Re: [ccp4bb] request for applications

> what would YOU do if you had $1e12 USD for your science? (a) Embezzle most of and (b) do sociologically relevant research with the rest, like https://www.ruppweb.org/Garland/PICD.html Best, BR ----- Bernhard Rupp

Re: [ccp4bb] Interface Configuration and Mapslicer Question

s any use. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com <mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail mobile Original Message On 18 Feb 2024, 03:29, Bernhard Rupp < hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> > wrote:

[ccp4bb] Interface Configuration and Mapslicer Question

ere, PS viewing works just fine). Cheers, BR -- Bernhard Rupp, Psilosopher <https://psilosophy.org/> https://psilosophy.org/ <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.

Re: [ccp4bb] How to make GDP.BeF3 solution ?

. Free lung X-rays -- Bernhard Rupp, Psilosopher <https://psilosophy.org/> https://psilosophy.org/ <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristalla

Re: [ccp4bb] what is isomorphous?

The Drenth rule of thumb makes sense. Whether 2 in the macromolecular sense isomorphous structures are isomorphous, is a matter or resolution, and it has to do with the reciprocal space overlap function aka G-function. So up to a certain resolution, 2 data sets may be isomorphous, but at high

[ccp4bb] Goniometer heads

/256336772397 Collecting home data - priceless. For everything else, there are beamlines. Cheers, BR -- Bernhard Rupp <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkri

[ccp4bb] Laser pointers for diffraction grating experiments

-23.htm Understanding diffraction: Priceless. For anything else, there is PayPal. Bargain for $10.50 so far. https://www.ebay.com/itm/256191715837 Cheers, BR -- Bernhard Rupp <http://www.hofkristallamt.org/>

Re: [ccp4bb] [ccpem] CCPEM Refmac servalcat error

> ADP values are constrained to be positive, because negative values do not > have physical meaning. Negative B-factors have physical meaning. It means Hell has frozen over. Regards, BR -- Bernhard Rupp http://www.hofkristallamt.

Re: [ccp4bb] About the A in AI

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 mailto:hofkristall...@gmail.com> > wrote: For those who concern themselves with such matters

[ccp4bb] About the A in AI

- Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 <mailto:b...@ruppweb.org> b...@ruppweb.org <mailto:hofkristall...@gmail.com> hofkristall...@gmail.com <http://www.hofkristallamt.org/> http://www.

Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

TCEP is known to form transition metal complexes. With the molecule alone already about 10A across, a ~11x11x46 cell is not unreasonable, and there might be alternatives to P3 (can’t tell from the single image). Would be interesting to collect and, as mentioned, toss into Direct methods

[ccp4bb] PhD/Postdoc positions in Structural Biology (cryo-EM) aiming at structural investigations of protein complexes involved in cell signaling

Hi Fellows, my former fellow Andreas Naschberger who advanced to a faculty position at KAUST has attractive and well-supported positions available. Please contact Andreas for details and inquiries. Best regards, BR From: Collaborative Computational Project in Electron

Re: [ccp4bb] binding pockets...

There is also a service from our Polish friends: called Spaceball (jokes aside) that calculates the volume of protein cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/). and the services in Hamburg are useful for visualization of binding pockets and channels https://proteins.plus/ Best, BR

[ccp4bb] windows 8.0.005 questions

reading, install in c:/wincoot? Thanks, BR - Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 <mailto:b...@ruppweb.org> b...@ruppweb.org <mailto:hofkristall...@gmail.com> hofkristall...@gmai

[ccp4bb] bond angle deviation listing in refmac log

version 5.8.0352 : 05/31/22## ### Thx, BR - Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 <mailto:b...@ruppweb.org> b...@ruppw

Re: [ccp4bb] ligand binds to one molecule

As you stated, you have multiple protomers in the asymmetric unit, where they are free from crystallographic symmetry constraints. Generally that means different local environment for each protomer. Inspecting the sites in the different protomers (frequently related by various

[ccp4bb] Affordable open access publishing is finally here!

Glad to bring this opportunity to your attention…. From: Dr. Adil Laskar Sent: Monday, February 21, 2022 01:14 Subject: Need To Response Respected Researcher, With our fastest growing Himalayan Journals platform, we have constructed a management team of highly Interested Scientists

Re: [ccp4bb] Negative density

Hmm…compliment, pretty darn good density map for 1.7 A….maybe look at the resolution cut-off. If it is at a significant level, it could be truncation ripples? Otherwise I second the noise opinion if it is already a well completed model. Cheers, BR From: CCP4 bulletin board On

[ccp4bb] PostDoc and PhD cryoEM positions SciLife lab Stockholm

, SciLifeLab Head of Unit, SciLifeLab CryoEM Facility Dept. Biochemistry & Biophysics, Stockholm University Tomtebodavägen 23 A, gamma2 17165, Solna Sweden Tel +468161013 Tel +46720181462 -- Bernhard Rupp k.k. Hofkri

[ccp4bb] Sir David Cox

https://www.wsj.com/articles/british-statistician-won-global-acclaim-for-his -methods-11643382040 The quote below is probably from him Regards, BR -- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristalla

Re: [ccp4bb] Off-topic: happy 2022

For those who want to riddle it out (and as structural biologists hopefully don’t come across mirror and glide planes) a ppt where you can take the International Tables and superimpose the tetragonal PG diagrams on the Kaleidoscope. Find the unit cell first, and then ferret out the rest.

[ccp4bb] The Magic of Mushrooms

-- Bernhard Rupp Institute of Genetic Epidemiology Medical University Innsbruck Schöpfstr. 41 A 6020 Innsbruck <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at +43 676 571 0536 -- k.k. Hofkristallamt San Diego, CA

Re: [ccp4bb] off-topic: structural motif / domain comparison

A lesser known service with very powerful search across domains and chains is TopSearch by Manfred Sippl & Cie.: https://topsearch.services.came.sbg.ac.at/ Its training set includes PDB entries up to 2018. Best, BR From: CCP4 bulletin board On Behalf Of Sam Tang Sent: Thursday,

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Maybe we should get to the root of this - what qualifies as machine learning and what not? Do nonparametric predictors such as KDE qualify? https://www.ruppweb.org/mattprob/default.html Happy toa dd to the confusion. -Original Message- From: CCP4 bulletin board On Behalf Of Tim

Re: [ccp4bb] Analysis of NMR ensembles

https://pubmed.ncbi.nlm.nih.gov/8744573/ Old but worked... Best br On Wed, May 26, 2021, 19:43 Tristan Croll wrote: > (sending properly this time, rather than just to Rasmus) > > I don't believe a "color by RMS" option is in ChimeraX right now (I'll > suggest it to the developers), but this

Re: [ccp4bb] Omit maps in phenix and ccp4

> setting occupancies of omitted atoms to zero has the danger of leaving a hole Not quite. We probably need Garib to confirm this, but I tried this many times, and if in refmac the occupancy is really zero (0.00), then this does not happen, and the ligand is treated as not present. An

[ccp4bb] New validation metric

-- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43 676 571 0536 - Doors

Re: [ccp4bb] ideal ligands

True. Sameer seems to be on it. In the meantime, I simly adjust my expectations of 'ideal' :-) Cheers br On Sat, Feb 6, 2021, 06:40 Tristan Croll wrote: > I know . Just suggesting the most likely cause of the problem. > > -- T > -- > *From:* Bernhar

Re: [ccp4bb] ideal ligands

(0,0,0) in > the PDBeChem script. > -- > *From:* CCP4 bulletin board on behalf of Bernhard > Rupp > *Sent:* 05 February 2021 20:51 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] ideal ligands > > > Hi Fellows, > > > > PDBeChem un

[ccp4bb] ideal ligands

-- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> +1 925 209 7429 +43 676 571 0536 -- Ma

[ccp4bb] PDBe cif directories

-- Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43

Re: [ccp4bb] Characterising potential drug-binding pockets

ICM PocketFinder might fit the bill (not free but academic license) eg in https://pubmed.ncbi.nlm.nih.gov/20977231/ Best, BR From: CCP4 bulletin board On Behalf Of Sergei Strelkov Sent: Monday, January 25, 2021 11:02 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Characterising potential

Re: [ccp4bb] The weekly nonsense

hat one ;-0 Sent from ProtonMail mobile Original Message On 22 Jan 2021, 23:03, Bernhard Rupp < hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> > wrote: Dear CCP4 Fellows, for the subscribers of my immensely popular show "The weekly nonse

[ccp4bb] The weekly nonsense

Cheers, BR -- Bernhard Rupp The Amt <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

db | sort -u` > > for atom in "$@" >do > if [ "$atom" != "$1" ] > then > echo -e "NWAV 1 $1\nATOM $atom\nEND\n" | crossec | awk '/^ > Lambda F/ {getline ; getline ; print $0}' > else >

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

...or you can use the old anoweb app http://www.ruppweb.org/new_comp/anomalous_scattering.htm http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr =1=100=K=Cu=1000=2=1=700=Submit HTH, BR From:

Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

number in the CIF as a workaround. Many thx, BR On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote: Dear Developers, running cif2mtz in ccp4i (or from the console) in the case of non-standard settings of space group 18 (which should be discoura

[ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

0 Not sure if this is a loss of information when generating the mmcif upon submission, or the SG is retrieved solely by SG number not symbol (the latter can give rise to a few more such situations). Best, BR -- Bernhard Rupp <http://www.hofkri

Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

In addition to the Debye-Waller correction, you have additional attenuation from the Lorenz and Geometry factor (specific for your powder diffraction geometry) that convolutes with the DB apodization. Meaning: the 400 will be more attenuated relative to 200 if you correct only for DBW.

Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

A situation like you are describing can happen in small molecule and power diffraction. If you explain what you are actually doing, it might be possible to speculate... Best, BR -Original Message- From: CCP4 bulletin board On Behalf Of Kamil Krawczyk Sent: Tuesday, December 22, 2020

Re: [ccp4bb] Anomalous signal to noise details

> I don't know the justification; maybe just experience? Surely the higher the > better. I've seen George Sheldrick deriving the value of ~0.8 when there is > _no_ anom signal but I forgot the details, sorry ... It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC, with

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

In reasonably compact format, the discussion topic is summarized in this CCP4 weekend introduction https://journals.iucr.org/d/issues/2013/02/00/wd5191/index.html As far as the solvent exclusion self-deception via low occupancy goes, fig 2 here:

[ccp4bb] [RESOLVED]partially restrained mode?

for ligand explosivity, for example) unrestrained? Best, BR -- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> +1 925 209 7429 +43

[ccp4bb] partially restrained mode?

-- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43 676 571 0536 -- Many plausible ideas vanish at the presenc

Re: [ccp4bb] Depositing structures of proteins of unknown sequence

At 25A the only discerning feature between Fabs is probably the elbow angle and a rigid body fit might be enough to discriminate between those. http://www.ruppweb.org/cvs/br/Stanfield_2006_JMB_antibody_elbow_angle.pdf Best br On Mon, Jul 27, 2020, 21:10 Roversi, Pietro (Dr.) wrote: > Dear

[ccp4bb] [refmac developers] unrestrained anisotropic

ADPs are violated. Are they also turned off when I select unrestrained - they should remain in effect regardless of how bad or unsupported my atoms are? Do I need to change/adjust/optimize the RBON/RIGU keywrd? Best, BR -- Bernhard

Re: [ccp4bb] Quote source inquiry

On Tue, 14 Jul 2020, Bernhard Rupp wrote: > Hi Fellows, > > > > afaicrimps (as far as I can recall in my progressing senility) > someone once wrote/stated/cursed somewhere that "Macromolecular > refinement is not a small molecule structure determination method".

[ccp4bb] Quote source inquiry

nks & best regards, BR ------ Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925

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

ng", as these tend to generate far more > heat than light. However, I do think it important to identify and describe > cultural differences when they start to impede scientific discussion. It is > OK to disagree. But let it be over interpretation of complete information &

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

.…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] number of frames to get a full dataset?

eople/view/126690-rizkallah-pierre From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp Sent: 29 June 2020 23:36 To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] number of frames to get a full dataset? I think

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

ndancy", 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, Ber

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

> 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 a. the position multiplicity (number of equivalent sites per unit cell, aka Wyckoff-Multiplicity), the only (!) cif

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

Tom makes a good point. The minimum RS coverage necessary to obtain a unique data set is just a simple calculation that involves no experimental reality. To judge the expected usefulness of the data, you need to have some idea about the possible errors, random and systematic. Random is

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

1/48th of reciprocal space is the minimum in certain SGs.. Table 6.6 in BMC or http://www.ruppweb.org/new_comp/spacegroup_decoder.htm Best, BR From: CCP4 bulletin board On Behalf Of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk Sent: Tuesday, June 23, 2020 08:11 To:

Re: [ccp4bb] visual mask editor - why

r genration, etc. Run the script with no arguments to get a list. Oh, but don't try it on an mtz file! mtz files are not maps. -James Holton MAD Scientist On 5/28/2020 12:11 PM, Bernhard Rupp wrote: Yes I have already pilfered useful parts of it in the scripts… Thx, BR From: Bo

Re: [ccp4bb] visual mask editor - why

package? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On May 28, 2020 21:17, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote: Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a ligand).

Re: [ccp4bb] visual mask editor - why

20, at 2:17 PM, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote: Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a ligand). Now, I would like to do a number of things without biasing towards a model. Like comparing these map regions, exclud

[ccp4bb] visual mask editor - why

be a compliment. Best, BR Brief question: Does something like a visual density mask editor exist? Thx, BR -- Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org <mailto:b...@hofkristallamt.

Re: [ccp4bb] visual mask editor?

, Stephen M Sent: Thursday, May 28, 2020 09:57 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor? You used to be able to do this in O (dating myself) From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp Sent: Thursday, May 28, 2020 12

[ccp4bb] visual mask editor?

Brief question: Does something like a visual density mask editor exist? Thx, BR -- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 2

[ccp4bb] Map grid passing from ccp4 refmac mask?

name despite selection (xyz.ccp4) gets changed to xyz.map in the actual output. Best, BR -- Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <

[ccp4bb] Oddity in CCP4 library signal mtz -error (developers)

anomalous maps. And oddly enough, for F-obs(-) and SIGF-obs(-)the G and L labels are not considered offending. So maybe it's not a real error just expecting F and Q . Best, BR -- Bernhard Rupp <http://www.hofkristallam

[ccp4bb] Refmac and hydrogens -developers

' or 'ignore', the stats and map are different and no H in output as requested - all as expected. Maybe that can be reproduced and, if it is not a feature, fixed. Best, BR -- Bernhard Rupp <http://www.hofkristallamt.org/>

Re: [ccp4bb] Using SFall for map conversion

//www-ibmc.u-strasbg.fr/spip-arn/ _ Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : Hi Fellows, I am failing on conversion of a ccp4 map to mtz using Sfall I provide as a scale reference a mtz with FP SIGFP and R

Re: [ccp4bb] Using SFall for map conversion

c.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/ _ Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : Hi Fellows, I am failing on conversion of a ccp4 map to mtz using Sfall I provide as a scale refere

Re: [ccp4bb] Using SFall for map conversion

and the problem went away. -James Holton MAD Scientist On 5/14/2020 1:44 PM, Bernhard Rupp wrote: Hi Fellows, I am failing on conversion of a ccp4 map to mtz using Sfall I provide as a scale reference a mtz with FP SIGFP and R free All cell constants and SG 20 and map headers seem t

[ccp4bb] Using SFall for map conversion

3 2 1 3 1 2 SFALL: Fatal disagreement between input info and map header How do I fix this ? In principle all the information is there to do the job. Many thx, BR -- Bernhard Rupp Crystallographiae Vindicis Militum Ord

Re: [ccp4bb] disinfecting keyboards

>This email was not typed but spoken by Siri on my laptop. Outing yourself? https://www.youtube.com/watch?v=7-SVvtxHJGU HTH BR > On Apr 29, 2020, at 2:59 PM, Sravya Mounika Kantamneni > wrote: > > How about using keyboard guards and dissecting them as usual? > > Regards, > Sravya > >> On

Re: [ccp4bb] disinfecting keyboards

>I do not know if any of the equipment may suffer damage in the medium or long >term due to the incidence of UV light. Hmm….everything made of cheap plastic….i.e. almost everything made in China…that must be the true conspiracy behind the virus! Cheers, BR On Wed, Apr 29, 2020 at

Re: [ccp4bb] on-topic: your opinions requested!

> go the Rupp Route: Name and Shame! Thanks for the character reference. Best, BR On 07/04/2020 16:08, Artem Evdokimov wrote: Dear CCP4ers, I would like to solicit your thoughts on the following (this is a real situation, but salient details are changed): Imagine that you're an

Re: [ccp4bb] New phasing approach

joke. Are you aware of K. Huemmer's and E. Weckert's three-beam experiments? See e.g. https://link.springer.com/chapter/10.1007/978-1-4615-5879-8_24 Best regards, Tim On Wednesday, April 1, 2020 4:00:19 AM CEST Bernhard Rupp wrote: > Hi Fellows, >

[ccp4bb] New phasing approach

-- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 -- Department of Genetic Epidemiology Medical University Innsbruck S

Re: [ccp4bb] Vote for cryoEM

So…Science has come down to a popularity contest on social media. Best, BR From: CCP4 bulletin board On Behalf Of Alessandro Vannini Sent: Tuesday, March 31, 2020 08:42 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Vote for cryoEM We are head to head with mass-spectrometry in the

[ccp4bb] [ccp4dev] Broken wiki link to dimple from ccp4i

ption(Object(Error)) #1 [internal function]: wfExceptionHandler(Object(Error)) #2 {main} thrown in /home/ccp4wiki/public_html/wiki/includes/Exception.php on line 168" Can you reproduce that behavior? Best, BR -- Bernhard Ru

Re: [ccp4bb] A question of density

A few figures in BMC re truncation effects: http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm

Re: [ccp4bb] refinement of 0.73A data in shelxl

Maybe the figures were just contoured odd...but my recollection of a good 0.8 A map appearance is differentwhich might be consistent with the high Rf...a look at the high res data or images/stats might help? Best, br On Mon, Feb 3, 2020, 14:58 George Sheldrick wrote: > Dear Matthias, > > >

[ccp4bb] Remember the turkey?

Hi Fellows - here some light Holiday entertainment (and puzzle) for you: Remember my thanksgiving posting below? Meant as a hoax or satire, it follows the classical pattern of throwing postmodern Critical Theory gibberish and Social Justice key words (successfully deployed by Alan Sokal)

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

raut & Kartoffelknödel > On Nov 28, 2019, at 4:38 PM, Bernhard Rupp wrote: > > Sorry for being late on this thread - > > but the completeness myth is one of these conventional wisdoms I am > seriously questioning and completeness as a global statistic is almost > uninformative, sho

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

can be found here https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 ------ Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org -- All models are wrong but some are us

[ccp4bb] Shelx and debian 10

Bernhard Rupp Department of Genetics and Pharmacology Institute of Genetic Epidemiology Medical University Innsbruck Schöpfstrasse 41 A 6020 Innsbruck – Austria +43 (676) 571-0536 bernhard.r...@i-med.ac.at

Re: [ccp4bb] A crystallisation screen pH query.

I would not take that for granted…see the comments by Tom Peat. It is easy to measure with some coarse and the fine strips both the unbuffered cocktail and drop pH – sometimes knowing the drop pH can be relevant for the physiological state. Mixing unbuffered cocktail and stock buffer also

Re: [ccp4bb] Figure of merit in refinement

s useful, BR -- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43 767 571 0536 -- All mode

Re: [ccp4bb] ITC question -dimer vs monomer

olekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 future. From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp Sent: Thursday, October 3, 2019 11:06 AM To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@J

Re: [ccp4bb] ITC question -dimer vs monomer

not occur in the future. From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp Sent: Thursday, October 3, 2019 11:06 AM To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] ITC question -dimer vs monomer Hi Fellows, pleas

[ccp4bb] ITC question -dimer vs monomer

the sites on the dimer are at least initially equivalent). Can someone guide me towards literature about this or perhaps share some first-hand experience? Many thanks, BR -- Bernhard Rupp http://www.hofkristallamt.org/ b

Re: [ccp4bb] Reg: water pentagon at dimer interface

Indeed they have been observed in quite a number of high resolution structures. http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-28.htm Chees, BR From: CCP4 bulletin board On Behalf Of Ronald E. Stenkamp Sent: Friday, September 27, 2019 17:22 To:

Re: [ccp4bb] Secrets of ZYMIT

Well, trade secret means exactly what it says. We were equally unable to extort it from the suppliers. MS fragment search as suggested might work. Best, BR From: CCP4 bulletin board On Behalf Of Jorg Stetefeld Sent: Monday, September 9, 2019 00:02 To: CCP4BB@JISCMAIL.AC.UK Subject:

[ccp4bb] Disable Phaser anisotropy correction in ccp4i classic

' - or is there a simpler external keyword or MODE command I can supply? Many thanks, BR -- Bernhard Rupp <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt

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

One practically HAS to do what Dale describes. The sigma levels of a difference map peak depends on how much it is above the mean noise level of the map. With high resolution (and given a cooperating molecule) it is very likely that the model is very good and complete, thus low mean map noise

[ccp4bb] Listserv problem

Dear Guardians of the List: I have been banned from the ccp4bb due to some temporary delivery problems and I cannot subscribe anymore - can someone please contact me off board please? Thx, BR -- Bernhard Rupp <h

Re: [ccp4bb] challenges in structural biology

> What about 'deep learning' applied to crystallization outcomes? Can it guide > individual trials better than intuition? Can it find previously unknown > promising combinations on a larger scale? I think several people were well aware of this need for some sort of sound machine learning

Re: [ccp4bb] Density questionable?

> Could there be two versions of each model: a "robustly-observed" and a "most-likely" version? We tried/suggested something in this spirit once. Not sure how it was received http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html Best, BR

Re: [ccp4bb] SA_flag vs PDB

: http://staraniso.globalphasing.org/deposition_about.html Cheers -- Ian Cheers -- Ian On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote: Hi Fellows – wondering if there is a particular reason the PDB cannot process a mt

[ccp4bb] SA_flag vs PDB

-- Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43

Re: [ccp4bb] beryllium chloride

The older fellows might well remember the huge Be windows on the ADSC multi-wire detectors – miraculously we survived them simply by common sense dictating (i) don’t eat it, (ii) don’t breathe it, and (iii) don’t rub your nose in it…. Cheers, BR From: CCP4 bulletin board On

Re: [ccp4bb] Against method: some warnings about model validation

Its still 31st here! -Original Message- From: Paul Emsley Sent: Sunday, March 31, 2019 6:59 PM To: b...@hofkristallamt.org Subject: Re: [ccp4bb] Against method: some warnings about model validation On 01/04/2019 02:55, Bernhard Rupp wrote: > I think we can be more specific h

Re: [ccp4bb] Against method: some warnings about model validation

I think we can be more specific here: Validation without electron density. One cannot wisecrack from the coordinates only. Otherwise this will be taken as a carte banc against any sort of validation. Best, BR From: CCP4 bulletin board On Behalf Of Robbie Joosten Sent: Sunday, March

Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

Hi Fellows, I'd really like to emphasize the point in the Buster instructions "be careful when examining fo-fc at low levels" when solvent is excluded. If the solvent contribution is omitted where you suspect the ligand (e.g. occupancy 0.02 in Refmac), there will be a fo contribution there from

Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

The most trivial procedure is probably to generate the symmetry mates in Coot (color by symop makes selection easier), pick the ones completing your known biological assembly, and saving those using File/Save Symmetry Coordinates. Once you have the correct model you can superimpose the

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