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

[David Waterman]

Hi Fred,

CCP4 distributes the shelxl binary on Linux. I've not checked yet, but
perhaps it is also part of CCP4 on Windows?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:38, Fred Vellieux 
wrote:

> Hello and thanks for the reply.
>
> My input file came from my checking SHELX manuals and SHELX instructions
> on the web, and trying to modify them to suit my case.
>
> I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux
> box, and only v1.3 was able to install on that Windows machine and not the
> latest v1.5). However, olex2 (the installation 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:
>
> 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?
>
> Cheers
> -- David
>
>
> On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
> wrote:
>
>> Hi folks,
>>
>> I have a simple question: is there an electronic bulletin board for
>> small-molecule crystallography? I have checked the list of CCP projects
>> and there is no CCP-project for small molecule crystallography in the
>> list.
>>
>> I am trying to run SHELXL, and it fails with the cryptic message "** BAD
>> ATOM OR UNKNOWN INSTRUCTION **".
>>
>> The alternative for me would be of course to use software meant for
>> macromolecular cystallography (that I know) on small molecule
>> diffraction data. And using the small molecule coordinate files
>> transformed to a suitable format. I don't know if this is feasible or
>> even advised. Probably not.
>>
>> Thanks,
>>
>> Fred.
>>
>> --
>> MedChem, 1st F. Medicine, Charles University
>> BIOCEV, Vestec, Czech Republic
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
>



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

[David Waterman]

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?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
wrote:

> Hi folks,
>
> I have a simple question: is there an electronic bulletin board for
> small-molecule crystallography? I have checked the list of CCP projects
> and there is no CCP-project for small molecule crystallography in the list.
>
> I am trying to run SHELXL, and it fails with the cryptic message "** BAD
> ATOM OR UNKNOWN INSTRUCTION **".
>
> The alternative for me would be of course to use software meant for
> macromolecular cystallography (that I know) on small molecule
> diffraction data. And using the small molecule coordinate files
> transformed to a suitable format. I don't know if this is feasible or
> even advised. Probably not.
>
> Thanks,
>
> Fred.
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[David Waterman]

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:
https://www.ccp4.ac.uk/schools/DLS-2015/course_material/Datareduction2015.pdf

Cheers
-- David


On Fri, 23 Feb 2024 at 10:17, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Graeme (I may well have mentioned this when we shared an office) et al
>
> I’ll add something from my small-molecule crystallography days, when we
> used point detectors - so this would be pre-1996 which was the last time I
> used one of these machines.
>
> I don’t remember which structure it was (feel free to go through the CSD
> to check on my behalf, but many structures were not deposited in those days
> and languish in a PhD thesis!); I had a dataset with three 90º angles, but
> the processing statistics (and overall cell volume) indicated quite plainly
> that it was monoclinic (probably P21). I re-refined the unit cell as if it
> were triclinic and the “best” 90 degree angle with the smallest ESD was the
> one that corresponded to the monoclinic beta; the two 90º angles refined
> away from their true value more.
>
> A result of that experiment was that (since then) I never assumed that the
> values of the angles from the data processing showed unambiguously that I
> had a high symmetry solution. I believe that Pointless arose after a
> hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be
> faulty here).
>
> Best wishes
>
> Harry
>
> > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hi Huw
> >
> > (first: thank to Phil for picking this up; it caused much confusion)
> >
> > While I get where you are coming from, it is still from a mathematical
> standpoint correct to consider e.g. a tetragonal crystal as monoclinic -
> P21 is a subgroup of P43212 (say) so strictly it is possible and correct -
> if experimentally unlikely - to have the situation we are discussing here
> occur.
> >
> > Also, under merging data to investigate twinning is a current bb topic.
> >
> > Telling users to “fiddle the parameters” so that the strict test is
> satisfied feels like a non-ideal answer: a warning when importing such data
> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this
> is unusual, I hope you know what you are doing” rather than a flat out
> error.
> >
> > Literally I got involved as I had a dials user ask me how to do this
> parameter fiddling in a more niche case and I thought that was a suboptimal
> solution to an artificial problem :-)
> >
> > On a personal note, I think it is important that the tools we develop
> still allow people to explore problems rather than railroading them down
> one true route which is the only allowed way to look at a problem: we learn
> a lot by exploring odd corners as here.
> >
> > Best wishes Graeme
> >
> >> On 23 Feb 2024, at 09:49, Huw Jenkins  wrote:
> >>
> >> [You don't often get email from h.t.jenk...@me.com. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification ]
> >>
> >> Hi Graeme,
> >>
> >>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>>
> >>> Processing a data set in lower than necessary symmetry e.g. tetragonal
> as monoclinic you _cannot_ import the merged MTZ file into i2 because it is
> impossible to have 90 degree angles for P21
> >>
> >> I had a look at the code in CCP4i2 that generates the errors in the
> screenshots you posted. The first one is only generated if two cell
> parameters are *exactly* equal and the second is generated when beta is
> between 89. and 90.0001 degrees.
> >>
> >> I think these tests should only fail if the data were processed
> assuming higher symmetry so that unit cell parameters were restrained and
> then the space group changed to a lower symmetry one. Isn't the correct
> approach when the true symmetry is lower than originally assumed to repeat
> the data processing without applying constraints imposed by the higher
> symmetry - because, for example, cell parameters refined assuming cell
> length/angle constraints may not predict the reflection positions as well
> as if these restraints were not applied, reflections assumed to be symmetry
> equivalent when they weren't may lead to suboptimal scaling etc etc?
> >>
> >>
> >> Huw
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright and
> or privileged material, and are for the use of the intended addressee only.
> If you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
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> > Any opinions expressed within this e-mail are those 

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

[David Waterman]

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
David


On Fri, 23 Feb 2024, 10:40 Huw Jenkins, <
288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:

> > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> >  so strictly it is possible and correct - if experimentally unlikely -
> to have the situation we are discussing here occur.
>
> I believe this is only technically possible because the MTZ format does
> not store esds on the unit cell parameters? In the thaumatin example
> processing the dataset here  - https://zenodo.org/records/4916649 -
> assuming monoclinic symmetry results in unit cell:
>
> 58.176(2), 150.543(4), 58.2050(18), 90.0, 90.1058(9), 90.0
>
> The situation you describe would result in for example:
>
> 58.1087(18), 150.543(4), 58.1087(15), 90.0, 90.(1), 90.0
>
> and the test should really only fail for:
>
> 58.1087(18), 58.1087(18), 150.400(5), 90.0, 90.0, 90.0
>
> i.e. where a=b have same value and esd (as they were constrained to be
> identical and esd on beta is 0 as it was constrained to be 90.
>
>
>
> > Telling users to “fiddle the parameters” so that the strict test is
> satisfied feels like a non-ideal answer: a warning when importing such data
> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this
> is unusual, I hope you know what you are doing” rather than a flat out error
>
> I think you have misunderstood here. I was suggesting telling users to
> integrate/scale the data without imposing higher symmetry was the correct
> thing to do? I don't see how "fiddling of parameters" is required.
>
> But I agree i2 should allow an override of this test.
>
>
> Huw
> 
>
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Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

[David Waterman]

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,
>
> Chatting to someone and wanted to provide some pointers on how to
> interpret the moments of E from truncate or ctruncate, and realised that I
> don't have any good *references*​ for this to hand i.e. what I am looking
> for and why, and my google search didn't come up with much that was useful
>
> Those of us who have a few orbits under out belts picked up a lot of this
> from osmosis but if you are trying to explain to someone new it's a bit
> more tricky
>
> What have I missed? Where would you point people today to understand e.g.
> Wilson stats and suchlike, from a user perspective (ie. not
> mathematics-first)
>
> Thanks in advance for any pointers
>
> Graeme
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
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> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
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> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
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Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

[David Waterman]

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,
> We have collected diffraction data on a Rigaku FR-X machine with a
> HyPix-6000HE detector. The images are in .rod_img format. We are trying to
> export the data in iMosflm compatible format using the options available in
> CrysAlisPro RED software provided by Rigaku. But the images generated show
> vertical strips instead of diffraction spots which gives error in
> processing. Can anyone suggest a method to convert the .rod_img images in
> iMosflm compatible format. Thank you!
>
> --
>  Vyankatesh Rajmane
> E-mail: vyankates...@gmail.com
>
>
> --
>
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[ccp4bb] DEADLINE APPROACHING: DLS/CCP4 data analysis workshop 2023

[David Waterman]

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 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 and early career scientists who have a focus on structural biology.
>
> This is again an in-person workshop, based at Diamond Light Source in the
> UK, but having learned from the online-only workshops during the pandemic,
> we will keep two remote setup days prior to the on-site element, and we
> will make use of a Slack workspace through the course.
>
> It is essential that applicants commit to attending the workshop in its
> entirety. Please note below the workshop days and timings involved:
>
> - First online preparation day (before fishing crystals): Monday 6 November
> - Second online preparation day (before data collection): Tuesday 21
> November
> - On-site: Monday 27 November to Tuesday 5 December
> - Day off: Saturday 2 December
>
> There is no fee to attend this online workshop, however attendance will be
> subject to an application process and a letter of support from the
> attendee's supervisor will be required. Both the application form and
> supervisor's letter of support will need to be submitted by 17:00 (UK time)
> on 9 October 2023.
>
> Some prior experience of crystallography and data collection is expected,
> and those who already have an interesting project (crystals and possibly
> previously collected datasets) will be given priority in selection.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2023/
> - Apply at the Diamond website:
> https://www.diamond.ac.uk/Home/Events/2023/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2023.html
>
> -- David (on behalf of the organisers)
>



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[ccp4bb] DLS/CCP4 data analysis workshop 2023

[David Waterman]

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,
postdocs and early career scientists who have a focus on structural biology.

This is again an in-person workshop, based at Diamond Light Source in the
UK, but having learned from the online-only workshops during the pandemic,
we will keep two remote setup days prior to the on-site element, and we
will make use of a Slack workspace through the course.

It is essential that applicants commit to attending the workshop in its
entirety. Please note below the workshop days and timings involved:

- First online preparation day (before fishing crystals): Monday 6 November
- Second online preparation day (before data collection): Tuesday 21
November
- On-site: Monday 27 November to Tuesday 5 December
- Day off: Saturday 2 December

There is no fee to attend this online workshop, however attendance will be
subject to an application process and a letter of support from the
attendee's supervisor will be required. Both the application form and
supervisor's letter of support will need to be submitted by 17:00 (UK time)
on 9 October 2023.

Some prior experience of crystallography and data collection is expected,
and those who already have an interesting project (crystals and possibly
previously collected datasets) will be given priority in selection.

- The course homepage: https://www.ccp4.ac.uk/schools/DLS-2023/
- Apply at the Diamond website:
https://www.diamond.ac.uk/Home/Events/2023/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2023.html

-- David (on behalf of the organisers)



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

[David Waterman]

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, 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 work :( $ cif2pdb --help
>>
>>  * ERROR *
>>   No cif file read on input
>>
>> Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif
>>
>>  * ERROR *
>>   No cif file read on input
>>
>>
>> Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif
>>
>>  * ERROR *
>>   No cif file read on input
>>
>>
>>
>> For someone who only used PDB files to get F^2 to validate processing,
>> how best to get one *from the command line* ?
>>
>> Thanks Graeme
>>
>>
>> --
>> This e-mail and any attachments may contain confidential, copyright and
>> or privileged material, and are for the use of the intended addressee only.
>> If you are not the intended addressee or an authorised recipient of the
>> addressee please notify us of receipt by returning the e-mail and do not
>> use, copy, retain, distribute or disclose the information in or attached to
>> the e-mail.
>> Any opinions expressed within this e-mail are those of the individual and
>> not necessarily of Diamond Light Source Ltd.
>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
>> attachments are free from viruses and we cannot accept liability for any
>> damage which you may sustain as a result of software viruses which may be
>> transmitted in or with the message.
>> Diamond Light Source Limited (company no. 4375679). Registered in England
>> and Wales with its registered office at Diamond House, Harwell Science and
>> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>>
>> 
>>
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Re: [ccp4bb] Outlawed PDB files, what should a muggle do

[David Waterman]

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 work :( $ cif2pdb --help
>
>  * ERROR *
>   No cif file read on input
>
> Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif
>
>  * ERROR *
>   No cif file read on input
>
>
> Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif
>
>  * ERROR *
>   No cif file read on input
>
>
>
> For someone who only used PDB files to get F^2 to validate processing, how
> best to get one *from the command line* ?
>
> Thanks Graeme
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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>



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Re: [ccp4bb] About the A in AI

[David Waterman]

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

The paper "Crystal Structure of PsiX Reveals a Trimethylating Enzyme" by
[Authors] (2023) reports the 1.0 angstrom crystal structure of the enzyme
PsiX. The authors conclude that PsiX is a trimethylating enzyme that
catalyzes the methylation of the C5 position of guanine.

Critique

There are several major flaws in the paper that call into question the
authors' conclusions. First, the authors' interpretation of the crystal
structure is based on a number of assumptions that are not supported by the
data. For example, the authors assume that the residues that are close to
the C5 position of guanine are involved in the methylation reaction.
However, there is no evidence to support this assumption. The residues
could be involved in other aspects of the enzyme's activity, such as
substrate binding or catalysis.

Second, the authors' experiments do not provide any direct evidence that
PsiX is a trimethylating enzyme. The authors show that PsiX can methylate
guanine in vitro. However, they do not show that PsiX is the only enzyme
that can methylate guanine in vivo. It is possible that there are other
enzymes that can methylate guanine, and that PsiX is not involved in this
reaction.

Third, the authors' experiments do not provide any information about the
mechanism of the methylation reaction. The authors suggest that PsiX uses a
SAM-dependent mechanism to methylate guanine. However, they do not provide
any evidence to support this suggestion. It is possible that PsiX uses a
different mechanism to methylate guanine.

Conclusion

The paper by [Authors] (2023) does not provide convincing evidence that
PsiX is a trimethylating enzyme. The authors' interpretation of the crystal
structure is based on a number of assumptions that are not supported by the
data. The authors' experiments do not provide any direct evidence that PsiX
is a trimethylating enzyme, and they do not provide any information about
the mechanism of the methylation reaction. Based on these criticisms, I
recommend that the paper be rejected.
thumb_upthumb_down
upload
Google it
more_vert

-- David


On Fri, 12 May 2023 at 16:50, Cowan, Richard H. (Dr.) 
wrote:

> The underlying model that drives Bing is ChatGPT, so perhaps not a
> surprise they produce the same output. Maybe giving Bard or Llama the same
> prompt might give different results.
>
>
>
> Thanks,
>
>
>
> *Richard Cowan*
>
> *Research Fellow*
>
>
>
> Leicester Institute of Structural and Chemical Biology
>
> Department of Molecular and Cell Biology
>
> University of Leicester | University Road | Leicester | LE1 7RH | UK
>
>
>
> *t:* +44 (0)116 229 7077
>
> *e:*  rc...@leicester.ac.uk 
> *w:* www.le.ac.uk
> [image:
> vxWQrlsJKAEloASUgBJQAkpg+xJQQbp9+eroSkAJKAEloASUgBJQAg0QUEHaACB9rASUgBJQAkpACSgBJbB9Cagg3b58dXQloASUgBJQAkpACSiBBgioIG0AkD5WAkpACSgBJaAElIAS2L4EVJBuX746uhJQAkpACSgBJaAElEADBFSQNgBIHysBJaAElIASUAJKQAlsXwIqSLcvXx1dCSgBJaAElIASUAJKoAECKkgbAKSPlYASUAJKQAkoASWgBLYvARWk25evjq4ElIASUAJKQAkoASWgBJSAElACSkAJKAEloASUwI5M4P8AZ4taSLRHMpYASUVORK5CYII=]
>
>
> Follow us on Twitter  or visit our
> Facebook  page
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Bruno
> KLAHOLZ 
> *Date: *Friday, 12 May 2023 at 16:36
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *Re: [ccp4bb] About the A in AI
>
> CAUTION: This email was sent from an *EXTERNAL* source. Think
> before clicking links or opening attachments.
>
>
>
> indeed, probably they are using the same databases and features.
>
> Same happens in translations btw.
>
>
>
> Cheers,
>
>
>
> Bruno
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Ian
> Tickle
> *Sent:* 12 May 2023 17:33
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] About the A in AI
>
>
>
>
>
> Hi Bernhard
>
>
>
> Methinks there's some cribbing going on between Bing and ChatGPT - not
> only deja-vu but the reviews are identical word for word!  How is that
> possible?
>
>
>
> Cheers
>
>
>
> -- Ian
>
>
>
>
>
> On Fri, 12 May 2023 at 16:15, Bernhard Rupp 
> wrote:
>
> For those who concern themselves with such matters, here the responses
> from Bing and ChatGPT to the prompt:
>
>
>
> “Please write a critical review report rejecting a scientific paper
> reporting that the 1.0 angstrom crystal structure shows that psiX is a
> trimethylating enzyme”
>
>
>
> Enjoy the frightening reading and then we can chat (LOL) about the creepy
> feeling of déjà-vu you might experience….
>
>
>
> https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0
>
> https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0
>
>
>
> Cheers, BR
>
>
>
> 

[ccp4bb] Continued issues with CCP4BB

[David Waterman]

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 to
CCP4BB@JISCMAIL.AC.UK" messages being received, even though the messages
have been distributed to the list. If you are unsure, you can always check
the public archive to see if your message has been sent, here:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4BB

Jiscmail's service update is on their webpage: https://www.jiscmail.ac.uk/.
Please bear with us for the time being while they resolve the current
issues.

Best wishes,

-- David



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

[David Waterman]

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 will be done for us by Jisc or if those subscribers should
re-subscribe themselves. Of course, deleted subscribers will not see this
message...

Cheers

-- David


On Tue, 10 Jan 2023 at 23:11, Bernhard Rupp 
wrote:

> I got unsubscribed from ccp4em yesterday with a similar message for
> b...@ruppweb.org. That one has a minor certificate problem that however
> does not affect other email recepients.
>
> For some reason, the ssl certificate for https://ruppweb.org/ is valid,
> but the mailserver still seems to have an issue. May be your IT can check
> yours
>
> Best br
>
>
> On Tue, Jan 10, 2023, 02:57 David Briggs  wrote:
>
>> I received this odd-looking message from the board address. Did anyone
>> else get anything similar?
>>
>> I'm sharing a screenshot because I'm not:
>> (a) going to click those links
>> (b) get others to click those links.
>>
>> Can the board admin confirm if this is legitimate or not?
>>
>> D
>>
>> --
>>
>> *Dr David C. Briggs CSci MRSB*
>>
>> Principal Laboratory Research Scientist
>>
>> Signalling and Structural Biology Lab
>>
>> The Francis Crick Institute
>>
>> London, UK
>>
>> ==
>>
>> about.me/david_briggs
>>
>> The Francis Crick Institute Limited is a registered charity in England
>> and Wales no. 1140062 and a company registered in England and Wales no.
>> 06885462, with its registered office at 1 Midland Road London NW1 1AT
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Test message

[David Waterman]

This is a test message to explore issues reported about automatic removals
from the BB.

-- David



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

[David Waterman]

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 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 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 and early career scientists who have a focus on structural biology.
>>
>> After the last two remote events limited to online-only using Zoom, we
>> are very happy to report that we intend to go back to an in-person workshop
>> this year! However, having learned from the online-only workshops, we will
>> keep two remote setup days prior to the on-site element, and we will make
>> use of a Slack workspace through the course.
>>
>> It is essential that applicants commit to attending the workshop in its
>> entirety. Please note below the workshop days and timings involved:
>>
>> - First online preparation day (before fishing crystals): Monday 17
>> October
>> - Second online preparation day (before data collection): Tuesday 22
>> November
>> - On-site: Monday 28 November to Tuesday 6 December
>> - Day off: Saturday 3 December
>>
>> There is no fee to attend this online workshop, however attendance will
>> be subject to an application process and a letter of support from the
>> attendee's supervisor will be required. Both the application form and
>> supervisor's letter of support will need to be submitted by 17:00 (UK time)
>> on 20 September 2022.
>>
>> Some prior experience of crystallography and data collection is expected,
>> and those who already have an interesting project (crystals and possibly
>> previously collected datasets) will be given priority in selection.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2022/
>> - Apply at the Diamond website:
>> https://www.diamond.ac.uk/Home/Events/2022/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2022.html
>>
>> -- David (on behalf of the organisers)
>>
>>



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

[David Waterman]

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 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 and early career scientists who have a focus on structural biology.
>
> After the last two remote events limited to online-only using Zoom, we are
> very happy to report that we intend to go back to an in-person workshop
> this year! However, having learned from the online-only workshops, we will
> keep two remote setup days prior to the on-site element, and we will make
> use of a Slack workspace through the course.
>
> It is essential that applicants commit to attending the workshop in its
> entirety. Please note below the workshop days and timings involved:
>
> - First online preparation day (before fishing crystals): Monday 17 October
> - Second online preparation day (before data collection): Tuesday 22
> November
> - On-site: Monday 28 November to Tuesday 6 December
> - Day off: Saturday 3 December
>
> There is no fee to attend this online workshop, however attendance will be
> subject to an application process and a letter of support from the
> attendee's supervisor will be required. Both the application form and
> supervisor's letter of support will need to be submitted by 17:00 (UK time)
> on 20 September 2022.
>
> Some prior experience of crystallography and data collection is expected,
> and those who already have an interesting project (crystals and possibly
> previously collected datasets) will be given priority in selection.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2022/
> - Apply at the Diamond website:
> https://www.diamond.ac.uk/Home/Events/2022/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2022.html
>
> -- David (on behalf of the organisers)
>
>



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[ccp4bb] DLS/CCP4 data analysis workshop 2022

[David Waterman]

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 and early career scientists who have a focus on structural biology.

After the last two remote events limited to online-only using Zoom, we are
very happy to report that we intend to go back to an in-person workshop
this year! However, having learned from the online-only workshops, we will
keep two remote setup days prior to the on-site element, and we will make
use of a Slack workspace through the course.

It is essential that applicants commit to attending the workshop in its
entirety. Please note below the workshop days and timings involved:

- First online preparation day (before fishing crystals): Monday 17 October
- Second online preparation day (before data collection): Tuesday 22
November
- On-site: Monday 28 November to Tuesday 6 December
- Day off: Saturday 3 December

There is no fee to attend this online workshop, however attendance will be
subject to an application process and a letter of support from the
attendee's supervisor will be required. Both the application form and
supervisor's letter of support will need to be submitted by 17:00 (UK time)
on 20 September 2022.

Some prior experience of crystallography and data collection is expected,
and those who already have an interesting project (crystals and possibly
previously collected datasets) will be given priority in selection.

- The course homepage: https://www.ccp4.ac.uk/schools/DLS-2022/
- Apply at the Diamond website:
https://www.diamond.ac.uk/Home/Events/2022/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2022.html

-- David (on behalf of the organisers)



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

[David Waterman]

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 event to the
members of the ccp4 community.  The registration deadline for in-person
attendees is the *17th of March* and the virtual registration deadline is a
week later on the *24thof March*.



If you have any questions about the event please let me know and I’ll be
happy to help.



Best wishes

Gillian



*Digital Research Infrastructure (DRI) Retreat*

*Manchester and online*

*Mon 28th March – Fri 1st April 2022*



Join the N8 Centre of Excellence in Computationally Intensive Research (N8
CIR; https://n8cir.org.uk/) this month for an exciting new event taking
place online and in-person from Monday 28 March – Friday 1 April.

Designed for people working at the interface between research and
technology and infrastructure, the event aims to help technology
specialists, such as research software and research infrastructure
engineers, to develop additional professional skills to support researchers
and accelerate discovery.

The 5 day event will feature more than 40 speakers and panellists who will
discuss all aspects of the Digital Research Infrastructure (DRI) landscape,
taking you on a journey from the first contact you may have with a
researcher, through identifying and meeting their needs, developing
leadership and working with vendors.

We are pleased to say that the event is free to attend due to generous
funding from EPSRC, regardless of your research area, funding source, UK
university or research institute.

The event is themed over the 5 days as follows:

   - Monday 28 March, The DRI Landscape
   - Tuesday 29 March, Engagement
   - Wednesday 30 March, Facilitation
   - Thursday 31 March, Leadership
   - Friday 1 April, Friends and Collaborators

The event will be fully hybrid, with in-person sessions taking place at the
University of Manchester's Barnes Wallis conference venue and remote
attendees joining us via the Airmeet platform.

*Join Us In-Person*

You are invited to join us in Manchester for as many days as you wish.
Overnight accommodation is available to attendees free of charge on a
dinner, bed and breakfast basis. There is also a conference dinner on the
Wednesday night open to all in-person attendees.

A number of travel bursaries are also available - please e-mail
enquir...@n8cir.org.uk for details of how to apply.

*Join Us Online*

There’s a strong offer for online attendees too. You will have complete
flexibility to attend as many sessions as you wish over the 5 days via our
Airmeet platform.  Airmeet will allow you to fully interact with the
in-person attendees and panellists in an immersive environment.

*Registration*

An overview of the programme can be found at:
https://n8cir.org.uk/dri-retreat/ Details of speakers are currently being
added so watch this space!

The deadline for registration for in-person attendance is *Thursday 17
March*, with remote registration closing on *Thursday 24 March*.  Register
now at https://n8cir.org.uk/dri-retreat/

We look forward to seeing you in Manchester (or online!) later this month.





Dr Gillian Sinclair

N8 CIR Programme Manager

University of Manchester



Mobile - 07778 890869

Email - gillian.sincl...@manchester.ac.uk

Website: https://n8cir.org.uk/

Twitter: https://twitter.com/N8CIR



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

[David Waterman]

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 okay, right?

Let's say I have two data processing protocols, A and B. Between these I
might be exploring some difference in options within one data processing
program, perhaps different geometry refinement parameters, or scaling
options. I expect the A and B data sets to be quite similar, but I would
like to evaluate which protocol was "better", and I want to do this
quickly, ideally looking at a single number. I don't like I/sigI because I
don't trust the sigmas, CC1/2 is often noisy, and I'm totally sworn off
merging R statistics for these purposes. I tend to use Rfree as an
easily-available metric, independent from the data processing program and
the merging stats. It also allows a comparison of A and B in terms of the
"product" of crystallography, namely the refined structure. In this I am
lucky because I'm not trying to solve a structure. I may be looking at
lysozyme or proteinase K: something where I can download a pretty good
approximation to the truth from the PDB.

So, what I do is process the data by A and process by B, ensure the data
sets have the same free set, then refine to convergence (or at least, a lot
of cycles) starting from a PDB structure. I then evaluate A vs B in terms
of Rfree, though without an error bar on Rfree I don't read too much into
small differences.

Does this procedure seem sound? Perhaps it could be improved by randomly
jiggling the atoms in the starting structure, in case the PDB deposition
had already followed an A- or B-like protocol. Perhaps the whole approach
is suspect. Certainly I wouldn't want to generalise by saying that A or B
is better in all cases, but I do want to find a way to assess the various
tweaks I can try in data processing for a single case.

Any thoughts? I appreciate the wisdom of the BB here.

Cheers

-- David


On Fri, 29 Oct 2021 at 15:50, James Holton  wrote:

>
> Well, of all the possible metrics you could use to asses data quality
> Rfree is probably the worst one.  This is because it is a cross-validation
> metric, and cross-validations don't work if you use them as an optimization
> target. You can try, and might even make a little headway, but then your
> free set is burnt. If you have a third set of observations, as suggested
> for Rsleep (doi:10.1107/S0907444907033458), then you have a chance at
> another round of cross-validation. Crystallographers don't usually do this,
> but it has become standard practice in machine learning (training=Rwork,
> validation=Rfree and testing=Rsleep).
>
> So, unless you have an Rsleep set, any time you contemplate doing a bunch
> of random things and picking the best Rfree ... don't.  Just don't.  There
> madness lies.
>
> What happens after doing this is you will be initially happy about your
> lower Rfree, but everything you do after that will make it go up more than
> it would have had you not performed your Rfree optimization. This is
> because the changes in the data that made Rfree randomly better was
> actually noise, and as the structure becomes more correct it will move away
> from that noise. It's always better to optimize on something else, and then
> check your Rfree as infrequently as possible. Remember it is the control
> for your experiment. Never mix your positive control with your sample.
>
> As for the best metric to assess data quality?  Well, what are you doing
> with the data? There are always compromises in data processing and
> reduction that favor one application over another.  If this is a "I just
> want the structure" project, then score on the resolution where CC1/2 hits
> your favorite value. For some that is 0.5, others 0.3. I tend to use 0.0 so
> I can cut it later without re-processing.  Whatever you do just make it
> consistent.
>
> If its for anomalous, score on CCanom or if that's too noisy the
> Imean/sigma in the lowest-angle resolution or highest-intensity bin. This
> is because for anomalous you want to minimize relative error. The
> end-all-be-all of anomalous signal strength is the phased anomalous
> difference Fourier. You need phases to do one, but if you have a structure
> just omit an anomalous scatterer of interest, refine to convergence, and
> then measure the peak height at the position of the omitted anomalous
> atom.  Instructions for doing anomalous refinement in refmac5 are here:
>
> https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html
>
> If you're looking for a ligand you probably want isomorphism, and in that
> case refining with a reference structure looking for low Rwork is not a bad
> strategy. This will tend to select for crystals containing a molecule that
> looks like the one you are refining.  But be careful! If it is an 

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

[David Waterman]

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 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 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 and early career scientists who have a focus on
>> structural biology.
>>
>> The workshop will take place online via Zoom over the course of two full
>> weeks, plus a preparation day in advance of the workshop. It is essential
>> that applicants commit to attending the workshop in its entirety. Please
>> note below the workshop days and timings involved:
>>
>> - Preparation day: Tuesday 23 November 2021
>> - Week 1: Monday 29 November to Friday 3 December 2021
>> - Week 2: Monday 6 December to Friday 10 December 2021
>> - The days will generally begin at 08:45 and will finish at 17:15 (UK
>> time)
>>
>> There is no fee to attend this online workshop, however attendance will
>> be subject to an application process and a letter of support from the
>> attendee's supervisor will be required. Both the application form and
>> supervisor's letter of support will need to be submitted by 17:00 (UK time)
>> on Friday 1 October 2021 (though see disclaimer below).
>>
>> Some prior experience of crystallography and data collection is expected,
>> and those who already have an interesting project (crystals and possibly
>> previously collected datasets) will be given priority in selection.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2021/
>> - Apply at the Diamond website:
>> https://www.diamond.ac.uk/Home/Events/2021/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2021.html
>>
>> *Disclaimer* Depending on the number of submissions we receive, we may
>> need to close applications earlier than the stated deadline to allow the
>> organisers time to process them. Applicants are therefore encouraged to
>> apply as soon as possible with all the required details requested,
>> including the letter of support. Incomplete applications will not be
>> processed.
>>
>> -- David (on behalf of the organisers)
>>
>



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

[David Waterman]

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 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 and early career scientists who have a focus on
> structural biology.
>
> The workshop will take place online via Zoom over the course of two full
> weeks, plus a preparation day in advance of the workshop. It is essential
> that applicants commit to attending the workshop in its entirety. Please
> note below the workshop days and timings involved:
>
> - Preparation day: Tuesday 23 November 2021
> - Week 1: Monday 29 November to Friday 3 December 2021
> - Week 2: Monday 6 December to Friday 10 December 2021
> - The days will generally begin at 08:45 and will finish at 17:15 (UK time)
>
> There is no fee to attend this online workshop, however attendance will be
> subject to an application process and a letter of support from the
> attendee's supervisor will be required. Both the application form and
> supervisor's letter of support will need to be submitted by 17:00 (UK time)
> on Friday 1 October 2021 (though see disclaimer below).
>
> Some prior experience of crystallography and data collection is expected,
> and those who already have an interesting project (crystals and possibly
> previously collected datasets) will be given priority in selection.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2021/
> - Apply at the Diamond website:
> https://www.diamond.ac.uk/Home/Events/2021/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2021.html
>
> *Disclaimer* Depending on the number of submissions we receive, we may
> need to close applications earlier than the stated deadline to allow the
> organisers time to process them. Applicants are therefore encouraged to
> apply as soon as possible with all the required details requested,
> including the letter of support. Incomplete applications will not be
> processed.
>
> -- David (on behalf of the organisers)
>



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[ccp4bb] DLS/CCP4 data analysis workshop 2021

[David Waterman]

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,
postdocs and early career scientists who have a focus on structural biology.

The workshop will take place online via Zoom over the course of two full
weeks, plus a preparation day in advance of the workshop. It is essential
that applicants commit to attending the workshop in its entirety. Please
note below the workshop days and timings involved:

- Preparation day: Tuesday 23 November 2021
- Week 1: Monday 29 November to Friday 3 December 2021
- Week 2: Monday 6 December to Friday 10 December 2021
- The days will generally begin at 08:45 and will finish at 17:15 (UK time)

There is no fee to attend this online workshop, however attendance will be
subject to an application process and a letter of support from the
attendee's supervisor will be required. Both the application form and
supervisor's letter of support will need to be submitted by 17:00 (UK time)
on Friday 1 October 2021 (though see disclaimer below).

Some prior experience of crystallography and data collection is expected,
and those who already have an interesting project (crystals and possibly
previously collected datasets) will be given priority in selection.

- The course homepage: https://www.ccp4.ac.uk/schools/DLS-2021/
- Apply at the Diamond website:
https://www.diamond.ac.uk/Home/Events/2021/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2021.html

*Disclaimer* Depending on the number of submissions we receive, we may need
to close applications earlier than the stated deadline to allow the
organisers time to process them. Applicants are therefore encouraged to
apply as soon as possible with all the required details requested,
including the letter of support. Incomplete applications will not be
processed.

-- David (on behalf of the organisers)



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Re: [ccp4bb] Anomalous signal to noise details

[David Waterman]

Hi all,

Thanks for the useful advice. Clemens, I was indeed reminded of the
 vs / discussion when I started this thread. The
reason I brought it up here is because the ratio-of-means form is the way
it is described in "Estimation of anomalous signal in diffraction data
<https://journals.iucr.org/d/issues/2006/08/00/dz5079/#SEC2>"
(Dauter 2006), and similarly in "Can I solve my structure by SAD phasing?
Anomalous signal in SAD phasing
<https://journals.iucr.org/d/issues/2016/03/00/ba5234/index.html#SEC1>"
(Terwilliger et al. 2015), where it appears as <|Δano|>/<σano>. Therefore,
I'm not sure it is true that everyone really means <|ΔF|/σ(ΔF)> when
discussing the anomalous signal to noise, but I am happy to adopt this
version. The problem is, we have different formulations and different
suggested cut offs, and given that we don't really have independent and
identically distributed random variables, these criteria surely produce
(slightly?) different results depending on which form is adopted.

There is a practical motive here: we want to report this metric in DIALS
and we want to provide some indicative guiding lines on a plot to help the
user make an interpretive judgement. It sounds like a plot of <|ΔF|/σ(ΔF)>
with guidelines at 0.8 and 1.2 would be a good start, but it does seem
there is scope for confusion, not immediately resolved by the literature.
At least we will write the formula out on the plot explicitly, rather than
hiding it behind an ambiguous name. Bernhard, unfortunately the copy of BMC
I use for reference is currently locked up at the office. One of the side
effects of working from home is that the group library of hardcopy
textbooks is sat gathering dust.

Cheers

-- David


On Fri, 18 Dec 2020 at 22:41, Petr Kolenko 
wrote:

> Dear David,
>
> Although this is not exactly a topic of your question, an alternative
> approach is to use the resolution screening and compare the results. I have
> implemented this approach to my program SHELIXIR (because it uses SHELX
> C/D/E), which can be found here:
>
> http://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir/
>
> It also has its GUI here:
>
> http://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir/gui/
>
> Once you have enough computational power, you can easily perform such
> testing (and no longer need to understand everything that is written in the
> manuscript :-) ).
>
> I hope that the program will soon be published and I would welcome if you
> (or someone else) used it and potentially gave me some feedback or
> suggestion. The program has other functions like parallelized solvent
> 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
> *Sent:* Friday, December 18, 2020 12:53 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Anomalous signal to noise details
>
>
>
> Hi folks
>
>
>
> The paper "Substructure solution with SHELXD
> <https://journals.iucr.org/d/issues/2002/10/02/gr2280/index.html>"
> (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 to below about 1.3
>
>
>
> Is this referring to the quantity <|ΔF|>/<σ(ΔF)> calculated in resolution
> shells, or the quantity <|ΔF|/σ(ΔF)> ?
>
>
>
> This entry
> <https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=SHELX_C/D/E#Resolution_cutoff_.28SHEL.29>
> on the ccp4wiki gives a cutoff
>
>
>
> where the mean value of |ΔF|/σ(ΔF) falls below about 1.2 (a value of 0.8
> would indicate pure noise)
>
>
>
> this version sounds to me like <|ΔF|/σ(ΔF)>
>
>
>
> which is the "better" metric, and what do people mean when they say
> DANO/SIGDANO? What is the justification for the 1.3 (or 1.2) value?
>
>
>
> Thanks!
>
> -- David
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Anomalous signal to noise details

[David Waterman]

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 to below about 1.3


Is this referring to the quantity <|ΔF|>/<σ(ΔF)> calculated in resolution
shells, or the quantity <|ΔF|/σ(ΔF)> ?

This entry

on the ccp4wiki gives a cutoff

where the mean value of |ΔF|/σ(ΔF) falls below about 1.2 (a value of 0.8
> would indicate pure noise)


this version sounds to me like <|ΔF|/σ(ΔF)>

which is the "better" metric, and what do people mean when they say
DANO/SIGDANO? What is the justification for the 1.3 (or 1.2) value?

Thanks!
-- David



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

[David Waterman]

>
> 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 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 and early career scientists who have a focus on
>> structural biology.
>>
>> The workshop will take place online via Zoom over the course of two
>> full weeks, as well as a preparation day in advance of the workshop.
>> It is essential that applicants commit to attending the workshop in
>> its entirety. Please note below the workshop days and timings
>> involved:
>>
>> - Preparation day: Monday 23 November 2020
>> - Week 1: Monday 30 November to Friday 4 December 2020
>> - Week 2: Monday 7 December to Friday 11 December 2020
>> Each day will begin at 08:45 and will finish at 17:15 (GMT - UK Time)
>>
>> Some prior experience of crystallography and data collection is
>> expected, and those who can bring an interesting project with them
>> (crystals and possibly previously collected datasets) will be given
>> priority.
>>
>> There is no fee to attend this online workshop, however attendance
>> will be subject to an application process and a letter of support from
>> the attendee's supervisor will be required. Both the application form
>> and supervisor's letter of support will need to be submitted by 17:00
>> (GMT) on Friday 16 October 2020.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2020/
>> - Apply at the Diamond website:
>>
>> https://www.diamond.ac.uk/Home/Events/2020/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2020.html
>>
>> *Disclaimer* Depending on the number of submissions we receive, we may
>> need to close applications earlier than the deadline to allow the
>> organisers time to process them. Applicants are therefore encouraged
>> to apply as soon as possible with all the required details requested,
>> including the letter of support - any incomplete applications will not
>> be processed.
>>
>> -- David (on behalf of the organisers)
>>
>



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

[David Waterman]

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 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 and early career scientists who have a focus on
> structural biology.
>
> The workshop will take place online via Zoom over the course of two
> full weeks, as well as a preparation day in advance of the workshop.
> It is essential that applicants commit to attending the workshop in
> its entirety. Please note below the workshop days and timings
> involved:
>
> - Preparation day: Monday 23 November 2020
> - Week 1: Monday 30 November to Friday 4 December 2020
> - Week 2: Monday 7 December to Friday 11 December 2020
> Each day will begin at 08:45 and will finish at 17:15 (GMT - UK Time)
>
> Some prior experience of crystallography and data collection is
> expected, and those who can bring an interesting project with them
> (crystals and possibly previously collected datasets) will be given
> priority.
>
> There is no fee to attend this online workshop, however attendance
> will be subject to an application process and a letter of support from
> the attendee's supervisor will be required. Both the application form
> and supervisor's letter of support will need to be submitted by 17:00
> (GMT) on Friday 16 October 2020.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2020/
> - Apply at the Diamond website:
>
> https://www.diamond.ac.uk/Home/Events/2020/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2020.html
>
> *Disclaimer* Depending on the number of submissions we receive, we may
> need to close applications earlier than the deadline to allow the
> organisers time to process them. Applicants are therefore encouraged
> to apply as soon as possible with all the required details requested,
> including the letter of support - any incomplete applications will not
> be processed.
>
> -- David (on behalf of the organisers)
>



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

[David Waterman]

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 and early career scientists who have a focus on
structural biology.

The workshop will take place online via Zoom over the course of two
full weeks, as well as a preparation day in advance of the workshop.
It is essential that applicants commit to attending the workshop in
its entirety. Please note below the workshop days and timings
involved:

- Preparation day: Monday 23 November 2020
- Week 1: Monday 30 November to Friday 4 December 2020
- Week 2: Monday 7 December to Friday 11 December 2020
Each day will begin at 08:45 and will finish at 17:15 (GMT - UK Time)

Some prior experience of crystallography and data collection is
expected, and those who can bring an interesting project with them
(crystals and possibly previously collected datasets) will be given
priority.

There is no fee to attend this online workshop, however attendance
will be subject to an application process and a letter of support from
the attendee's supervisor will be required. Both the application form
and supervisor's letter of support will need to be submitted by 17:00
(GMT) on Friday 16 October 2020.

- The course homepage: https://www.ccp4.ac.uk/schools/DLS-2020/
- Apply at the Diamond website:
https://www.diamond.ac.uk/Home/Events/2020/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2020.html

*Disclaimer* Depending on the number of submissions we receive, we may
need to close applications earlier than the deadline to allow the
organisers time to process them. Applicants are therefore encouraged
to apply as soon as possible with all the required details requested,
including the letter of support - any incomplete applications will not
be processed.

-- David (on behalf of the organisers)



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

[David Waterman]

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 package
gsfonts-x11 installed made an absolute mess of things, so if you do have
that please try removing it.

Cheers
-- David


On Tue, 29 Sep 2020 at 15:39, Kay Diederichs 
wrote:

> hmm, should have looked more carefully! Now I see the letters that should
> be greek (e.g. phi) and look like a strike-through epsilon.
>
> Maybe somebody else has xubuntu 18 without this problem?
> Do you use non-standard repositories?
>
> Kay
>
> On Tue, 29 Sep 2020 14:34:07 +0100, Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
> ...
> >However, the screenshot looks as expected (i.e. good) to me; no tiny
> fonts. Not sure what I overlook.
> >
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] diffdump in CCP4 7.1

[David Waterman]

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 available at the command line with a CCP4 environment set up.

Cheers
-- David


On Sat, 22 Aug 2020 at 01:48, Tim Gruene  wrote:

> Dear David,
>
> Kay Diederich's generate_XDS.INP
>
> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
> creates the full XDS.INP for you for a large number of frame formats.
> It is not CCP4, but I think there are no restrictions for using it.
>
> Best regards,
> Tim
>
> On Fri, 21 Aug 2020 14:29:26 -0700
> Jan Abendroth  wrote:
>
> > Hi all,
> >
> > It looks as if the utility ‘diffdump’ is no longer part of the
> > standard linux CCP4 7.1 distribution.
> >
> > It has been a very handy tool for preparing XDS input files.
> >
> > Does anyone know if there is an equivalent script in CCP4 7.1?
> >
> >
> >
> > Thanks,
> >
> > Jan
> >
>
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] Two scientist / software developer positions on neutron diffraction at RAL

[David Waterman]

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 Waterman  wrote:

> 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 package and be made available within the Mantid framework.
>
> The two positions are closely related, and indeed the successful
> candidates will be expected to work together, and with others, in a
> cross-campus collaboration at the Rutherford Appleton Laboratory. Broadly,
> the ISIS post has a stronger focus on crystallographic algorithm
> development while the SCD post emphasises implementation of the software,
> but there is much overlap and a similar skillset is required. Those
> interested may prefer to apply for both positions! The posts are initially
> for 18 months.
>
> Please see here for further details and to apply:
>
> https://www.topcareer.jobs/Vacancy/irc254133_10766.aspx (closes 2nd
> August)
> https://www.topcareer.jobs/Vacancy/irc254236_10785.aspx (closes 9th
> August)
>
> Please feel free to contact david.water...@stfc.ac.uk or
> silvia.cape...@stfc.ac.uk if you have any questions.
>
> Best wishes
>
> -- David
>



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

[David Waterman]

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 package and be made available within the Mantid framework.

The two positions are closely related, and indeed the successful candidates
will be expected to work together, and with others, in a cross-campus
collaboration at the Rutherford Appleton Laboratory. Broadly, the ISIS post
has a stronger focus on crystallographic algorithm development while the
SCD post emphasises implementation of the software, but there is much
overlap and a similar skillset is required. Those interested may prefer to
apply for both positions! The posts are initially for 18 months.

Please see here for further details and to apply:

https://www.topcareer.jobs/Vacancy/irc254133_10766.aspx (closes 2nd August)
https://www.topcareer.jobs/Vacancy/irc254236_10785.aspx (closes 9th August)

Please feel free to contact david.water...@stfc.ac.uk or
silvia.cape...@stfc.ac.uk if you have any questions.

Best wishes

-- David



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

[David Waterman]

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 <
42fef00af26b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> I need assistance with solving my protein structure.
> I have attempted (using remote access)  to integrate my diffraction images
> (.h5 format) using xia2 but I keep getting the following error message:
>
> The program run with command: xia2 /dls/i04/data/2020/
> has failed with error message
> child process exited abnormally
>
>
> #CCP4I TERMINATION STATUS 0 "child process exited abnormally"
>
> I will appreciate suggestions on how to overcome this.
>
> Thanks.
>
> Adewumi Adeyeye, (PhD Candidate)
> Department of Biochemistry, Genetics, and Microbiology
> Structural Biology Group,
> Room 3-7, Agricultural Sciences Building,
> University of Pretoria
> c/o University & Lynnwood Roads
> Hatfield
> Pretoria
> 0083
>
> Cell: +27630996979
> South Africa
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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

[David Waterman]

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
remove them (they constitute a tiny part of the full install size, after
all) and the policy of the core team is to keep anything that passes the
"if it ain't broke" test.

I know this because I once suggested that pdbset should be removed and
replaced with a script that uses Gemmi. This is because pdbset has some
problems (it removes LINK records for example). However removing it was
strongly resisted by others in the core team. The maintenance burden of
removing such a program far outweighs the negligible cost of simply keeping
it around.

Cheers
-- David


On Wed, 8 Jul 2020 at 15:36, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> I fully agree, I have some old scripts I infrequently use. Making these
> programs inaccessible would break these scripts, forcing me to reinvent a
> couple of wheels.
>
>
>
> My 2 cnts worth of junk to your mailbox,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Oganesyan,
> Vaheh
> *Gesendet:* Mittwoch, 8. Juli 2020 16:23
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Accessing full list of programs in
> CCP4I2
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Thank you for explanation. There are many small programs in CCP4 that have
> not been updated for years and they still work despite being in unsupported
> folder. By making them inaccessible (or more difficult to access) nobody
> gets easier/cheaper life. Even if there are newer programs that may do the
> same it is not a good reason to forget the old ones. It is like forgetting
> the history and the culture. Then making new discoveries just to find that
> it is the same old “wheel” just a bit more round. It is probably very
> personal, but I do not throw away old edition of Thermodynamics text book
> when new one is coming out. And I’m not a hoarder, do not have OCD or ADHD.
>
>
>
> This is already 4 cents together. Sorry to clutter your mailbox.
>
>
>
> Vaheh (CCP4 user since 1992)
>
>
>
> *From:* Christian Roth 
> *Sent:* Tuesday, July 7, 2020 12:42 PM
> *To:* Oganesyan, Vaheh 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>
>
>
> I understand that one is used to the programs one is familiar with and
> Eleanor especially is very fond of these things, but there are several
> things which can be done for example in Coot (symmetry coordinates etc) .
> It is just another way to do it. I had the chance and pleasure to work for
> a while with the programmers of some of these programs in one building and
> such decisions are not taken lightly. But one cannot support all programs
> and write for every program interfaces or even keep two interfaces alive.
> There are just not enough people and money to do that. Also most scientific
> programmers don't get paid to keep the things just running. Would it be
> better to have also programmers to keep legacy up to date and write and
> update GUI's, maybe? But again someone needs to pay for that.
>
> Just my 2 cents.
>
>
>
> Cheers
>
> Christian
>
>
>
>
>
> On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
>
> … and how all these changes being justified?
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Eleanor
> Dodson
> *Sent:* Tuesday, July 7, 2020 12:25 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>
>
>
> Yes - there are things I use all the time which are not part of the CCP4I2
> list
>
> pdbset to generate symmetry equivalents  or find the centre of mass etc etc
>
> coordconv to turn orthogonal coordinates to fractional - after all we are
> crystallographers and need to relate models to unit cells..
>
> distang to do a quick check on crystal contacts..
>
> nd there must be more..
>
> Eleanor
>
>
>
> On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
> wrote:
>
> For occasions like Laus, it would be useful to further on have access to
> the
> CCP4 v7.0 Program Documentation,
>
> even if the programs are not updated as Christian explained.
>
> I was for instance looking for translating coordinates as in pdbset, but
> couldn't find a replacement in the ccp4i2 gui.
>
> Greetings
>
>   Gottfried
>
>
>
>
> On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote:
>
> Ah I see! Great I can run it that way
>
>
>
> And yes, Eleanor, after I realized that list was gone, I was panicking
> that there are some random things I used to do with those programs would no
> longer be possible. Good to know that the command line versions are still
> there in the 7.1 distro.
>
>
>
> Best,
>
>
>
> Kelvin
>
>
>
> --
> Kelvin Lau
>
> https://people.epfl.ch/kelvin.lau
> 

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

[David Waterman]

Hi Herman,

I started googling and ended up completely lost down a rabbit hole (have a
look here if you want to see what I mean:
https://plato.stanford.edu/entries/measurement-science/). As a result I'm
no longer sure I know what the word "measurement" means! I tried to
simplify things with a practical example. Let's say I take a set of clearly
real world measurements (temperature values over time, say). I can take the
mean of subsets of these values and maybe that is a "measurement" too -
especially for readings taken in quick succession, expressly done to reduce
measurement error. But what if I fit a line to a series of values, is the
gradient of the line also a "measurement"? Maybe?

Anyway, for MPR it probably doesn't matter if the measurement is of a
response variable, rather than something "raw". That's because MPR isn't
actually affected by the values themselves (ignoring the thorny issue of
outlier rejection), it is just a count of them.

Cheers
-- David


On Fri, 3 Jul 2020 at 11:22, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear David,
>
>
>
> Thank you for your reaction. It has become clear to me that although most
> people understand what I intended with “measurement”, in practice it is
> very much in the eye of the beholder. It was suggested in the BB to use
> observation instead, but I am fairly sure that some people will also have
> issues with that.
>
>
>
> 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 stay.
>
>
>
> Best regards,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* David Waterman 
> *Gesendet:* Freitag, 3. Juli 2020 10:49
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Betreff:* Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number
> of frames to get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is dgwater...@gmail.com
>
>
>
> 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
> summation and profile-fitted intensities. I think *these* are the
> measurements, not the intensity derived during the scaling procedure. Sure,
> anyone who wants to be even more pedantic than me will point out that these
> "raw measurements" are also the result of fitting procedures. However, to
> my eyes, the difference is that we don't consider the profile and summation
> integrated intensities to change as a result of the procedure that
> ultimately determines the statistic (MPR) of interest. During that
> procedure they are independent, not dependent variables.
>
>
>
> Maybe I am worrying about nothing. It agree it is *fairly clear* what you
> mean by MPR. I just wanted to explore if there was any opportunity for
> further reducing ambiguity.
>
>
>
> Cheers
>
> -- David
>
>
>
>
>
> On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Dear Ian,
>
>
>
> Since some very advanced countries still use miles, Fahrenheit and inches,
> I did not expect anything to change. It was an escalating discussion in
> this thread on data completeness(!) on the use of multiplicity vs
> redundancy that made me suggest a different term. Except for an occasional
> discussion in the BB, there is nothing against people using the term they
> are most comfortable with.
>
>
>
> However, I insist that trying to impose a different definition of
> “measurement” for MPR vs the definition used for the calculation of
> redundancy/multiplicity is not a valid argument against MPR.
>
>
>
> Cheers,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Ian
> Tickle
> *Gesendet:* Donnerstag, 2. Juli 2020 22:06
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to
> get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
>
>
> Well I very much doubt that many software developers are going to trawl
> through all their code, comments, output statements & documentation to
> change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
> agreed on (assuming of course we do manage to come to an agreeme

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

[David Waterman]

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.

-- David


On Fri, 3 Jul 2020 at 09:56, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi James,
>
> At your offline suggestion I tried this myself and observe the same fit
> inducing flashing - however when I shared the desktop (which had a
> full-screen NX session running) it worked fine
>
> The performance seems good enough to be able to follow along with data
> collection at the very least
>
> Best wishes Graeme
>
> > On 3 Jul 2020, at 09:44, Sandy, James (DLSLtd,RAL,LSCI) <
> james.sa...@diamond.ac.uk> wrote:
> >
> > Hi all,
> >
> > I have had problems trying to share my screen using Teams when using the
> NX client. I have experienced the screen flashing in a manner which may
> induce fits! This may be related to sharing a window rather than the whole
> desktop but something to be aware of. I have taken to using Zoom if I want
> to work with others sharing an NX session.
> >
> > Cheers,
> >
> > James
> >
> >
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Winter,
> Graeme (DLSLtd,RAL,LSCI)
> > Sent: 03 July 2020 09:33
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Relaying a remote data collection on using moodle
> collaborate or Microsoft Teams
> >
> > Hi Nick
> >
> > I’ll offer a vote in favour of teams, as it is possible with the desktop
> application to hand over control as well for a shared window (e.g. NX) so
> your student could perform the collection themselves under your supervision
> rather than just watching.
> >
> > I’ve not tried teams + NX as a combination but I can see no reason why
> this would not work, it’s not like the network load will be much different
> to watching a room full of happy faces… you could also try this out in
> advance, connecting to nx.diamond for e.g. processing and confirming that
> the screen share works so you lose no time on data collection day.
> >
> > FWIW I prefer zoom for meetings as it’s got better sound & copes better
> with large groups (IMHO) however for small groups / 1:1 teams has worked
> quite well in my experience, and I was particularly impressed with the
> screen sharing.
> >
> > Best wishes Graeme
> >
> >
> >
> >> On 3 Jul 2020, at 09:18, Nicholas Keep 
> wrote:
> >>
> >> We are going to be doing a data collection for an MRes student at
> Diamond in the next couple of weeks.  These are his first crystals.  It
> would be good if he could be involved in watching it.
> >>
> >> I was wondering if anyone had tried sharing screen and voice via moodle
> collaborate or Microsoft Teams while doing a data collection?  Zoom is
> deprecated by our institution but if anyone had succeeded on zoom that
> would also be interesting.
> >>
> >> I am on Virgin media 100 MB broadband which is pretty much achieving
> that (upload is only around 9 MB though).
> >>
> >> Alternatively we can try and set him up to connect via nx and watch,
> but that would lose the sound connection unless I have a phone tucked under
> my chin.
> >>
> >> We could just record my screen and sound and he could watch later.
> >>
> >> Any tips?
> >>
> >> Best wishes
> >>
> >> Nick
> >>
> >>
> >>
> >> --
> >> Prof Nicholas H. Keep
> >> Executive Dean of School of Science
> >> Professor of Biomolecular Science
> >> Crystallography, Institute for Structural and Molecular Biology,
> >> Department of Biological Sciences Birkbeck,  University of London,
> >> Malet Street, Bloomsbury LONDON WC1E 7HX
> >>
> >> Dean Email;  scid...@bbk.ac.uk
> >> Dept email n.k...@mail.cryst.bbk.ac.uk
> >> Telephone 020-7631-6852  (Room G54a Office)
> >> 020-7631-6800  (Department Office)
> >> Fax   020-7631-6803
> >> If you want to access me in person you have to come to the
> >> crystallography entrance and ring me or the department office from the
> >> internal phone by the door
> >>
> >> ##
> >> ##
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright and
> or privileged material, and are for the use of the intended addressee only.
> If you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> > Any opinions expressed within 

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

[David Waterman]

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
summation and profile-fitted intensities. I think *these* are the
measurements, not the intensity derived during the scaling procedure. Sure,
anyone who wants to be even more pedantic than me will point out that these
"raw measurements" are also the result of fitting procedures. However, to
my eyes, the difference is that we don't consider the profile and summation
integrated intensities to change as a result of the procedure that
ultimately determines the statistic (MPR) of interest. During that
procedure they are independent, not dependent variables.

Maybe I am worrying about nothing. It agree it is *fairly clear* what you
mean by MPR. I just wanted to explore if there was any opportunity for
further reducing ambiguity.

Cheers
-- David


On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Ian,
>
>
>
> Since some very advanced countries still use miles, Fahrenheit and inches,
> I did not expect anything to change. It was an escalating discussion in
> this thread on data completeness(!) on the use of multiplicity vs
> redundancy that made me suggest a different term. Except for an occasional
> discussion in the BB, there is nothing against people using the term they
> are most comfortable with.
>
>
>
> However, I insist that trying to impose a different definition of
> “measurement” for MPR vs the definition used for the calculation of
> redundancy/multiplicity is not a valid argument against MPR.
>
>
>
> Cheers,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Ian
> Tickle
> *Gesendet:* Donnerstag, 2. Juli 2020 22:06
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to
> get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
>
>
> Well I very much doubt that many software developers are going to trawl
> through all their code, comments, output statements & documentation to
> change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
> agreed on (assuming of course we do manage to come to an agreement, which I
> doubt).  And good luck with persuading wwPDB to change 'redundancy' in
> their mmCIF dictionary!  That would be not only pointless but also a lot of
> work, partly because terms get abbreviated in code and in outputs (e.g. to
> 'redund' in mine, or 'mult').  And don't say I can keep the code & comments
> the same and only change the outputs and documentation: that will really
> tax my brain!  Also don't say this need only apply to new code: no code is
> ever completely new, and mixing up old & new terminology would be a
> disaster waiting to happen!  Also it won't end there: someone will always
> find terminology that they disagree with: I can think of plenty cans of
> worms that we could open, but I think one is already one too many!
>
>
>
> By the way, "measurements per reflection" won't float, because some
> measurements will be rejected as outliers (that's why we need redundancy! -
> as opposed to simply measuring intensities for longer).  What I call
> redundancy is "the count of _contributing_ measurements per reflection"
> (CCMPR, sigh).  Personally I think that adding one more term is going to
> confuse things even more since if I'm right most people will continue to
> use the old terms in parallel anyway.
>
>
>
> IMO we should all be free to use the terminology we are most comfortable
> with, and it's up to the receivers of the information to perform the
> translation.  That's how it always has been, and IMO always will be.  Of
> course it behoves (behooves?) the sender to point to or make available any
> necessary translation tools, such as a dictionary or glossary, but once
> that is done it is the responsibility of the receiver to make use of those
> tools.  Even better if you can point to formally-published information
> (i.e. book or peer-reviewed paper), since information on the web is so
> ephemeral.  As a receiver of information myself that's what my brain is
> doing constantly, i.e. converting others' terminology into concepts my
> brain can process.  If I'm forced to write code using a different set of
> terms it's inevitable that I will unconsciously lapse into my old bad ways
> and I'll end up with a dog's breakfast!  If I'm constantly having to
> convert my terminology into some standardised (standardized?) terminology
> before committing it to code, I'm going to use up what little brainpower I
> have left!
>
>
>
> The absolutely critical thing surely is to DEFINE all terms that might be
> unfamiliar or ambiguous (yes Bernhard, I abhor a definitional vacuum for
> this very reason!).  That way the developers feel 

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

[David Waterman]

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 terminal.
On a Mac this will be something like "source
/Applications/ccp4-7.1/bin/ccp4.setup-sh". Please note that not everything
is guaranteed to work in CCP4i.

Best wishes
-- David


On Sun, 28 Jun 2020 at 07:42, Luca Mazzei  wrote:

> Dear CCP4 people,
> Can you help me with this?
> At the end of installation of CCP4 7.1 on Mac with OS Mojave, CCP4 folder
> contains ccp4i2 icon, whereas ccp4 icon is not present. This way I can not
> launch the old interface, neither by clicking on the invisible icon nor
> using the terminal. I just fixed the problem by a copy-and-paste of the
> ccp4 icon coming from another Mac on which CCP4-7.0 is installed and It
> seems to work well (I ran Refmac, Coot and Molrep with success usingthe old
> interface)! Do you have any suggestion on why this occurs and how to
> overcome this problem in a more efficient way?
>
> Thanks in advance,
>
> Luca
>
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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

[David Waterman]

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 many ways: the summation integration and profile-fitted
intensities are separate measurements, are they not? Also, one can measure
the background intensity, the position, spot skewness and an
inexhaustible number of other quantities from a single observed Bragg spot.
So perhaps Observations Per Reflection (OPR) is better, but is there really
a difference between observation and measurement? Perhaps each reflection
is already a separate event, in which case Reflections Per Miller Index
(RPMI) looks better. However, what about the term "reflection" itself, is
that precise enough for us...?

-- David


On Wed, 1 Jul 2020 at 19:52, James Holton  wrote:

>
> Sorry to take this thread on a detour/diversion: What I was attempting to
> point out below, perhaps unclearly, is that the different interpretations
> of the word "redundant" are a cultural difference.  As a student of
> multiple English languages perhaps I can explain:
>
> Few US English speakers know that in UK/European/Australian English the
> word "redundant" has a strong negative connotation. I, for one, was
> surprised to learn that the phrase "made redundant" is used in the UK to
> describe loss of employment.  That is, a layoff, firing or perhaps a
> furlough. So, I think it important to spell out for my fellow US English
> speakers that the emotional ties to this negative connotation can be strong
> ones.
>
> Conversely, many UK English speakers do not know that in US English the
> word "redundant" has a strong positive connotation.  We never use the
> phrase "made redundant" to describe a lost job.  Most Americans I think
> would be confused by such a turn of phrase. If a US English speaker was
> told their jobs was "made redundant" they would most likely think that a
> new hire was onboarded to back them up.  This would imply that their job
> was so important that the company wanted at least two people doing it, just
> in case you got hit by a bus. This strong positive connotation also has
> emotional roots.
>
> Personally, I prefer the positive connotation. Perhaps that is my cultural
> bias, or perhaps I just generally believe that positivity is better than
> negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has
> changed enormously over the last few hundred years, and I don't think we're
> going to change that any more than we are going to change the meaning of
> "redundant" in these two major forms of English.
>
> However, just because a word has slightly different meanings in two
> slightly different languages does not mean we should abandon it.  Are we
> going to stop eating "chips" just because we are not sure if our fried
> potato will come as sliced wedges or thin crispy wafers? If you are unhappy
> with your meal, is it the fault of the culture you are visiting? or the
> customer for forgetting where they are? Context is everything.
>
> So, for those unfamiliar with one or more of the major English-speaking
> cultures, here are a few other important differences to be aware of:
> "Football" may not be the game you think it is.
> If you are offered a "biscuit" in the US, do not expect it to be sweet.
> If you want to leave a building you should take the "lift" to the "ground
> floor", but if you take an "elevator" get off on the "1st floor".
> A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it
> only means an unintelligent person, or a plastic replica of one.
> "please" and "thank you" are considered baseline politeness in some
> English cultures, but their excessive use in others, such as the US, can be
> seen as rude.
> A "tap" in the US dispenses beer, water comes out of a "faucet".
> A "flat" in the US is not a place to live, but rather where we test rocket
> cars.
> "Gas" can be a liquid in the US.
> "Rubber" is a substance in both languages, but in the US a lump of it
> meant for erasing pencil marks is an "eraser". Do not ask for a "rubber" at
> the shop unless you are sure which country you are in.
> A "holiday" in the US is a special day on the calendar when everyone gets
> off work, not just when an individual takes a "vacation".
> If you go walking down the "pavement" you are risking getting hit by a car
> in the US, because that is what we call the road bed, not the "sidewalk".
> A "torch", is a handheld electric light in the UK, but in the US it is a
> flaming stick of wood.
> A "queue" is a line of people in the UK, but in the US it is known only to
> computer scientists submitting jobs on a cluster.
>
> Then there are words like "capillary", which means the same thing in both
> languages but the alternate pronunciations never fail to enrage someone. It
> is perhaps odd that since US 

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

[David Waterman]

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 David Waterman,  wrote:

> 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
>> > least not replace them when they fail?
>> >
>> > On 06/29/2020 06:24 PM, Andreas Förster wrote:
>> >> I like to think that the reflections I carefully measured at high
>> >> multiplicity are not redundant, which the dictionary on my computer
>> >> defines as "not or no longer needed or useful; superfluous" and the
>> >> American Heritage Dictionary as "exceeding what is necessary or
>> >> natural; superfluous" and "needlessly repetitive; verbose".
>> >>
>> >> Please don't use the term Needless repetitivity in your Table 1.  It
>> >> sends the wrong message.  Multiplicity is good.
>> >>
>> >> All best.
>> >>
>> >>
>> >> Andreas
>> >>
>> >>
>> >>
>> >> On Tue, Jun 30, 2020 at 12:03 AM James Holton > >> <mailto:jmhol...@lbl.gov>> wrote:
>> >>
>> >> I have found that the use of "redundancy" vs "multiplicity"
>> >> correlates very well with the speaker's favorite processing
>> >> software.  The Denzo/HKL program scalepack outputs "redundancy",
>> >> whereas scala/aimless and other more Europe-centric programs output
>> >> "multiplicity".
>> >>
>> >> At least it is not as bad as "intensity", which is so ambiguous
>> >> as to be almost useless as a word on its own.
>> >>
>> >> -James Holton
>> >> MAD Scientist
>> >>
>> >> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
>> >>>
>> >>> > Oh, and some of us prefer the word 'multiplicity' ;-0
>> >>>
>> >>> Hmmm…maybe not. ‘Multiplicity’ in crystallography is context
>> >>> sensitive, and not uniquely defined. It can refer to 
>> >>>
>> >>>  1. the position multiplicity (number of equivalent sites per
>> >>> unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of
>> >>> multiplicity
>> >>>  2. the multiplicity of the reflection, which means the
>> >>> superposition of reflections with the same /d/  (mostly powder
>> >>> diffraction) 
>> >>>  3. the multiplicity of observations, aka redundancy.
>> >>>
>> >>> While (a) and (b) are clearly defined, (c) is an arbitrary
>> >>> experimental number.
>> >>>
>> >>> How from (a) real space symmetry follows (b) in reciprocal space
>> >>> (including the epsilon zones, another ‘multiplicity’) is explained
>> >>> here 
>> >>>
>> >>> https://scripts.iucr.org/cgi-bin/paper?a14080
>> >>> <
>> https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/paper?a14080__;!!GobTDDpD7A!Z-SrnEqSZwQOXWOwbMCkZ1GB3fvdFuQ5lzYUYwQdUVTCALc3j9O3xqX7-s72_nF7$>
>>
>> >>> 
>> >>>
>> >>> and also on page 306 in B

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

[David Waterman]

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
> > least not replace them when they fail?
> >
> > On 06/29/2020 06:24 PM, Andreas Förster wrote:
> >> I like to think that the reflections I carefully measured at high
> >> multiplicity are not redundant, which the dictionary on my computer
> >> defines as "not or no longer needed or useful; superfluous" and the
> >> American Heritage Dictionary as "exceeding what is necessary or
> >> natural; superfluous" and "needlessly repetitive; verbose".
> >>
> >> Please don't use the term Needless repetitivity in your Table 1.  It
> >> sends the wrong message.  Multiplicity is good.
> >>
> >> All best.
> >>
> >>
> >> Andreas
> >>
> >>
> >>
> >> On Tue, Jun 30, 2020 at 12:03 AM James Holton  >> > wrote:
> >>
> >> I have found that the use of "redundancy" vs "multiplicity"
> >> correlates very well with the speaker's favorite processing
> >> software.  The Denzo/HKL program scalepack outputs "redundancy",
> >> whereas scala/aimless and other more Europe-centric programs output
> >> "multiplicity".
> >>
> >> At least it is not as bad as "intensity", which is so ambiguous
> >> as to be almost useless as a word on its own.
> >>
> >> -James Holton
> >> MAD Scientist
> >>
> >> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
> >>>
> >>> > Oh, and some of us prefer the word 'multiplicity' ;-0
> >>>
> >>> Hmmm…maybe not. ‘Multiplicity’ in crystallography is context
> >>> sensitive, and not uniquely defined. It can refer to 
> >>>
> >>>  1. the position multiplicity (number of equivalent sites per
> >>> unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of
> >>> multiplicity
> >>>  2. the multiplicity of the reflection, which means the
> >>> superposition of reflections with the same /d/  (mostly powder
> >>> diffraction) 
> >>>  3. the multiplicity of observations, aka redundancy.
> >>>
> >>> While (a) and (b) are clearly defined, (c) is an arbitrary
> >>> experimental number.
> >>>
> >>> How from (a) real space symmetry follows (b) in reciprocal space
> >>> (including the epsilon zones, another ‘multiplicity’) is explained
> >>> here 
> >>>
> >>> https://scripts.iucr.org/cgi-bin/paper?a14080
> >>> <
> https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/paper?a14080__;!!GobTDDpD7A!Z-SrnEqSZwQOXWOwbMCkZ1GB3fvdFuQ5lzYUYwQdUVTCALc3j9O3xqX7-s72_nF7$>
>
> >>> 
> >>>
> >>> and also on page 306 in BMC.
> >>>
> >>> Too much multiplicity might create duplicity… 
> >>>
> >>> Cheers, BR
> >>>
> >>> __ __
> >>>
> >>> Jon Cooper
> >>>
> >>> __ __
> >>>
> >>> On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)"
> >>> mailto:tom.p...@csiro.au>> wrote:
> >>>
> >>> I would just like to point out that for those of us who have
> >>> worked too many times with P1 or P21 that even 360 degrees will not
> >>> give you 'super' anomalous differences. 
> >>>
> >>> I'm not a minimalist when it comes to data- redundancy is a
> >>> good thing to have. 
> >>>
> >>> cheers, tom 
> >>>
> >>> __ __
> >>>
> >>> Tom Peat
> >>> Proteins Group
> >>> Biomedical Program, CSIRO
> >>> 343 Royal Parade
> >>> Parkville, VIC, 3052
> >>> +613 9662 7304
> >>> +614 57 539 419
> >>> tom.p...@csiro.au  
> >>>
> >>> __ __
> >>>
> >>>
> 
> > --
> >>>
> >>> *From:*CCP4 bulletin board  >>> > on behalf of
> >>> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk
> >>> 
> >>> 

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

[David Waterman]

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 surprised me greatly. I wondered if perhaps you were referring to the
ccp4i2 GUI for xia2, for which I must admit responsibility. However, I
can't find "Copyright (C) 2013 David Waterman" anywhere within the current
release of CCP4, so I am perplexed.

I would like to make it clear that xia2 is not distributed under the terms
of the CCP4 licence. It has a permissive free software licence, namely
BSD-3, which must surely conform to any reasonable definition of Open
Source. See here https://github.com/xia2/xia2/blob/master/LICENSE

While xia2 has certain modes that run non-open software, Graeme's point is
that the default mode runs DIALS, which is BSD-3 as well.

-- David


On Thu, 7 May 2020 at 18:56, Ethan A Merritt  wrote:

> On Thursday, 7 May 2020 10:18:38 PDT Roversi, Pietro (Dr.) wrote:
> > Thank you Ethan for taking the the time to answer and explain.
> > Yes I am sure I have asked a vague and imprecise question.
> >
> > Practically, I am going to point to xia2 for data processing:
> >
> https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Xia2/manual.html
> >
> > and hope it is "Open Source enough" - without too much scrutiny on
> dependencies?
>
> I may misundertand the full scope of xia2, but I believe it is a scripted
> pipeline
> that invokes other programs.  Those other programs individually may have
> their own very different licensing or distribution or use restrictions.
> The user guide you linked to says
> if you use xia2 in published work please include the references
> for the programs it has used, which are printed at the end of the
> output.
>
> 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.
>
> So I guess the first question is whether the CCP4 License Agreement
> meets your definition of Open Source.
>
> The next question would be what programs did xia2 choose to run?
> Some of these may meet your criteria for Open Source, others not.
> For example, does xia2 invoke shelx?  Does shelx meet your criteria?
>
> Ethan
>
>
>
> >
> > So, what about a refinement suite of programs that is "just as Open
> Source" as xia2 is for data processing?
> >
> > Unless this second message of mine is making my re-drafted question
> worse than the original one .
> >
> > with best wishes,
> >
> > Pietro
> >
> >
> > Pietro Roversi
> >
> > Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
> >
> > LISCB Wellcome Trust ISSF Fellow
> >
> > <https://bit.ly/2I4Wm5Z>
> https://le.ac.uk/liscb/research-groups/pietro-roversi
> >
> >
> > Leicester Institute of Structural and Chemical Biology
> > Department of Molecular and Cell Biology, University of Leicester
> > Henry Wellcome Building
> > Lancaster Road, Leicester, LE1 7HB
> > England, United Kingdom
> >
> > Skype: roversipietro
> > Mobile phone  +44 (0) 7927952047
> > Tel. +44 (0)116 2297237
> >
> >
> >
> > 
> > From: Ethan A Merritt 
> > Sent: 07 May 2020 18:08
> > To: Roversi, Pietro (Dr.) 
> > Cc: CCP4BB@jiscmail.ac.uk 
> > Subject: Re: [ccp4bb] What refinement programs are fully Open Source?
> >
> > On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
> > > Dear all,
> > >
> > > we are in the editorial stages of a manuscript that I submitted to
> Wellcome Open Research for publication.
> > >
> > > The journal/editor ask us to list fully Open Source alternatives to
> the pieces of software we used, for example for data processing and
> refinement.
> > >
> > > What refinement programs are fully Open Source?
> >
> > There are recurring battles and philosophical fractures over what exactly
> > "open source" means, either in practice or aspirationally.
> > You would do well to provide a definition before asking people for
> > suggestions that meet your criteria.
> >
> > At one point the Open Source Foundation (OSF) claimed to have the
> authority
> > to declare something was or was not "open source" and kept lists of
> &

Re: [ccp4bb] CCP4 7.1 released

[David Waterman]

o have contributed to CCP4
> 7.1, and all of those who have helped in testing it. The following
> publication should be used to cite the use of CCP4:
>
> M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R.
> Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J.
> McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R.
> J. Read, A. Vagin and K. S. Wilson (2011) *Overview of the CCP4 suite and
> current developments*, Acta Cryst *D67* 235-242.
>
> Use of individual CCP4 programs should be acknowledged also by the
> citation of respective publications, where required (please cf. from
> program documentation). CCP4 is supported by the BBSRC UK through grant
> BB/S006974/1 (CCP4 Advanced Integrated 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 underlying
> libraries. Despite all the effort we've made, bugs and unforeseen
> “features” will most certainly be found in the Suite, which has grown
> substantially in size. When bugs and errors are discovered, the best way to
> deal with them is to report them to us at c...@stfc.ac.uk. We value
> highly all feedback from our users, and together we will bring CCP4 yet
> closer to community expectations and standards.
>
> Many thanks for being CCP4 users,
>
> Eugene Krissinel
>
> on behalf of CCP4 Core Group:
>
> Charles Ballard
> Andrey Lebedev
> Ronan Keegan
> David Waterman
> Kyle Stevenson
> Ville Uski
> Oleg Kovalevskiy
> Tarik Drevon
> Karen McIntyre
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> -
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Vote for cryoEM

[David Waterman]

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 personally don't tweet.
>>
>>
>> On Tue, Mar 31, 2020 at 12:21 PM Sweet, Robert <
>> 27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Real Men (and possibly Women too) Don't Tweet.
>>>
>>> Bob
>>>
>>> 
>>> From: CCP4 bulletin board  on behalf of James
>>> Holton 
>>> Sent: Tuesday, March 31, 2020 12:18 PM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] Vote for cryoEM
>>>
>>> Allessandro,
>>>
>>> The link you provide directs to a website hosted at someting called "
>>> twitter.com".  My spam filter flagged it as junk.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 3/31/2020 8:41 AM, Alessandro Vannini wrote:
>>> We are head to head with mass-spectrometry in the #JBCMethodsMadness
>>> CHAMPIONSHIP. This can’t happen!
>>>
>>> Get out and VOTE! 15 min to go!
>>>
>>> https://twitter.com/jbiolchem/status/1244655631316987905?s=20<
>>> https://urldefense.com/v3/__https://twitter.com/jbiolchem/status/1244655631316987905?s=20__;!!P4SdNyxKAPE!QXCVmZuWG8FEmwM9FbPP-f3LEbH6bMcORBgYwRGHCpxZF7cWEHW9OsXmS5uQ_Q$
>>> >
>>>
>>> [cid:part2.4691618D.6AA0935A@lbl.gov]
>>>
>>> Sent from my iPhone
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<
>>> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!QXCVmZuWG8FEmwM9FbPP-f3LEbH6bMcORBgYwRGHCpxZF7cWEHW9OsUFmMKe0Q$
>>> >
>>>
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<
>>> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1__;!!P4SdNyxKAPE!QXCVmZuWG8FEmwM9FbPP-f3LEbH6bMcORBgYwRGHCpxZF7cWEHW9OsUFmMKe0Q$
>>> >
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
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[ccp4bb] PRACE fights against COVID-19 - fast track call for proposals is open!

[David Waterman]

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 track review process to provide
> swift feedback to the applicants.
> This call is open until further notice. Applications are evaluated within
> one week and start as soon as possible if awarded.
>
> Please find full details of the call here:
> https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/
> <
> https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/
> >
>
> Best regards,
> Marc
> --
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baa...@smplinux.de  -  http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217



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Re: [ccp4bb] CCP4BB vs COVID19

[David Waterman]

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 community is pretty good with this too. Perhaps
there are some opportunities to help out here, for those who can still get
to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  That, I believe, is interesting.  Espeically since they are
> so far apart I expect this selective pressure might work in trans: as in
> a super-infection. That is, the S and L genome types may interfere with
> each other.
>
> The authors fall short of claiming evidence of interference upon
> super-infection, and indeed they have already been criticised for
> calling "L" the "aggressive" type.  But it is still interesting and
> points a finger at ORF8.
>
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a
> stretch of 60 residues.  This homologous region contains the S84L site
> (Val I544 in 5o32).  I had a quick look and appears to be a
> cavity-filling mutation to me.  Not very big, but maybe something could
> fit in there.  To be sure we'd need a structure of ORF8.
>
> Good luck to you all, and stay healthy.
>
> -James Holton
> MAD Scientist
>
> 

Re: [ccp4bb] Running CCP4_Blend on Mac

[David Waterman]

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 trying to run Blend program from CCP4interface (7.0.078) to merge
> multiple datasets (9). I am running the CCP4 on Mac mojave 10.14.6 OS and
> installed R program in /usr/local/bin/R. In the CCP4 interface, the same
> path is added under system administration/configure interface/external
> programs/add a program/. When i start the blend program, it is showing
> Dependency error: BLEND requires R. Am I missing something here.
> Please advise me running blend through ccp4 interface?
>
>
> Thank you,
> --
> ravi kumar
>
> --
>
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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Waterman]

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 lack of POINTLESS and AIMLESS lines within the
history. As Graeme says, I think there are opportunities here for more
sophisticated tracking of provenance - certainly going back as far as
telling us where and when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Not quite relevent but is there some way of stamping these files with a
> record of where they were generated ?
> I used to use my ability to read - name them myself as
> SAMPLEX-dialsprocessing-unmerged.mtz then
> SAMPLEX-dialsprocessing-unmerged-staranisod.mtz
>
> and there is an mtz feature which wrote a history with dates as well but
> now with automated file naming it is hard to keep track of how a file was
> generated.
>
>
> It seems likely that lots of Table !s do not describe the data set that
> was actually used for structure solution and deposition!
>
> Eleanor
>
> On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:
>
>> Dear  Dave, Star Aniso Developers,
>>
>> If this turns out to be because we are “missing something” i.e. there is
>> an expectation on a property being present in the output files but it’s not
>> there in our MTZ output, please let us know :-)
>>
>> Best wishes Graeme
>>
>> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
>> wrote:
>>
>> Dear ccp4bb
>>
>> I am trying to get the staraniso server to accept a scaled but unmerged
>> mtz file from DIALS processing, but it reports an “Internal Server Error”
>> after thinking about it for a while. Should this be possible? The file is
>> 31 MB, so not huge.
>>
>> It works fine for a merged mtz from DIALS, but this is not the preferred
>> option and I don’t get the full statistics I need for Table 1.
>>
>> Thanks in advance
>>
>> Dave Lawson
>>
>> ---
>>
>> Prof. David M. Lawson
>> Department of Biological Chemistry,
>> John Innes Centre,
>> Norwich,
>> NR4 7UH, UK.
>> Tel: +44-(0)1603-450725
>> Web: https://www.jic.ac.uk/people/david-lawson
>> Email: david.law...@jic.ac.uk
>>
>>
>> --
>>
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>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>>
>>
>> --
>>
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>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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>>
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>>
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>
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[ccp4bb] Study Weekend 2020 live stream

[David Waterman]

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



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Re: [ccp4bb] CCP4 Computational Scientist

[David Waterman]

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 scientist to work on a research project
> in Electron Diffraction. The Project is funded by BBSRC UK, and will be
> conducted in CCP4 Core Group based in Rutherford Appleton Laboratory, UK.
>
> For full job details and direct links to online application portal, please
> visit one of the following web-sites:
>
> https://www.topcareer.jobs/Vacancy/irc250548_10011.aspx
> https://findajob.dwp.gov.uk/details/3026333
> https://brightrecruits.com/jobs/ccp4-computational-scientist
>
> All informal enquires may be sent to eugene.krissi...@stfc.ac.uk
>
> Kind regards,
> Eugene Krissinel.
>
>
>
>
>
>
> --
>
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[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2019

[David Waterman]

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 and early career scientists,

Please consider applying for the sixth joint DLS/CCP4 workshop on MX data
collection and structure solution, to be held at Diamond Light Source, UK
from the 1st to the 8th December 2019.

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2019/

The workshop has been very successful in previous years, as shown by
acknowledgements given in publications from attendees of the course:

http://www.ccp4.ac.uk/schools/DLS-school/index.php

The application period is now open and will* close on the 18th October*.
Applicants will be required to submit a CV/resume, 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)



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[ccp4bb] DLS/CCP4 data analysis workshop 2019

[David Waterman]

PhD students, postdocs and early career scientists,

Please consider applying for the sixth joint DLS/CCP4 workshop on MX data
collection and structure solution, to be held at Diamond Light Source, UK
from the 1st to the 8th December 2019.

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2019/

The workshop has been very successful in previous years, as shown by
acknowledgements given in publications from attendees of the course:

http://www.ccp4.ac.uk/schools/DLS-school/index.php

The application period is now open and will* close on the 18th October*.
Applicants will be required to submit a CV/resume, 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)



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

[David Waterman]

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 Peligro, 
wrote:

> Following my last question I was searching for a redundant PDB and found
> this paper https://doi.org/10.1016/j.str.2007.07.012. I went to the
> methods section and found out that the link to the database of redundant
> protein structures is now gone (http://dper.burnham.org/). Anyone knows
> of a similar database? Or anyone knows how to make one?
>
> Thanks again for your help.
>
>
> Murph
>
> El jue., 19 de sep. de 2019 a la(s) 19:04, Dale Tronrud (
> de...@daletronrud.com) escribió:
>
>>
>>My recollection is that gamma-chymotrypsin crystals will persist in
>> pHs all the way from 3 to 9.  I don't know if the crystals will grow
>> over that range.
>>
>>There are a fair number of phage T4 lysozymes variants in the PDB.  I
>> don't think this is considered "overpopulation" but a valuable
>> contribution to humanity.  ;-)
>>
>> Dale Tronrud
>>
>> On 9/19/2019 4:03 PM, Murpholino Peligro wrote:
>> > A quick glance at the entries of hen egg white lysozyme in the PDB show
>> > that it can be crystallized at different pH values, but the space group
>> > is not always the same. I still have to refine the analysis but I was
>> > wondering that maybe there are a few proteins that can crystallize at a
>> > wide range (maybe not that wide) of pH values and still have the same
>> > space group?
>> >
>> > To refine the analysis a wee further: By any chance do you know any
>> > proteins overpopulating the PDB (i.e. besides HEWL)?
>> >
>> > Lots of thanks as always.
>> >
>> > Murphy
>> >
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> >
>>
>
> --
>
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>



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

[David Waterman]

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 RAM (and that
might not be enough if you've got a big unit cell, low dose, fine-slicing
and want to use > 1 processor). However, I'm led to believe that fewer
people process synchrotron data sets off site these days.

Cheers

-- David


On Wed, 14 Aug 2019 at 08:37, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> A 10 year old laptop (64 bit) with Linux on it will be absolutely fine ;-)
>
> Sent from Yahoo Mail on Android
> 
>
> On Wed, 14 Aug 2019 at 6:22, Matthew Bratkowski
>  wrote:
> Hi,
>
> Can anyone recommend a good desktop computer for running crystallography
> programs?  I am looking for a Mac or Linux computer that is relatively fast
> and moderately priced.  I am not interested in building my own system; I
> want a computer that ready to use right out of the box.  Any suggestions
> would be appreciated.
>
> Thanks,
> Matt
>
> --
>
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>
>
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>
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[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2018

[David Waterman]

Dear all,

The application period for this year's DLS/CCP4 workshop closes this
Sunday. Please get your applications in soon if you would like the
opportunity to collect data at the UK's national synchrotron light source,
and get help from leading experts on your own projects.

Best wishes
-- 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 2nd
> to the 9th December (with accommodation from the 1st).
>
> This course offers the opportunity for you to work alongside leaders in
> the field of MX on data from your own crystals. For more details please
> check here:
>
> http://www.ccp4.ac.uk/schools/DLS-2018/
>
> The application period is now open and will close on the *7th October*.
> Applicants will be required to submit a CV/resume, 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)
>
>



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

[David Waterman]

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 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 2nd
> to the 9th December (with accommodation from the 1st).
>
> This course offers the opportunity for you to work alongside leaders in
> the field of MX on data from your own crystals. For more details please
> check here:
>
> http://www.ccp4.ac.uk/schools/DLS-2018/
>
> The application period is now open and will close on the *7th October*.
> Applicants will be required to submit a CV/resume, 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)
>
>



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

[David Waterman]

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:
https://dials.github.io/documentation/tutorials/correcting_poor_initial_geometry_tutorial.html.
As the tutorial states,

This is a challenging dataset to process. There are a combination of
problems, including:

   - A ‘reversed’ rotation axis
   - Incorrect beam centre recorded in the image headers
   - Split spots
   - Multiple lattices
   - Systematically weak spots that may correspond to pseudocentring

Cheers
-- David


On Tue, 25 Sep 2018 at 18:27, Whitley, Matthew J  wrote:

> Dear colleagues,
>
> I want to thank the following people for providing suggestions and
> comments about ‘difficult’ datasets suitable for teaching data processing:
>
> Tim Craig
> Jacob Keller
> Graeme Winter
> Aleksandar Bijelic
> Clemens Vonrhein
> Loes Kroon-Batenburg
> James Holton
>
> If anyone else has suggestions for good datasets for teaching processing,
> I would still be happy to hear them.
>
> Finally, several people asked me to make available a list of all the
> dataset suggestions I receive.  I am happy to do so, and I will post a
> message to this list when the information is up and available, probably
> later in the fall.
>
>
> Sincerely,
> Matthew
>
>
>
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
>
>
>
>
> On 9/19/2018 5:15 PM, Whitley, Matthew J wrote:
>
> Dear colleagues,
>
> For teaching purposes, I am looking for a small number (< 5) of
> macromolecular diffraction datasets (raw images) that might be
> considered 'difficult' for a beginning crystallography student to
> process.  By 'difficult' I generally mean not able to be processed
> automatically by a common processing package (XDS, Mosflm, DIALS, etc)
> using default settings, i.e., no black box "click and done" processing.
> The datasets I am looking for would have some stumbling block such as
> incorrect experimental parameters recorded in the image headers,
> multiple lattices that cause indexing to fail, datasets for which
> determining the correct space group is tricky, datasets for experiments
> in which the crystal slipped or moved in the beam, or anything else you
> can think of.  The idea is for these beginning students to examine
> several datasets that highlight various phenomena that can lead one
> astray during processing.
>
> A good candidate dataset would also ideally comprise a modest number of
> images so as to keep integration time to a minimum.  Factors that are
> mostly irrelevant for my purpose: resolution (as long as better than
> ~3.5 Å), source (home vs synchrotron), presence/absence of anomalous
> scattering,  presence/absence of ligands, monomeric vs oligomeric
> structures, etc.  Also, to be clear, I am not looking for datasets that
> have so many pathologies that they would require many long hours of work
> for an expert to process correctly.
>
> I have checked public repositories such as proteindiffraction.org and
> SBGrid databank, but all of the datasets I acquired from these sources
> process satisfactorily with little effort, and in any event I know of no
> way to search for 'challenging' datasets.  (I also wonder whether
> anybody is in the habit of depositing, shall we say, less-than-pristine
> images to public repositories?)
>
> If you know of such a dataset that is already publicly available, or if
> you have such a dataset that you are willing to share for solely
> educational purposes, I would appreciate hearing from you, either on- or
> off-list.
>
> Thank you in advance for your suggestions.
>
> Matthew
>
>
>
>
> --
>
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>



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

[David Waterman]

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:

> 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 2nd
> to the 9th December (with accommodation from the 1st).
>
> This course offers the opportunity for you to work alongside leaders in
> the field of MX on data from your own crystals. For more details please
> check here:
>
> http://www.ccp4.ac.uk/schools/DLS-2018/
>
> The application period is now open and will close on the *7th October*.
> Applicants will be required to submit a CV/resume, 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)
>
>



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[ccp4bb] DLS/CCP4 data analysis workshop 2018

[David Waterman]

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 2nd
to the 9th December (with accommodation from the 1st).

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2018/

The application period is now open and will close on the *7th October*.
Applicants will be required to submit a CV/resume, 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)



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

[David Waterman]

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 from the most
recent) and then the last few updates applied. This will help improve the
speed of installation, while still allowing a few updates to be rolled
back, if required. The final kinks are being ironed out from the new
installers at the moment, so these should be available fairly soon. There
will eventually be a new release of CCP4, resetting the update count to
zero, but that's a longer term plan.

Cheers
-- David


On Sat, 7 Jul 2018 at 19:12, Boaz Shaanan  wrote:

> Hi,
>
>
> For now, until there is a complete new version, I think that if you pick
> up the latest build from the ccp4 site it includes all the updates. I could
> be wrong though, but the CCP4 people will confirm this (or not).
>
>
> Cheers,
>
>
>   Boaz
>
>
>
>
>
>
>
>
>
>
>
>
> *Boaz Shaanan, Ph.D. Dept. of Life
> Sciences  Ben-Gurion University of the
> Negev  Beer-Sheva
> 84105
> Israel
> E-mail:
> bshaa...@bgu.ac.il  Phone: 972-8-647-2220
>Fax:   972-8-647-2992 or 972-8-646-1710*
>
>
>
>
>
>
>
> --
> *From:* CCP4 bulletin board  on behalf of Jan
> Stransky 
> *Sent:* Saturday, July 7, 2018 8:52 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Last few months updates, updated coot, ccp4i2,
> imosflm, etc
>
> Dear Charles,
> is there a plan to release new base package of CCP4 which would contain
> all updates, so we don't have to go through the already quite lengthy
> update process with new installations?
> Best regards,
> Jan
>
> On 07/05/2018 03:15 PM, Ballard, Charles (STFC,RAL,CSE) wrote:
> > For those of you not applying updates, the last few months updates have
> > included
> >
> > * phaser 2.8
> > * ccp4i2
> > * dials 1.9 (1.10 coming soon)
> > * ccp4mg
> > * coot 0.8.9.1
> >  * imosflm/ipmosfm 7.2.2
> >
> > plus interfaces to simbad, ample arcimboldo, and a dials gui DUI
> >
> > Update ID: 7.0.050
> > Date: 17.01.18
> >
> > Component  Description  Mac OS 64-bit   Linux 32-bitLinux
> 64-bitWindows
> > 32-bitWindows 64-bit
> > coot  0.8.9   yes yes yes -   -
> > aimless   0.6.2   yes yes yes yes yes
> >
> >
> > Update ID: 7.0.051
> > Date: 09.02.18
> >
> > Component  Description  Mac OS 64-bit   Linux 32-bitLinux
> 64-bitWindows
> > 32-bitWindows 64-bit
> > phaser2.8.2   yes yes yes yes yes
> > ccp4i updates for phaser 2.8  yes yes yes yes yes
> > arcimboldoupdates for phaser 2.8  yes yes yes yes yes
> > ample update to 1.4.1 yes yes yes yes yes
> > simbadupdate to 0.1.10yes yes yes -   -
> > dials update to 1.8.4 yes yes yes yes yes
> > ccp4i update for ampleyes yes yes yes yes
> >
> > Update ID: 7.0.052
> > Date: 28.02.18
> >
> > Component  Description  Mac OS 64-bit   Linux 32-bitLinux
> 64-bitWindows
> > 32-bitWindows 64-bit
> > ccp4i2Numerous bug fixes, improvments to stability, speed and
> > efficiencyyes yes yes yes yes
> >New: Arcimboldo yes yes yes -   -
> >New: Simbad yes yes yes -   -
> >New: Ample  yes yes yes yes yes
> >Enhancements to existing interfaces yes yes yes
> yes yes
> >New crystal definition and interface introduced yes yes
> yes yes yes
> >
> > Update ID: 7.0.053
> > Date: 19.03.18
> >
> > Component  Description  Mac OS 64-bit   Linux 32-bitLinux
> 64-bitWindows
> > 32-bitWindows 64-bit
> > ccp4mgfix issues with some refmac output  yes yes
> yes yes yes
> > pointless update to 1.11.10, read nXDS files  yes yes
> yes yes yes
> > buccaneer Bug fixes   yes yes yes yes yes
> > refmacBug fixes and speed enhancementsyes yes
> yes yes yes
> > crank2Bug fixes and enhancements  yes yes yes
> yes yes
> > arcimboldoBug fixes   yes yes yes yes yes
> > molrepBug fiesyes yes yes yes yes
> > fragon0.1.0, MR pipeline  yes yes yes -   -
> > acedrgNew features and bug fixes  yes yes yes
> yes yes
> > rabdamradition damage detection, command line onlyyes
> yes yes yes yes
> > clipper   bug fix in mtz writing routine  yes yes 

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

[David Waterman]

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. In a CCP4Console window cd to the directory C:\CCP4-7\7.0\
   5. Run the script InstallSetup.cmd by typing that name and pressing Enter
   6. Examine the log file called Installdisp.log (notepad.exe
Installdisp.log).
   You should see many lines with no errors, only some warnings.

Please let us know if this fixes the problem. We will release a fixed
installer soon.

-- David

On 12 February 2018 at 14:00, Vries, R.M.J.M. de 
wrote:

> Dear all,
>
>
>
> Although I normally use Linux for all my work with CCP4i2, I now use the
> Windows because of a workshop I will be giving. Here the audience is using
> Windows almost exclusively, therefore I chose to adapt to it.
>
>
>
> After using the xia2/DIALS pipeline I wanted to use the
> dials.reciprocal_lattice_viewer which, fortunately, worked absolutely
> fine (truly an amazing tool). I had to use the *CCP4 console *to make the
> dials-commands work. When I tried to apply the same method for the
> dials.image_viewer, it did not work. This is the console error message:
>
> https://pastebin.com/JNGRmu7G
>
>
>
> Which ends with:
>
> 1.  WindowsError: [Error 3] The system cannot find the path specified:
> 'c:\\ccp4-7\\7.0\\lib\\checkout\\cctbx-phaser\\cctbx_
> project\\rstbx\\slip_viewer/*.*'
>
> My slip_viewer is located in this directory by default:
>
> 'C:\CCP4-7\7.0\lib\py2\site-packages\cctbx_project\rstbx\slip_viewer'
>
>
>
> For me, the checkout folder in lib does not even exist. Any ideas to get
> around this problem?
>
>
>
> I am running CCP4i2 7.0.051 on Windows 7 (64 bit), but this error was also
> present on CCP4i2 7.0.051 on Windows 10 (64 bit).
>
>
>
> All the best,
>
>
>
> Rens de Vries
>
>
>

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

[David Waterman]

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> wrote:

> PhD students, postdocs and early career scientists,
>
> Please consider applying for the fourth joint DLS/CCP4 workshop on MX data
> collection and structure solution, to be held at Diamond Light Source, UK
> from the 30th November to the 7th December 2017.
>
> This course offers the opportunity for you to work alongside leaders in
> the field of MX on data from your own crystals. For more details please
> check here:
>
> http://www.ccp4.ac.uk/schools/DLS-2017/
>
> The application period is now open and will close on the 6th October.
> Applicants will be required to submit a CV/resume, 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)
>

[ccp4bb] DLS/CCP4 data analysis workshop 2017

[David Waterman]

PhD students, postdocs and early career scientists,

Please consider applying for the fourth joint DLS/CCP4 workshop on MX data
collection and structure solution, to be held at Diamond Light Source, UK
from the 30th November to the 7th December 2017.

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2017/

The application period is now open and will close on the 6th October.
Applicants will be required to submit a CV/resume, 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)

[ccp4bb] Senior scientist in crystallography - NovAliX

[David Waterman]

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

[David Waterman]

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

-- David

On 9 December 2016 at 14:59, "Weiergräber, Oliver H." <
o.h.weiergrae...@fz-juelich.de> wrote:

> Hello Paul and ccp4 devs,
>
> as I mentioned, the crashing coot version is the one provided with the
> latest ccp4 update(s), i.e.
>
> ---
> 0.8.7 (revision-count 6498)
> [with guile 1.8.8 embedded]
> [with python 2.7.10 embedded]
> Binary type: Linux-x86_64-centos-5-python-gtk2
> Builder_info: CCP4, Oxfordshire
> ---
>
> Running CentOS 6.8 here, but any EL6 incarnation should behave in the same
> way.
>
> This is the console output after invoking geometry analysis:
> ---
>  Unknown element ::
> /usr/local/ccp4-7.0/bin/coot: line 284: 17416 Segmentation fault
> (core dumped) $coot_bin "$@"
> coot-exe: "/usr/local/ccp4-7.0/libexec/coot-bin"
> coot-version:
> /usr/local/ccp4-7.0/libexec/coot-bin
> platform:
> /bin/uname
> core: #f
> No core file found.  No debugging
> ---
>
> Line 284 is just the final fi statement, without obvious (to me at least)
> relation to geometry analysis ...
>
> Hope this helps
> Oliver
>
> 
>   PD Dr. Oliver H. Weiergräber
>   Institute of Complex Systems
>   ICS-6: Structural Biochemistry
>   Tel.: +49 2461 61-2028
>   Fax: +49 2461 61-9540
> 
>
>
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul
> Emsley [pems...@mrc-lmb.cam.ac.uk]
> Sent: Friday, December 09, 2016 3:31 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Bug in latest COOT
>
> On 09/12/16 14:13, "Weiergräber, Oliver H." wrote:
> > Hello,
> >
> > after installing the latest ccp4 updates today, I found that coot will
> consistently crash (core dump) if geometry analysis is run on _any_
> structure containing an OXT atom.
> >
> >
>
> Hello Oliver,
>
> When reporting a bug you should try to include as much information as
> possible so that the developer can reproduce it.
>
> Ideally include a backtrace, but at the minimum you should include the
> operating system and version of coot that you are using:
>
> $ coot --version-full
>
> Having said that, I don't really follow what CCP4 do to Coot before they
> distribute the binaries.  Official coot binaries are tested before
> publication - so I'd recommend you use those.
>
> It goes without saying that I can't reproduce the problem that you
> mentioned - and even CCP4's build of Coot 0.8.7 (on Macintosh 10.10)
> seems not to have this problem.
>
> http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
>
> Paul.
>
>
> 
> 
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
> 
> 
>

[ccp4bb] Scientist Biacore SPR

[David Waterman]

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 &
development (medicinal

chemistry, protein x-ray crystallography, biophysics analysis). NovAliX
offers a complete

range of services in the field of small molecules early drug discovery. The
company has a

team of 90 scientists, its headquarters in Strasbourg-Illkirch (France) and
staff in France,

Spain and Belgium.

Location: Illkirch, France

Job description: Responsibilities of this role include:

- Ensure the good execution of the SPR Biacore projects.

- Design of assays & execute Biosensor experiments, such as compound
screening, hit

confirmation, determination of interactions affinity and kinetic analyses
thereof

using biosensor equipment such as Biacore T200.

- SPR data analysis and interpretation, troubleshooting.

- Reviewing, evaluating and communicating experience findings to the
customer.

- Reporting of results in a written format.

- Communicate regularly internally and with clients.

- Training lab staff when required.

Profile: We are looking for a dynamic and passionate scientist expert in
Biacore SPR to join our

Screening and Interaction Unit.

Major requirements:

- PhD in biophysics.

- At least 2 years of relevant experience in the SPR field with a proven
track record of

biological molecules characterization/analysis using SPR .

- Good practice of Biacore instruments in particular, and know-how in method

development using such instruments.

- Autonomous in conducting experiments, interpreting numerical data and
drawing

conclusions.

- Excellent written and verbal communication skills coupled with the
ability to

prioritize multiple tasks and have the confidence to challenge existing
systems &

processes.

Please send your application in English or French (CV, research work,
references) by email to:

pos...@novalix-pharma.com

NovAliX, BioParc, Boulevard Sébastien Brant, BP30170, F-67405 Illkirch CEDEX

Tel : +33 (0) 368 330 200 - Fax : +33 (0) 368 330 201 - Email :
i...@novalix-pharma.com

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

[David Waterman]

Dear all,

There are just two days left to submit applications for this year's
DLS/CCP4 workshop. If you are thinking of applying, please be aware that
the application form takes a bit of thought, so I would advise you to look
at it as soon as possible.

Thanks to all those who have already 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 who have submitted
> applications so far.
>
> Best wishes
>
> -- David
>
> On 1 September 2016 at 16:34, David Waterman <dgwater...@gmail.com> wrote:
>
>> PhD students, postdocs and early career scientists,
>>
>> Please consider applying for the joint DLS/CCP4 workshop on MX data
>> collection and structure solution, to be held at Diamond Light Source, UK
>> this December. This workshop is the third in an annual series styled on the
>> well-known APS/CCP4 summer schools and offers the opportunity for you to
>> work alongside leaders in the field of MX on data from your own crystals.
>> For more details please check here:
>>
>> http://www.ccp4.ac.uk/schools/DLS-2016/
>>
>> The application period will close on the 7th October. Applicants will be
>> required to submit a CV/resume, 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] Offtopic: Software to closely visualize interacting partnets in protein complex

[David Waterman]

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,

 Apologies for this little off-topic inquiry. I want to closely visualize
 the interacting residues in an multimeric protein complex to understand the
 nature of interactions. Is there any good software to give this information
 with good clarity.
 Any suggestion is highly appreciated.

 Thanks,
 Best !!!

 Debasish Kumar Ghosh

 CSIR- Junior Research Fellow (PhD Scholar)
 C/o: Dr. Akash Ranjan
 Computational and Functional Genomics Group
 Centre for DNA Fingerprinting and Diagnostics
 Hyderabad, INDIA

 Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
 Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
 Lab URL:
 http://www.cdfd.org.in/labpages/computational_functional_genomics.html

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

[David Waterman]

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 greater
moment of inertia than the case where there is one mass at each position.
This tells me that changes to the masses in the further spread case would
be more effective (faster) at changing the orientation of the rod. Then
it's a bit of leap I admit, but I felt that measurements of a line's height
made in such a way would be more effective at determining the fit
parameters than the evenly spread case.

But I decided not to rely on intuition when I could simulate it. At the
bottom of the message is a script in the R language that does 2 line
fits of the function y = m*x + c, where c = 100, m = 1 and x is the
sequence 1..10 for the first 1 fits and (1, 1, 1, 1, 1, 10, 10, 10, 10,
10) for the rest of them. The data being fit to are 'measurements' taken by
adding a standard normal deviate to x + 100 at each position.

After running all these simulations (it takes a few seconds) the script
then calculates the mean and standard deviations of the fit parameters, m
and c. The standard deviations are interesting:

mean intercept of fit1: 99.99619
sd of intercept of fit1 0.6833687

mean intercept of fit2: 99.99909
sd of intercept of fit2 0.498759

mean gradient of fit1: 1.00076
sd of gradient of fit1 0.1100296

mean gradient of fit2: 0.9996967
sd of gradient of fit2 0.07021113

Fit 2 has a tighter distribution for both the intercept and the gradient.
It is therefore the more precise way of fitting the line, and this was the
'heavy-ended' case.

Script follows:

line_fit - function(x_seq)
{
  y_seq - 100 + x_seq + rnorm(length(x_seq))
  return(coef(lm(y_seq~x_seq)))
}

even_spaced_x - seq(1,10)
heavy_ended_x - c(rep(1,5), rep(10,5))

fit1 - replicate(1, line_fit(even_spaced_x))
fit2 - replicate(1, line_fit(heavy_ended_x))

cat(mean intercept of fit1:, mean(fit1[1,]), \n)
cat(sd of intercept of fit1, sd(fit1[1,]), \n\n)

cat(mean intercept of fit2:, mean(fit2[1,]), \n)
cat(sd of intercept of fit2, sd(fit2[1,]), \n\n)

cat(mean gradient of fit1:, mean(fit1[2,]),\n)
cat(sd of gradient of fit1, sd(fit1[2,]), \n\n)

cat(mean gradient of fit2:, mean(fit2[2,]), \n)
cat(sd of gradient of fit2, sd(fit2[2,]), \n\n)


Cheers

-- David

On 22 January 2015 at 22:20, Keller, Jacob kell...@janelia.hhmi.org wrote:

 Dear Crystallographers,

 This is more general than crystallography, but has applications therein,
 particularly in understanding fine phi-slicing.

 The general question is:

 Given one needs to collect data to fit parameters for a known function,
 and given a limited total number of measurements, is it generally better to
 measure a small group of points multiple times or to distribute each
 individual measurement over the measureable extent of the function? I have
 a strong intuition that it is the latter, but all errors being equal, it
 would seem prima facie that both are equivalent. For example, a line (y =
 mx + b) can be fit from two points. One could either measure the line at
 two points A and B five times each for a total of 10 independent
 measurements, or measure ten points evenly-spaced from A to B. Are these
 equivalent in terms of fitting and information content or not? Which is
 better? Again, conjecture and intuition suggest the evenly-spaced
 experiment is better, but I cannot formulate or prove to myself why, yet.

 The application of this to crystallography might be another reason that
 fine phi-slicing (0.1 degrees * 3600 frames) is better than coarse (1
 degree * 3600 frames), even though the number of times one measures
 reflections is tenfold higher in the second case (assuming no radiation
 damage). In the first case, one never measures the same phi angle twice,
 but one does have multiple measurements in a sense, i.e., of different
 parts of the same reflection.

 Yes, 3D profile-fitting may be a big reason fine phi-slicing works, but
 beyond that, perhaps this sampling choice plays a role as well. Or maybe
 the profile-fitting works so well precisely because of this diffuse-single
 type of sampling rather than coarse-multiple sampling?

 This general math/science concept must have been discussed somewhere--can
 anyone point to where?

 JPK

 ***
 Jacob Pearson Keller, PhD
 Looger Lab/HHMI Janelia Research Campus
 19700 Helix Dr, Ashburn, VA 20147
 email: kell...@janelia.hhmi.org
 ***

Re: [ccp4bb] HKL2000 Display

[David Waterman]

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 
muhammad.bashir.k...@univie.ac.at wrote:

 Hi All;

 Could somebody explain why my Display image in HKL2000 look like that.
 Image attached.
 Thanks for help in advance.

 Bashir

 
 Department of Biochemistry
 University of Alberta
 Edmonton Canada

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

[David Waterman]

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 easily though, and I would be happy to provide one
off-list if you are interested. Scripts like this already exist in the
DIALS project (http://dials.sourceforge.net/ - try e.g. dials.import
/my/images/*.cbf; dials.show_models datablock.json).

Note that the dxtbx way is not giving you direct access to header values,
but will print information about experimental models constructed from the
headers. Usually this is what you want. If not, ADXV (
http://www.scripps.edu/tainer/arvai/adxv.html) is a useful tool that can
display image header values, but I don't know if this can be scripted to
print to console.

Cheers

-- David

On 1 December 2014 at 11:22, Takaaki Fukami fukami...@chugai-pharm.co.jp
wrote:

 Dear all,

 I'd like to dump header information of a diffraction image file.
 CCP4 diffdump is a good tool, though it outputs the same angle
 for both oscillation start and end for .cbf image. (bug?)

 Are there any other tools to get diffraction image header info?

 Regards

 -
 Takaaki Fukami (mailto:fukami...@chugai-pharm.co.jp)
 Discovery Research Dept. (Biostructure Gr.)
 Chugai Pharmaceutical Co.,Ltd.

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

[David Waterman]

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) you may
directly run a command like

$CCP4/share/python/CCP4Dispatchers/bin/refmac5

What happens here is that a Python dispatcher script is first started. This
sets the environment just prior to running the job as a subprocess, to
which it passes the command line and stdin. We developed this system a
little while back as an approach to avoid exporting the heavyweight
environment that CCP4 required. In practice, since then we have cleaned the
environment up so much that it is hardly a worry any more. The dispatchers
may still be of interest though for people who think it is barbaric to set
anything else other than PATH, or for people who regularly swap between
different versions of CCP4.

There is a side effect of creating the CCP4Dispatchers package that is in
fact much more interesting than avoiding explicit environment set up. That
is there is now a Python interface for running CCP4 programs that comes
free with the suite. This makes development of simple scripts and pipelines
very easy in Python. Please see the documentation for details (
http://www.ccp4.ac.uk/html/CCP4Dispatchers.html).

Cheers


-- David

On 16 November 2014 08:43, Folmer Fredslund folm...@gmail.com wrote:

 Dear Peter,

 Put your source command in your .bashrc file.

 It's a hidden file (because of the dot in the start) in your home folder
 and will be run every time you open a terminal, so any command inside
 will be executed.

 You can edit the file by typing
 gedit .bashrc
 Just after opening a terminal.

 If you just started using Linux and you're interested in an introduction
 to how Linux works, I'd recommend the Linux Foundations free online course

 https://www.edx.org/course/linuxfoundationx/linuxfoundationx-lfs101x-2-introduction-5386

 Especially if you are not working in a lab were people can help you with
 questions like the one you just asked.

 Venlig hilsen/Best regards
 Folmer Fredslund
 Den 16/11/2014 07.34 skrev 陈昂 angsc...@outlook.com:

 Dear all:

 I have installed CCP4 suit on my computer. The OS IS fedora 18. Every
 time I open the software, I have to

 use the command source. Does anyone else can run it in terminal without
 that command?

 Thank u so much!

 best regards,

 Peter

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

[David Waterman]

Dear all,

Please be aware that the application period for the first DLS/CCP4 data
analysis workshop closes on the 31st October. Successful applicants will be
notified shortly after that date.

As a reminder, the workshop is intended for PhD students, postdocs and
early career scientists who are *currently working on a project in MX, and
who are able to bring crystals or data with them*. The workshop will
consist of a mixture of lectures and tutorials, plus hands-on practical
sessions, in which the students will work alongside the leading software
developers and scientists on their own data. Applicants please note that
you must provide the e-mail address of a supervisor who will write a letter
in support of your application.

More details may be found here:
http://www.ccp4.ac.uk/schools/DLS-2014/index.php

The online application form is at Diamond's Events site:
http://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

[David Waterman]

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
package so you do not need to install it separately. In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk

Many thanks for using CCP4.

The CCP4 Core Team

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

[David Waterman]

Dear all,

Please be aware that the application period for the first DLS/CCP4 data
analysis workshop closes on the 31st October. Successful applicants will be
notified shortly after that date.

As a reminder, the workshop is intended for PhD students, postdocs and
early career scientists who are currently working on a project in MX, and
who are able to bring crystals or data with them. The workshop will consist
of a mixture of lectures and tutorials, plus hands-on practical sessions,
in which the students will work alongside the leading software developers
and scientists on their own data. Applicants please note that you must
provide the e-mail address of a supervisor who will write a letter in
support of your application.

More details may be found here:
http://www.ccp4.ac.uk/schools/DLS-2014/index.php

The online application form is at Diamond's Events site:
http://www.diamond.ac.uk/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

[David Waterman]

PhD students, postdocs and early career scientists,

Please consider applying for the first joint DLS/CCP4 workshop on MX data
analysis, this December. This workshop is styled on the highly successful
APS/CCP4 summer schools and offers the opportunity for you to work
alongside leaders in the field 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

[David Waterman]

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: BLEND example script
* iMosflm: Correct link to iMosflm web pages

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
package so you do not need to install it separately. In addition, all
available updates will be installed automatically if you are using
Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

Re: [ccp4bb] error in starting imosflm

[David Waterman]

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 April 2014 11:59, Ian Tickle ianj...@gmail.com wrote:

 Hi Felix

 You're very trusting!  Bugs in new versions of software are not unknown!
 The bug may not manifest itself in a program crash (though it makes life
 easier if it does), rather it may simply give different numerical results
 that you may not spot for some after.  This is why CCP4 distributes test
 data (in $CEXAM) for users to test the software (though the examples there
 are hardly comprehensive).  Most major software packages (e.g. LAPACK)
 provide comprehensive test suites that test all possible ways in which the
 software may be used so you can verify that the new version at least gives
 the same results as the distributor's test suite (this also checks whether
 there are machine dependencies).  So I need to run tests on the new version
  compare with results from the old one before I release it to users, for
 which I obviously need access to both versions.  Also the man pages are
 missing from the new version: I just find it quicker  easier to type 'man
 fft' or whatever than to fire up the browser.

 Cheers

 -- Ian


 On 29 April 2014 11:23, Felix Frolow mbfro...@post.tau.ac.il wrote:

 Hi Tim,
 What can be a reason to work with an obsolete version of CCP4?
 I remember reading somewhere that 6.3.0 version is obsolete.

 FF

  Dr Felix Frolow
 Professor of Structural Biology and Biotechnology, Department of
 Molecular Microbiology and Biotechnology
 Tel Aviv University 69978, Israel

 Acta Crystallographica F, co-editor

 e-mail: mbfro...@post.tau.ac.il
 Tel:  ++972-3640-8723
 Fax: ++972-3640-9407
 Cellular: 0547 459 608

 On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Sreetama, dear Ian,

 I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
 need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
 open a new terminal to make sure everything refers to v6.3 and vice versa.

 Best,
 Tim


 On 04/28/2014 04:51 PM, Ian Tickle wrote:

 Harry,

 I've run into this problem before with other programs when I switch
 between v6.3  v6.4.  I think the problem is this code in
 ccp4.setup-sh:

 if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
 $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} else
 PATH=${PATH}:${dir} fi fi

 Ignore the 'ccp4_first_in_path' business, unless the user has
 hacked the script it always takes the 'then' clause of the 'if' so
 it's actually doing this:

 if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
 $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} fi fi

 So what happens is that the first time you source the setup for
 v6.4 it prepends the directories for that version.  If you then
 source the setup for v6.3 it prepends the directories for that and
 you will use the v6.3 executables.  So far so good.  Now what
 happens if you source the setup for v6.4 again?  The code above
 ensures that the v6.4 directory is NOT prepended again and so it
 will continue to use v6.3 until you logout  in again  reset the
 path.

 Cheers

 -- Ian







 On 28 April 2014 14:54, Harry Powell ha...@mrc-lmb.cam.ac.uk
 wrote:

 Hi Sreetama

 That's the problem - sourcing the old ccp4 6.3 distro has set up
 MOSFLM_EXEC to point to an old copy of ipmosflm that will not run
 with the latest iMosflm.

 Mosflm version 7.0.9  for Image plate and CCD data 14th May
 2012


 which cannot be used with iMosflm 7.1.0.

 So it looks like there might be an issue with the ccp4 6.4 setup
 not over-writing the environment variable MOSFLM_EXEC as it
 should. The immediate way round this would be to not source ccp4
 6.3 in any terminal that you want to run iMosflm from.

 Can you send me  c...@stfc.ac.uk (*not* to the ccp4bb, please)
 the output of

 echo $PATH which $MOSFLM_EXEC

 (1) before you source ccp4-6.3 (2) after you source ccp4-6.3
 (3) after you source ccp4-6.4

 So that we can get a clear idea of what is happening to your PATH
 when you do each of these three things.

 On 28 Apr 2014, at 14:38, sreetama das wrote:

 Dear Sir, If I sorce ccp4-6.3, and then change in the bashrc
 file 

 source ccp4-6.4, (and source the modified .bashrc file in either
 case) but don't close the previous terminal, then opening imosflm
 gives the aforementioned error. After closing the imosflm GUI, if
 I type at the terminal, I get the following:


 sreetama@sreetama-laptop:~/data $ $MOSFLM_EXEC BFONT
 COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML
 LOGFILE -- hr !--SUMMARY_END--/FONT/B


  Mosflm version 7.0.9  for Image plate and CCD data
 14th

 May 2012  ***

 Andrew Leslie and Harry Powell, MRC Laboratory of Molecular
 

Re: [ccp4bb] error in starting imosflm

[David Waterman]

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 machine typing
/path/to/ccp4-6.4.0/share/python/CCP4Dispatchers/bin/imosflm starts imosflm
without anything needed to be sourced in the terminal beforehand. Of course
this is more useful if dispatchers are also generated for the other
versions of CCP4 you want to use. There are some instructions for doing
that in the link above, and the files you need are located in $CCP4/libexec
of a ccp4-6.4.0 install.

Cheers

-- David


On 28 April 2014 17:01, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Sreetama, dear Ian,

 I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
 need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
 open a new terminal to make sure everything refers to v6.3 and vice versa.

 Best,
 Tim


 On 04/28/2014 04:51 PM, Ian Tickle wrote:
  Harry,
 
  I've run into this problem before with other programs when I switch
  between v6.3  v6.4.  I think the problem is this code in
  ccp4.setup-sh:
 
  if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
  $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} else
  PATH=${PATH}:${dir} fi fi
 
  Ignore the 'ccp4_first_in_path' business, unless the user has
  hacked the script it always takes the 'then' clause of the 'if' so
  it's actually doing this:
 
  if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
  $ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} fi fi
 
  So what happens is that the first time you source the setup for
  v6.4 it prepends the directories for that version.  If you then
  source the setup for v6.3 it prepends the directories for that and
  you will use the v6.3 executables.  So far so good.  Now what
  happens if you source the setup for v6.4 again?  The code above
  ensures that the v6.4 directory is NOT prepended again and so it
  will continue to use v6.3 until you logout  in again  reset the
  path.
 
  Cheers
 
  -- Ian
 
 
 
 
 
 
 
  On 28 April 2014 14:54, Harry Powell ha...@mrc-lmb.cam.ac.uk
  wrote:
 
  Hi Sreetama
 
  That's the problem - sourcing the old ccp4 6.3 distro has set up
  MOSFLM_EXEC to point to an old copy of ipmosflm that will not run
  with the latest iMosflm.
 
  Mosflm version 7.0.9  for Image plate and CCD data 14th May
  2012
 
  which cannot be used with iMosflm 7.1.0.
 
  So it looks like there might be an issue with the ccp4 6.4 setup
  not over-writing the environment variable MOSFLM_EXEC as it
  should. The immediate way round this would be to not source ccp4
  6.3 in any terminal that you want to run iMosflm from.
 
  Can you send me  c...@stfc.ac.uk (*not* to the ccp4bb, please)
  the output of
 
  echo $PATH which $MOSFLM_EXEC
 
  (1) before you source ccp4-6.3 (2) after you source ccp4-6.3
  (3) after you source ccp4-6.4
 
  So that we can get a clear idea of what is happening to your PATH
  when you do each of these three things.
 
  On 28 Apr 2014, at 14:38, sreetama das wrote:
 
  Dear Sir, If I sorce ccp4-6.3, and then change in the bashrc
  file 
  source ccp4-6.4, (and source the modified .bashrc file in either
  case) but don't close the previous terminal, then opening imosflm
  gives the aforementioned error. After closing the imosflm GUI, if
  I type at the terminal, I get the following:
 
  sreetama@sreetama-laptop:~/data $ $MOSFLM_EXEC BFONT
  COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML
  LOGFILE -- hr !--SUMMARY_END--/FONT/B
 
 
   Mosflm version 7.0.9  for Image plate and CCD data
  14th
  May 2012  ***
  Andrew Leslie and Harry Powell, MRC Laboratory of Molecular
  Biology, Hills Road, Cambridge CB2 0QH, UK E-mails:
  and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk References:
  Mosflm: A.G.W. Leslie and H.R. Powell (2007), Evolving Methods
  for Macromolecular Crystallography, 245, 41-51 ISBN
  978-1-4020-6314-5
  New auto-indexing based on DPS: I. Steller R. Bolotovsky and
  M.G.
  Rossmann
  (1997) J. Appl. Cryst. 30, 1036-1040 New iMosflm GUI:  T.G.G.
  Battye, L. Kontogiannis, O. Johnson, H.R.
  Powell
  and A.G.W. Leslie.(2011) Acta Cryst. D67, 271-281)
 
 
 
 
 
 How much of this information is useful in diagnosing user problems?
  Mosflm run on Monday, April 28 2014 at 19:01 by sreetama
  Compiler command: gfortran Compiler version: GNU Fortran (GCC)
  4.4.7 Copyright (C) 2010 Free
  Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to
  the extent permitted by law. You may redistribute copies of GNU
  Fortran under the terms of the GNU General Public License. For
  more informatio
  Executable type:  ELF 32-bit LSB executable, Intel 80386,
  version
  1 (SYSV), 

Re: [ccp4bb] Merging Data from Multiple Crystals

[David Waterman]

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 slightly from
what is finally released. Your comments are welcome.

I hope this helps. Cheers,

-- David


On 29 March 2014 13:38, Andreas Förster docandr...@gmail.com wrote:

 Contact James Foadi.

 http://diamond.ac.uk/Beamlines/Mx/I24/Staff/Foadi.html


 Andreas




 On 29/03/2014 1:21, Alexander Batyuk wrote:

 Dear Tassos,

 Do you know by chance whether BLEND is available?

 Best wishes,

 Alex

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

[David Waterman]

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 (ϕ, ω, κ) can be visualised as
 rotation ϕ about Z, rotation ω about the new Y, rotation κ about the new Z.
 It seems the same as the ZXZ convention of eulerian angle definition.
 What's the difference between the CCP4 polar angle definition and eulerian
 angle ZXZ definition?

 And what's the definition of polar angle XYK convention in GLRF program?

 Thank you very much!

 Best wishes,

 --
 Qixu Cai
 Email: caiq...@gmail.com
 School of Life Sciences,
 Xiamen University, Fujian, China
 **from thunderbird**

Re: [ccp4bb] refining nucleic acids with Coot

[David Waterman]

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 ashley.p...@sgc.ox.ac.uk

  Hi Almudena - I came across this issue recently as well with an old pdb
 file. As Paul says you need to convert from v2.3 to v3.2 pdb formats. In
 addition to the link he gave, you can also accomplish this using the iotbx
 toolbox that comes with phenix.

  iotbx.pdb_remediator file_name=in.pdb output_file=out.pdb



 will rename * atom names to ' (eg O4* to O4') which can then be
 regularised in coot.



 Ashley



 *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
 *Almudena Ponce Salvatierra
 *Sent:* 14 January 2014 15:52
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* [ccp4bb] refining nucleic acids with Coot



 Dear all,

 I am trying to refine an oligonucleotide chain in Coot and I get the
 following message when I try:

 Fail to match (to the dictionary) the following model atom names:

 G

 O5* C5* O4* etc

 That would cause exploding atoms so the refinement did not start

 Does anyone know how to solve this?

 Best wishes,

 Almudena.


 --

 Almudena Ponce-Salvatierra

 Macromolecular crystallography and Nucleic acid chemistry

 Max Planck Institute for Biophysical Chemistry

 Am Fassberg 11 37077 Göttingen

 Germany






 --
 Almudena Ponce-Salvatierra
 Macromolecular crystallography and Nucleic acid chemistry
 Max Planck Institute for Biophysical Chemistry
  Am Fassberg 11 37077 Göttingen
 Germany

[ccp4bb] CCP4-6.4.0 Update 005

[David Waterman]

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): better handling of resolution limits for tests
   - crank (all): fixes for use of ARP/wARP 7.4
   - aimless (all): inclusion of history in MTZ
   - pointless (all): fix axial reflection bug

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 package so you do not need to
install it separately.
In addition, all available updates will be installed automatically if you
are using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

-- David

Re: [ccp4bb] iMosflm bug?

[David Waterman]

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. Unfortunately I can't remember how I set fonts up on my machine,
but it may help to:

1) install the ttf-mscorefonts-installer package
2) ensure the package gsfonts-x11 is *not* installed (this causes an
incorrect mapping of unicode symbols so you get things like the registered
trademark symbol appearing - an effect apparently known as mojibake...)

Cheers

-- David


On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com wrote:

 Has anyone else encountered this?  When I go to processing options in
 iMosflm 1.0.7, many of the parameters on the right hand side of the window
 are cut off, and there is no way to scroll over so that I can enter them.
  I've attached link to a picture of what it looks like.

 https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png

 Thanks,
 Thomas Cleveland

Re: [ccp4bb] Philosophical question

[David Waterman]

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
cells. This does not answer why that particular convention was chosen,
but it does count against the idea that it is the best possible system, or
indeed should continue to be selected for (except that mutations to this
machinery tend to be very much deleterious).

-- David


On 19 March 2013 14:34, Jacob Keller j-kell...@fsm.northwestern.edu wrote:

 Never one to shrink from philosophizing, I wonder generally why the codon
 conventions are the way they are? Is it like the QWERTY keyboard--basically
 an historical accident--or is there some more beautiful reason? One might
 argue that since basically all organisms share the convention (are there
 exceptions, even?), that it must be the best of all possible conventions.
 I have often wondered whether maybe this particular convention allows for
 the most effective pathways between proteins of significant function, e.g.,
 through the fewest mutations perhaps? One certainly cannot maintain that
 every possible protein sequence has been made at some time or another in
 the history of the biological world (go quantitate!) so there must be a way
 to ensure that mostly the best ones got made. On the other hand, since
 many organisms share DNA, maybe they had to agree on a system (I think
 this is the dogma?). Was there a United Organisms convention at some
 point, reminiscent of Les Immortels of the French language or POSIX or
 something, to ensure compliance? What was the penalty for non-compliance?

 Anyway, I like the question about the methionines,

 Jacob


 On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.eduwrote:

 Opher Gileadi wrote:

 Hi Theresa,

 To add to Anat's comments: Although the AUG codon for the first
 methionine and all other methionines in a protein coding sequence look the
 same, they are read in a very different way by the ribosomal machinery. The
 first AUG is recognized by the initiation complex, which includes the
 separate small ribosomal subunit (40s), a special tRNA-methionine, and
 initiation factors (proteins) including eIF2. This leads to assembly of a
 complete ribosome and initiation of protein synthesis. Subsequently, in the
 process of elongation, AUG codons are read by a different tRNA, which is
 brought to the 80s ribosome bound to a protein called elongation factor 1a.
 This is an oversimplification, of course, but the point is that the
 initiation codon (=the first amino acid to be incorporated to the protein)
 is read by a special tRNA, hence the universal use of methionine.

 Opher

  Yes, but why methionine? Half the time it has to be removed by
 N-terminal peptidase to give a small first residue, or by leader sequence
 processing. Why use a big expensive amino acid instead of choosing one of
 the glycine codons? Is there an obvious reason, or just it had to be
 something, and Met happened to get selected?

 And why sometimes alternate start codons can be used? and why doesn't
 initiation occur also at methionines in the middle of proteins? I'm
 guessing it has to do with 5' untranslated region and ribosome binding
 sites. So could the start codon actually be anything you want, provided
 there is a strong ribosome binding site there?

 Just being philosophical, and not afraid to display my ignorance,
 eab




 --
 ***

 Jacob Pearson Keller, PhD

 Looger Lab/HHMI Janelia Farms Research Campus

 19700 Helix Dr, Ashburn, VA 20147

 email: kell...@janelia.hhmi.org

 ***

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

[David Waterman]

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 List,

 Does anyone know of a source of quantification of membrane proteins in
 garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally,
 it just occurred to me that probably all HeLa cells are XX--seems right,
 no?) I am looking for the highest-expressed, particularly, and definitely
 want to include single-pass proteins as well.

 Jacob

 --
 ***

 Jacob Pearson Keller, PhD

 Looger Lab/HHMI Janelia Farms Research Campus

 19700 Helix Dr, Ashburn, VA 20147

 email: kell...@janelia.hhmi.org

 ***

[ccp4bb]

[David Waterman]

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 trolling.
It is a credit to the subscribers that this system works. We are a
self-governing community in which it is only natural that contentious
messages generate vigorous responses. Only very rarely have subscriptions
been cancelled because of an abuse of the system. Indeed in most such cases
this has been a result of the subscriber's email account being hacked and
used without their permission.

The sort of comment removed type moderation you might see on e.g.
newspaper websites is neither possible on our email-based Bulletin Board,
nor I believe desirable, as it goes against the spirit of the CCP4BB.

-- David


On 30 October 2012 05:15, Kavyashree Manjunath ka...@ssl.serc.iisc.inwrote:

 Dear CCP4 users,

 It is extremely sad that CCP4BB has failed to moderate/screen
 for such spam mails!

 Thanks
 kavya


   Dear Friends,
 
 
 
  There is no need to apply to this position, we suggest. It is a
  PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement,
  screening, selection board, selection and approval) is just the
 procedure.
  
 
  It does not matter whether you apply or not. If you apply and called for
  interview, then you have to waste your valuable time as well as huge
 travel
  money unless some Big Boss is fixing you to the post.
 
  Interestingly Indian Institute of Science recruits and carries faculties
  and trains them in such a way that it has become a epicentre of
 recruitment
  scams across India and it make rest of Indian Scientists/Faculties in
 their
  path of scams and CRIME. Students also inherit the character of their
 boss.
  They do not participate in any form of fair selection in the country.
  Almost all cases they select and load many times inferior candidates even
  though candidate was not seen by anybody or interviewed. Similarly they
  distribute various national awards among themselves and within their
 group.
  THEY ARE NOT ASHAMED AT ALL.
 
  This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks
  who are good for nothing but worst for everything. 
 
 
 
  Sham
 


 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.

[ccp4bb] CCP4 update

[David Waterman]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes.

For Linux and Mac:

   - *areaimol*: fixed segmentation fault due to a bug in dynamic memory
   allocation
   - *cprodrg*: HETATM notations synchronised with refmac
   - *ccp4i*: fixes in refmac harvesting

In addition to the above, on Windows:

   - *ccp4i*: added kill job functionality

The easiest way to obtain the update is to install the CCP4 update
clienthttp://www.ccp4.ac.uk/download/update_manual.html, if
you have not done so already. Note that autoupdates will work correctly
only with CCP4 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

[David Waterman]

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 tried this on SL 6.3, so can't tell you in advance what you'll get)

Cheers

-- David


On 19 September 2012 17:12, Fred. Vellieux frederic.velli...@ibs.fr wrote:

 Hi all,

 The question is in the Subject line of this email: which version of Coot
 should I download and install on a Scientific Linux 6.3 box ?

 Ta very much in advance,

 F.V.

 --
 F.M.D. Vellieux (B.Sc., Ph.D., hdr)
 IBS / ELMA
 41 rue Jules Horowitz
 38027 Grenoble Cedex 01
 France
 Tel: +33 438789605
 Fax: +33 438785494

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

[David Waterman]

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 the
following link, and please let us know if it fixes the problem.

ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/updates/windows/

-- David
(CCP4)


On 14 September 2012 16:52, Laurie Betts laurie.betts0...@gmail.com wrote:

 Dear ccp4,

 WE installed ccp4 6.3.0 GUI under Windows 7, and tried to run AREAIMOL on
 a single coordinate file with protein and some nucleic acid.  It crashes
 with a child killed segmentation violation error, however the exact same
 input coordinate file runs fine on ccp4 6.3.0 under MacOSX.  So it's not
 the input file it's something about that program under Windows???

Re: [ccp4bb] protein interactions

[David Waterman]

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 it
won't work. It looks as though you can only put in one query
sequence/structure and will then have to scan the results for the
appearance of the second.

I hope this helps.

-- David


On 6 September 2012 07:43, Careina Edgooms careinaedgo...@yahoo.com wrote:

 Anybody know of any software out there that can predict potential
 interaction sites between two proteins? They have been shown to interact
 via y2h screens but I have no idea if they would interact on their own in
 vitro. Before I clone them into a vector and purify them I would like some
 sort of confirmation that the interaction could occur in the absence of
 other cellular factors.
 There are 2 interactions I am looking at. For the one, the structures of
 both proteins are known. For the other only one structure is known.
 So, is there software that uses 2 known structures to predict binding
 sites and (I know this is a long shot), but is there any software around
 that could predict an interaction based on the sequences only (or one 3D
 structure and one sequence)?

 Thanks
 Careina

[ccp4bb] Old Newsletter News

[David Waterman]

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 occasionally received requests for old articles, we hope that this
complete archive will be of use to the community. Certainly browsing the
old editions will be useful for anybody interested in the history of CCP4 -
and dare I say a little nostalgic for some of you out there ;-). The first
issue, dated October 1979, and when the newsletter was called the Daresbury
Laboratory Information Quarterly for Protein Crystallography, describes the
nascent days of the Collaborative Computational Project in Protein
Crystallography, shortly after the project was first approved. The first
article proper is perhaps unsurprisingly about a data format; a regular
theme for the newsletter. The editorial of that first edition ends with
this paragraph, which of course remains true today:

Please note that the main aim of the newsletter is to keep people informed
 of the work being carried out by the CCP and of which programs are
 available for general use. We will therefore rely upon your contributions
 for future editions!


Happy reading.

-- David

[ccp4bb] CCP4 Newsletter 48

[David Waterman]

Hi folks,

After a brief hiatus (okay, more than four and a half years) the CCP4
Newsletter on Protein Crystallography is back!

The latest issue is now available from the website
http://www.ccp4.ac.uk/newsletters.php in both HTML and PDF. This edition
follows hot on the heels of the 6.3.0 release of the CCP4 Suite, and
correspondingly it focuses mainly on new and improved programs found in the
Suite. There are articles on the new programs ViewHKL, GESAMT, comit,
nautilus, ProSMART, Zanuda and AMPLE. We also have news of the latest
improvements to the mosflm package and the current xia2 manual. Finally,
two articles about the new GUI project, CCP4i2, give a taste of things to
come from CCP4 developers.

We intend to get back to a semi-regular schedule of Newsletter
publications. To that end, submissions are accepted immediately for the
next issue, with a target publication date 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

[David Waterman]

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 knows if the PISA software could be
 used/modified to detect potential interfaces of interaction of different
 proteins? This would be very useful as a tool to validate protein-protein
 interactions detected by in vivo methods such as yeast 2 hybrid screens. If
 PISA is not quite there yet, does anyone know of other software that could
 do a similar thing?

 Best
 Careina

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

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 releases, only an increase in
the maximum number of allowed batches from 5000 to 1. If this limit is
a problem for you, then Phil's advice is to use Aimless instead.

Best regards

-- David


On 3 August 2012 19:02, Peter Goettig peter.goet...@sbg.ac.at wrote:

 In the Windows version of the new CCP4 release SCALA produces a summary
 table (same in the full text) that contains only some rudimentary data,
 such as

   Overall  InnerShell
  OuterShell
   Low resolution limit   19.97 0.00  0.00
   High resolution limit 3.00 0.00  0.00

   Rmerge  0.000 0.000 0.000
   Rmerge in top intensity bin0.115- -
   Rmeas (within I+/I-)   0.000 0.000 0.000

   aso

 while the final statement of SCALA is ** Normal termination **

 Has anyone else experienced similar problems and found a way to solve
 them? Otherwise, I would ask the developpers to take care of the bugs.
 However, the corresponding tables generated by AIMLESS contain the full
 information.

 Regards,

 Peter


 Peter Goettig
 Structural Biology
 University of Salzburg
 Billrothstrasse 11
 Salzburg, Austria

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

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 week.

Sorry about this.
David
(CCP4)
On Aug 3, 2012 7:13 PM, Peter Goettig peter.goet...@sbg.ac.at wrote:

 In the Windows version of the new CCP4 release SCALA produces a summary
 table (same in the full text) that contains only some rudimentary data,
 such as

   Overall  InnerShell
  OuterShell
   Low resolution limit   19.97 0.00  0.00
   High resolution limit 3.00 0.00  0.00

   Rmerge  0.000 0.000 0.000
   Rmerge in top intensity bin0.115- -
   Rmeas (within I+/I-)   0.000 0.000 0.000

   aso

 while the final statement of SCALA is ** Normal termination **

 Has anyone else experienced similar problems and found a way to solve
 them? Otherwise, I would ask the developpers to take care of the bugs.
 However, the corresponding tables generated by AIMLESS contain the full
 information.

 Regards,

 Peter


 Peter Goettig
 Structural Biology
 University of Salzburg
 Billrothstrasse 11
 Salzburg, Austria

Re: [ccp4bb] CCP4-6.3.0 installation

[David Waterman]

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 Aug 4, 2012 9:39 PM, james09 pruza james09x...@gmail.com wrote:

 Dear CCP4bbers,

 I am facing CCP4-6.3.0 installation problem. Unable to run make.
 Configuration is done. Getting error while running make (command not
 found). Please help.
 Thanks in advance, James

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

Yep, it's definitely our problem not yours, Phil ;-). I believe the only
change to scala source since 6.2.0 was to up the maximum number of batches
again. This new bug is probably related to the change of compiler for 6.3.0.

We'll be trying to make sense out of this next week.

Cheers
D
On Aug 4, 2012 2:34 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:

 This must be a problem on Windows as it doesn't show up on OSX or Linux,
 and this code hasn't changed for a long time, I think

 David I guess you will feed this back to me: I don't have any way of
 testing on Windows

 Anyway, Aimless 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 to 6.2.0's
 version of scala from the problems page as a workaround early next week.
 
  Sorry about this.
  David
  (CCP4)
 
  On Aug 3, 2012 7:13 PM, Peter Goettig peter.goet...@sbg.ac.at wrote:
  In the Windows version of the new CCP4 release SCALA produces a summary
 table (same in the full text) that contains only some rudimentary data,
 such as
 
Overall
  InnerShell  OuterShell
Low resolution limit   19.97 0.00  0.00
High resolution limit 3.00 0.00  0.00
 
Rmerge  0.000 0.000
 0.000
Rmerge in top intensity bin0.115- -
Rmeas (within I+/I-)   0.000 0.000 0.000
 
aso
 
  while the final statement of SCALA is ** Normal termination **
 
  Has anyone else experienced similar problems and found a way to solve
 them? Otherwise, I would ask the developpers to take care of the bugs.
 However, the corresponding tables generated by AIMLESS contain the full
 information.
 
  Regards,
 
  Peter
 
 
  Peter Goettig
  Structural Biology
  University of Salzburg
  Billrothstrasse 11
  Salzburg, Austria

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

[David Waterman]

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 big-endian
machine and adapt appropriately. For example, one of the header entries
encompassed by your 'REST' array is a machine stamp. You can check that and
see that it is 0x44, 0x41, 0x00, 0x00 for a little endian file, or 0x11,
0x11, 0x00, 0x00 for a big endian file. If neither, give up.

Also, check that sizeof(long) and sizeof(float) are both 4 bytes on your
machine. This might not be specified by the format (
http://www.ccp4.ac.uk/html/maplib.html#description) either, but I have only
ever seen map files with the header entries coming in 32 bit units.

Cheers

-- David


On 2 July 2012 14:41, Soares, Alexei soa...@bnl.gov wrote:

  Hello, Alex here.

 Ten years ago, I read CCP4 maps this way, but it no longer works ... can
 anyone tell me why?  Note that map1 is an integer so that multiple headers
 can be read.  Also, supposedly the map header is text, but a simple head
 -1 dumps lots of digital garbage from the map header.

 Thanks, and sorry for the beginner question!

//    READ MAP HEADER 

fread( MAP_H[map1].NC , sizeof(long) ,   1, read1);
fread( MAP_H[map1].NR , sizeof(long) ,   1, read1);
fread( MAP_H[map1].NS , sizeof(long) ,   1, read1);

fread( MAP_H[map1].MODE   , sizeof(long) ,   1, read1);

fread( MAP_H[map1].NCSTART, sizeof(long) ,   1, read1);
fread( MAP_H[map1].NRSTART, sizeof(long) ,   1, read1);
fread( MAP_H[map1].NSSTART, sizeof(long) ,   1, read1);

fread( MAP_H[map1].NX , sizeof(long) ,   1, read1);
fread( MAP_H[map1].NY , sizeof(long) ,   1, read1);
fread( MAP_H[map1].NZ , sizeof(long) ,   1, read1);

fread(  MAP_H[map1].CELL   , sizeof(float),   6, read1);

fread( MAP_H[map1].MAPC   , sizeof(long) ,   1, read1);
fread( MAP_H[map1].MAPR   , sizeof(long) ,   1, read1);
fread( MAP_H[map1].MAPS   , sizeof(long) ,   1, read1);

fread( MAP_H[map1].AMIN   , sizeof(long) ,   1, read1);
fread( MAP_H[map1].AMAX   , sizeof(long) ,   1, read1);
fread( MAP_H[map1].AMEAN  , sizeof(long) ,   1, read1);

fread( MAP_H[map1].ISPG   , sizeof(long) ,   1, read1);

fread( MAP_H[map1].NSY, sizeof(long) ,   1, read1);

fread(  MAP_H[map1].REST   , sizeof(float),   32, read1);

fread(  MAP_H[map1].LAB, sizeof(char) , LAB_LEN, read1);
fread(  MAP_H[map1].SYM, sizeof(char) , MAP_H[map1].NSY, read1);

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

[David Waterman]

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 be better off using the API
 (http://www.ccp4.ac.uk/dist/html/C_library/cmaplib_8h.html): that way
 your program will have a good chance of still working in another 10
 years' time!

 Cheers

 -- Ian

 On 2 July 2012 14:41, Soares, Alexei soa...@bnl.gov wrote:
  Hello, Alex here.
 
  Ten years ago, I read CCP4 maps this way, but it no longer works ... can
  anyone tell me why?  Note that map1 is an integer so that multiple
 headers
  can be read.  Also, supposedly the map header is text, but a simple head
  -1 dumps lots of digital garbage from the map header.
 
  Thanks, and sorry for the beginner question!
 
 //    READ MAP HEADER 
 
 fread( MAP_H[map1].NC , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NR , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NS , sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].MODE   , sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].NCSTART, sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NRSTART, sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NSSTART, sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].NX , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NY , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].NZ , sizeof(long) ,   1, read1);
 
 fread(  MAP_H[map1].CELL   , sizeof(float),   6, read1);
 
 fread( MAP_H[map1].MAPC   , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].MAPR   , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].MAPS   , sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].AMIN   , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].AMAX   , sizeof(long) ,   1, read1);
 fread( MAP_H[map1].AMEAN  , sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].ISPG   , sizeof(long) ,   1, read1);
 
 fread( MAP_H[map1].NSY, sizeof(long) ,   1, read1);
 
 fread(  MAP_H[map1].REST   , sizeof(float),   32, read1);
 
 fread(  MAP_H[map1].LAB, sizeof(char) , LAB_LEN, read1);
 fread(  MAP_H[map1].SYM, sizeof(char) , MAP_H[map1].NSY, read1);
 

Re: [ccp4bb] Failure in Phaser EP

[David Waterman]

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 10 December 2011 15:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Arko,

 your input script reads
 LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-)

 Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-.

 Tim

 On 12/10/2011 09:33 AM, arka chakraborty wrote:
  Hi CCPers!
 
  I have a strange problem..I am trying to obtain phases for a dna decamer
  structure from  cobalt SAD data. In the Phaser EP module when I input the
  mtz generated by Ctruncate and the heavy atom PDB file generated from
  shlelxC/D and run the program it fails. Below is the log file for one of
  the runs. Plz help me out!
 
  Thanks in advance!
 
  ARKO
 
  #CCP4I VERSION CCP4Interface 2.0.7
  #CCP4I SCRIPT LOG phaser_EP
  #CCP4I DATE 10 Dec 2011  13:45:46
  #CCP4I USER 'UNKNOWN'
  #CCP4I PROJECT decamer
  #CCP4I JOB_ID 37
  #CCP4I SCRATCH C:/Ccp4Temp
  #CCP4I HOSTNAME dell-pc
  #CCP4I PID 3412
 
  pre
  BFONT COLOR=#FF
  html!-- CCP4 HTML LOGFILE --
  !--SUMMARY_BEGIN--
 
 
 #
 
 #
 
 #
  ### CCP4 PROGRAM SUITE: Phaser
  2.2.1 ###
 
 #
  Run time: Sat Dec 10 13:45:46 2011
  Version:  2.2.1
  Release Date: Tue Aug 24 18:17:37 2010
 
  If you use this software please cite:
  $TEXT:Reference1: $$ $$
  Phaser Crystallographic Software
  A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni 
  R.J. Read
  J. Appl. Cryst. (2007). 40, 658-674
 
  $$
  !--SUMMARY_END--
  !--END--/FONT/B
  !--SUMMARY_BEGIN--
 
 
 *
  *** Phaser Module: PREPROCESSOR
  2.2.1 ***
 
 *
 
 
  !--SUMMARY_END--
  ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
  !--SUMMARY_BEGIN--
  TITLE phasing_with_phaser_10_12_11
  MODE EP_AUTO
  HKLIN
 
 E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz
  
  RESOLUTION 21.659 2.900
  HAND BOTH
  LLGCOMPLETE NCYC 50
  LLGCOMPLETE CRYSTAL DECAMER COMPLETE ON
  LLGCOMPLETE CRYSTAL DECAMER SIGMA 6.0
  LLGCOMPLETE CRYSTAL DECAMER CLASH DEFAULT
  LLGCOMPLETE CRYSTAL DECAMER SCATTERING ELEMENT CO
  ATOM CRYSTAL DECAMER PDB
 L:/decamer/scala_NGAT-1-P1X8-pk_1_001_shelx2.pdb
  CRYSTAL DECAMER DATASET Cobalt 
  LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-)
  CRYSTAL DECAMER DATASET Cobalt 
  SCATTERING WAVELENGTH 1.60428
  CRYSTAL DECAMER DATASET Cobalt 
  FIXDP
  COMPOSITION NUCLEIC MW 9084 NUMBER 1
  ROOT L:/manual_model_esrf_NG/ccp4_work/decamer_37
  ## This script run with the command   ##
  # phaser
  
  !--SUMMARY_END--
 
  
  EXIT STATUS: SUCCESS
  
 
  CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs)
  Finished: Sat Dec 10 13:45:46 2011
 
  /pre
  /html
  pre
  BFONT COLOR=#FF
  html!-- CCP4 HTML LOGFILE --
 
 
 #
 
 #
 
 #
  ### CCP4 PROGRAM SUITE: Phaser
  2.2.1 ###
 
 #
  Run time: Sat Dec 10 13:45:46 2011
  Version:  2.2.1
  Release Date: Tue Aug 24 18:17:37 2010
 
  If you use this software please cite:
  $TEXT:Reference1: $$ $$
  Phaser Crystallographic Software
  A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni 
  R.J. Read
  J. Appl. Cryst. (2007). 40, 658-674
 
  $$
  !--END--/FONT/B
 
  !--SUMMARY_BEGIN--
 
 *
  *** Phaser Module: READ DATA FROM MTZ FILE
  2.2.1 ***
 
 *
 
  TITLE phasing_with_phaser_10_12_11
  HKLIN
 
 E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz
  
  RESOLUTION 21.659 2.900
  CRYSTAL DECAMER DATASET Cobalt 
  LABIN F+ = F(+) SIGF+
  !--SUMMARY_END--
 
 
  BFONT COLOR=#FF8800
  --
  SYNTAX ERROR: Use SIGFPOS SIGF(+) or SIG+