Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

n program) does not come with > Shelx program executables, and I could not locate the installers for the > shelx software on Windows. > > Hence I am running SHELXL in line command mode on my Linux box. > > Thank you again, > > Fred. > On 12/03/2024 10:12, David Waterman wrote:

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

Hi Fred, I find Olex2 and shelxle are both convenient interfaces to SHELXL refinement, that take care of some of the details of .ins file format for you. However, maybe you are stuck in the starting gate, depending on what is malformed in your input file. Where did your input files come from?

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Harry, I remember the C222/P622 confusion from some of Phil's old slides, and I thought that was an impressive case! It probably appears in a few places on the internet, but one I found just now is slide 15 of this presentation:

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Huw, This is tricky because in certain situations the cell parameter esds can get lost. For example if best_unit_cell= has been passed during scaling or merging with DIALS. Or, if cell parameter refinement was done using the LFBGS engine, in which case the esds are not calculated. Cheers

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

Norman Stein's article at the back of this newsletter is the one I like! https://legacy.ccp4.ac.uk/newsletters/newsletter47/newsletter47.pdf -- David On Wed, 14 Feb 2024 at 15:14, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Good afternoon all, > >

Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

Hi, The latest version of DIALS may be able to read this format. If you can send me an image off-list I would be happy to check. Once in DIALS, it also may be possible to export the dataset in CBF format. Best wishes David On Tue, 10 Oct 2023, 06:28 Vyankatesh Rajmane, wrote: > Dear all, >

[ccp4bb] DEADLINE APPROACHING: DLS/CCP4 data analysis workshop 2023

Hi folks, Please be reminded that the deadline for applying to attend this year's DLS/CCP4 workshop is *Monday 9th October at 17:00 UK time*. Best wishes, -- David On Tue, 26 Sept 2023 at 17:07, David Waterman wrote: > We are pleased to announce that the 10th joint Diamond-CCP4 Works

[ccp4bb] DLS/CCP4 data analysis workshop 2023

We are pleased to announce that the 10th joint Diamond-CCP4 Workshop on MX data collection and structure solution is now open for applications! Bringing together leading experts in the field of MX to teach best practice in data collection and analysis, this course is aimed at PhD students,

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

Of course the proper answer should be to fix dimple to read mmCIF (for which I would also recommend gemmi) -- David On Wed, 20 Sept 2023 at 16:35, David Waterman wrote: > gemmi convert --shorten 7qgf.cif foo.pdb > > ? > -- David > > > On Wed, 20 Sept 2023 at 15:57, Winte

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Looks like PDB files have been outlawed because mmCIF > > But dimple needs PDB files > > cif2pdb says nope > > Grey-Area

Re: [ccp4bb] About the A in AI

Bard (draft 2 of 3) Sure, here is a critical review report rejecting a scientific paper reporting that the 1.0 angstrom crystal structure shows that psiX is a trimethylating enzyme: Title: Critical Review Report: PsiX is not a Trimethylating Enzyme Author: Bard Date: 2023-05-12 Introduction

[ccp4bb] Continued issues with CCP4BB

Hi folks, We are continuing to experience some issues with the BB. Jiscmail are aware of the problems earlier that led to automatic deletion of ~1400 subscribers and we hope they will reinstate those subscriptions soon. In the meantime, there appear to be some odd effects like "Rejected posting

Re: [ccp4bb] Is this Spam? This looks like Spam.

It looks like there were about 1400 automatic deletions like this across the CCP4BB. Jisc are aware of the issue, which affects multiple lists (see https://twitter.com/jiscmailhelp/status/1612756687919742979). We have requested that these deletions be reverted, but we have not yet heard if this

[ccp4bb] Test message

This is a test message to explore issues reported about automatic removals from the BB. -- David To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

[ccp4bb] CLOSING SOON: DLS/CCP4 data analysis workshop 2022

Hi all, The application period for the DLS/CCP4 workshop closes 17:00 (UK time) on Tuesday the 20th. Don't leave it to the last minute to apply! :) Cheers -- David On Tue, 13 Sept 2022 at 12:02, David Waterman wrote: > Hi folks, > > A reminder: there is one week left to apply for th

[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 data analysis workshop 2022

Hi folks, A reminder: there is one week left to apply for this year's DLS/CCP4 workshop. Please see below for details. Best wishes -- David On Tue, 6 Sept 2022 at 13:31, David Waterman wrote: > We are pleased to announce that the 9th joint Diamond-CCP4 Workshop on MX > data coll

[ccp4bb] DLS/CCP4 data analysis workshop 2022

We are pleased to announce that the 9th joint Diamond-CCP4 Workshop on MX data collection and structure solution is now open for applications. Bringing together leading experts in the field of MX to teach best practice in data collection and analysis, this course is aimed at PhD students, postdocs

[ccp4bb] Digital Research Infrastructure (DRI) Retreat March 2022

Posted on behalf of Gillian Sinclair. -- *From:* Gillian Sinclair *Sent:* 09 March 2022 10:10 *To:* CCP4 *Subject:* [CCP4] For dissemination - Digital Research Infrastructure (DRI) Retreat March 2022 Hello I would be grateful if you could please disseminate this

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

Hi James, What you wrote makes lots of sense. I had not heard about Rsleep, so that looks like interesting reading, thanks. I have often used Rfree as a simple tool to compare two protocols. If I am not actually optimising against Rfree but just using it for a one-off comparison then that is

[ccp4bb] LAST CHANCE TO APPLY: DLS/CCP4 data analysis workshop 2021

Hi folks, The application deadline for this year's online DLS/CCP4 workshop is today, 17:00 UK time. If you haven't yet applied but want a chance to come you still have a few hours to submit your application! Cheers -- David On Fri, 24 Sept 2021 at 13:23, David Waterman wrote: > Hi fo

[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 data analysis workshop 2021

Hi folks, A reminder: there is one week left to apply for this year's DLS/CCP4 workshop. Please see below for details. Best wishes -- David On Tue, 14 Sept 2021 at 16:12, David Waterman wrote: > We are pleased to announce that the 8th joint Diamond-CCP4 Workshop on MX > data coll

[ccp4bb] DLS/CCP4 data analysis workshop 2021

We are pleased to announce that the 8th joint Diamond-CCP4 Workshop on MX data collection and structure solution is now open for applications. Bringing together leading experts in the field of MX to teach best practice in data collection and analysis, this course is aimed at PhD students,

Re: [ccp4bb] Anomalous signal to noise details

vent > content screening, etc. ;-) Feel free to ask for more. > > Best regards, > > Petr > > > > PS: Although tested on a number of cases, the command line is more stable > than the GUI. > > > > *From:* CCP4 bulletin board *On Behalf Of *David > Waterman >

[ccp4bb] Anomalous signal to noise details

Hi folks The paper "Substructure solution with SHELXD " (Schneider & Sheldrick, 2002) describes how data can be truncated at the resolution at which [ΔF to its estimated > standard deviation as a function of the resolution] drops

[ccp4bb] ONE DAY TO APPLY: DLS/CCP4 Data Collection and Structure Solution Workshop, 30 Nov - 11 Dec 2020

> > Dear all, > > Please note there is now just one day left to apply for this year's > DLS/CCP4 workshop (details below)! > > Best wishes > -- David > > > On Tue, 6 Oct 2020 at 10:03, David Waterman wrote: > >> We are pleased to announce that the 7th

[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 Data Collection and Structure Solution Workshop, 30 Nov - 11 Dec 2020

Dear all, Please note there is one week left to apply for this year's DLS/CCP4 workshop (details below). Best wishes -- David On Tue, 6 Oct 2020 at 10:03, David Waterman wrote: > We are pleased to announce that the 7th joint Diamond-CCP4 Workshop on > MX data collection and str

[ccp4bb] DLS/CCP4 Data Collection and Structure Solution Workshop, 30 Nov - 11 Dec 2020

We are pleased to announce that the 7th joint Diamond-CCP4 Workshop on MX data collection and structure solution is open for applications. Bringing together leading experts in the field of MX to teach best practice in data collection and analysis, this course is aimed at PhD students, postdocs

Re: [ccp4bb] font issues in imosflm under xubuntu 18

Dear Wim, Are you using imosflm distributed by CCP4, the LMB build, or something else? I don't see the same problem with the version in the current CCP4 on standard Ubuntu 18.04.5 (not xubuntu). I do remember seeing similar issues in the past though. It used to be the case that having the

Re: [ccp4bb] diffdump in CCP4 7.1

Dear Jan, If you just want to generate XDS input files then Tim's suggestion of using generate_XDS.INP is exactly right. If you or others miss the functionality of diffdump in CCP4 for reading image headers, then I suggest this command as a replacement: dials.show /path/to/image_file This is

Re: [ccp4bb] Two scientist / software developer positions on neutron diffraction at RAL

Dear all, Please be reminded about the two posts advertised below. You can ignore the closing date of 2nd August shown here - the first post has been adjusted to close on the 9th August as well, to be in line with the other position. Best wishes -- David On Thu, 23 Jul 2020 at 19:25, David

[ccp4bb] Two scientist / software developer positions on neutron diffraction at RAL

Dear all, The STFC Scientific Computing Department and ISIS neutron source are looking for two programmer scientists, who will develop the next generation of single-crystal neutron diffraction analysis software for the time-of-flight technique. The software will extend the DIALS data processing

Re: [ccp4bb] CCP4I TERMINATION STATUS 0 "child process exited abnormally"

Dear Adewumi Adeyeye, The ccp4i interface to xia2 is no longer supported and I suspect it might be completely broken. You should be able to process your data using the ccp4i2 interface though. Best wishes -- David On Wed, 22 Jul 2020 at 10:32, Adewumi Adeyeye <

Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

Hi all, Please be reassured that there are no plans at the moment to remove programs from CCP4, at least none of which I am aware. The newer GUIs might not provide interfaces to run all of these programs, but they are still there to run from the command line. There is currently no good reason to

Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

; > > The advantage of multiplicity/redundancy is that it does not mention what > is multiple or redundant and that one can refer to the program > documentation for an exact definition. Since most people are happy with the > multiplicity/redundancy they grew up with, that is the way it will

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

I should say I also saw flashing during screen share in a Zoom call. This might also be because only a single window was shared, and this window overlaid another on the speaker's desktop. I saw flickering glimpses of the Word document underneath the window the speaker was trying to share. --

Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Hi Herman, I like the idea of MPR, but I continue to worry about the term "measurement". The intensity associated with a particular reflection is a fit based on a scaling model, and ultimately, depending on your integration software, may be linked to a weighted sum of two raw measurements: the

Re: [ccp4bb] unable to launch ccp4 old interface on mac

Dear Luca, Thanks for your email. CCP4i is no longer supported by the CCP4 Core Team. The main interfaces in CCP4 7.1 are CCP4i2 and the CCP4cloud client. However, ccp4i is still included with the suite, as you found, and can be run from the command line if you source the CCP4 environment in a

Re: [ccp4bb] number of frames to get a full dataset?

It is hard for us to rise above these cultural differences, so perhaps the adoption of a third, precisely-defined, and neutral term is indeed warranted. MPR seems a good start, but it forces us to think about what we mean by measurement. My feeling is that a diffraction spot can be measured in

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Ok, the analogy is not great because most reflection data sets have some "fault tolerance" whereas RAID 0 does not. But the point is that anything that is not an exact copy and brings actual information should not be considered "redundant" On Tue, 30 Jun 2020, 09:00 Da

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Reflections are as "redundant" as the disks in a RAID 0 array On Tue, 30 Jun 2020, 02:49 James Holton, wrote: > What could possibly go wrong? > > -James Holton > MAD Scientist > > On 6/29/2020 6:17 PM, Edward A. Berry wrote: > > Now can we get rid of all the superfluous disks in our RAID? Or at

Re: [ccp4bb] What refinement programs are fully Open Source?

Dear Ethan, The copy of xia2 that I have on my machine says at the top of the source > # Copyright (C) 2013 David Waterman > # > # This code is distributed under the terms and conditions of the > # CCP4 Program Suite Licence Agreement as a CCP4 Application. This surprise

Re: [ccp4bb] CCP4 7.1 released

tegrated Approaches to Macromolecular > Structure Determination), as well as by our industrial users. > Final remarks > > CCP4 7.1 is out now. A considerable effort has been put into developing, > compiling, bundling and testing its many new components and

Re: [ccp4bb] Vote for cryoEM

If this were a tweet, I would like and retweet it. -- David On Tue, 31 Mar 2020 at 20:07, Rangana Warshamanage wrote: > What's the purpose of this contest? > Why one method needs to be crowned over another? > > Rangana > > On Tue, Mar 31, 2020 at 7:01 PM Gloria Borgstahl > wrote: > >> I

[ccp4bb] PRACE fights against COVID-19 - fast track call for proposals is open!

Posted on behalf of Dr. Marc Baaden: Dear colleagues, the Partnership for Advanced Computing in Europe (PRACE) is welcoming > project proposals requesting computing resources to contribute to the > mitigation of the impact of the COVID-19 pandemic. > This call for proposals will follow a fast

Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help fill the testing shortfall in the UK (see https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers). This is a worthy initiative, if it is accepted (logistics are the main problem). The structural biology

Re: [ccp4bb] Running CCP4_Blend on Mac

Dear Ravi Kumar If I remember correctly, Blend requires the path to the executable Rscript rather than R. I can't check this now but I can look into it on Monday if you are still having trouble. Best wishes David On Fri, 6 Mar 2020, 21:02 Reddiravikumar Kumar, wrote: > Hi all, > > I am

Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Hi Eleanor, MTZ history is still useful, so from a recent xia2 run I can see (with mtzdmp): * HISTORY for current MTZ file : From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT It isn't possible to tell that the data were actually scaled in DIALS too though, apart from the

[ccp4bb] Study Weekend 2020 live stream

Hi everybody, For those wishing to view the CCP4 Study Weekend live stream, please click here: https://ukri.zoom.us/j/195886424 We are about to start. Cheers -- David To unsubscribe from the CCP4BB list, click the

Re: [ccp4bb] CCP4 Computational Scientist

Dear all, Here's a reminder that CCP4 is looking for a computational scientist to investigate corrections for electron diffraction data. Job details are below. Best wishes -- David On Mon, 23 Sep 2019 at 13:20, Eugene Krissinel wrote: > Dear All, > > CCP4 is looking for computational

[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2019

Dear all, Please note the application period for this year's DLS/CCP4 workshop closes *this Friday*. Best wishes -- David -- Forwarded message - From: David Waterman Date: Tue, 1 Oct 2019 at 15:30 Subject: DLS/CCP4 data analysis workshop 2019 To: PhD students, postdocs

[ccp4bb] DLS/CCP4 data analysis workshop 2019

with crystals and/or data will be given priority. Best wishes on behalf of the organisers, David Waterman (CCP4) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB

Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

archive.org suggests the database existed up to December 2018, but appears to be no more. What to do when scientific resources associated with published papers disappear like this? It seems to be a problem that is not very well addressed. Cheers David On Fri, 20 Sep 2019, 04:26 Murpholino

Re: [ccp4bb] Recommendations for a Desktop Computer for Crystallography Programs

Dear Matthew, One factor that might influence your decision is whether you want to do data processing on that computer or not. Large data sets collected on e.g. EIGER detectors may challenge a standard Linux laptop. To get the best out of DIALS I would certainly recommend no less than 16 GB of

[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2018

-- David On Wed, 19 Sep 2018 at 14:17, David Waterman wrote: > PhD students, postdocs and early career scientists, > > Please consider applying for the fifth joint DLS/CCP4 workshop on MX data > collection > and structure solution, to be held at Diamond Light Source, UK from the 2

[ccp4bb] FINAL WEEK: DLS/CCP4 data analysis workshop 2018

Dear all, Just one week remains to apply for the DLS/CCP4 December 2018 workshop (see below). Applications are judged on merit and require a letter of support from a supervisor. Best wishes, David On Wed, 19 Sep 2018 at 14:17, David Waterman wrote: > PhD students, postdocs and early car

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

Hi Matthew, I'm a little late to the thread, but I thought I would still like to add DPF3b, kindly provided by Wolfram Tempel. This dataset is available on zenodo and forms the basis of a tutorial for using DIALS:

[ccp4bb] REMINDER: DLS/CCP4 data analysis workshop 2018

Two weeks remain to apply for the DLS/CCP4 December workshop. Applications are judged on merit and require a letter of support from a supervisor, so if you are interested please don't leave it too late to apply. Best wishes David On Wed, 19 Sep 2018 at 14:17, David Waterman wrote: >

[ccp4bb] DLS/CCP4 data analysis workshop 2018

, describe their projects and obtain a letter of support from a supervisor, so please do not wait until the last minute to apply! Those with crystals and/or data will be given priority. Best wishes on behalf of the organisers, David Waterman (CCP4

Re: [ccp4bb] Last few months updates, updated coot, ccp4i2, imosflm, etc

Dear Boaz, Jan, Currently the base version 7.0.0 is installed and all updates are then applied on top of this. This is very costly in terms of time and bandwidth. To mitigate this, a new mechanism is being developed by CCP4. A checkpoint version will be installed (something like minus 10 updates

Re: [ccp4bb] dials.image_viewer problem on Windows [CCP4 console]

Dear Rens de Vries, Sorry for the trouble. Can you please try the following? 1. Open the file C:\CCP4-7\7.0\InstallSetup.cmd in a text editor 2. Change the string "--skip-phenix-dispatchers" to "--skip_phenix_dispatchers" (i.e. last two dashes to underscores) 3. Save the file 4.

[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2017

Hi all, The application period for this year's DLS/CCP4 workshop has been extended by one week. So, if you are interested in joining us this December, please apply by 10 am on Monday the 16th October. Thanks! -- David On 12 September 2017 at 21:44, David Waterman <dgwater...@gmail.com>

[ccp4bb] DLS/CCP4 data analysis workshop 2017

and obtain a letter of support from a supervisor, so please do not wait until the last minute to apply! Those with crystals and/or data will be given priority. Best wishes on behalf of the organisers, David Waterman (CCP4)

[ccp4bb] Senior scientist in crystallography - NovAliX

Please see the attached, posted on behalf of Carole Meyer at NovAliX. Reply to post...@novalix-pharma.com Poste Senior Scientist crystallography Saclay NovAliX.pdf Description: Adobe PDF document

Re: [ccp4bb] Bug in latest COOT

Dear Oliver, I just tried this on 1D2F using computers at Diamond (Red Hat Enterprise Linux Workstation release 6.8 (Santiago)) with coot in CCP4 7.0.025 and all was well. Could you send me, or point me towards, a PDB that causes the issue - and exact instructions for how to trigger it? Cheers

[ccp4bb] Scientist Biacore SPR

Posted on behalf of Carole Meyer at NovAliX *Job offer* Position: Scientist Biacore SPR (Surface Plasmon Resonance) (M/F) Type of contract: Temporary contract (12 months) - Starting date: November 2016 Employer: NovAliX is a company specialized in outsourced research

[ccp4bb] TWO DAYS REMAIN to apply for the DLS/CCP4 data analysis workshop 2016

submitted their applications. Best wishes, -- David On 23 September 2016 at 16:27, David Waterman <dgwater...@gmail.com> wrote: > Dear all, > > Please be aware that the application period for this year's DLS/CCP4 > workshop closes on the 7th October. Thanks to all those

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

Dear Debasish, Unless I have misunderstood your query this is very much on-topic and sounds a lot like the sort of thing PISA is designed to give you. See http://www.ccp4.ac.uk/html/pisa.html Cheers -- David On 10 March 2015 at 10:25, Debasish Kumar Ghosh dkgh...@cdfd.org.in wrote: Dear All,

Re: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling

Hi Jacob, My intuition for the line fit case was exactly the opposite to yours. My reasoning is a sort of physical one. If you imagine the line as a stiff rod with hooks for masses evenly spread along its length at 10 positions, then the object where you put 5 masses at positions 1 and 10 has a

Re: [ccp4bb] HKL2000 Display

Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan

Re: [ccp4bb] how to dump diffraction image header info?

Dear Takaaki, dxtbx provides a way to do this (see http://journals.iucr.org/j/issues/2014/04/00/jo5001/jo5001.pdf). It is available in ccp4-python (try 'import dxtbx'), however there is no script currently in CCP4 that uses this to print the header information. One could write such a script

Re: [ccp4bb] How to run CCP4 without source command

Hi all, Folmer's advice is exactly right. However, just for the curious I'd like to point out a way to run CCP4 programs without having to explicitly source a setup script. For example (and for demonstration purposes, ignoring the fact that $CCP4 is only defined when the environment is sourced)

[ccp4bb] 10 DAYS REMAIN to apply for the DLS/CCP4 data analysis workshop

://www.diamond.ac.uk/Home/Events/2014/Diamond-CCP4-Data-Collection-and-Analysis-workshop.html Many thanks for your interest David Waterman, on behalf of the organisers.

[ccp4bb] CCP4-6.4.0 Update 022

Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes: • BLEND: – update to version 0.5.9 Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the

[ccp4bb] REMINDER: apply now for the first DLS/CCP4 data analysis workshop

/Home/Events/2014/Diamond-CCP4-Data-Collection-and-Analysis-workshop.html Many thanks for your interest -- David Waterman

[ccp4bb] Save the dates for the first DLS/CCP4 data analysis workshop

of MX on data from your own crystals. For more details please check here: http://www.ccp4.ac.uk/schools/DLS-2014/ A further announcement will be made when the application pages are ready. Best wishes on behalf of the organisers, -- David Waterman (CCP4)

[ccp4bb] CCP4-6.4.0 Update 015

Dear CCP4 users, An update for the CCP4-6.4.0 series has just been released, consisting of the following changes: * BLEND: New program for optimum selection of multi-crystal datasets for merging * Documentation: Help for BLEND * CCP4i: BLEND interface and allow view of PNG files * Examples:

Re: [ccp4bb] error in starting imosflm

Hi Ian, Improving the CCP4 tests is a priority. We (the core team) have a project looking into that. If developers have their own tests for components of the suite that have not made it into the distribution, then we'd be happy to collect them for the new test set. Best wishes -- David On 29

Re: [ccp4bb] error in starting imosflm

Dear all, For experiments that involve switching between different versions of CCP4 you might like to try the CCP4Dispatchers scripts (see http://www.ccp4.ac.uk/html/CCP4Dispatchers.html). On a binary install of ccp4 6.4.0 these will have been generated automatically. For example, on my Linux

Re: [ccp4bb] Merging Data from Multiple Crystals

Dear Alex BLEND will be released soon through the CCP4 Updates. In the meantime, the easiest way to try it out is to install one of the nightly builds from here: http://www.ccp4.ac.uk/dev/nightly/. The usual warnings apply. What you obtain that way may not be (fully) tested, and may differ

Re: [ccp4bb] difference between polar angle and eulerian angle

This is a helpful introductory paper on the topic: http://journals.iucr.org/d/issues/2001/10/00/ba5006/ba5006.pdf -- David On 27 March 2014 06:11, Qixu Cai caiq...@gmail.com wrote: Dear all, From the definition of CCP4 (http://www.ccp4.ac.uk/html/ rotationmatrices.html), the polar angle

Re: [ccp4bb] refining nucleic acids with Coot

For reference, the CCP4 tool is called 'pdb2to3' -- David On 14 January 2014 18:32, Almudena Ponce Salvatierra maps.fa...@gmail.comwrote: Thank you all very much for your very helpful advices! I managed to solve my problem! :-) Best, Almudena. 2014/1/14 Ashley Pike

[ccp4bb] CCP4-6.4.0 Update 005

Dear CCP4 Users, An update for the CCP4-6.4.0 series has just been released, consisting of the following changes: - Documentation (all): new documentation for othercell and updated documentation for pointless and aimless - cprodrg (Mac): fix for segfault on OSX - ctruncate (all):

Re: [ccp4bb] iMosflm bug?

This might be a problem with fonts. On my laptop the menu items use a sans serif font and that particular window is just wide enough to fit all the items. The font also looks more attractive and readable than your screenshot. I'm guessing (from your desktop background!) that you also use Ubuntu.

Re: [ccp4bb] Philosophical question

I believe that the reason all organisms share the convention (more or less) is that it dates back to LUCA - the Last Universal Common Ancestor of all extant life. LUCA must have had the basic transcription and translation machinery that we now see somewhat divergently-evolved versions of in all

Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

I wouldn't be so sure that HeLa is just XX, or that it should be called garden variety after what I read today. http://www.nature.com/news/most-popular-human-cell-in-science-gets-sequenced-1.12609#/b1 -- David On 18 March 2013 15:08, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear

[ccp4bb]

Dear Kavya, The CCP4BB is a closed community, in the sense that a user must subscribe to the list before being able to post and that subscription requests are handled manually rather than being granted by default. This is generally sufficient to stop spam, irrelevant advertisements and blatant

[ccp4bb] CCP4 update

release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- David Waterman

Re: [ccp4bb] Which Coot for Scientific Linux 6.3

Dear Fred, You may like to try the CCP4 Package Manager, available from the downloads page: http://www.ccp4.ac.uk/download/#os=linux This allows installation of CCP4 components, including Coot, automatically and will attempt to identify the appropriate version for you (disclaimer: I have not

Re: [ccp4bb] Areaimol under CCP46.3.0 under Windows 7 crashes

Dear Laurie, A similar issue was found recently with the 64 bit Linux binary of areaimol. After fixing that, we prepared a new binary for Windows in case the same problem turned up. It looks probable that is indeed the case. Could you please replace areaimol.exe on your system with the one from

Re: [ccp4bb] protein interactions

Hi Careina, For the first question, it sounds as though IBIS would do what you want: http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to answer your second question, although sequences are compared to known structures, so if your sequence is dissimilar to anything in the PDB

[ccp4bb] Old Newsletter News

We at CCP4 are pleased to announce that the online archive of CCP4 Newsletter articles is now finally complete. We located hard copies of the previously missing editions 1 to 29, scanned them and are hosting the resulting PDFs on our website: http://www.ccp4.ac.uk/newsletters.php As we

[ccp4bb] CCP4 Newsletter 48

in the winter. Articles may cover any topic of interest to macromolecular crystallographers, though we are particularly interested in articles on software or methodology, and short items of news. Have a good weekend. -- David Waterman

Re: [ccp4bb] Pisa application

Perhaps IBIS does what you want? http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi IBIS ... infers/predicts interacting partners and binding sites by homology -- David On 8 August 2012 07:33, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear ccp4ers I just wonder whether anybody

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

Hi Peter, We're still working on the resolution of this bug. In the meantime you may wish to replace 6.3.0's scala.exe with the one from 6.2.0, which is linked to from the Windows Problems pageshttp://www.ccp4.ac.uk/problems/windows.php#ccp4-6.3.0. Scala has not changed much between the two

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

Dear Peter, You are not alone with this. We have just found out about this bug. It appears to just be a problem with output formatting (the MTZ should be fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's version of scala from the problems page as a workaround early next

Re: [ccp4bb] CCP4-6.3.0 installation

Please note that we do now offer both 32 and 64 bit binary bundles of the CCP4 suite on Linux. With the new Package Manager, binary installation is supposed to be 'painless'. So you may like to try this, rather than feeling to ought to compile your own. Your feedback is welcome. Cheers David. On

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

should be better :-) Phil On 4 Aug 2012, at 14:26, David Waterman wrote: Dear Peter, You are not alone with this. We have just found out about this bug. It appears to just be a problem with output formatting (the MTZ should be fine). We'll get a fix as soon as we can and will provide a link

Re: [ccp4bb] How do I read a CCP4 map header?

Hi Alex, The map header is binary, not text, which explains the junk you saw in your terminal. One thing to be careful of is where the map file came from. The map format doesn't specify the byte order written to disk, so your reading routine has to identify whether it was written by a little- or

Re: [ccp4bb] How do I read a CCP4 map header?

Hi Alex Out of the possible issues I suggested earlier I suspect most strongly you have sizeof(long) != 4. But Ian is indeed right to promote the canonical answer. Avoid such mess by using the API ;-) -- David On 2 July 2012 15:48, Ian Tickle ianj...@gmail.com wrote: Hi Alex Wouldn't you

Re: [ccp4bb] Failure in Phaser EP

Dear Arko, Is it possible that your Phaser installation is out of sync with your CCP4 installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and 'SIGF(-) =' to the LABIN line. Best regards -- David On

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