Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Roger Rowlett
The first step would be to verify consistent, convincing electron density for the proposed thioketal adduct. A good way to start might be an "omit" map of the region by mutating the Cys residues to Ala, truncating them to the beta-carbon. The resulting difference density may be suggestive of a

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Roger Rowlett
To verify the presence of a non protein ligand, you need to come at this from an unbiased perspective. 1. Remove what you think is not there (e.g. disulfide bond) by truncating the Cys residues 2. Examine the difference density map to see if it conforms to your expectations of what is proposed to

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

2020-06-30 Thread 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

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Lumbini Yadav
Hi Daniele, Do you see Fo-Fc density near disuphide bond where you are trying to fit acetone? On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi wrote: > Dear CCP4bb, > > I'm trying to insert an Acetone molecule between two cysteine residues in > coot or modifying the pdb. I'm working on this

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Daniele Veggi
Hi Yadav, yes, this is only a representation of what I would like to do. If during the refinement will continue to appear density, probably I'm on the good track..but currently my big issue is inserting the ACN covalently linked to both cys. many thanks Daniele Veggi GSK Vaccines Siena Italy

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

2020-06-30 Thread 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: >

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

2020-06-30 Thread Winter, Graeme (DLSLtd,RAL,LSCI)
Or, we could accept the fact that crystallographers are kinda used to multiplicity of an individual Miller index being different to multiplicity of observations, and in Table 1 know which one you mean?  Given that they add new information (at the very least to the scaling model) they are

[ccp4bb] insertion of a chemical

2020-06-30 Thread Daniele Veggi
Dear CCP4bb, I'm trying to insert an Acetone molecule between two cysteine residues in coot or modifying the pdb. I'm working on this modified molecule where the disulfide bridge was chemichally opened and inserted an acetone molecule between the two cysteine. MS data confirm this modification

[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

2020-06-30 Thread lyguo
The Multiscale Research Institute for Complex Systems (MRICS) at Fudan University is located at the Zhangjiang Campus of Fudan University and is supported by the Shanghai High-level Talents Program. MRICS is strongly committed to the development of novel and effective multi-scale imaging

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Lumbini Yadav
As also suggested by Dr. Roger you should first see the density then the next step of molecule addition is suggested. Omit is also a good idea for further confirmation. On Tue, Jun 30, 2020 at 4:55 PM Daniele Veggi wrote: > Hi Yadav, > yes, this is only a representation of what I would like to

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

2020-06-30 Thread Phil Jeffrey
The people that already use multiplicity are going to find reasons why it's the superior naming scheme - although the underlying reason has a lot to do with negative associations with 'redundant', perhaps hightened in the current environment. And conversely redundant works for many others -

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

2020-06-30 Thread Phil Evans
I changed the annotation from “Redundancy” to “Multiplicity” in Scala, later in Aimless, after I was taken to task by Elspeth Garman with the argument as stated, that if it’s redundant why did you bother to measure it? (this one could run and run …) Phil > On 30 Jun 2020, at 14:07, Ian Tickle

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

2020-06-30 Thread John R Helliwell
Dear Colleagues, In an effort to break this naming deadlock, and with Massimo and Ian not showing up as yet, I checked the IUCr Dictionary. “Redundancy“ and “Multiplicity“ are not listed. The more generic term “Statistical Descriptors“ is though and even offers Recommendations:-

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

2020-06-30 Thread John R Helliwell
Dear Herman, I think that MPR is a very neat and tidy, excellent, proposal. Moreover it uses the word “measurements”, and we are an experimental based science. I support it. Great. Greetings, John Emeritus Professor John R Helliwell DSc > On 30 Jun 2020, at 15:10, Schreuder, Herman /DE >

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

2020-06-30 Thread David Schuller
By all means, if you still have "disks" you should get rid of them, and replace them with some modern storage. On 2020-06-29 21:17, 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,

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

2020-06-30 Thread Edwin Pozharski
Replicate is a good option with its own problems as it can be seen as referring to exact copy which multiple measurements clearly aren't. It does have an advantage of being the word used by non-crystallographers though. As a lame attempt at joke, use of terms redundancy and multiplicity to

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

2020-06-30 Thread Ian Tickle
I agree about RAID but I would go a lot further. There seems to be some confusion here over the correct meaning of 'redundant' as used in a scientific context. I don't think looking it up in an English dictionary is very helpful. So as has been mentioned the non-scientific and rather imprecise

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Paul Emsley
On 30/06/2020 10:51, Daniele Veggi wrote: Dear CCP4bb, I'm trying to insert an Acetone molecule between two cysteine residues in coot or modifying the pdb. I'm working on this modified molecule where the disulfide bridge was chemichally opened and inserted an acetone molecule between the two

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

2020-06-30 Thread Schreuder, Herman /DE
Dear BB, Since there does not seem a generally accepted term for the subject of this discussions, and since even the IUCR scriptures do not give any guidance, I would propose to introduce a completely new term: Measurements per reflection or MPR This term is politically neutral, should

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

2020-06-30 Thread Gerard Bricogne
Dear Phil, I would like to make an attempt to not let this question get mired in exchanges of well-researched linguistic arguments at risk of being drowned in a cacophony of sound bites :-) . You refer to the days of SCALA, at which time data were collected on CCD detectors, whose

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

2020-06-30 Thread Bernhard Rupp
.…but there is a difference whether I measure the same identical hkl over again or ‘preferably in more than one symmetry-equivalent position’, to quote the IUCr. So do we have a MPSR for the same reflection and a MPRR for the related reflections? Cacophonically yours, BR From: CCP4

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

2020-06-30 Thread Gerard Bricogne
Dear Bernhard, That is true, and the discrepancies between repeated measurements of the same hkl would have to be parametrised differently from those between symmetry-related ones (e.g. in terms of radiation damage only, while the others would also involve absorption effects). However I am

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

2020-06-30 Thread Frank von Delft
Gerard, fantastic proposal - let's call it "abundancy"!!! Which developer will be the first to change their logfile? On 30/06/2020 16:38, Gerard Bricogne wrote: Dear Phil, I would like to make an attempt to not let this question get mired in exchanges of well-researched linguistic

[ccp4bb] 60th Anniversary Meeting of The British Biophysical Society 14-17 September via Zoom

2020-06-30 Thread Dave Scott
Update: 60th Anniversary Meeting of The British Biophysical Society 14-17 September via Zoom Registration is now OPEN and is FREE. Please register at: REGISTER URL: https://bit.ly/31p61xC The British Biophysical Society Biennial meeting is the largest national meeting of the UK biophysics

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

2020-06-30 Thread Gerard Bricogne
Dear Ed, Concerning your remark that "use of terms redundancy and multiplicity to describe the same concept is by itself redundant", one could perhaps say that redundancy is an abstract property of a dataset, while multiplicity is a numerical attribute. Redundancy is desirable because if

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

2020-06-30 Thread 00000c2488af9525-dmarc-request
Hello JohnDoes the IUCr dictionary list 'degeneracy'?Jon CooperOn 30 Jun 2020 17:11, Gerard Bricogne wrote:Dear Bernhard, That is true, and the discrepancies between repeated measurements of the same hkl would have to be parametrised differently from those between symmetry-related ones

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

2020-06-30 Thread 00000c2488af9525-dmarc-request
I think it is quite an interesting question in principle for Laue crystallography (now probably only relevant in the neutron world?) since, for example, if one had a crystal in the 432 point group, you could collect an essentially complete dataset with one 'image'. Given that each image can take