL CryoARM200) and associated equipment within the Electron Microscopy Imaging Centre (EMIC), for provision of

Re: [ccp4bb] Topology diagram

My Google search led directly to https://www.ccp4.ac.uk/html/topdraw.html HTH > Le 30 mai 2024 à 17:32, Lionel a écrit : > > Dear community, > > A biochemist asks me if I knew a webserver/tool to draw topology diagram of > protein from a deposited pdb or part of it, ideally allowing

[ccp4bb] Topology diagram

Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I

Re: [ccp4bb] Skimming crystal

Hello This is a common issue with volatile organics in the drop. Solutions that have worked in the past include: 1. covering the drop in oil (some people prefer light oil, I personally prefer heavy/viscous oil, as it makes harvesting easier) 2. diluting the drop with a much larger volume of

Re: [ccp4bb] Skimming crystal

We had exactly the same thing happening with some crystals grown in tBuOH. The evaporation of tBuOH leads to currents in the drop and crystals tumbling about. Our first solution was patience and persistence, trying to trap a goodlooking crystal near the edge and loop it out. After a time

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

Many thanks to all who replied, and thank you for your insight and advice. I'll make sure I add a bit in the SI that explains why the R-factors are high. Kay - yes, apologies I did mean 'high' R factors lol. Andy - both molecules in the AU are well defined. Best wishes, Cat Dr Catherine R.

[ccp4bb] Free CryoEM Webinar - May 30th, 2024, 12pm (Eastern)

Dear all, Please remember to join us tomorrow for our next NIH sponsored Joint CryoEM Service Centers Webinar: "Building Bridges: Selenocysteine Synthase as a Model for Efficiently Managing Interactions between Researchers and National Facilities" by Dr. Vitor Hugo Balasco Serrão at 12 PM

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

There's nothing wrong with translational NCS. It is what it is ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 29 May 2024, 15:49, Kay Diederichs wrote: > Hi Catherine, I think you meant to write "giving high

[ccp4bb] Postdoc position available at LNBR/CNPEM

Postdoctoral position available in carbohydrate enzymology and structural biology We are looking for candidates who are interested in exploring the microbial dark matter from Brazilian mega biodiversity aiming at elucidating novel mechanisms involved in carbohydrate breakdown and modification

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

Hi Catherine, I think you meant to write "giving high R-factors". To add to what Esko and Eleanor wrote: There is nothing wrong with your data or spacegroup or refinement; it is just that the tNCS produces two sets of reflections: half or your reflections are statistically "normal" (as if no

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

With that translation (x,1/2,1/2) lots of your reflections with k and l Odd will be relatively weak and those zones usually have higher r factors. Look at the plots of reflection zones in hklview and you will probably notice weak and strong zones. The translation will make selecting the

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

Hi Cat, If your pseudo-centering actually leads to significant change in your cumulative intensity distribution, you might have a convincing explanation as to why the R-values would remain on the high side. I had a pseudo-body centered case a long time ago

[ccp4bb] Translational non-crystallographic symmetry giving low R-factors

Hi, I have collected data for a protein which solved easily to 1.6 Å using MR. However, during data analysis and refinement it clearly has translational NCS. According to Xtriage on Phenix: Frac. coord.: 0.072, -0.498, 0.5 Distance to origin: 68.798 Height relative to origin: 51.479% p-value

[ccp4bb] CryoEM@NOVA: International Summer School at Nova FCT, Caparica, Lisbon region, Portugal

Join us for this International Summer school as we explore exciting advancements and trends in Cryo-EM and Crystallography: “1st CryoEM – X-ray Crystallography Synergy workshop” This training school presents a unique opportunity for researchers to combine the strengths of both techniques:

[ccp4bb] Structural Biology Facility Position at the University of Edinburgh

Dear colleagues, We are looking for a Structural Biology Technologist (at post-doctoral level) to manage the protein crystallography, biophysics and computational modelling facilities of the Structural Biology Core of the Discovery Research Platform for Hidden Cell Biology at the University of

[ccp4bb] Postdoc positions at Francis Crick Institute/Imperial College London

Postdoc positions are available in my group (www.imperial.ac.uk/people/xiaodong.zhang). We are currently seconded to the Francis Crick Institute (www.crick.ac.uk/research/labs/xiaodong.zhang),

[ccp4bb] Postdoctoral Research Fellow Position Available - Join Our Team at Harvard Medical School

Dear Colleagues, I am pleased to announce an exciting opportunity for a Postdoctoral Research Fellow in my laboratory at the Beth Israel Deaconess Medical Center/Harvard Medical School. We are seeking a talented researcher to join our team in studying proteins that regulate triglyceride

Re: [ccp4bb] Data Processing questions

Hello Marco, There are schools that will teach you about the software (and theory) used in crystallography and they tend to be very good, so one suggestion is to enroll in one of these 1-2 week courses to learn everything properly. You should process all of your data sets- it is only after

[ccp4bb] Data Processing questions

Hi All, I just collected a lot of data for native crystals and Seleno-methionine derivative crystals. I have a couple of questions 1. How do I know which images to process and which ones to exclude which might be radiation damaged and not be good to further process? I have been told it is

Re: [ccp4bb] Search for similar geometric arrangement in PDB database

May I point you towards the shape similarity search available at the rcsb.org site? https://www.rcsb.org/news/feature/63933da0e543b6038c4fc5dd The news suggests that you need to upload via URL - but there is a file upload option in the source pull down. On 5/22/24 5:03 PM, Das, Abhinaba

[ccp4bb] Search for similar geometric arrangement in PDB database

Dear community, Is it possible to conveniently search the PDB for specific geometrical shapes, disregarding the input residues and specifically focusing on finding similar topologies? Thanks in advance To unsubscribe

[ccp4bb] ccp4um broken on EL8

Dear community, It seems a recent update has broken ccp4um on EL8 (reproduced this on RHEL8 and AlmaLinux v8). The tool crashes with [...]ccp4um-bin: symbol lookup error: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b This usually results from an

[ccp4bb] Program Available - The inaugural Gateway Ion Channel Symposium (the deadline for registration is May 31)

Dear Colleagues, This email is to remind you to register or support your trainees in registering for the inaugural Gateway Ion Channel Symposium (GICS). The deadline for registration is May 31, 2024. https://www.vai.org/event/gateway-ion-channel-symposium/ GICS is designed to feature junior

Re: [ccp4bb] ccp4 monomer library atom name change

Dear Charis, Please see: https://www.wwpdb.org/news/news?year=2023#654a801dd78e004e766a96bd Because wwPDB has changed these atoms names, the monomer library was updated accordingly. More than 800 monomers were affected. We have added the old atom names in _chem_comp_atom.alt_atom_id to help

[ccp4bb] Out from May 21 to May 28 (no internet)

Hi, I will be out of the office from May 21 to May 28. I will not have access to the internet during this time. Thanks Yousif Yousif Shamoo, Ph.D. Rice University Ralph and Dorothy Looney Professor Professor, Department of Biosciences MS-140 P.O. Box 1892 Houston, TX. 77251-1892

[ccp4bb] ccp4 monomer library atom name change

Dear colleagues, We have recently discovered a change in the monomer library and specifically a change in the atom names of PYR.cif. The atom names of this monomer were changed between ccp4 version 8.0.016 and version 8.0.018. We were wondering if this change was on purpose and if these new

[ccp4bb] A favour to ask - EMBL-EBI user survey

Dear all, I would like to encourage you to participate in EMBL-EBI’s user survey, which aims to understand the usage, impact and improvement areas of the open data resources managed by EMBL-EBI and collaborators. If our data resources have ever saved you 10 minutes, here’s your chance to give

[ccp4bb] NIGMS Mature Synchrotron Program Evaluation

Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program:

[ccp4bb] CBMS LECTURE SERIES - May 22 @13:30 (EDT)

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Valerie Garcia-Negrón Sustainable, Biofuels, and Co-products Research Eastern Regional Research Center in Wyndmoor WEDNESDAY, MAY 22, 13:30 (EDT) "Evaluation of

[ccp4bb] JNJ Entry-Level Opportunity for Tomography Specialist

Hi All, We have one entry-level opening for a tomography expert (Please follow the link for the job application): https://jobs.jnj.com/en/jobs/2406188377w/senior-scientist-cryo-et/ Thanks, Xiaodi JOB TITLE Senior Scientist, Cryo-ET FUNCTION Discovery & Pre-Clinical/Clinical Development

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

On Fri, 17 May 2024 08:27:02 -0700, James Holton wrote: ... > >With a bit of a caveat on how many photons/pixel you need for stable >background subtraction. XDS starts having issues around 1 photon/pixel >or less, and DIALS claims to be able to get to 0.01 photons/pixel, but I >have not

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