[ccp4bb] Fw: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES TODAY - 4TH DECEMBER!

Quick reminder - last call for CCP4 Study Weekend in person registration is today (Monday 4th Dec)! From: CCP4 bulletin board on behalf of Karen McIntyre - STFC UKRI <6f4fce69ead1-dmarc-requ...@jiscmail.ac.uk> Sent: 01 December 2023 14:31 To: ccp4bb Subjec

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

Another point of confusion worth pointing out: * Many US medical-school-affiliated faculty positions are “12 months” but you may be expected (and heavily pressured) to recover well over 50% of your salary from your grants. The fine print varies widely as to what you will be paid if you fa

[ccp4bb] FW: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

Hi The current version of coot in ccp4 (on osx and linux) is 0.9.8.8, since update 12 in June Charles -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: 18 July 2023 17:11 To: ccp4bb Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is

[ccp4bb] FW: [ccp4bb] CCP4 Study Weekend 2023 - Early bird registration extended to 20th November

Early bird registration for the in-person CCP4 Study Weekend 2023 has been extended to 20th November! Register now before the price goes up!!! We have also continued the standard student bursaries which cover the cost of registration plus one night's accommodation. If you are a student (or stand

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

restricted lens aperture. > > > > Good debate though. > > > > Colin > > *From:* John R Helliwell > *Sent:* 17 February 2020 16:36 > *To:* Nave, Colin (DLSLtd,RAL,LSCI) > *Cc:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolut

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

well > Sent: 17 February 2020 16:36 > To: Nave, Colin (DLSLtd,RAL,LSCI) > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution? > > Hi Colin, > Neutrons are applied to the uranyl hydrides so as to make their scattering > lengths much more e

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear Colin Great that you mention the Rose equation and its consequences for cryo-EM! I have actually written a paper on that topic some 40 years ago [Marin van Heel: Detection of object in quantum-noise limited images. Ultramicroscopy 8 (1982) 331-342]. I honestly have not thought about it for a

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Sent: 17 February 2020 16:36 To: Nave, Colin (DLSLtd,RAL,LSCI) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution? Hi Colin, Neutrons are applied to the uranyl hydrides so as to make their scattering lengths much more equal than with X-rays, and so side step

[ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear Marin For electron microscopy, the Rose criterion (a measure of contrast/noise) is sometime used to distinguish low contrast features within polymers (see for example Libera, M. & Egerton, R. (2010). Polymer Reviews. 50, 321-339.). A particular value of the Rose criterion implies a partic

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

uraged from applying some I/sigI type cut off. > > Cheers > Colin > > > > From: John R Helliwell > Sent: 17 February 2020 12:09 > To: Nave, Colin (DLSLtd,RAL,LSCI) > Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution? > > Hi Colin, > I think the ph

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

/ch4o8v0001/ ). For protein crystallography perhaps series termination errors have become less important as people are discouraged from applying some I/sigI type cut off. Cheers Colin From: John R Helliwell Sent: 17 February 2020 12:09 To: Nave, Colin (DLSLtd,RAL,LSCI) Subject: Re: [ccp4bb] FW

[ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear all. Would it help to separate out the issue of the FSC from the value of the threshold? My understanding is that the FSC addresses the spatial frequency at which there is a reliable information content in the image. This concept should apply to a wide variety of types of image. The issue

[ccp4bb] FW: [ccp4bb] CCP4 Study Weekend 2020: early bird period closes on Sunday 17th November!!!

Just a reminder that the early bird period for the CCP4 Study Weekend closes on Sunday 17th November. After this date no standard student bursaries will be available and registration will cost £290 for everyone (an increase of £50). Get in before the price goes up!!! Regards Karen McIntyre CC

Re: [ccp4bb] FW: [ccp4bb] old data - headers

ow >> :) >> >> >> -Original Message- >> From: Pedro Matias [mailto:mat...@itqb.unl.pt] >> Sent: den 31 januari 2019 11:46 >> To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers >> >>

Re: [ccp4bb] FW: [ccp4bb] old data - headers

e thanks everyone.. what a response. All good now > :) > > > -Original Message- > From: Pedro Matias [mailto:mat...@itqb.unl.pt] > Sent: den 31 januari 2019 11:46 > To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers >

Re: [ccp4bb] FW: [ccp4bb] old data - headers

huge thanks everyone.. what a response. All good now :) -Original Message- From: Pedro Matias [mailto:mat...@itqb.unl.pt] Sent: den 31 januari 2019 11:46 To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers Hi Dean, I reckon that it is an

Re: [ccp4bb] FW: [ccp4bb] old data - headers

Hi Dean, I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the images with mosflm or adxv you should see the characteristic 2x2 tile pattern. Note how the header format is similar to the one you posted from the ESRF. Pedro Às 10:21 de 31/01/2019, Dean Derbyshire escreveu: >

[ccp4bb] FW: [ccp4bb] old data - headers

thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I right in assuming MARCCD or are we going back as far as image plate? here is the image header Harry what do you think HEADER_BYTES= 512; DIM=2; BYTE_ORDER=little_endian; TYPE=unsigned_short; PIXEL_SIZE=0.08160; BIN=none; ADC=

Re: [ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

[cid:a3a4faea-08e2-46af-88de-3bde456d9124@fed.cclrc.ac.uk] Sorry for spamming you all on this, but these images keep on getting stripped for Armin and myself. On 2 Aug 2018, at 16:51, Charles Ballard - UKRI STFC wrote: > Begin forwarded message (on behalf of Armin Wagner) > From: ahw78 mailto:

[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

Begin forwarded message (on behalf of Armin Wagner) From: ahw78 mailto:armin.wag...@diamond.ac.uk>> Date: 2 August 2018 at 09:17:48 BST To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>> Subject: Re: [ccp4bb] Sulphate or phosphate? Dear Eleanor, We can

[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

Dear all, Sorry, now with the attachment of an anomalous difference fourier above and below the sulphur edge. Best regards, Armin On 02/08/2018, 09:17, "CCP4 bulletin board on behalf of armin.wag...@diamond.ac.uk" wrote: Dear Eleanor, We can tune the wavelength over a lar

[ccp4bb] FW: [ccp4bb] Resolution mismatch aimless/refmac

Dear All, Thanks everyone for the suggestions and clarifications. As Eleanor and Garib wrote, I cannot find real differences in map quality or statistics after refinement depending if I set or not the resolution edges. This is more a matter of how the remarks in the pdb are recorded for validat

Re: [ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Hi Sutapa, Slow expression did work in my case. I had to induce with 100uM IPTG, and grow cells at 10C for 48 hours. It left at least 50% of expressed protein in soluble fraction. Best, Swarna On Wed, Apr 5, 2017 at 1:52 AM, AJV wrote: > Hi Sutapa, > > The input from other commenters has been

Re: [ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Hi Sutapa, The input from other commenters has been great, so I'll stick to discussing only the portion of your question regarding baculovirus. In our experience, codon-optimization has resulted in little to no improvement of total protein yields or protein solubility in baculovirus. We routine

Re: [ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Dear Sutapa There has been wonderful suggestions, particularly from Bert, size matters! Considering that all is in order, i would share my experience with retroviral integrase, a sparingly soluble protein when expressed in E. coli. The protein exists in mammalian cells as a multi-protein complex

[ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Dear Supta, If I may make another type of suggestion, we have had success in crystallizing sparingly soluble proteins in the presence of up to 2M urea (Dines et al. Journal of Structural Biology, 2007). It is enough to avoid non-specific associations, but not enough to denature the protein. It

Re: [ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

CCP4 pdbset is very good for this. Find the symops in $CCP4/lib/data/symop.lib and use symgen and chain commands to create each with a different chain ID. The six-fold screw is generated by: X,Y,Z -Y,X-Y,2/3+Z Y-X,-X,1/3+Z -X,-Y,1/2+Z Y,Y-X,1/6+Z X-Y,X,5/6+Z X,Y,1+Z but the two-fold defines

Re: [ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

that's neat - I have used chimera to build filaments from fibre diffraction where you specify the rise and angle rather than symmops. 'Sym' command specifying 'group h' then rise and angle. Martyn On Fri, Dec 9, 2016 at 1:34 PM, Paul Emsley wrote: > > I would use the function new_molecule_by_symo

Re: [ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

I would use the function new_molecule_by_symop e.g. # python imol = new_molecule_by_symop(0, "Y,-X+Y,Z+1/6", 0,0,0) then do this 5 more times selecting the other symmetry operators that generate the helix around the z axis.. or the attached script (adjust as necessary) Paul. On 09/12/16 1

Re: [ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

Yes I would do it that way by clicking on the ones I want to see - then saving them and then reading them back in. You can change the chainids so Coot makes them different colours which might help. Things might be easier in PyMol if you want interactive control over the colours for a picture say. c

[ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

Dear All, I mean if the radius set in the Coot "Cell Symmetry" was too small, not enough monomers (less than 6) can be displayed to show the "continuous helix with a six-fold screw axis". If the radius was too large, as for the "continuous helix with a six-fold screw axis" can be regarded as

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

From the Washington Post (https://www.washingtonpost.com/news/speaking-of-science/wp/2016/11/09/what-will-president-trump-mean-for-science/): Last year, Trumptold conservative radio host Michael Savage, “I hear

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

It is better to light a candle than curse the darkness... Enviado desde mi iPhone > El 10/11/2016, a las 01:17, William G. Scott escribió: > > Dear Edward et al: > > I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I > think it is a mistake, and perhaps a missed oppo

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Dear Edward et al: I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I think it is a mistake, and perhaps a missed opportunity, to ignore politics completely. For example, Newt Gingrich is currently in the running for Sec HHS. He has previously written editorials in t

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

We got 4K0F! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radu Aricescu Sent: Thursday, 10 November 2016 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Hi JPK, Not sure about them, but I was

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

PDBID of 5HIT. I wonder what the authors thought when they got this ID back from RCSB! > >   > > JPK > >   > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten > Sent: Wednesday, November 09, 2016 4:18 PM > To: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... There is nothing wrong with discussing sex at work, either theorethical http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1sex or experimental http://www.rcsb.org/pdb

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

edu> Verzonden: woensdag 9 november 2016 21:43 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... I Agree with Edward. No discussion of politics, religion, or sex at work. Best wishes,

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

: Wednesday, November 9, 2016 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Eddie Snell for President On Wed, Nov 9, 2016 at 11:02 AM, Edward Snell mailto:esn...@hwi.buffalo.edu>> wrote: As a Brexit and Trumpet af

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Eddie Snell for President On Wed, Nov 9, 2016 at 11:02 AM, Edward Snell wrote: > As a Brexit and Trumpet affected person having a foot in both countries > ,this topic is too far off the normal discussion on CCP4 and probably > better taken up privately. CCP4 is not a political discussion site.

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

I would concur with Ed. I can understand the emotions, but political shouting should be done elsewhere. Let’s remain civil. Klaus === Dr. Klaus Fütterer Deputy Head of School Undergraduate Admissions Room 717, Biosciences

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } I totally agree with you, Edward! James Sent from Yahoo Mail for iPhone On Wednesday, November 9, 2016, 5:02 pm, Edward Snell

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

As a Brexit and Trumpet affected person having a foot in both countries ,this topic is too far off the normal discussion on CCP4 and probably better taken up privately. CCP4 is not a political discussion site. With CCP4 the signal is unusually high and the noise low when compared to any discuss

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

You are kidding right? Artem On Nov 9, 2016 11:53 AM, "John Hardin" wrote: > Greetings, > > I fully understand that I will be labeled as ignorant and that I will > likely be hated because of my views, > but I am thrilled that Hillary lost this election. > > The United States has embarked on a p

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Moral? Donald Trump? Really? On Wed, Nov 9, 2016, 17:53 John Hardin wrote: > Greetings, > > I fully understand that I will be labeled as ignorant and that I will > likely be hated because of my views, > but I am thrilled that Hillary lost this election. > > The United States has embarked on a pa

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Greetings, I fully understand that I will be labeled as ignorant and that I will likely be hated because of my views, but I am thrilled that Hillary lost this election. The United States has embarked on a path of immorality, and I am excited by the possibility of restoring the moral character a

[ccp4bb] Fw: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Good job they did'nt dead heat otherwise it would have been Trumpton. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7 - Forwarded Message - From: Ian Tickle To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 9 November 2016, 12:

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

US elections, UK BREXIT, Colombia referendum . . . if you are fed up with democracy, consider kingdoms. Middle East is still investing into science, technology and education! Cheers, Stefan On 9 November 2016 at 16:22, Noam Adir wrote: > Dear Ian, > > > > I have always thought that this saying

[ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Dear Ian, I have always thought that this saying, attributed to Lincoln, is sorely lacking the finishing touch, which is: “in a democracy, it is sufficient to fool enough of the people at the right time”. Today’s results are a prime example. --Noam From: CCP4 bulletin board [mailto:CCP4BB@J

[ccp4bb] FW: [ccp4bb] Please post this message

 Hi,  I just subscribed to CCP4BB but I am trouble posting this message. Could  you please upload this Job advertisement.  Thanks much, Sudha  Postdoctoral Position in Structural Biology, Department of Physiology and Biophysics at Case Western Reserve University, Cleveland OH Laboratory of Dr

[ccp4bb] FW: [ccp4bb] dynapro DLS cuvettes

Some memories from the dark recesses of my mind… Hope it helps! Bryan From: Prince, D Bryan Sent: Thursday, August 14, 2014 6:07 PM To: 'Gloria Borgstahl' Subject: RE: [ccp4bb] dynapro DLS cuvettes Dear Gloria, I seem to remember that we had a DynaPro DLS system and used disposable plastic cuv

Re: [ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

2014-05-15 9:53 GMT-03:00 Colin Nave : > Of course exponential growth can’t go on forever – the hidden point behind > my question. > A nice example from another biological database is Swissprot. It had an exponential-like growth until 2009, and now it's somewhat linear: http://web.expasy.org/doc

[ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

Roger Thanks for this reply. Sometime in the next millennium I guess. I did get replies from several well wishers implying that it would be a good idea if I retired as soon as possible. More usefully, Marjolein Thunnissen reminded me of the article http://www.uic.edu/labs/caz/downloads/Abad-Zap

[ccp4bb] FW: [ccp4bb] which space group?!?

Hi, The density in both space groups looks very similar, with no obvious differences. The data was processed in XDS followed by refinement in REFMAC and then PHENIX. Yes, the statistics of the orthorhombic structure is probably more realistic. But when both are refined in REFMAC these statistic

[ccp4bb] FW: [ccp4bb] PIMS & XtalView Help

Hi Dwayne, Please send me a copy of your stack traces. I have just release PiMS4.4. I would like to review the errors that have affected you before building a release of xtalPiMS. Regards, Chris Morris From: "McCully, Dwayne (NIH/NIAMS) [C]" mailto:dmccu...@mail.nih.gov>> Date: 21 June 2013

[ccp4bb] FW: [ccp4bb] validating ligand density

You are the one who should judge your statement, but it looks plausible to me. Now that I think of it: why do we need referees if every scientist should judge their own hypothesis? Publication will be a lot faster if we no longer need to heed the remarks of some grumpy referees and send in revis

Re: [ccp4bb] FW: [ccp4bb] [ccp4bb] disulfide engineering

We have had some good luck with hydrogen peroxide [for technical details plus validation via a crystal structure see Van der Meeren et al JBC 288(2):1214-1225, (2013)]. best of luck Savvas On 28 Feb 2013, at 12:14, "McEwan, Paul" wrote: > Rather than looking at “anti-DTT” it is more import

[ccp4bb] FW: [ccp4bb] disulfide engineering

Rather than looking at "anti-DTT" it is more important to set up an appropriate redox system. This can be a combination of reduced and oxidised glutathione or cysteine. If you check some of the commercial protein refolding screens this should give you an idea about relative concentrations. Bes

[ccp4bb] FW: [ccp4bb] off topic: DSSP

--- Begin Message --- Hi, I thought the latest version of dssp ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz contains the fixes to build a Mac version. However, it may be you have to remove the -static flag from the Makefile. If so, please let me know, I have no Mac capable of run

[ccp4bb] FW: [ccp4bb] refining against weak data and Table I stats

           From: בעז שאנן Sent: Thursday, December 13, 2012 11:42 AM To: Frank von Delft Subject: RE: [ccp4bb] refining against weak data and Table I stats Hi Frank, Also tNCS screw up the CC*/CC1/2 measure. I played with it on a structure that I'm working on, which has a huge off-o

[ccp4bb] Fw: [ccp4bb] structural homology

I recommend Swiss Pro's Deep View for homology modeling with a single template. You should use VAST searching for the most diverse sequences to find suitable pdb homologs. Best to align your protein sequence with the choices from VAST, being careful to align turns (pro's, gly's etc) and if you

[ccp4bb] Fw: [ccp4bb] Question on Symmetry Axis Notation Convention

The standard notation is 21 axis parallel to [100]?   Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com   From: James Stroud To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 14 June 2012, 20:06 Subject: [ccp4bb] Questi

Re: [ccp4bb] Fw: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

Yep, works for me too. 1w2i-sf.cif contains no pdbx entries. Did you perhaps first download the mmcif format coordinate file? On the RCSB site, the "mmCIF File" are coordinates, and "Structure Factor (text)" are reflections in mmCIF format. Cheers Martyn On Wed, 2012-02-29 at 02:33 -0800, Dial

[ccp4bb] Fw: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

I just have it successfully done:  Import reflection file in mmCIF format and create MTZ file In 1w2i-sf.cif - Forwarded Message - From: Jayashankar To: Dialing Pretty Cc: CCP4BB@jiscmail.ac.uk Sent: Wednesday, 29 February 2012 7:05 PM Subject: Re: [ccp4bb] CCP4i Reflection DataUtili

Re: [ccp4bb] FW: [ccp4bb] highly glycosylated protein

d (on behalf of Wei Li >) >Subject: [ccp4bb] FW: [ccp4bb] highly glycosylated protein >To: CCP4BB@JISCMAIL.AC.UK > > > > Dear Pascal and Matthias, > > I am sorry for the delay of reply, thanks very much > for your suggestions on the glycosylation protein. >

Re: [ccp4bb] FW: [ccp4bb] highly glycosylated protein

; > BR > > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wei Li > Sent: Tuesday, May 17, 2011 9:36 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] FW: [ccp4bb] highly glycosylated protein > > > > > > Dear Pascal an

Re: [ccp4bb] FW: [ccp4bb] highly glycosylated protein

– surprised the cells live at all. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wei Li Sent: Tuesday, May 17, 2011 9:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] FW: [ccp4bb] highly glycosylated protein Dear Pascal and Matthias, I am sorry for the delay of

[ccp4bb] FW: [ccp4bb] highly glycosylated protein

Dear Pascal and Matthias, I am sorry for the delay of reply, thanks very much for your suggestions on the glycosylation protein. Now I am trying to do a stable cell line with CHO lec 3.8.2.1 cells, this cell line could express protein with shorter glycans. I hope several weeks later I could ge

Re: [ccp4bb] **Possible spam**Re: [ccp4bb] FW: [ccp4bb] diffraction of spherulites

> Sent: 06 April 2011 18:16 > To: Nave, Colin (DLSLtd,RAL,DIA) > Cc: CCP4BB@jiscmail.ac.uk > Subject: **Possible spam**Re: [ccp4bb] FW: [ccp4bb] diffraction of > spherulites > > It seems hard to imagine what there is anything in his solutions other > than protein that would

Re: [ccp4bb] FW: [ccp4bb] diffraction of spherulites

It seems hard to imagine what there is anything in his solutions other than protein that would make spherulites, no? PEG 8000 at 12% seems pretty benign, unless the trays or screens have been sitting around for quite a while... JPK On Wed, Apr 6, 2011 at 12:04 PM, Colin Nave wrote: > > > Stefan

[ccp4bb] FW: [ccp4bb] diffraction of spherulites

Stefan Could the low angle reflections be from lamellar liquid crystals of the PEG (or a mixed PEG/water phase). Seems like you have 1st,2nd and 4th order reflections with presumably the 2nd order about 20A. I think 40A lamellar spacing is characteristic of some PEG liquid crystals. Colin From

[ccp4bb] FW: [ccp4bb] Merging data to increase multiplicity

Herman Thanks. 5-10 degrees is certainly high whatever definition one uses. In the list I gave, I didn't include "relative to the angular separation of the diffraction spots in reciprocal space." I would like to say that I didn't include it to see if anyone else came up with this one.

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Dont forget all the "atomic resolution" 3Å structures! From: Pavel Afonine [pafon...@gmail.com] Sent: Thursday, January 06, 2011 6:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accu

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distanceaccuracies

@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and > distanceaccuracies > > Dear Colin, > > Wladek Minor has just drawn my attention to the following recent > paper: > > Acta Cryst. (2010). D66, 1041.1042 > &g

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

ariables (the single-bond torsion angles)" > > > > > > > > Overall this seems a reasonable claim. > > > > Colin > > > > > > > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Charles W. Carter, Jr > &g

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

ile at the same time using a minimal set of > variables (the single-bond torsion angles)" > > > > Overall this seems a reasonable claim. > > Colin > > > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Charles > W. Carter,

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Maybe if you are really into this, you could "go public" by writing a letter to the editor (from the CCP4BB?), and I am sure there will be a good response from the authors... Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Behalf Of Charles W. Carter, Jr Sent: 06 January 2011 09:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies Begin forwarded message: From: "Charles W. Carter, Jr" Date: January 6, 2011 10:51:20 AM GMT+01:00

[ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Begin forwarded message: > From: "Charles W. Carter, Jr" > Date: January 6, 2011 10:51:20 AM GMT+01:00 > To: Gerard Bricogne > Subject: Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies > > I echo Gérard's thought. > > Pascal Retailleau

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Dear Axel, On Sun, Dec 26, 2010 at 01:15:44PM -0800, Axel Brunger wrote: > We defined "super-resolution" in our DEN paper as > achieving coordinate accuracy better than the resolution > limit d_min of the diffraction data. We proposed this > definition in analogy to its use wide-spread use in

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

We defined "super-resolution" in our DEN paper as achieving coordinate accuracy better than the resolution limit d_min of the diffraction data. We proposed this definition in analogy to its use wide-spread use in optical microscopy: "super-resolution" methods such as STORM, PALM, and STED achi

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

> I find the "super-resolution" claims in this paper a bit of a conjuring trick. I think it is understood that information cannot come from nothing. You cannot cheat in basic physics. Interestingly, I had the same discussion with bioinformatics colleagues a short time ago. The problem is the same

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Dear Gerard, Actually, for some of the tests we turned off the DEN network restraints for the last two refinement macrocycles, so, at least for these particular cases, the DEN method truly found a better minimum rather than forcing the system to the higher resolution structure. Cheers, Axel O

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Extrapolating to the infinite, I wonder how super-resolution fits into MD models or structure predictions? Jacob On Thu, Dec 23, 2010 at 5:04 PM, Gerard Bricogne wrote: > Dear Bernhard, > >     I must say that I find the "super-resolution" claims in this paper a > bit of a conjuring trick. If th

Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Dear Bernhard, I must say that I find the "super-resolution" claims in this paper a bit of a conjuring trick. If the final refined model has greater accuracy than one would expect from the resolution of the data it has been refined against, it is because that extra accuracy has been lifted fr

[ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Oops I am outdated: Axel just emailed me that he describes an improved coordinate estimate beyond the Rayleigh criterion in his recent paper Schroder GF, Levitt M, & Brunger AT (2010) Super-resolution biomolecular crystallography with low-resolution data. Nature 464(7292), 1218-1222. For the defo

[ccp4bb] FW: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Dear Tim, Interesting discussion, and I agree with your last description of the issues. When I started playing with this for oxymyoglobin [J. Mol. Biol. 142, 531-544 (1980)] it seemed immediately apparent (i.e. by thinking about it before starting to write programs) that the simple Babinet app

[ccp4bb] Fw: [ccp4bb] protein turns brown

Yellow or brown tinge is very common especially if you have used sonication to lyse the cells. It helps to wash the cells with buffer or even high salt and spin them down again before lysis. If you want brown then you should see what happens when you work with yeast. Probably flavins or some

[ccp4bb] FW: [ccp4bb]

Dear Changyi, If refmac distorts the ring to fit INTO the density, the first question I would ask myself is whether the sugar ring has been fitted correctly. Sugars can be a pain in the neck with different puckers, chair/boat conformations, different anomers etc. If the sugar is somewhat disorder

[ccp4bb] FW: [ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?

>Is there any easy to convert a colume in mtz file (say fom) into a fixed >value? I tried to convert to ascii first, but mtz2various only takes 1 >single FP colume (unfortunately I have 2). Thanks! Can't think why you might want to do this, but sftools will do it. shellscript: #!/bin/bash sftoo

[ccp4bb] Fw: [ccp4bb] degradation of protein durring freez thaw

Sounds like good advice - I suppose that since pure water un-freezes last, you could have protein concentration inhomogeneities? So in areas where the protein concentration is raised it could start to feel like crashing out. All the best Martyn Martyn Symmons Cambridge - Original Messag

[ccp4bb] FW: [ccp4bb] Refining against images instead of only reflections

Jacob Yes, discussions have taken place but perhaps more private than on the CCP4 bulleting board! So I am glad someone has raised the issue. The present approximation that people make works very well in the majority of cases. The approximation is implied during the integration of a spot and is

[ccp4bb] FW: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Dear ALL: Thanks a lot for the valuable guidance. Here are some updates of my problem. The current model is 100% complete now. The two good molecules fit into the density very well. I am currently using P2221 space group. I split the data according to suggestions I got using mtzutils

Re: [ccp4bb] Fw: [ccp4bb] cracking crystal

ost. Kris - Kris F. Tesh, Ph D Director, Macromolecular Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA 001 281 362 2300 x 144 From: Kris Tesh To: CCP4BB@JISCMAIL.AC.UK Date: 09/01/2009 04:20 PM Subject: [ccp4bb] Fw: [ccp4bb

[ccp4bb] Fw: [ccp4bb] cracking crystal

I have been asked about a supplier. I know of at least 4: 1. Aldrichwww.sigmaalldrich.com Fomblin Y LVAC 14/6Cat # 317934-100G100g 2. Lancaster/Alfa Aesar www.alfa.com/CGI-BIN/LANSAWEB?WEBEVENT+L0178567F6B740600C68505B+ALF+ENG

Re: [ccp4bb] FW: [ccp4bb] X-Ray versus NMR Structure

Correct, this special NMR issue of NSMB does not have any pdfs for some reason. The presubmission manuscript can be downloaded from my site: http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 On Nov 18, 2008, at 8:26 PM, Kantardjieff, Katherine wrote: In regards to the reference below,

[ccp4bb] FW: [ccp4bb] X-Ray versus NMR Structure

In regards to the reference below, it does not appear to be in the online archive of NSMB... Those pages are mysteriously missing between volumes 10 and 11. > > You might find this review useful: X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Bi

Re: [ccp4bb] FW: [ccp4bb] .getTwoTheta() in DiffractionImage library

Dear Francois Remacle, One example images for the mar225 is available under: http://www.mx.bessy.de/temp_stuff/mar225_5_theta_1_001.img.bz2 The output for this image using DiffractionImage library looks like this (using the function listed below): DEBUG OUTPUT ===

[ccp4bb] FW: [ccp4bb] .getTwoTheta() in DiffractionImage library

From: Remacle, F (Francois) Sent: 02 July 2008 09:46 To: 'Georg Zocher' Subject: RE: [ccp4bb] .getTwoTheta() in DiffractionImage library Dear Georg, Normally the getTwoTheta function should pick up the angle information from the image header. Obviously in

[ccp4bb] FW: [ccp4bb] 2mhb

Thanks, Mitch - this explains it. So it is a remediation issue, because I READ the remediated file remarks in search for an answer, and there is NO more corresponding REMARK 3. Now, I don't want to be more of a pest than usual, but I am slowly getting worried about this remediation business. Wh

  1   2   >