[ccp4bb] Fwd: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

-- Forwarded message - From: Arpita Goswami Date: Sun, Sep 8, 2024, 03:11 Subject: Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O To: John R Helliwell Dear Dr. John and others, Good day! Thank you all for the clarifications, corrections

[ccp4bb] Fwd: [ccp4bb] Crystal optimization

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

[ccp4bb] Fwd: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, Unfortunately, I did not see that the latest binary update was from 2008. I do not have access to any newer binaries for Linux, as I'm on MacOS. Maybe you can use the MineProt software from the quote I mentioned previously to (in a roundabout way) accomplish the CIF file generation? "“

Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 -- Forwarded message - From: Nicholas Clark mailto:ndcla...@buffalo.edu>> Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot an

[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

-- Forwarded message - From: Nicholas Clark Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 To: Julia Griese Julia, I have the same issue with PyMOL. After it opens the blank session, if you return to the file explorer an

[ccp4bb] Fwd: [ccp4bb] Another folding AI

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Another folding AI Date: November 5, 2022 at 12:13:04 PM EDT To: "Nave, Colin (DLSLtd,RAL,LSCI)" mailto:colin.n...@diamond.ac.uk>> As notable a scientist as Maxwell was, he also has been ha

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

] Fwd: [ccp4bb] Validation of structure prediction Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers, etc. I would definitively

Re: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

04 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers,

[ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers, etc. I would definitively recommend everybody to go through the model in detail a

[ccp4bb] Fwd: [ccp4bb] Co-crystallization and thermal shift assay

Hello, we had an interesting case in the lab many years ago... Using the shift-assay, a student managed to identify conditions that markedly stabilized the protein of interest. To cut a long story short, in the end it turned out conditions were identified that gave monomers while the biologic

[ccp4bb] Fwd: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

in case it might be of interest for someone @CNB: > Begin forwarded message: > > From: Bjørn Panyella Pedersen > Subject: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane > Proteins (Denmark) > Date: 5 February 2021 at 17:20:38 GMT+1 > To: CCP4BB@JISCMAIL.AC.UK > Reply-To: Bjørn

[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

Agreed. In fact, as a matter of course, when die Rechnung arrives I endeavor to head for die Tur… > > > >> On 20 Oct 2020, at 10:23 AM, Schreuder, Herman /DE >> wrote: >> >> Looks more like crowd-phishing to me! 😉 >> The original message did not make it through my spam filter and it may not

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Guys, Thanks for all the help. I figured out what's wrong with the sequence file. I had accedently entered an "X' to one of the sub-chains. Cheeres ! Gihan To unsubscribe from the CCP4BB list, click the following link: h

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

, this is not a mutation at all but points to the origin of this virus. /Michel. From: CCP4 bulletin board On Behalf Of Carter, Charlie Sent: March 21, 2020 7:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19 Begin forwarded message: From: "char

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] CCP4BB vs COVID19 Date: March 21, 2020 at 8:07:53 AM EDT To: James Holton mailto:jmhol...@lbl.gov>> Brilliant post, James. Thanks so much! I also find what you describe interesting, because

[ccp4bb] Fwd: [ccp4bb] Fw: protein protein interactions

Dear Careina, I would recommend you our partner-specific binding site predictor: BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the binding site of the two partners. http://bipspi.cnb.csic.es/xgbPredApp/ Kind regards, Ruben Quoting "careinaedgo...@yahoo.com" <0

Re: [ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

FliS and FliC Artem On Sun, Nov 10, 2019, 03:42 Gianluca Cioci wrote: > ps: the 3D structure > of the complex should > be solved at high resolution > > ;o) > > > > > Dear All, > > I am looking for examples of two small proteins A and B that can form a > tight complex AB. > Each protein should

[ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

ps: the 3D structure of the complex should be solved at high resolution ;o) Dear All, I am looking for examples of two small proteins A and B that can form a tight complex AB. Each protein should be straightforward to express in E.coli, well folded and stable in the isolated form. Also, if

[ccp4bb] Fwd: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

-- Forwarded message - From: Daniel M. Himmel, Ph. D. Date: Mon, Aug 5, 2019 at 12:45 PM Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ To: Pentagonal phosphate geometry would be a transition state, except that three oxygens woul

[ccp4bb] Fwd: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Date: July 19, 2019 at 1:32:53 PM EDT To: Patrick Loll mailto:pjl...@gmail.com>> Hi Pat, I, too have fallen into this rabbit hole while Mark Ro

[ccp4bb] Fwd: [ccp4bb] AKTA FPLC fractionation peak by peak

Thank you both for your answers! *Upasana* - the chromatogram was randomly selected to ilustrate the point - we do a careful equilibration of the column and degas the mobile phase(s) before starting. I'm not really sure what you mean by oligomeric state of the protein - we are working with complex

Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

This can be done at Diamond I23 beamline. https://doi.org/10.1016/j.nimb.2016.12.005 Best regards, Jan Dne 16.02.2019 v 18:49 Patrick Loll napsal(a): > S has about 0.56 anomalous electrons at 8 keV, whereas P has about > 0.44. This is a small difference between two weak signals—unlikely to > gi

[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This is a small difference between two weak signals—unlikely to give a clear result. If you could get to the sulfur & phosphorus edges, then you could (in principle) answer this, but that’s a very hard experiment to accompl

[ccp4bb] Fwd: [ccp4bb] VERY old mtz file..

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] VERY old mtz file.. Date: November 14, 2018 at 10:16:23 AM EST To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> I’ve found this thread to be most interesting and out of near pathologica

[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

Begin forwarded message: [cid:image001.png@01D42A41.AE0B8B60] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Fwd: [ccp4bb] suggestions on a microscope for Crystallography

-- Forwarded message -- From: Daniel M. Himmel, Ph. D. Date: Wed, Mar 7, 2018 at 12:23 AM Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography To: Chandramohan Kattamuri My best experience was with Leica microscopes, such as the S6E. Leica microscopes have optic

Re: [ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

Hi, Yuvraj, I can suggest two methods: 1) collect a dataset at room temperature 2) crystallize your protein in cryoconditions. That is add 25 % of glycerol to your crystallization conditions and perform small optimization in terms of precipitant concentration. 2017-12-29 7:55 GMT+03:00 Prem Praka

[ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

-- Forwarded message -- From: Prem Prakash Date: Fri, Dec 29, 2017 at 10:22 AM Subject: Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings To: zaigham mahmood khan Hi, Yuvraj Initially I also faced similar problems, then I tried various combin

Re: [ccp4bb] Fwd: [ccp4bb] shadow at the edge

Depends on the geometry of the goniometer/pin relative to the X-ray beam. If the pin is too close, it will possibly cast a shadow. If the pin is aligned at a shallow angle relative to the X-ray source beam, the pin or the goniometer may get in the way regardless of how far away the crystal is from

[ccp4bb] Fwd: [ccp4bb] Contouring 2Fo-Fc map, large blobs in Fo-Fc

I searched for 4 copies, but Phaser only found 3. It's possible there is an additional copy of the molecule in the ASU On Wed, Apr 26, 2017 at 2:40 AM, Randy Read wrote: > Dear Roger, > > You didn’t mention this, but did you search for 2 copies (or an even > number of copies) and, if so, did Pha

[ccp4bb] Fwd: [ccp4bb] No improvement in R-factor after Refmac.

-- Forwarded message -- From: Polisetty Satya Dev Date: Mon, Mar 20, 2017 at 1:35 PM Subject: Re: [ccp4bb] No improvement in R-factor after Refmac. To: Sudipta Bhattacharyya Hi, I had tried running xtriage but it does not show any sign of NCS. But pointles is showing the followi

[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa Reply-To

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

P4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Anindito Sen mailto:andysen.to...@gmail.com>> Sent: Sunday, December 11, 2016 12:45:16 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit G

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

Phishing spam. Don't click. T Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 11 Dec 2016, at 17:45, Anindito Sen wrote: > > Guys > > are you all receiving the same??? What on earth is this ? > > Andy > > > >> Begin for

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

The Nigerian Prince wants your money. Get Outlook for Android<https://aka.ms/ghei36> From: CCP4 bulletin board on behalf of Anindito Sen Sent: Sunday, December 11, 2016 12:45:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Remittance

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

Sorry - didn't realise that was going out to the whole list, and just made a liar out of myself. Will bow out now. On 2016-11-10 10:20, Tristan Croll wrote: Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income, low

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

Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income, low-employment environment myself this has the ring of truth to it. I totally agree with you (and worry just as much) regarding the proliferation of anti-exper

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

Hi Tristan, I’m afraid I don’t get the logic in the article you sent. In this case the farmers who are crying for the attention of the people in shiny palaces have voted for one who lives in golden mansions. For me the really worrying thing here is how can so many people be misled by a false

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

From letters in yesterday’s Guardian:- today is 9/11 Make America grate again > On 10 Nov 2016, at 08:00, Marjolein Thunnissen > wrote: > > Dear Bill, > > I fully agree with you, awareness has to be spread and one should not ignore > politics completely, especially when there are so stron

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

In the interests of promoting understanding... the link below is to an article on what is ostensibly a comedy website and contains a bit of coarse language, but nevertheless is quite possibly the most insightful exposition of the situation I've come across. The two-sentence synopsis: don't thin

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

Dear Bill, I fully agree with you, awareness has to be spread and one should not ignore politics completely, especially when there are so strong anti-intellectual (anti-science) statements out there. best regards Marjolein On 10 Nov 2016, at 04:17, William G. Scott mailto:wgsc...@ucsc.edu>>

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 ...

6, 12:25 Subject: Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes!), Illinois: "You can fool all of the people some of the time, and some of the people a

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

rom:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ian > Tickle > *Sent:* Wednesday, November 9, 2016 2:25 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity > ... > > > > > > Abraham Lincoln wa

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

@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, November 9, 2016 2:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes

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

Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes!), Illinois: "You can fool all of the people some of the time, and some of the people all of the time, but you cannot fool all the people all the time." https://www.academia.edu/2506

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

A note of optimism ... in Italy we could survive to Berlusconi ... Best, Roberto. Inizio messaggio inoltrato: > Da: "William G. Scott" > Data: 09 novembre 2016 06.37.30 GMT+01.00 > A: CCP4BB@JISCMAIL.AC.UK > Oggetto: [ccp4bb] just out of totally idle curiosity ... > Rispondi a: "William G. Scot

Re: [ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

Dear Chen, On Thu, May 14, 2015 at 10:05:05AM -0400, Chen Zhao wrote: > Thanks a lot for your reply! I am a little surprised to learn that the > centrosymmetry is always considered as a point groups symmetry component. > That might explain why all the anomalous data I have seen have higher Rmeas >

[ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

From: Chen Zhao Date: Thu, May 14, 2015 at 10:04 AM Subject: Re: [ccp4bb] XDS Rmeas in space group determination To: Kay Diederichs Hi Kay, Thanks a lot for your reply! I am a little surprised to learn that the centrosymmetry is always considered as a point groups symmetry component. That migh

[ccp4bb] Fwd: [ccp4bb] XDS INP

Dear Lu you can freely download the tutorial from here: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page You can check if your detector is supported here: http://xds.mpimf-heidelberg.mpg.de/html_doc/detectors.htm Best Fulvio > Il giorno 07/mag/2015, alle ore 10:33, luzu

[ccp4bb] Fwd: [ccp4bb] Structural classification

Dear Deepa, When classifying structures you need to first ask "why?". For example, if you want to get an idea about evolutionary relations, you must try to find their DNA sequences and analyse those in the light of a multiple sequence alignment (MSA) that follows the protein alignment. In phar

[ccp4bb] Fwd: [ccp4bb] how to recover my data

Inizio messaggio inoltrato: > Da: "Fulvio Saccoccia, Sapienza" > Oggetto: Re: [ccp4bb] how to recover my data > Data: 05 marzo 2015 13:48:34 CET > A: Smith Lee > > Dear Smith, >It is curious; I am not sure about what I am going to suggest since I > never had that problem but the simplest

Re: [ccp4bb] Fwd: [ccp4bb] adjusting bad Ramachandran angles

Jeremy, apparently I was unclear (and possibly moving off-topic) since I got other emails off list about this. I did not mean to imply that I would use Ramachandran restraints to fix a register error since this obviously needs to be addressed in real space. Rather, inspection of the Ramachandran

[ccp4bb] Fwd: [ccp4bb] adjusting bad Ramachandran angles

Dear Kevin Please re-read my earlier email paying particular attention to the words "explicitly" and "expressly". To my mind, the notion of moving a Ramachandran outlier by moving a dot across a graph (which you feel is a danger) is identical to expressly forcing that residue into a favoured Ra

Re: [ccp4bb] Fwd: [ccp4bb]

And what is the NC translation vector (in fractional coordinates)? If it is x, 1/2, z then your SG could be P2 - the NC translation will generate absences along the 0k0 diffraction vector. Eleanor On 28 November 2014 at 14:01, rohit kumar wrote: > yes...right know its monoclinic (p21) space g

Re: [ccp4bb] Fwd: [ccp4bb]

yes...right know its monoclinic (p21) space gp. On Fri, Nov 28, 2014 at 7:24 PM, Eleanor Dodson wrote: > Are you testing all SGs? for your known point group? > > Eleanor > > On 28 November 2014 at 13:34, rohit kumar wrote: > >> >> >> Dear all, >> >> i am solving a structure of 2.5 A resolution

Re: [ccp4bb] Fwd: [ccp4bb]

Are you testing all SGs? for your known point group? Eleanor On 28 November 2014 at 13:34, rohit kumar wrote: > > > Dear all, > > i am solving a structure of 2.5 A resolution by PHASER but every time i > got this following warning. > > $TEXT:Warning: $$ Baubles Markup $$ > > ---

[ccp4bb] Fwd: [ccp4bb]

Dear all, i am solving a structure of 2.5 A resolution by PHASER but every time i got this following warning. $TEXT:Warning: $$ Baubles Markup $$ - Large non-origin Patterson peak indicates that translational NC

Re: [ccp4bb] Fwd: [ccp4bb] B-factor blurring

Dear Mike, I am not sure what you mean by 'reference'. When you multiply your data with exp(-Bs^2) with B > 0 you weight your reflections depending on resolution so that high resolution data (probably including noise) are supressed while low resolution data a underlined. Using the term 'B' with it

[ccp4bb] Fwd: [ccp4bb] B-factor blurring

My sincere thanks to all who are responding to my request below. To be explicit, my question relates to B-factor blurring (+B correction), not to B-factor sharpening (-B correction). thanks Mike Begin forwarded message: > From: Mike Lawrence > Subject: [ccp4bb] B-factor blurring > Date: 18

[ccp4bb] Fwd: [ccp4bb] : MTZ for a protein fragment and R factors, Masking and Maps

George, Remember that scattering from every point in the cell contributes to every reflection; the R-value is a global metric of agreement between the model and the data. Hence, calculating the R-value for a few selected residues is not a sensible thing to do, unless you want to ask how well yo

[ccp4bb] Fwd: [ccp4bb] phaser issue MR

Dear all, thank you for your suggestions, I finally fix the problem as follows. I'll write a summary here for future reference. 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

On Tue, Mar 04, 2014 at 01:33:58PM +0800, wu donghui wrote: > > Here I attached the config.log file for your help. I have tried to use > either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1), or There is some confusion here. The number 4.

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

On Tuesday, 04 March 2014 01:33:58 PM wu donghui wrote: > Dear Tim, > > Here I attached the config.log file for your help. I have tried to use > either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1), or > g++-4.2.1(/Applications/Xcode.app/

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

BTW, we got one report from a sysadmin who has built ccp4 using Clang (Apple compiler 5.0) + gfortran 4.8 from: http://gcc.gnu.org/wiki/GFortranBinaries#MacOS So it's likely that at least one lab is using CCP4 built with Clang. I'm not aware of any benchmarks, though. Marcin On Mon, Mar 03, 2014

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

Hi I think you must be doing something wrong if you can't run Mosflm from the ccp4 binary install - it runs for me. How are you trying to run it? If you need the compilers to build Mosflm then I *very* strongly recommend using the compilers I mentioned in my earlier e-mail - they are what the

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51

[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

-- Forwarded message -- From: wu donghui Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from b

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

Hi If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing either the High Performance Computing gcc/gfortran or investing in the Intel Compilers. http://hpc.sourceforge.net/ http://software.intel.com/en-us/intel-compilers (if you have ) Performance-

[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

-- Forwarded message -- From: wu donghui Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify

[ccp4bb] Fwd: [ccp4bb] out of topic: liquid handling robot for optimisation

I would like to thank all the people who answered my question. I can forward a summary upon request. Best, Valerie Le 29 nov. 2013 à 11:02, Valerie Biou a écrit : > Dear all, > > We are looking for a robot to mix solutions and prepare optimisation plates > for crystallisation. > Ideally, t

[ccp4bb] Fwd: [ccp4bb] Add C-terminal amide - solved

Thanks for the help, the issue is solved. Here a short summary in case anybody else has the same problem: 1) Add pointer atom in Coot NH2 and create link to C-terminal residue 2) create cif file with correct link description 3) modify LINK record in PDB to correct residues/ link name 4) refine in

[ccp4bb] Fwd: [ccp4bb] move ligand to fit the density in coot

Dear Wei, It seems that coot detects some discrepancies between cif file and your ligand. It is not uncommon that the program used to generate your ligand pdb produces atom definitions that are not correctly read by programs used to generate restrains, such as PRODRG. In order to overcome the

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

: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ethan A Merritt [merr...@u.washington.edu] Sent: 03 October 2013 00:53 To: ccp4bb Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 On Wednesday, 02 October, 2013 17:31:06 wtempel wrote: > Tim,

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

sage ------ > From: Tim Gruene > Date: Wed, Oct 2, 2013 at 4:13 PM > Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 > To: wtempel > Cc: CCP4BB@jiscmail.ac.uk > > > Dear W., > > if P21 is a proper subgroup of C2221, scaling a P21 data se

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

do this. HTH D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com] Sent: 02 October 2013 22:31 To: ccp4bb Subject: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 Tim, I agree with your

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

P21 with properly transfered free flags. I just do not know how to accomplish that transfer. W. -- Forwarded message -- From: Tim Gruene Date: Wed, Oct 2, 2013 at 4:13 PM Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel Cc: CCP4BB@jiscmail.ac.uk -

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

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear W., if P21 is a proper subgroup of C2221, scaling a P21 data set in C2221 would try to make non-equivalent reflections equal, would it not? I would reintegrate the data in the correct point group and scale in the correct space group. Best, Tim

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

Hello Appu and Boaz, my suspicion arises from failure to refine (as in reducing crystallographic R-factor from the 40%s) a related, virtually isomorphous crystal structure in the original C2221 setting. Scaling statistics are very nice even in C2221. If I drop the symmetry to P21, the R-factor drop

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

Thanks, Randy. Molrep must be failing due to some other flaw in my procedure, as it clearly uses the P21 cell, as evidenced by the output CRYST1 and ViewHKL in qtRView of ccp4i. Can you suggest any alternative procedures that would expand that C-centered data set into the primitive setting? W. ---

Re: [ccp4bb] Fwd: [ccp4bb] tricky mr problem

I've had good luck using the CCP4 DM program PARROT to improve poor initial MR maps with twinned data. (Based on some suggestions from this bb.) I think it works especially well if you have a lot of NCS symmetry, but it's worth a try, and doesn't take long. Cheers, ___

[ccp4bb] Fwd: [ccp4bb] tricky mr problem

I would try phase improvement, especially since you have two molecules per a.u. In other words averaging, solvent flattning, histogram matching. The best way is to start at low(er) resoltuion and extend to the highest resolution vailable. The best criterium for success is a improved and interpretab

[ccp4bb] Fwd: [ccp4bb] CCP4 Support 32 bit OSX - request for feedback

PS Please consult http://support.apple.com/kb/ht3696 for how to determine your CPU type. Many thanks -- Eugene Begin forwarded message: From: Eugene Krissinel mailto:eugene.krissi...@stfc.ac.uk>> Date: 12 July 2013 12:47:26 GMT+01:00 To: mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] CCP4 Sup

[ccp4bb] Fwd: [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

Dear Rain Field, A new xia2 release is now available please see: http://xia2.blogspot.com for details. This version should be included in the next CCP4 update. Once again apologies for the inconvenience. Best wishes, Graeme On 4 July 2013 08:18, Graeme Winter wrote: > Dear Rain Field, > >

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