Re: [ccp4bb] Future Diffraction Methods

My (limited) experience of the Diffraction Methods GRC suggests that the most valuable part of these meetings is when people get together outside the talks - so independent of the session chairs (apart from the people that they invite) and of any instructions given to speakers. Just my two

Re: [ccp4bb] Future Diffraction Methods

Whether cross-pollination happens depends on the session chairs, and the remit they're given, and the instructions given to the speakers:  if early on everybody sets the tone, to inform as much as advertise, then it could be a rip-roaringly interesting meeting. At least, I've never

Re: [ccp4bb] Future Diffraction Methods

Hi all, I'm a big believer in cross-pollination between disciplines. I think there could be room for a multidisciplinary methods meeting (MMM) provided the right topics are chosen. If these are things that concern NMR-ists, X-ray-ans and cryo-EM-ers equally you might get the right mix of

Re: [ccp4bb] Future Diffraction Methods

Hi, everybody, hi, Nukri and Pavel ! I fully agree with Pavel that, if the speakers are not exceptional, if they are (as usually) concentrated on their specific and narrow problems, cross-discipline meetings make us lost quite fast, they are annoying and useless. Richard Feynmann had the same

Re: [ccp4bb] Future Diffraction Methods

.@gmail.com>> Date: Monday, 30 January 2023 at 11:40 am To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Future Diffraction Methods Hi Pavel, Your description of the current status is exactly correct. And

Re: [ccp4bb] Future Diffraction Methods

of The University of Queensland. From: CCP4 bulletin board on behalf of Nukri Sanishvili Reply to: Nukri Sanishvili Date: Monday, 30 January 2023 at 11:40 am To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] Future Diffraction Methods Hi Pavel, Your description of the current status

Re: [ccp4bb] Future Diffraction Methods

Hi Pavel, Your description of the current status is exactly correct. And that's exactly what I am proposing to change or, more accurately, try to change. By seeking out and bringing together people who do complementary and collaborative work, so they can set an example for others. This, of

Re: [ccp4bb] Future Diffraction Methods

Nukri, IMO, the idea of cross-discipline meetings is great conceptually, at least for reasons you pointed out, but utopical in practice. When we attend our field-specific meetings we meet colleagues we know, we talk to collaborators from the past or find new ones, we have things in common that we

Re: [ccp4bb] Future Diffraction Methods

Hi James, This meeting has indeed been one of the best ones by its format, content, and atmosphere. Many thanks to all the organizers and attendees of the past. Nevertheless, it is not surprising that it was cancelled, given the trends in structural biology research. Straightforward evolutionary

Re: [ccp4bb] Future Diffraction Methods

board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Frank von Delft Sent: Monday, December 19, 2022 10:21 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Future Diffraction Methods This Message is from an External Sender. Do not click links or open attac

Re: [ccp4bb] Future Diffraction Methods

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Future Diffraction Methods This Message is from an External Sender. Do not click links or open attachments unless you trust the sender. Shoot... that sucks. Yes, we do need something! "Structural Biology Methods"? More interesting quest

Re: [ccp4bb] Future Diffraction Methods

Excellent idea. From: CCP4 bulletin board on behalf of Debanu Das Date: Saturday, December 24, 2022 at 5:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Future Diffraction Methods Consider merging with the Annual ACA meeting. The ACA meeting can also benefit from more X-ray diffraction

Re: [ccp4bb] Future Diffraction Methods

: +44 (0) 1235 567505 > > Mobile: +44 (0) 7471 026061 > > email: allen.orvi...@diamond.ac.uk > > > > AMO site: > https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub/Staff/Orville.html > > XFEL-Hub site: https://www.diamond.ac.uk/Instruments/Mx/XFEL-Hub.html > > >

Re: [ccp4bb] Future Diffraction Methods

at 09:22 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Future Diffraction Methods Shoot... that sucks. Yes, we do need something! "Structural Biology Methods"? More interesting question: does it need the GRC to host? What about reimagining the CCP4 study weekend - the question keeps

Re: [ccp4bb] Future Diffraction Methods

Shoot... that sucks. Yes, we do need something! "Structural Biology Methods"? More interesting question:  does it need the GRC to host?  What about reimagining the CCP4 study weekend - the question keeps coming up there anyway. That's one for CCP4 WG1 to discuss - they're meeting straight

[ccp4bb] Future Diffraction Methods

I want to thank everyone who attended the 2022 Gordon Research Conference and Gordon Research Seminar on Diffraction Methods in Structural Biology, as well as all those who contributed to these great gatherings in the past.  It was an outstanding meeting if I do say so myself. Not just because

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

___ > >> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> Bijvoet Center for Biomolecular Research > >> Utrecht University > >> Padualaan 8, 3584 CH Utrecht > &

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

and correct meta data. > >> > >> Best wishes, > >> Loes > >> > >> ___ > >> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> B

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

; >> cloud services. And as Graeme mentioned: when archiving raw data > >> make sure to add sufficient and correct meta data. > >> > >> Best wishes, > >> Loes > >> > >> ___________ >

[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

t; Best wishes, > >> Loes > >> > >> ___ > >> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> Bijvoet Center for Biomolecular Research > >> Utrecht

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear all, as a follow-up to our initial message (and similar to other activities from the MX community), we added some content to our BUSTER wiki at https://www.globalphasing.com/buster/wiki/index.cgi?Covid19 to show interested users how to (re-)refine existing PDB entries with BUSTER and how

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

nsdag 18 maart 2020 23:30 Aan: CCP4BB@JISCMAIL.AC.UK  Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures Dear colleagues, Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease structures in the PDB seems to indicate that that there migh

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear Colleagues, I would like to add my voice to those advocating making available raw diffraction images and point out another resource for raw data deposition, https://cxidb.org, particularly for the case of emerging methods such as serial crystallography. Cheers, Filipe On Thu, 19 Mar 2020

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi > While those text files would be heavy, they'd be still lighter than raw > images and the whole useless white space they carry with them between > reflections. At the risk of extending this thread into a different direction, the "white space (the images) carry with them between

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

This last, very important point made by Graeme gives me the chance to plug a satellite workshop at the IUCr Congress (end of August, so fingers crossed that this will go ahead) on "MX raw image data formats, metadata and validation". This is organized by Herbert Bernstein, Loes Kroon-Batenburg,

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

gt;> Dr. Loes Kroon-Batenburg >> Dept. of Crystal and Structural Chemistry >> Bijvoet Center for Biomolecular Research >> Utrecht University >> Padualaan 8, 3584 CH Utrecht >> The Netherlands >> >> E-mail : l.m.j.kroon-batenb...@uu.nl >> ph

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

AIL.AC.UK>> namens Gerard Bricogne mailto:g...@globalphasing.com>> Verzonden: woensdag 18 maart 2020 23:30 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures Dear

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear Julien, On Thu, Mar 19, 2020 at 08:47:20AM +, Julien Cappèle wrote: > Though I agree with you Clemens that raw images are amazing to work > with as you can use any software you are confortable with, we cannot > forget that depositing several TB of data for each lab would be bad > for

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear all, On Thu, 19 Mar 2020, Winter, Graeme (DLSLtd,RAL,LSCI) wrote: Date: Thu, 19 Mar 2020 09:08:21 From: "Winter, Graeme (DLSLtd,RAL,LSCI)" To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures No matter how much data

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Van: CCP4 bulletin board namens Gerard Bricogne Verzonden: woensdag 18 maart 2020 23:30 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures Dear colleagues, Perusal and some initial (re-)refinement of the various SARS

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi Folks, Quick note on "Like a super raw image diet-plan for the incoming summer” - the bslz4 compression used with Eiger works really well, and the data are pretty close to entropy limit in terms of size - which means if you measure your data carefully (i.e. low background etc.) you can

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi everyone, There are some very interesting ideas. Though I agree with you Clement that raw images are amazing to work with as you can use any software you are confortable with, we cannot forget that depositing several TB of data for each lab would be bad for ecological reason. And because

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi Clemens, this is curious. You are right that there's a direct link to the raw data on 6vs4, but there isn't one on http://www.rcsb.org/structure/6H56. I'll contact RCSB to see where the problem lies. All best. Andreas On Thu, Mar 19, 2020 at 8:34 AM Clemens Vonrhein wrote: > Hi

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear Petr, On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote: > For those of you who are in touch with these data, would deposition > of unmerged intensities in P1 in the whole detector range instead of > complete dataset be good enough to „correctly“ re-evaluete the > structure? Or is

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi Andreas, On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote: > - The link to the raw data can be found inside the mmCIF file under > _pdbx_related_exp_data_set.data_reference. Whether it's also shown on one > of the PDB sites is up to the designers of these sides. I cannot find

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

people could offer their spare time to help the others with someting? Best regards, Petr From: CCP4 bulletin board On Behalf Of Andreas Förster Sent: Thursday, March 19, 2020 7:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

As someone who's done this (for one structure of minor significance), I would like to make a few comments: - I highly encourage deposition of raw data. Why would you not? Now that many labs are shut is the time to do it for all these datasets hiding somewhere on abandoned hard disk. These

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

A wonderful idea Gerard and Clemens. Sent from my iPhone > On Mar 18, 2020, at 6:31 PM, Gerard Bricogne wrote: > > EXTERNAL EMAIL – Use caution with any links or file attachments. > > Dear colleagues, > > Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease >

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

) From: CCP4 bulletin board on behalf of Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, March 18, 2020 5:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures EXTERNAL MAIL

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

What a great idea? Have you approached the depositors? Eleanor On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne wrote: > Dear colleagues, > > Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease > structures in the PDB seems to indicate that that there might be potential >

[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear colleagues, Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease structures in the PDB seems to indicate that that there might be potential to improve these if refinements could be repeated after some reprocessing and further analysis of the raw diffraction images,

Re: [ccp4bb] Powder diffraction database

Regarding X-ray Powder Diffraction software http://www.ccp14.ac.uk/ Regarding search match procedures and databases there are several https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ http://www.icdd.com/?gclid=EAIaIQobChMI1NGPpIOZ5gIVhkPTCh3E4gcyEAAYASAAEgIQhPD_BwE

Re: [ccp4bb] Powder diffraction database

eath Campus, Cardiff, CF14 4XN email: rizkall...@cardiff.ac.uk        phone: +44 29 2074 2248 http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre -Original Message- From: CCP4 bulletin board On Behalf Of Peer Mittl Sent: 02 December 2019 09:51 To: CCP4BB@JISCMAIL.AC.UK Subject: [cc

Re: [ccp4bb] Powder diffraction database

From memory, I’d look at the ICSD first; I think it’s got lots of powder information. From what I remember, CSD is entirely single crystal (though there might be some powder structures there), and is not what many people would call “publicly available”. You may or may not have some luck

[ccp4bb] Powder diffraction database

Could someone please give me some advice on how to query a publicly available powder diffraction database? Upon (protein) crystallization we always get large spherulites of an inorganic compound and I would like to know what it is. It should be possible to use the scattering angles of these

[ccp4bb] Workshop "Diffraction Data Collection Using Synchrotron Radiation"

I would hereby like to announce the 6th edition of the workshop "Diffraction Data Collection Using Synchrotron Radiation", which will take place from July 04-06, 2019 at the BESSY II storage ring of the Helmholtz-Zentrum Berlin for

Re: [ccp4bb] Weird diffraction pattern

Dear all Thanks for all the input both on- and off- the list. We shall definitely look into these suggestions further and report again here in due course. Kind regards Sam On Tue, 9 Oct 2018 at 19:12, Sam Tang wrote: > Dear all > > Hello. We recently shot a crystal (a protein with small

[ccp4bb] AW: [EXTERNAL] [ccp4bb] Weird diffraction pattern

To me, it looks like some intergrown salt crystal. HS Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang Gesendet: Dienstag, 9. Oktober 2018 13:13 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Weird diffraction pattern Dear all Hello. We recently shot

Re: [ccp4bb] Weird diffraction pattern

raised previously on CCP4bb From: Sam Tang Sent: 09 October 2018 15:02 To: Nave, Colin (DLSLtd,RAL,LSCI) Cc: ccp4bb Subject: Re: [ccp4bb] Weird diffraction pattern Hello Colin Although the unit cell dimensions from mosflm should be largely unreliable in this case, the software actually

Re: [ccp4bb] Weird diffraction pattern

*Sent:* 09 October 2018 12:13 > *To:* ccp4bb > *Subject:* [ccp4bb] Weird diffraction pattern > > > > Dear all > > > > Hello. We recently shot a crystal (a protein with small molecule as > ligand) at a synchrotron source and see a weird pattern. ( > https://drive.google.

Re: [ccp4bb] Weird diffraction pattern

Sam Would this unit cell index some of the spots? a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A. Colin From: CCP4 bulletin board On Behalf Of Sam Tang Sent: 09 October 2018 12:13 To: ccp4bb Subject: [ccp4bb] Weird diffraction pattern Dear all Hello. We recently shot a crystal

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

> À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Lundi 12 mars 2018 12h54 Objet : [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal? Dear all: I would like to seek your wisdom on our latest diffraction pattern. We have been working on protein/DNA complex. The prot

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

The diffraction patterns clearly show an overlap of two or more lattices, which either means you didn’t have a single crystal at the start or it was damaged during the flash-cooling process. PEG 400 is generally a good cryoprotectant at ≥20%, but I would recommend using at least 25% to be

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

Dear Xiao and Hans: Thanks for your reply. We tried to index it but failed. Joseph On Mon, Mar 12, 2018 at 11:15 PM, Xiao Lei wrote: > did you try to index it? the cell dimensions may give you hint. > > On Mon, Mar 12, 2018 at 4:40 AM, Joseph Ho

Re: [ccp4bb] weird diffraction pattern

Hello Tang, 1) For MR, you might want to try a range of homologs, or even a stack of overlapping homologs. A normal modes server like elNemo might also help if it can predict the "bend" your molecule undergoes upon binding. A long shot perhaps, but stranger things have happened. You also

Re: [ccp4bb] weird diffraction pattern

July 28, 2017 2:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] weird diffraction pattern Hi, Thanks to all who gave me suggestions concerning the weird diffraction pattern and I really appreciate it that Kay Diederichs help me processing my data set and answer my questions. Although the dat

Re: [ccp4bb] weird diffraction pattern

Hi, Thanks to all who gave me suggestions concerning the weird diffraction pattern and I really appreciate it that Kay Diederichs help me processing my data set and answer my questions. Although the data set can be processed using HKL3000, XDS without problems, the Rwork/Rfree values are still

Re: [ccp4bb] weird diffraction pattern

Dear Gerd, I wasn't really giving much attention to the poke between the ribs ;-) - for me the more serious matter was to see the merits of pixel detectors over CCDs made light of, as if they didn't really make much difference. If some people get carried away in the way you describe,

Re: [ccp4bb] weird diffraction pattern

Dear Gerard, my "sound like a sales person" was meant as poking a little fun - nothing serious, of course. I and our users like our not-so-new-anymore Pilatus3 6M. It's a great detector in many ways. But, there is a lot of hype that this detector solves all-problem, for instance fine

Re: [ccp4bb] weird diffraction pattern

Thanks for spelling it out! Would that advice still hold if the mosaicity of the crystal is 0.7 degrees? (I know, I should go read the paper., but . . .) eab On 07/13/2017 03:00 PM, Gerard Bricogne wrote: Dear Gerd, I can assure you that I have no shares in Dectris nor any commecial

Re: [ccp4bb] weird diffraction pattern

Dear Gerd, I can assure you that I have no shares in Dectris nor any commecial connections with them. What I do have is a lot of still vivid memories of CCD images, with their wooly point-spread function that was affected by fine-grained spatial variability as well as by irredicible

Re: [ccp4bb] weird diffraction pattern

Dear Gerard, you sound like a sales person for Dectris. Fine slicing is perfectly fine with CCD detectors - it takes a bit longer because of the step scan instead of continuous scan. The read noise issue is often overstated compared to the sample induced scatter background. If for fine

Re: [ccp4bb] weird diffraction pattern

Hi Chenjun, Few suggestions from my side. Process the data with XDS and look into acentric intensity distribution (it indicates any twinning possibility). Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation possibilities. Twinning can confuse the program and suggest you

Re: [ccp4bb] weird diffraction pattern

d. > > JPK > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??? > Sent: Thursday, July 13, 2017 3:56 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] weird diffraction pattern > > hello everyone, > I w

Re: [ccp4bb] weird diffraction pattern

Dear Tang, I noticed that your diffraction images seem to have been recorded on a 3x3 CCD detector. With this type of detector, fine slicing is often discouraged (because of the readout noise), and yet with the two long cell axes you have, any form of thick (or only semi-fine) slicing would

[ccp4bb] AW: [ccp4bb] weird diffraction pattern

on. Depending on the nature of the disorder, you may or may not correct for it. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tang Chenjun Gesendet: Donnerstag, 13. Juli 2017 14:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb

Re: [ccp4bb] weird diffraction pattern

Hi Jacob, I have tried seeding approaches but it didn't help. All best, Chenjun Tang

Re: [ccp4bb] weird diffraction pattern

Hi David, Thanks for your comments. Although the spots become streaky in certain directions, I have processed the data in HKL3000 and imosflm, which suggested the C2221 space group (66.59, 246.95 and 210.17). The Rmerge(0.14), completeness(94.8%), redundancy(4.6) are OK. When I tried to run

Re: [ccp4bb] weird diffraction pattern

You've got multiple lattices--try seeding approaches mentioned in a recent/current thread. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??? Sent: Thursday, July 13, 2017 3:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] weird diffraction

Re: [ccp4bb] weird diffraction pattern

M To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] weird diffraction pattern hello everyone, I would like to seek your opinion on my crystal hits. I am working on a helicase of which the native structure is solved and the all solution statistics are fine. I am trying to crystallize and solve t

[ccp4bb] weird diffraction pattern

hello everyone, I would like to seek your opinion on my crystal hits. I am working on a helicase of which the native structure is solved and the all solution statistics are fine. I am trying to crystallize and solve the structure of the protein/ssDNA complex. I recently got some hits from

Re: [ccp4bb] Anisotropic diffraction

Dear Roberto, I think you should try different special orientations of your crystals in the loop to find the one in which the measurable reflections stay away from the slow moving region (usually aligned with the beamstop holder, so horizontal in your image), in which reflections cannot be

Re: [ccp4bb] Odd diffraction

Dear Fang Lu, These spots are from a small molecule crystal. There is one very short axial length (large distance between reciprocal lattice rows) and one quite long axis (the spots are close together in the straight reciprocal lattice row near the bottom of your diffraction pattern) You can

Re: [ccp4bb] Odd diffraction

The spots at the very edge is around 2.5A. 2015-02-18 12:15 GMT+00:00 Fang Lu fangluwork...@gmail.com: Hi all, I got this odd diffraction. Not sure what it is, detergent or protein? Any ideas? The crystallisation condition is 2.4M Sodium Malonate. GF buffer contains HEGA-10,Tris,

[ccp4bb] Odd diffraction

Hi all, I got this odd diffraction. Not sure what it is, detergent or protein? Any ideas? The crystallisation condition is 2.4M Sodium Malonate. GF buffer contains HEGA-10,Tris, KAcetate, MgAcetate, EDTA and DTT. Protein size is around 100kDa. Thank you for your time. Fang [image: 内嵌图片 1]

[ccp4bb] GRC Diffraction 2014 Instruct fellowships

Dear all, Unfortunately something went wrong in email archiving, and I recall receiving more applications from specific people, than what are now in my mailbox. May I kindly ask the people that did send an application, to re-send me their PDF file by reply to this email? Sorry again to

[ccp4bb] IUCr Diffraction Data Deposition Working Group

Dear Colleagues, We wish to let you know that the Triennial report for 2011 to 2014 on diffraction data deposition matters, prepared by the IUCr Diffraction Data Deposition Working Group (DDD WG) is now available at:- http://forums.iucr.org/viewtopic.php?f=21t=343 Best wishes, John, Brian and

Re: [ccp4bb] Strange diffraction

Small unit cell and strong diffraction -- I agree with Artem. D. Muhammed bashir Khan wrote: Hi All; I have a strange diffraction pattern from a membrane protein in one of the PEG containing conditions. Could somebody suggest/comments about this diffraction pattern. Please find the

[ccp4bb] Pittsburgh Diffraction Conference: registration extended to August 21, 2013

Dear colleagues, This is a reminder that the 71st Pittsburgh Diffraction Conference will be held at the Hauptman-Woodward Medical Research Institute in Buffalo, NY on September 18-20, 2013. Program topics include crystallization approaches for recalcitrant proteins and protein complexes,

Re: [ccp4bb] Improve diffraction ...any ideas?

Hi Urmi, When you say antibody you mean Fab fragments? If so, bear in mind that Fab fragments can be quite flexible about the region inbetween the variable and constant domains, which may be detrimental to the quality of your crystals ... in this case, further to the advice of others on here, you

[ccp4bb] AW: [ccp4bb] Improve diffraction ...any ideas?

! Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Urmi Dhagat Gesendet: Freitag, 24. Mai 2013 04:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Improve diffraction ...any ideas? Hi, I am working on a protein antibody complex which

Re: [ccp4bb] Improve diffraction ...any ideas?

Use random microseeding to pick up new conditions, and work with those. See http://www.douglas.co.uk/mms.htm and http://www.douglas.co.uk/MMS_proc.htm for theory, references and practical details On 24 May 2013 03:20, Urmi Dhagat udha...@svi.edu.au wrote: Hi, I am working on a protein

Re: [ccp4bb] Improve diffraction ...any ideas?

Rajiv, I don't quite get your idea. Once the crystals of the single proteins have grown, you can't soak the other protein in, can you? Or do you mean something else? Umri, if you do get crystals of one of the components it's well worth trying cross-seeding into the complex, again using random

Re: [ccp4bb] Improve diffraction ...any ideas?

I think this is an advice not to follow. Vaheh -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajiv K Bedi Sent: Friday, May 24, 2013 1:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Improve diffraction ...any ideas? Dear Umri

Re: [ccp4bb] Improve diffraction ...any ideas?

I think you can soak another protein into a protein crystal if it is small enough to pass through water channels, I guess. More info: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483499/

Re: [ccp4bb] Improve diffraction ...any ideas?

Hello Scott Setting up rMMS by hand works fine, but it's a bit slow and uses more protein and (sometimes much more important!) more seed stock. We recommend using a Hamilton syringe, preferably with a rounded needle, to set up by hand. 1.0 protein + 0.7 reservoir solution + 0.3 seed stock works

Re: [ccp4bb] Improve diffraction ...any ideas?

Dear Umri, I think the main problem is co-crystallization. What I would do is crystallize protein and antibody separately and then soak protein crystals into reservoir solution containing antibody or vice versa. And do try to get crystals from different conditions which may alter the space

Re: [ccp4bb] Strange diffraction image

Could be an organic crystal - what's the resoution of the lowest order reflections? Jan D. On Fri, Oct 12, 2012 at 8:11 AM, Chang Qing robie0...@gmail.com wrote: Hi, everyone: I just got some strange diffraction images from crystals with triangular pyramid shape. I think this should not be

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange diffraction image Hi, everyone: I just got some strange diffraction

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

part de Chang Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange diffraction image Hi, everyone: I just got some strange diffraction images from crystals with triangular pyramid shape. I think this should

Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

message -- From: Tim Gruene t...@shelx.uni-ac.gwdg.de Date: 2012/10/12 Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image To: Chang Qing robie0...@gmail.com 抄送： CCP4BB@jiscmail.ac.uk -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, What makes you think spots from salt

Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image

and finally I got crystals like this. Is it possible that I get some strange crystals such as CsMgCl3 or something else? Best regard Chang -- Forwarded message -- From: Tim Gruene t...@shelx.uni-ac.gwdg.de Date: 2012/10/12 Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction

[ccp4bb] Pittsburgh Diffraction Conference 2012

The 70th Pittsburgh Diffraction Conference will be held at SSRL between September 30th and October 2nd 2012 and will feature 2 full days of lectures and poster presentations. The conference starts with a welcome reception on September 30 and there will be a banquet on the evening of October

Re: [ccp4bb] Anisotropic diffraction

: Friday, April 27, 2012 3:18 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Anisotropic diffraction Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6

Re: [ccp4bb] Anisotropic diffraction

-- From: chen c chenc...@gmail.com Sent: Sunday, April 29, 2012 6:09 PM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] Anisotropic diffraction I accept your advice. In fact, this is the first time I am involved in anisotropic issue. And I learned a lot from all

Re: [ccp4bb] Anisotropic diffraction

: [ccp4bb] Anisotropic diffraction Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa

[ccp4bb] Anisotropic diffraction

Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa

Re: [ccp4bb] Anisotropic diffraction

Anisotropic truncation should have no effect on the space group symmetry. On 04/27/12 15:18, Theresa Hsu wrote: Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is

Re: [ccp4bb] Anisotropic diffraction

Birtley and Curry used a novel optimization method, in their paper Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy, which might be inspiring for you. 在 2012年4月28日 上午3:21，David Schuller dj...@cornell.edu 写道： Anisotropic

Re: [ccp4bb] No diffraction

This might be obvious, but make sure you washed the crystals thoroughly before dissolving them for SDS-PAGE or mass spec -Jesse On Thu, Jan 26, 2012 at 10:48 AM, Katherine Sippel katherine.sip...@gmail.com wrote: Might I suggest consulting the CCP4 user community wiki on the topic:

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