Re: [ccp4bb] How to address deposited structures poorly modeled?

There are a few helpful things to remember: First, absolute values of global reciprocal space metrics, like R and R free, are not informative about local real space errors. So the R-value number does only inform you whether a model is perhaps complete rubbish or rather not. It also informs you abo

Re: [ccp4bb] Words to avoid

Then: on the poop list of the postmodernists: Transgressing conventional boundaries: Postmodern Structural Biology. * B. Rupp. IUCR Keynote. Aug. 21-29, 2011* Now: on the poop list of the new order: Correcting cis-trans-transgressions in macromolecular structure models. F. Waibl, K. R. Liedl, B. Ru

Re: [ccp4bb] Words to avoid

Baja de gringo loco On Wed, Mar 12, 2025, 19:41 Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > "_golf_ of America” particularly apt with current POTUS… > > Harry > > > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh < > vaheh.oganes...@astrazeneca.com> wrote: > > > > You never

Re: [ccp4bb] Key bindings WinCoot 0.9

This (.coot-preferences) is where the key bindings script should be installed to (*). Not sure why it didnt happen in your case. I assume some permission issue. Difficult to say from your description. Anyway, good that it works now. B (*) which actually resides in %COOT_HOME% which by default

Re: [ccp4bb] Crystal optimization

) and methanol (protein, unpublished). Best regards Bernhard To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to mem

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

On 15/05/2024 19:03, Paul Emsley wrote: On 13/05/2024 17:38, Otsile Mojanaga wrote: *From:*Otsile Mojanaga *Sent:* Monday, May 13, 2024 3:29 PM *To:* Paul Emsley *Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC Dear Paul/All Thank

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

w if that'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> &

[ccp4bb] Interface Configuration and Mapslicer Question

ep, and there, 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...@hofkr

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 re

[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.

[ccp4bb] Two postdoc positions in Ubiquitin Signalling, WEHI, Melbourne, Australia

and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Officer---Structural-Biology-of-E3-Ubiquitin-Ligases_JR1578-3 Contact: Dr. Bernhard Lechtenberg, lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au> The Komander lab seeks to recruit a postdoc with stru

Re: [ccp4bb] About the A in AI

My bad. Both ChatGPT, here is bing: https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0 From: Ian Tickle Sent: Friday, May 12, 2023 17:33 To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] About the A in AI Hi Bernhard Methinks there's

[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] To Trim or Not to To Trim

results of 240 respondents were: Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Bernhard From: CCP4

Re: [ccp4bb] To Trim or Not to To Trim

trimming the side-chains. Bernhard Bernhard C. Lechtenberg PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division​​ E lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au> T +61 3 9345 2217 From: CCP4 bulletin board on behalf of Rhys G

Re: [ccp4bb] Postdoc opportunity at WEHI, Melbourne, Australia

There are still a few days to apply for this postdoc position in my lab at WEHI in Melbourne. Application deadline is 11 March 2023 (AEDT; closer to 10 March for those in the US). For questions please email me at lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au> Bernhard

[ccp4bb] Postdoc opportunity at WEHI, Melbourne, Australia

ease email me at lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au>. Best wishes, Bernhard Bernhard C. Lechtenberg PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division​​ E lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au> T

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 assisted

[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 cryo-Microscop

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

preference 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> hofkrista

[ccp4bb] bond angle deviation listing in refmac log

CCP4 8.0.005: Refmac version 5.8.0352 : 05/31/22## ### Thx, BR ----- Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 <mailto:b...@ruppwe

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 non-crystallogra

[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 Behalf

[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] PDB deposition of structure solved with a Robetta model

, which is a mandatory item for the deposition. How can I keep the information that I used the Robetta calculated model? In advance thanks for your valuable answers. Cheers, Bernhard -- Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und

[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. htt

[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, Augu

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 Gruene

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 wi

Re: [ccp4bb] Co crystalization with less soluble ligand.

Dear Gourab, You might just want to add the ligand in pure, solid form to the edge of the crystallization drop. This worked in our case beautifully (see Angew. Chem. Int. Ed. 2012, 51, 3354). We had to soak it for 4 weeks. Good luck! Best regards Bernhard

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 occupa

[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

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, > > > > P

[ccp4bb] ideal ligands

Thx, BR -- 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

[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 dr

Re: [ccp4bb] The weekly nonsense

referees should have spotted that 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 popul

[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

ents > > #!/bin/bash > #egrep '^ATOM|^HETATM' | cut -c77-78 file.pdb | sort -u` > > for atom in "$@" >do > if [ "$atom" != "$1" ] > then > echo -e "NWAV 1 $1\nATOM $atom\nEND\n" | crossec

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 &iano=1&nresi=10

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

SG 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 dis

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

ure 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. A

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 1

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 hel

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: https://febs.onlinelibrary.wiley.com/doi/epdf/1

[ccp4bb] [RESOLVED]partially restrained mode?

t (to check 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

[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] A Problem of my Research Protein

? Good luck, Bernhard From: CCP4 bulletin board on behalf of Guohui SHANG Reply to: Guohui SHANG Date: Tuesday, 15 September 2020 at 4:22 pm To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] A Problem of my Research Protein Hi Everyone， Well,My Research Protein is easily Dimerzation

Re: [ccp4bb] Cell disruption

Dear colleagues, The CCP4BB community is amazing, as always. I received many comments by happy users of the Avestin Emulsiflex C3 (and C5); not so much on the Microfluidics LM20. Thanks for that, it will be a great help to decide which instrument to purchase. Best, Bernhard From: CCP4

[ccp4bb] Cell disruption

more about ease of use, maintenance, reliability and if anybody operates these in a cold room (4°C). Thanks in advance, Bernhard -- Bernhard C. Lechtenberg, Ph.D. Laboratory Head Ubiquitin Signalling Division The Walter and Eliza Hall Institute 1G Royal Parade Parkville VIC 3052 Australia Phone

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 all,

[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

e) 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&qu

[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?

correct"/"incorrect" and "right"/"wrong", 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 d

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 b

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 it is

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

"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 A

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 use

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 eas

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: CCP4BB@JISCMAI

Re: [ccp4bb] visual mask editor - why

editor - why Bernhard, Sounds like you are plotting something similar to what I was tinkering with once. A script you may find useful is this one: https://bl831.als.lbl.gov/~jamesh/bin_stuff/map_func.com I wrote this because although mapmask, maprot, etc have very useful functionalities I

Re: [ccp4bb] Question about small molecule crystallography

questions. You will find descriptions about different crystallization techniques and which (organic) solvents you can use for a start. If you have further questions, just send me an email. Best regards Bernhard Prof. Dr. Bernhard Spingler Department of

Re: [ccp4bb] visual mask editor - why

Yes I have already pilfered useful parts of it in the scripts. Thx, BR From: Boaz Shaanan Sent: Thursday, May 28, 2020 11:59 To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor - why Hi Bernhard, Did you consider trying 'polder' in

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, excluding

[ccp4bb] visual mask editor - why

would 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...@hofkristal

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 12:39

[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?

e map file 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.

[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.hofkrist

[ccp4bb] Refmac and hydrogens -developers

e input PDB and 'use if present' 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 --

Re: [ccp4bb] Using SFall for map conversion

...@hofkristallamt.org Subject: Re: [ccp4bb] Using SFall for map conversion Dear Bernhard, Is it an old map ? Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I think I was using

Re: [ccp4bb] Using SFall for map conversion

rc-requ...@jiscmail.ac.uk <mailto:0d88e888355a-dmarc-requ...@jiscmail.ac.uk> > wrote: Dear Bernhard, Is it an old map ? Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map format

Re: [ccp4bb] Using SFall for map conversion

ing SFSG 1 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 head

[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] Coot "Fix nomenclature error" window

, e.g. “.coot.py”, I think you have to change this to “set_nomenclature_errors_on_read ignore”. HTH, Bernhard -- Bernhard C. Lechtenberg, Ph.D. Laboratory Head Ubiquitin Signalling Division The Walter and Eliza Hall Institute 1G Royal Parade Parkville VIC 3052 Australia Phone: +61 3 9345 2217

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 A

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 2:53

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 ind

Re: [ccp4bb] New phasing approach

ses through the interferometer cutting down tremendously the intensity of reflections from macromolecular crystals which tend to be far from parallel. Gerd On 01.04.2020, 16:02, "CCP4 bulletin board on behalf of Tim Gruene" wrote: Dear Bernhard, your paper is actually not so much of

[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 Schö

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 #JBCMethodsM

[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] Overrefinement considerations and Refmac5.

In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie. (summarized in BMC) and a figure of the empirical distributions http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm which are broad and – as mentioned - the actual delta values

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 http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomo

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) ht

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

, mit Rotkraut & 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 > uninform

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

ty representation 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 w

[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

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