Re: [ccp4bb] Co-Crystallization with drug molecule

Dear Amit, If you will decide to try soakings, you could also try to dehydrate the drop to increase ligand concentration, as well as avoiding to wash the crystals in cryo-protection solutions, as described here (https://journals.iucr.org/j/issues/2022/02/00/ap5042/index.html). Good luck! D

Re: [ccp4bb] Rwork and Rfree the same?

Dear Justin, Be careful of the reported “fill-in” effect of unobserved data by some refinement programs (not sure if this is your case or even if it was, whether it may cause the Rfactor to be identical) when using anisotropic cut-off. It is documentated here: https://staraniso.globalphasing.

Re: [ccp4bb] Fragile Crystals

Hi Morgan Elizabeth, You could try this protocol (paper title below, shameless plug), it can cryo-protect your crystals without the need of touching the crystal drop, while at the same time it is likely to make your crystals more robu

Re: [ccp4bb] What could these crystals be?

Shameless plug, did you try Fusion screen (available from MD). It has been outperforming all the other 22 screens in our bank, either giving exclusive hits or always giving crystals when other screens did too (sure we still had cases when nothing work). It has shown to be very powerful in our e

Re: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

Hi Rafael, Once I inherited a protocol with a problem similar to yours and they told me that the precipitation was caused by nickel leaking out during the elution with 250 mM imidazole. I am not sure whether this was true, however, their fix was to place something like 20 ul of 200 mM EDTA at t

Re: [ccp4bb] TEV vs HRV3C

/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.u

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone 01223 267839 To uns

Re: [ccp4bb] symmetry possibilities

Hi Jorge, > > Should I look at anything else to establish twin P1 is the best way to refine > this structure? You could feed your refined model and map coefficients to Zanuda (CCP4 program) which automatically will check which higher symmetry space group will give lower Rfactors in refinement

Re: [ccp4bb] ligand binds to one molecule

4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-b

Re: [ccp4bb] SHELXD for help

the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue

Re: [ccp4bb] freezing in ethane / propane - unipucks ?

il.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

On 17 Jan 2022, at 09:07, Clemens Vonrhein wrote: > > Dear Dom, > >> On Fri, Jan 14, 2022 at 10:56:32PM +, Dom Bellini wrote: >> Thanks for your inputs. I wonder why the PDB doesn’t allow to submit >> two separate mtz files, > > Ideally, these would actual

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

2 and > Ccp4 Cloud can combine MTZ files. > > I'll think about supporting multiple merged MTZs in mxdepo.html in the future. > > Best, > Marcin > >> On Fri, 14 Jan 2022 at 17:42, Dom Bellini - MRC LMB >> wrote: >> >> Hi Marcin, >> >>

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

mmCIF) - scaled unmerged data (MTZ or XDS_ASCII) to this converter: https://project-gemmi.github.io/wasm/mxdepo.html and then you can upload the resulting cif file to the wwPDB deposition system. Best wishes Marcin On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB wrote: Dear Jasmine, But can w

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

445-0103 ext 4920 Fax: (732)445-4320 === To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Fa

Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

k the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenu

Re: [ccp4bb] Problems with refining covalently linked heme cofactor

link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Camb

Re: [ccp4bb] unknown density in 1.6 A structure

uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB

Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

Hi Kamil, Ok this gives a better picture of the experiment. Although electron density contribution to diffraction is a bit more complicated than what I said in my previous email, in essence though the diffracting angles of 200 and 400 are indeed related as you said, with sin(theta) equal to l

Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

> > For example, the 400 and 200 reflections in a diffractogram are related to > the 100 family of crystallographic planes; I'd imagine, that in real space, > the higher order plane (e.g. the 400) corresponds to atoms 'closer' to the > center of the crystal/unit cell. > If it can help you to

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

nately, the data were collected more than 30/40 days ago so I > requested them via TOPCAT - unless there is a way round this? > > All the best, > > Irwin > From: Dom Bellini > Sent: 22 December 2020 18:54 > To: Irwin Selvam ; > CCP4BB@JISCMAIL.AC.UK > Subject: Re:

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

-- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dom Bellini, Xray Crystallography Facility (1S205) M

Re: [ccp4bb] Residual density feature

Dear Colin, I believe people usually refer to it as "unidentified blob" when depositing/writing in these cases. But I wonder whether others may suggest better options. Best, D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Levy [c.

Re: [ccp4bb] off topic pymol

Dear Almudena, Those letter represents different peptide chains. I guess in your cases they were probably peptide fragments built by automatic building programs such as arp/warp or buccaneer. Some programs do create PDB files with that extra column, which seems to send Pymol a bit awry. B

Re: [ccp4bb] Resolve Domain Sequence Ambiguities

Did you try ShelxE autotrace? At that resolution it should work nicely, or at least be able to distinguish between the two sequences. D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: 05 February 2015 15:49 To: ccp4bb Subject:

Re: [ccp4bb] Resolve Domain Sequence Ambiguities

Dear Jacob, Are you sure your MR solution is correct? What is your resolution? Best, D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: 05 February 2015 15:21 To: ccp4bb Subject: [ccp4bb] Resolve Domain Sequence Ambiguities H

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

Dear Andre, In the past I had some good fitting results with SITUS (it was a case where the matched the crystal structure). Best, D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Adam Round [aro...@embl.fr] Sent: 02 February 2015 11:13 To

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

Dear Jacob, To add one more thing to the many ones from James, despite air scattering noise being flat and easily subtractable over time, that noise wont be the same if you take images with and without the sample. Since some of the photons will be absorbed and diffracted by the crystal, the air

Re: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal

Dear Dialing, Just in case, make sure you get the residue numbering right. I.e., if you are try to insert a new residues between two residues already consecutively numbered, for example 96-97 or 134-135, then Coot will not to create the connection with the new residue. HTH D -Original Me

Re: [ccp4bb] Metal ion differentiation - reg

Dear Dhanasekaran, I am not sure from your email whether is important for you to resolve this ambiguity with crystallographic techniques. If not, an easy and simple way would be to shoot your crystals at energies above the Zn absorption edge (which is at highest energy of the two metals) and th

Re: [ccp4bb] Problem with Rfactor

Dear Sudarshan, I have the feeling the your R factor after Molrep is really high because the program has failed to produce a correct/not-partial solution, which could be due to many things, but usually the main problem is how good your search model is. The difference in spacegroups is not a pro

Re: [ccp4bb] Thermofluor assay

Dear Theresa,, , I would not advice to use thermofluor with membrane proteins as thefluorescent dye used in the assay binds to exposed hydrophobic patches of unfolding proteins. Therefore the presence of detergents would cause much unwanted fluorescence which would likely swamp your signal of in

Re: [ccp4bb] suggestion on improving sea urchin like crystals

Dear William, When in doubt, I would usually harvest a few needle clusters (especially as it sounds like you got plenty now), wash them with crystallization reservoir and then run them on SDS-PAGE gel. If you see a band of the right molecular weight you have most probably crystallized your pro

Re: [ccp4bb] Comparison of Water Positions across PDBs

Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest

Re: [ccp4bb] changes in small sections of secondary structure

Dear Mahesh, You could also run the CCP4 program CONTACT/ACT (Tadeusz Skarzynski & Andrew Leslie/Wojtek Rypniewski & Howard Terry) for inter residue contacts and compare the NH-OC bonds in the different structures. Best, D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JI

Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

horombic lattice. D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dom Bellini [dom.bell...@diamond.ac.uk] Sent: 03 October 2013 08:21 To: ccp4bb Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 QUICK ERRATUM Sorry W, I forgot a v

Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

QUICK ERRATUM Sorry W, I forgot a very important bit (I was half asleep ;-)). As the unit cells are, it would not be correct to import one set of Rfree flags from one dataset to the other in sftools as the axes are moved around and the indexing is no longer consistent between the two mtzs. Firs

Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

Dear W., If you really want to do a comparison on the Rfree, the only way would be to start off how described by Tim, i.e., rescaling your images to create a P21 mtz and then further reducing them to create a second higher symmetry C2221 mtz. Then you could create a set of Rfree flags for one

Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

com/s/gljckhw7ui6df6c/Booklet.pdf?m Best, D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent: 22 August 2013 23:38 To: ccp4bb Subject: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law Dear Community, I have

Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

Hi Some people emailed me saying that the attachment did not get through. I hope this will work. Sorry. D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry [ber...@upstate.edu] Sent: 23 August 2013 00:01 To: ccp4bb Subject

Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

Dear Community, I have attached a short booklet written some 6 years ago during rainy evenings to teach principle of crystal diffraction with biologist students in mind, never used it as I don't have students, but I now believe its mission was this thread ;-) It uses lots of real space diffrac

Re: [ccp4bb] Dependency of theta on n/d in Bragg's law

Dear Pietro, Ladd & Palmer book does explain it, just first example that springs to mind. HTH D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pietro Roversi Sent: 20 August 2013 15:37 To: ccp4bb Subject: [ccp4bb] Dependency of theta on n/d in

Re: [ccp4bb] ctruncate bug?

20, 2013, at 12:45 PM, Dom Bellini wrote: > Wouldnt be possible to take advantage of negative Is to extrapolate/estimate > the decay of scattering background (kind of Wilson plot of background > scattering) to flat out the background and push all the Is to positive values? >

Re: [ccp4bb] ctruncate bug?

Wouldnt be possible to take advantage of negative Is to extrapolate/estimate the decay of scattering background (kind of Wilson plot of background scattering) to flat out the background and push all the Is to positive values? More of a question rather than a suggestion ... D From: CCP4 bulle

Re: [ccp4bb] popular piece on X-ray crystallography

I would like to add/support James comments. Once it used to bother me the fact that diffraction was observed from the crystal even though the beam does not possess a space-time coherence (or even worse in the case of in-house diffractometers). This is because in text books they always illustrate

Re: [ccp4bb] Alternate sugar conformations in refmac 5.5.0110

Dear Markus, You could also try the "inse" keyword, which will tell refmac two mutually exclude two atoms occupying the same position but we occupancy for example of 0.6 and 0.4, stopping them from repelling each other. Here is an example in the case of an Fe site which was contaminated by Mn i

Re: [ccp4bb] Puzzling electron density upon heavy metal soaking

Hi, I have enocountered a similar effect with WO4- derivatives, I found a huge blob with some little resemblence to icosahedral features, some kind of mini 10 x W bucky ball. I was wondering whether there could be any slightly possibility that your protein may be able of some kind of yet unkno

Re: [ccp4bb] PNAS on fraud

Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Be