Re: [ccp4bb] Help crystalizing protein

Hello Marco, I know you said you would prefer keeping the full-length protein. But have you looked at an AlphaFold2 prediction? Ideally of the monomer and homo- and hetero-dimers you mentioned. It’s often a good guide for construct design. If you see a lot of “spaghetti” with low pLDDT, that mi

Re: [ccp4bb] replacing B-factor column and color accordingly

Hello, Just thought I would add one actionable suggestion to Robbie’s good advice. At least one program is well equipped to do this type of operations without doing PDB file surgery: ChimeraX. See relevant documentation: - the setattr command can set named "attributes" to atom selections, and c

Re: [ccp4bb] enzyme or other protein with multiple cofactors

Hello Harry, I can think of an example of multiple protein chains with multiple cofactors: photosystems I and II. There are several structures in the PDB, take a look, they are full of chlorophylls, carotens, and other things. Definitely more than one per protein chain. If you are going to use

Re: [ccp4bb] NAR impact factor

al figures to Kay’s (or does the LLM know that we’ve both developed integration programs, and bias accordingly?) Harry > On 19 Dec 2024, at 15:00, Tim Gruene wrote: > > On Thu, 19 Dec 2024 10:19:58 + > Guillaume Gaullier wrote: > >> Hello, >> >> I clicked this

Re: [ccp4bb] NAR impact factor

Hello, I clicked this link, and got this conclusion: "The adjusted impact factor of Nucleic Acids Research, excluding citations from special issues dedicated to databases and web servers, is approximately 25.9. This indicates a significant impact when focusing solely on the regular articles pu

Re: [ccp4bb] Modelling unidentified ligand

Good luck with the deposition! And if you later manage to identify this ligand, the PDB allows updating an already processed and released entry with a new atomic model, without changing the accession code. It is a relatively simple process if you saved the deposition ID and password, even easi

Re: [ccp4bb] Cryo-EM rigid body with 1 ADP per chain

Hello Derek, You might receive more answers if you post cryoEM questions to the CCPEM list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccpem Not sure why you need to refine a B-factor, at this resolution it won't tell you much, even with only one per chain or per tetramer. For the rigid-

Re: [ccp4bb] Recommendations for crystallization screens

Hello Saniya, For protein-DNA complexes, the set of conditions described in this article has been helpful in the past: https://doi.org/10.1107/S1744309112025316 You will find more info in a message I posted in a discussion from earlier this year: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A

Re: [ccp4bb] cryoEM molecular replacement

Hello Johan and Natesh, There is more info about the terminology in this article: https://doi.org/10.1038/s41586-024-07215-4 In brief, yes, "Coulomb potential map" or "electrostatic potential map" is most correct (as far as I remember). But "cryoEM map" is widely accepted as a shortcut, and is

Re: [ccp4bb] cryoEM molecular replacement

Hello Matthew, This is a very good point. With good maps one can tell if it’s the correct hand by visually inspecting the alpha-helices (or from features of the quaternary structure for some complexes), but sometimes it is more difficult. I don’t know how em_placement and emplace_local behave w

Re: [ccp4bb] cryoEM molecular replacement

Hello, Manual fitting in ChimeraX followed by its fitmap command is indeed quick and easy, and many people's go-to. If you want to skip the manual step, read the documentation for fitmap (the command "help fitmap" will open it), there are options for global search that can do large steps so yo

Re: [ccp4bb] PDBe access issue

It works here, I entered an accession code and it took me to the entry page. Guillaume On 15 Nov 2024, at 08:04, Xavier Brazzolotto wrote:  Dear all, I am currently experiencing an issue when accessing PDBe (https://www.ebi.ac.uk/pdbe/) Any maintenance or server error, or does this issue co

Re: [ccp4bb] contour level for cryoEM deposition: coot vs chimera

I read somewhere (I don’t have the ref, sorry) that it is because the phases are directly measured in cryoEM (since it is an imaging technique), and they are often more accurate than the phases of crystallographic maps. On this basis, if you can find a structure that has been solved both by cryo

Re: [ccp4bb] contour level for cryoEM deposition: coot vs chimera

There is some more info in the documentation of the corresponding command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ChimeraX and Coot report different numbers probably because they have different defaults: ChimeraX computes statistics on the whole box (per its d

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Hello Javier, Placing atoms implies that you know they are present somewhere (possibly with some uncertainty on exactly where), but setting their occupancies to zero implies that you know they are nowhere at all. This is a paradox. I think atoms with zero occupancy make no sense in a final depo

Re: [ccp4bb] Plasmids for Fluorescent proteins

Hi Prerna, I agree with Reza: AddGene is a good place to source the plasmids from. In addition, the fluorescent protein database can help you choose your fluorescent proteins: https://www.fpbase.org/ There doesn’t seem to be systematic cross-references between FPbase and AddGene (I only checke

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: W

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

Hello, > What if instead of images we just collected a list of x-y coordinates of > photon hits vs time? This already exists, but for electrons: https://doi.org/10.1107/S205225252000929X This is the technology in Falcon4 detectors. The advantage is that it allows you to decide how to slice

Re: [ccp4bb] replacement for Scientific Linux

Hello, I don’t know if crystallographic software is commonly GPU-accelerated. Most software we use to process cryoEM data is and requires CUDA, which only works on Nvidia hardware with their driver. Also seems to be the case for a lot of deep learning software. Like it or not, it’s simply a fac

Re: [ccp4bb] Crystals with DNA

Hello Careina, In addition to all the good suggestions you already got, I can point to these very good references: - Pryor EE Jr, Wozniak DJ & Hollis T (2012) Crystallization of Pseudomonas aeruginosa AmrZ protein: development of a comprehensive method for obtaining and optimization of protein

Re: [ccp4bb] [EXT] [ccp4bb] Crystallizing a tough target

Hello, Regarding this question: A curious question - is it logical to say that if the protein is highly charged (either negative or positive), it is likely to be more soluble and resist crystallization due to electrostatic repulsion? Our protein has highly positively charged surface, although

Re: [ccp4bb] Automated refinement convergence

a biological question or if you want to benchmark refinement strategies... Here is an interesting resource if you worry about the sustainability of your computing: https://www.green-algorithms.org/ The calculator is nice too: https://calculator.green-algorithms.org/ Cheers, Guillaume --- Guil

Re: [ccp4bb] [External] Re: [ccp4bb] alternatives to Consurf server

Hello, ChimeraX can also color an atomic model by sequence conservation score: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html This tutorial uses an output from ConSurf, but as far as I understand any multiple sequence alignment can serve as the source of

Re: [ccp4bb] Alternatives to X

> Yes, it [Twitter/X] is quite unfiltered nowadays, but I actually like to have > things in the open whether I agree with them or not. It puts more > responsibility on the community and the community notes help with that. This would be fine without algorithmic promotion of posts and accounts. Bu

Re: [ccp4bb] Alternatives to X

Hello, I can also recommend posting on a Mastodon instance. There is no algorithmic promotion of posts or accounts, which means you have to work a bit more to find interesting people to follow, but the reward is generally nicer, with more genuine interactions (since all the "popularity contest"

Re: [ccp4bb] skewness in a good EM map?

Hello, This was discussed on the CCPEM list recently, see this discussion: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCPEM;dda7f5e8.2310 (you can navigate to the answers with the "By topic: Next" link at the top). I hope this helps, Guillaume From:

Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

Maybe a naive question, and definitely going off-topic… but what if the successful candidate decides they are happy with the 9-month salary and instead of seeking grants decides to go on vacation during the 3 unpaid months? Would a hiring department be cool with that in general? (not asking abou

Re: [ccp4bb] Intractable outliers in wwPDB validation report

A good example of such expected outliers can be found in structures of nucleosomes: the validation report always flags almost all DNA bases as geometry outliers. But we have no end of evidence that these structures are correct: for instance, the many ensemble and single-molecule FRET studies of

Re: [ccp4bb] CentOS 7 end of life (july 2024)

Hello, I have never tried any of the migration tools you listed, so can't advise on their use. But regarding your first option of doing a backup, reformatting from btrfs to a different filesystem, restoring the backup and proceeding with the upgrade with a non-official tool: you might as we

Re: [ccp4bb] AI and cis-peptides

Interesting. Has someone similarly looked at whether AlphaFold predicts disulfide bridges? Guillaume On 13 Jul 2023, at 15:12, Randy John Read mailto:rj...@cam.ac.uk>> wrote: I’m not sure about other methods, but AlphaFold does predict peptides in both cis and trans configurations. In a rece

Re: [ccp4bb] happy/sad maps

Hello James, Thank you for sharing! As usual, these messages and the answers they attract are very educational, and I enjoyed reading. Regarding "all-or-nothing real space maps", in single-particle cryoEM the masks we use always have a soft edge (continuously and smoothly decaying from 1 to 0

Re: [ccp4bb] To Trim or Not to To Trim

others, are better off showing maps than not. Cheers, Guillaume On 17 Mar 2023, at 23:57, Huw Jenkins mailto:h.t.jenk...@me.com>> wrote: On 17 Mar 2023, at 15:01, Guillaume Gaullier mailto:guillaume.gaull...@kemi.uu.se>> wrote: CryoEM papers often show a map in a main figure, and a

Re: [ccp4bb] To Trim or Not to To Trim

Hello, I think Rams’ last remark is very important. People with every preference regarding modelling (trimmed, zero-occupancy or high-B), past their disagreement on this particular question, are all concerned about how their models will be interpreted by non-experts. Since all experimental sci

Re: [ccp4bb] Solubility of Aluminum Fluoride

ded to use AlCl3 and NaF > hoping to form AlF3 in the reaction mix. > > Best > > Faisal > > > On Tue, Jun 21, 2022 at 2:08 PM Guillaume Gaullier > mailto:guillaume.gaull...@univ-tlse3.fr>> > wrote: > Hi Firdous, > > I have read a fair amount of pa

Re: [ccp4bb] Solubility of Aluminum Fluoride

Hi Firdous, I have read a fair amount of papers about ATP-dependent chromatin remodelers in which ADP-BeF3 is often cited. It is made as follows (quoting from one of these papers): "ADP-BeF3 was prepared as a 10x stock (10 mM ADP, 30 mM BeSO4, 150 mM NaF, 10 mM MgCl2), freshly before use." So

Re: [ccp4bb] REFMAC5 refinement: nucleic acid residues with bad geometry

Hello Pradeep, Have you visually checked the model at these locations? Is this non-ideal geometry of the DNA supported by the map? At 2.3 A resolution, the DNA should be well resolved (both backbone and nucleic bases planes). Some (most?) DNA-binding proteins distort DNA when binding to it, so

Re: [ccp4bb] Search for a particular motif [off-topic]

Hello, ScanProsite almost does what you want, but since it only searches sequence databases, it has no notion of secondary structures and therefore cannot exclude motifs found in a secondary structure. https://prosite.expasy.org/scanprosite/ I don’t know of any tool that would search structures

Re: [ccp4bb] am I doing this right?

I am not qualified to comment on anything in the rest of this discussion, but regarding the excerpt quoted below: this way of recording an "image" seems very similar to the EER (electron event representation) of the Falcon 4 direct electron detector used in cryoEM. See https://doi.org/10.1107/S2

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Hello, In the particle picking section, you may want to include these two: Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P, Sitsel O, Raisch T, Prumbaum D, et al (2019) SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biolog

Re: [ccp4bb] interesting paper...

And for completeness, this other paper describing an independent replication of these results, also formally published yesterday (but a preprint was posted some time ago, so you may have seen it already): https://doi.org/10.1126/science.abj8754 Cheers, Guillaume On 16 Jul 2021, at 12:58, Harr

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hello, Have you tried ISOLDE? Interactive MDFF is really powerful both for fixing models with poor geometry and for improving fit to the map. There is a good tutorial for refinement of a model against a cryoEM map with ISOLDE: https://isolde.cimr.cam.ac.uk/static/isolde/doc/tutorials/intro/cry

Re: [ccp4bb] Structural Alignment

Hi Armando, This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ More specifically, its matchmaker command will align two structures and print the corresponding sequence alignment: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmak

Re: [ccp4bb] Vote for cryoEM

Thank you for pointing out nitter.net, Veronica! This is great for read-only access, especially with RSS feed (I have been missing this feature ever since Twitter removed it), although it cannot replace regular Twitter (yet?) for posting. Guillaume > On 2 Apr 2020, at 11:25, V F wrote: > >>

Re: [ccp4bb] Vote for cryoEM

One remark about Jürgen’s comment (quoted below). It is great that well established scientists use Twitter, because by doing so they implicitly accept to be contacted publicly and to engage in public conversations (assuming their account is public, which is the default when you sign up on Twitt

Re: [ccp4bb] incorporating disulfide linkage

Hi Kahkashan, This paper shows a nice example with specific crosslinks in the nucleosome: https://doi.org/10.1016/j.jmb.2017.10.029 Of course, having a high-resolution structure helps a lot to design specific crosslinks like they did… You may not have

Re: [ccp4bb] Crystal screen for DNA binding proteins

Hi Sylvia, A screen specifically designed to crystallize protein-DNA complexes is described in this paper: https://www.ncbi.nlm.nih.gov/pubmed/22869139 Back when it was just published, I manually prepared the 48 conditions and it was not too diff

Re: [ccp4bb] Sequence variability mapped on a PDB

Hello Reza, Have you tried ConSurf? http://consurf.tau.ac.il/2016/ I just noticed they now also have precalculated results for proteins deposited in the PDB: http://bental.tau.ac.il/new_ConSurfDB/ Hope this helps, Guillaume > On Mar 16, 2019, at 17:42, Reza Khayat wrote: > > ​Hi, > > >