Re: [ccp4bb] how to create a figure of a blob

Hi I was wondering if moorhen might be useful for this? Harry > On 18 Jul 2024, at 18:35, Paul Emsley wrote: > > On 7/18/24 15:33, Andrea Smith wrote: >> >> I have a “green blob” in my map and I want to create a picture of it. What >&g

Re: [ccp4bb] Error in mosaicity estimation by iMOSFLM

” in the “Images” window after you have loaded images - for “modern” crystals I find that a value of 5 - 10 microns here is often useful. Best wishes Harry > On 18 Jul 2024, at 05:01, Arpana Shikha wrote: > > Dear CCP4 Users, > > I recently updated the CCP4 package from version 8 to

Re: [ccp4bb] message yesterday on the CCP4BB

Hi Pandora’s box comes to mind… Harry > On 10 Jul 2024, at 07:14, Grant Hansman > <db9e83c7f6ed-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi, > > I sent a message yesterday on the CCP4BB (below). I received so many > enquires. Can I edit or stop this messa

Re: [ccp4bb] PDBE - HTTP Status 404?

Ok, it seems to be back again. Maybe the servers had a hangover after yesterday’s celebrations… Harry > On 5 Jul 2024, at 11:43, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > https://www.ebi.ac.uk/pdbe > &g

[ccp4bb] PDBE - HTTP Status 404?

Hi folks https://www.ebi.ac.uk/pdbe HTTP Status 404 - Not Found ?? Harry 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

Re: [ccp4bb] CCP4 Cloud Server Structure Prediction Task Unavailable

predicted models from the DB). Harry > On 26 Jun 2024, at 06:00, YASH MISRA PHD222012 > wrote: > > Dear all, > > Can someone help me with this? > > Until yesterday it was working fine but today when I tried running this task > I am getting the following error. I tr

[ccp4bb] PDBE website down - scheduled "maintenance" or not?

Hi folks I’m just having issues seeing the PDBe website - does anyone know if this is scheduled or if there is another issue? Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk

Re: [ccp4bb] List of 3-letter codes of modified amino acids

people to raise the issue directly with me…) Once more, I knew this would be the place to ask! Harry > On 24 Jun 2024, at 13:40, Robbie Joosten wrote: > > Hi Harry, > > A BSc student in our lab just had a look at this. Here is the list of > mappings pdb-redo uses: > h

[ccp4bb] List of 3-letter codes of modified amino acids

(if not recently), but a quick search through ccp4bb postings has not revealed it to me. Can anyone help? Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1

Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

Hi Presumably Wladek would know about this - I believe that he is an occasional visitor to this BB! Harry > On 13 Jun 2024, at 10:40, Martin Malý wrote: > > Dear John, > Thank you for the link. It would be great if https://proteindiffraction.org/ > (IRRMC) was rescu

Re: [ccp4bb] Computational crystallography in 2024

Hi Lucas This one? https://www.iucr.org/resources/commissions/crystallographic-computing/schools/kyoto-2008-crystallographic-computing-school IUCr’s Commission on Crystallographic Computing still holds these - next one (probably) in Alberta! Harry > On 16 May 2024, at 01:51, Lucas Bleic

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Robbie I’m not actually using PDB files of proteins - I’m using the PDB format files in PDBeChem, because at the moment I’m interested in doing stuff with ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what I’d expect, but I’m prepared to work around that. Harry

Re: [ccp4bb] a dinosaur asks ... PDB format query

read the atomic charge as well, which is useful for my purposes) so I’m hoping that this will be reliable. Harry > On 15 May 2024, at 12:38, Marcin Wojdyr wrote: > >> >>> • Alignment of one-letter atom name such as C starts at column 14, while >>> two-lett

Re: [ccp4bb] a dinosaur asks ... PDB format query

Sorry - just read that > • Alignment of one-letter atom name such as C starts at column 14, while > two-letter atom name such as FE starts at column 13. indicating a rule does exist. Harry > On 15 May 2024, at 11:54, Harry Powell > <193323b1e616-dmarc-requ...@jiscma

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Ezra Thanks for this. In other words, would it be true to say that there are no actual rules about what appears in columns 13-16 because “it's a rose by any other name”? Harry > On 15 May 2024, at 11:38, Ezra Peisach wrote: > > If you take a look at > https://w

[ccp4bb] a dinosaur asks ... PDB format query

8.307 6.456 -11.669 6.00 11.00 C > HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 C I’m sure that someone here will say “why don’t you look at *, it’s obvious”, in which case - many thanks! help Harry

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

ndroid >>>> From: CCP4 bulletin board on behalf of Rafael >>>> Marques >>>> Sent: Monday, May 13, 2024 3:13:16 PM >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility >>>

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hi With this in mind, I have found the easiest way to generate AlphaFold models (for those not in the DB) is actually in CCP4 Cloud-remote - makes MR using AF models a real doddle. See the Tutorials (in particular on MR) available with CCP4 Cloud. Harry > On 14 May 2024, at 09:20, Ra

[ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Hi folks This arrived in my inbox this morning, and I believe that it may provoke some discussion… Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν Best wishes! Harry >From: Stephanie Wankowicz >Sent: Saturday, May 11, 2024 3:31 PM >To: James Fraser ; Pedr

[ccp4bb] replacement for Scientific Linux

? Harry 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

Re: [ccp4bb] Microscope camera

have their own webcam utility to turn your DSLR/mirrorless into a suitable device, and this would be most likely to use the SLR mount. E-Bay have Nikon bodies starting at around $200 today. Harry > On 24 Apr 2024, at 22:15, Patrick Loll wrote: > > Greetings, hive mind, > >

Re: [ccp4bb] Rescale merged data?

Hi Clemens I’m “quite”* surprised. Do the authors of these programs offer any explanation as to why the scaling programs (given that these are the ones that usually provide F/I information for subsequent programs) bother to calculate sigmas if they’re going to be ignored? Harry * for “quite

Re: [ccp4bb] Rescale merged data?

tion limit is (I’d choose CC -1/2 = 0.30, as Doeke suggests)? Do HKL or XSCALE do the same (sorry, I haven’t looked at their output for quite some time)? Just my two ha’porth Harry > On 17 Apr 2024, at 21:35, Hekstra, Doeke Romke > wrote: > > Hi Matt, > > I appreciate disagree

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

and be able to answer you directly - 30 years ago I *would* have been able to spot problems in these files at a glance, but lack of practice means that I doubt I could do the same these days! best wishes Harry > On 12 Mar 2024, at 09:00, Fred Vellieux wrote: > > Hi folks, > >

Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

Hi Marco You could always try the CCP4 tools (since this is the CCP4 BB…) “superpose” or “gesamt” to superpose (or is it “superimpose”? discuss…). Harry > On 28 Feb 2024, at 00:53, Marco Bravo wrote: > > Hello all, > Does anyone know how to save a superimposed pymol or chim

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

it was an unrecognised system, and the most recent binary was built in 2008). Many thanks to everyone who took the time to read and answer my question! Harry To unsubscribe from the CCP4BB list, click the following link: https

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

(when) things go wrong! best wishes and thanks again Harry > On 23 Feb 2024, at 14:00, Nicholas Clark > <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Harry, > > Unfortunately, I did not see that the latest binary update was from 2008. I > do not

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

are wonderful - that’s why there are so many of them. Have a great weekend Harry > On 23 Feb 2024, at 12:46, Ida de Vries wrote: > > Dear Harry, > > You could also try to use pdb2cif from the cif-tools: > https://github.com/PDB-REDO/cif-tools. The only strict requirement for

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

.. any version > SGI IRIX ... version 5.3-6.4 > make: *** [Makefile:32: compile] Error 1 which is odd, because this is a new Linux system installed this week > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release > Rocky Linux release 9.3 (Blue Onyx) best wishe

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

til I retire ;-)); I’ve found with other web resources that this can trigger DDOS protection systems (e.g. being temporarily banned…). best wishes Harry > On 23 Feb 2024, at 11:41, Marta Martínez wrote: > > Hi Harry > > I use this link: https://mmcif.pdbj.org/converter/ &

[ccp4bb] mmCIF files from PDB format for AlphaFill

A-coot-0.cif filled.cif > Error reading file ‘protein_A-coot-0.cif' > >> parse error at line 2: This file does not seem to be an mmCIF file Harry To unsubscribe from the CCP4BB list, click the following link: https://ww

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

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 (DLS

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

collection. You don’t say which beamline at ALS you used, but if it’s got a kappa or similar fitted the beamline staff should be able to help. best wishes Harry > On 20 Feb 2024, at 09:20, Pedro Matias wrote: > > Hi Marco, > > Further to Zhen's comment, that can also happen if

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue RMSD Harry > On 5 Jan 2024, at 10:49, Tomas Malinauskas > wrote: > > Dear All, > > I apologize for asking a somewhat off-topic question. > > I have multiple aligned PDB files loaded in

Re: [ccp4bb] what is isomorphous?

detailed than people have mentioned here, there’s a “Methods in Enzymology” chapter by Charlie Carter (?) et al from the early part of this century on the subject - again, I can’t remember exactly who or when. Have a good break (which reminds me to register for the CCP4 Study Weekend)! Harry

Re: [ccp4bb] RMSF calculation in pymol

models in the file Harry > On 14 Dec 2023, at 21:55, Krieger, James M wrote: > > I don’t have one for pymol, but there is a function in prody for it. > > Best wishes > James > >> On 14 Dec 2023, at 21:41, Srivastava, Dhiraj >> wrote: >> >>  &g

Re: [ccp4bb] What could these crystals be?

, some places will also grow your crystals for you on site, using your conditions. Unfortunately, I don’t know where “yahoo” is, so I can’t make a suggestion as to which might be closer/easier for you to access! best wishes Harry > On 24 Nov 2023, at 08:59, careinaedgo...@yahoo.

Re: [ccp4bb] Fragile Crystals

to get samples to (from Birmingham) than one of the European facilities. Harry > On 23 Nov 2023, at 09:31, Jose A. MARQUEZ wrote: > > Dear Elizabeth, > > In situ data collection is a good approach to try in your case. You could use > the CrystalDirect technology for automated

[ccp4bb] HH-Suite, HHBLits, HHSearch query

be associated with the project losing funding (which is a huge loss to the community at large). Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1

Re: [ccp4bb] Video link for RSC meeting on "British X-ray Crystallographers."

Hi Jon many thanks for this! For those interested in Peter Morris, there was an interview with him in Chemical and Engineering News at the end of September - https://cen.acs.org/people/CEN-talks-with-Peter-J-T-Morris-science-historian/101/i32 Harry > On 9 Nov 2023, at 22:57,

Re: [ccp4bb] radiation damage and image discard

Hi I’ve never actually used it in anger (one should never be angry when processing data…), but doesn’t AutoProc, developed by the good folks at Global Phasing do a lot of these analyses? Clemens, Claus etc may have something pertinent to say. Harry > On 30 Oct 2023, at 13:23, Jorge Iu

Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

) - > https://cen.acs.org/careers/great-tenure-debate-again/101/i29 If you have a free 10 -15 minutes… Harry > On 16 Oct 2023, at 08:15, Tim Gruene wrote: > > On Sun, 15 Oct 2023 19:44:45 + > "Hekstra, Doeke Romke" wrote: > >> Mark is, of course, right that

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

in the right direction. Best wishes Harry > On 10 Oct 2023, at 06:17, 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 t

Re: [ccp4bb] naturally obsessed - the movie

Okay, I’ve found a DVD with it on… Harry > On 3 Oct 2023, at 14:51, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Good idea, but amazon.com.be tells me - > > "Actuellement indisponible. > Nous ne savons pas quand cet article sera

Re: [ccp4bb] naturally obsessed - the movie

t… so it should be somewhere in my “archives" Harry > On 3 Oct 2023, at 14:22, F.Xavier Gomis-Rüth wrote: > > You can purchase it from Amazon. > > On 3/10/23 15:21, Burak Veli Kabasakal wrote: >> Dear all, >> >> Sorry I realized the movie is only 10 mi

Re: [ccp4bb] naturally obsessed - the movie

to see if I can find it. Do you have a deadline? Harry > On 3 Oct 2023, at 11:02, Chris Ulens wrote: > > Dear members of the ccp4bb, > I have a somewhat unusual question. For many years I have shown the movie > “Naturally Obsessed - the making of a scientist” for educative

Re: [ccp4bb] Intractable outliers in wwPDB validation report

effort on your part - another tool to your collection. Harry > On 25 Sep 2023, at 07:00, Guillaume Gaullier > wrote: > > A good example of such expected outliers can be found in structures of > nucleosomes: the validation report always flags almost all DNA bases as > geometr

Re: [ccp4bb] the structures of Nucleic acid

occupancy); the structure solution was actually carried out in the laboratory of one G.M. Sheldrick, using software that I think may have never been released to the public. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/ for details... Harry > On 19 Sep 2023, at 20:53, Di

Re: [ccp4bb] the structures of Nucleic acid

to them appearing in Acta D), available at - https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html Contributions at the same meeting by others whose names will be instantly recognizable may well be more use than mine… Best wishes Harry > On 19 Sep 2023, at 19:32, Wag

Re: [ccp4bb] Determining Second Lattice

Hi Matt Call me old-fashioned but I’d use Mosflm for this. The multiple lattice autoindexing is easy to run and easy to interpret. Harry > On 30 Aug 2023, at 16:20, Matt McLeod wrote: > > Hi all, > > I have a lot of large datasets that I want to screen to determine if t

Re: [ccp4bb] mmciif pdb file editor.

whatever text editor you have on your system - so on LInux or Mac, something like vim, emacs, nano, on Windows Notepad. No need for anything special. But I’d also be wary about screwing up the file completely with your edits - it’s easy to turn a compliant file into something invalid. Harry > On

Re: [ccp4bb] ILLUSTRATE in PYMOL

Hi Since this is the ccp4 bulletin board, it’s always worth mentioning CCP4MG for producing images & movies of macromolecules. Comes with the package, and you can get help from the author directly if you have any issues. Harry > On 17 Aug 2023, at 02:09, khaja faisal tarique

Re: [ccp4bb] An unknown but strong positive electron density in my crystal

Hi > Has anyone seen similar density to this before and/or can suggest how to > model this positive density? Many thanks. Romulan bird of prey? Harry > > Regards, > > Yue Li > > > > To unsubscribe from the CCP4BB list, click the following link: > http

Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

nly takes a short time... best wishes Harry > On 2 Aug 2023, at 20:20, Phil Jeffrey wrote: > > 1. Completeness is primarily an issue with using the right point group and > crystal system, not the actual space group (e.g. in primitive point group mmm > the space groups P222, P2221

[ccp4bb] Macs, XQuartz, ccp4i2, Coot, iMosflm....

” with a pleasing appearance? Harry 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

Re: [ccp4bb] Patenting ligand binding?

clear of lawyers and the law... Harry > On 28 Jul 2023, at 12:36, John R Helliwell wrote: > > Dear Graeme, > Yes indeed, interesting. > There are clearly aspects of microED of proteins which might be documented as > non-obvious otherwise it wouldn’t have been a bi

Re: [ccp4bb] On the production of a two domain protein

easy to run (submitting a job would take less time than it’s taken me to type this sentence), and has very helpful user support (see http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) It would at least give you something to think about before spending time in the lab. Harry > On 26

Re: [ccp4bb] 1990s-style stereo viewer

) because they had the set-up your pictures are of. However, these pics may still be of use to me. Thanks everyone who has replied to this - I knew this would be the right place to ask! Harry > On 25 Jul 2023, at 00:23, Jon Cooper > <488a26d62010-dmarc-requ...@jiscmail.ac.

Re: [ccp4bb] 1990s-style stereo viewer

Hi Alastair YES! Those are the ones. Many thanks Harry > On 24 Jul 2023, at 16:46, Alastair MC EWEN wrote: > > Hi Harry, > > Are these the ones you mean? > > Best, > Alastair > > ~ > Alastair McEwen, PhD > Integrated Structural Biology Platform &

Re: [ccp4bb] 1990s-style stereo viewer

Can’t have been a PS300 in that case! I’ve since been reminded that they were made of wood (the stereo viewers, not the Evans and Sutherland. But I’m probably wrong about that as well…) Harry > On 24 Jul 2023, at 16:03, Wim Burmeister wrote: > > Hi, > the E PS300 already us

[ccp4bb] 1990s-style stereo viewer

that were used for advanced computer graphics machines like E PS300. From my somewhat dim memory, they had an adjustable mirror on one side so that the two views could be coalesced (with the adjustment knob on the top of the box). More in hope than expectation… Harry

Re: [ccp4bb] PDB, mmCIF, chain ID

to tell me that the chain ID in legacy PDB format in _atom_site.auth_asym_id in the mmCIF, and not in either of the two items I mentioned previously. best wishes and happy Solstice! Harry > On 9 Jun 2023, at 15:57, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: &

Re: [ccp4bb] checkCIF alert

tps://journals.iucr.org/e/issues/2020/01/00/su5533/index.html > > https://doi.org/10.1107/S2056989019016244 > > checkCIF validation ALERTS: what they mean and how to respond > > Anthony L. Spek best wishes Harry > > On 12 Jun 2023, at 10:29, Aaron Finke >

[ccp4bb] PDB, mmCIF, chain ID

read the entries? (the refinement program for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably phenix.refine, but I wouldn’t bet my house on it). Harry To unsubscribe from the CCP4BB list, click the following

Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path

but not quite 100%) that work for Linux will also work for Macs (as you suspect). Harry > On 5 Jun 2023, at 12:31, David J. Schuller wrote: > > I am not familiar with Macs, but on Linux the first problem could be easily > solved by having the desktop shortcut call a brief shell script

Re: [ccp4bb] British X-ray Crystallographers

Hi Gerard I’ve mentioned it to the organiser - we shall see how long the Garmen will be there! Harry > On 24 May 2023, at 10:27, Gerard Bricogne wrote: > > Dear Jon, > > Quite a line-up indeed. > > Might someone at the RSC correct the typo in Elspeth's sur

Re: [ccp4bb] British X-ray Crystallographers

so expensive and the results were not that good. > > But I agree that many (all?) of the talks will be of lasting value. I will > think about how we could record it without incurring great expense. So (being an optimist, as those who know me well know :-)) I’d say “maybe”. Harry > &g

Re: [ccp4bb] British X-ray Crystallographers

Hi Boaz No informaiton on the website about this but I have asked the organiser. Harry > On 24 May 2023, at 09:58, Boaz Shaanan wrote: > > Indeed! Will it perhaps be possible to watch the event by zoom? Or will a > recording of it be availabe later on? Any idea? > Cheers, &

Re: [ccp4bb] British X-ray Crystallographers

Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at 23:16, Jon Cooper > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > I am biased, but this looks like an interesting meeting: > > https://www.rsc.org/events/detail/76719/british-x-ray-crystallog

Re: [ccp4bb] choosing an NMR structure from PDB

, Rfree 0.222) is at #6 - why? looking at the PDB-REDO entries is educational), so it’s challenging to write scripts that will scrape the whole DB and give the “best” model for each. Harry > Hi Harry, > > A useful starting point when looking for the 'best' [insert criteria here] &g

[ccp4bb] choosing an NMR structure from PDB

of these are from the same paper, so may be in different conditions (e.g. pH). All except the first (1A3P) cover the same bit of sequence. Specifically, what should I look for in the downloadable files (mmCIF, for example) from the PDB? Thoughts? Harry

Re: [ccp4bb] COOT crash in ccp4i2 - Error in wrapper coot_rebuild 0.0

I hadn’t noticed until just now, but this also happens on Linux machines at SLAC - > Distributor ID: Debian > Description: Debian GNU/Linux 10 (buster) > Release: 10 > Codename: buster :-( Harry > On 29 Mar 2023, at 15:02, Joseph Cockburn wrote: > > D

[ccp4bb] Fwd: Crystallographic Computing School

of previous events held by the IUCr Commission for Crystallographic Computing which are are available here - > https://www.iucr.org/resources/commissions/computing/schools Harry > Begin forwarded message: > > From: "Lutz, M.H. (Martin)" > Subject: Crystallographic Co

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

Whoops! A quick glance at the PDB entry indicates I must have been clairvoyant to have read it 20 years ago. Harry > On 20 Mar 2023, at 10:35, Harry Powell wrote: > > And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or > not cramin is a protein, since

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

And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or not cramin is a protein, since it has “only” 46 amino acids) where (from memory, I haven’t read the paper for at least 20 nyears…) they modelled multiple water networks. 3NIR, for reference. Harry > On 20 Mar 2

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

Hi Jürgen You might think so, but I’d disagree. Not going too far away from your line of reasoning I could also put in a completely fictitious ligand or cofactor and assign its occupancies to zero (I really, really knew it was there but I just couldn’t find any evidence… :-)) Harry > On

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

there in the crystal _before_ exposure to the beam. The coordinates are supposed to be what you actually find, not what you hope is there. Just my two ha’porth Harry To unsubscribe from the CCP4BB list, click

Re: [ccp4bb] Structural alignment and classification

Hi Eleanor According to https://www.ccp4.ac.uk/html/gesamt.html "Gesamt aligns two or more structures…” and https://www.ccp4.ac.uk/html/superpose.html "superpose aligns and superposes two or more protein structures…” But the real expert is probably Eugene. Har

Re: [ccp4bb] Structural alignment and classification

Or you could use Gesamt - also in CCP4. Harry > On 6 Mar 2023, at 13:15, Kay Diederichs > wrote: > > Dear Armando, > > besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign > (https://zhanggroup.org/US-align/). > In my tests, THESEUS sometimes crashed in

Re: [ccp4bb] Tools for structure-based multiple sequence alignment

Hi Manoj If the structures are in the PDB, then PDB-KB may have already done the work for you - https://www.ebi.ac.uk/pdbe/pdbe-kb/ They run Gesamt on homologous structures for the whole PDB every week (as I understand it). Harry > On 2 Mar 2023, at 07:45, Manoj N wrote: >

[ccp4bb] Bioinformatics post

we’re processing > 1000 models a day (project supervised by Prof Mike Sternberg). Missense-3D predicts the structural changes introduced by an amino acid substitution (project supervised by Dr Alessia David). > http://www.sbg.bio.ic.ac.uk/phyre2/ > http://missense3d.bc.ic.ac.uk/mis

Re: [ccp4bb] Future Diffraction Methods

ha’porth Harry > On 30 Jan 2023, at 11:54, Frank von Delft wrote: > > Whether cross-pollination happens depends on the session chairs, and the > remit they're given, and the instructions given to the speakers: if early on > everybody sets the tone, to inform as much as advertise

Re: [ccp4bb] binding pockets...

is the surface of the pocket as vertices and faces in a file with the extension “.obj” (the other programs fill the pocket with dummy atoms). Result looks most similar to that from parKVFinder. Again, many thanks for the input Harry > On 12 Jan 2023, at 11:26, Harry Powell wrote: > >

Re: [ccp4bb] binding pockets...

Hi Mike Interesting. I haven’t looked at Java stuff for quite some time… Harry > On 4 Jan 2023, at 12:53, Mike S wrote: > > Have you tried P2Rank? It is quite fast, and there is a standalone version > that has command line options to run against all coordinate files in a >

Re: [ccp4bb] binding pockets...

tons gets a little boring! Sorry my initial post wasn’t clearer Harry 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

[ccp4bb] binding pockets...

Hi folks I was wondering what people’s favourite program is to find binding pockets in proteins. I’ve had a look at a couple but each has its own idiosyncrasies. HNY Harry To unsubscribe from the CCP4BB list, click

Re: [ccp4bb] ligands found in ChEBI...

g that with “64119” as the argument gives me a file ChEBI_64119.sdf with 3D coords. Many thanks to all who got me out of my hole! Harry > On 6 Dec 2022, at 12:19, Harry Powell wrote: > > Hi Julie > > Ta. > > Do you know if there’s an API (pref. Python 3.9 or later) f

Re: [ccp4bb] ligands found in ChEBI...

Hi Oliver I’d just worked that out when I tried an obviously non-planar molecule (that I didn’t include with my breakfast this morning)! PubChem looks like a useful way forward - many thanks. Harry > On 6 Dec 2022, at 11:55, Oliver Smart wrote: > > Hi Harry, > > The SDF

Re: [ccp4bb] ligands found in ChEBI...

! Harry > On 6 Dec 2022, at 11:31, Harry Powell wrote: > > Hi folks > > Can anyone help with this? > > I must have missed something in the documentation, because I don’t understand > why the .mol and .sdf files downloaded from > > https://www.ebi.ac.uk/chebi

[ccp4bb] ligands found in ChEBI...

0 0 > 4 3 2 0 0 0 0 > 7 4 1 0 0 0 0 > 1 5 1 0 0 0 0 > 5 3 1 0 0 0 0 > 12 5 1 0 0 0 0 > 6 2 1 0 0 0 0 > 6 4 1 0 0 0 0 > 11 6 2 0 0 0

Re: [ccp4bb] occupancy factors for alternate conformations and alternate ligands

atoms in different partially occupied conformations, but I’m not sure there is a real justification for this apart from making the solution refine more stably. No doubt someone here will correct me! Harry > On 28 Nov 2022, at 19:31, Michael Colaneri wrote: > > Dear colleagues, &g

Re: [ccp4bb] ChEBI and SMILES

) ChEBI ≠ ChEMBL, although there is an overlap (a considerable ione…). Harry > On 7 Oct 2022, at 10:29, jeet balraj wrote: > > Hi Harry > To search the ligand of interest in the ChEMBL database, you can follow these > simple steps: > 1. download the ChEMBL database and extr

[ccp4bb] ChEBI and SMILES

Hi Probably a silly question, but I was wondering how to search for a ligand in ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning mind ... Harry To unsubscribe from the CCP4BB list, click

Re: [ccp4bb] Lower b-factors with increasing T

Hi Graeme good to know that I haven’t forgotten everything. Rgarding the data collection - I don’t think the OP mentioned how many crystals were used in the data collection (unless, of course, I’ve been reading even less carefully than normal…). Harry > On 8 Sep 2022, at 10:29, Win

Re: [ccp4bb] Lower b-factors with increasing T

hi folks I’ve been away from data processing for a while, but am I alone in thinking that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3. Harry > On 7 Sep 2022, at 19:46, Matt McLeod

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

Crambin (quick search for “Martha Teeter” and “Crambin” should yield dividends)? There are some very high resolution structures of that with multiple conformations. Harry > On 23 Aug 2022, at 23:02, Pavel Afonine wrote: > > Dear community, > > I’m looking for an examp

Re: [ccp4bb] scitbx issue....

Hi Billy Many thanks for this - unfortunately, there are other dependencies that appear not to be included in > conda create -n new_environment -c conda-forge cctbx-base python=3.9 e.g. > [MacPro:~] harry% conda activate phenix_env > (phenix_env) [MacPro:~] harry% python > P

[ccp4bb] scitbx issue....

this is on a freshly installed conda... The error I get when trying to run process_predicted_model.py is - > [MacPro:~/icl/test] harry% python3 process_predicted_model.py > pae/AF-Q8W3K0-F1-predicted_aligned_error_v2.json > Traceback (most recent call last): > File "/Volumes/Use

Re: [ccp4bb] Regarding the correct space group identification

hope not freezing…) the crystal, I would take some time to optimise the cryocooling conditions. I’d also think about moving the detector further away (maybe 300mm?) so you aren’t “wasting” so much of it - the diffraction only goes ~2/3 of the way to the edge. Just some thoughts. Harry

Re: [ccp4bb] Regarding the correct space group identification

Sorry - meant to add this: I know that (of the “free” programs) Mosflm, DIALS and Eval15 can process multiple lattices. Harry > On 28 Jul 2022, at 14:36, Harry Powell wrote: > > Hi Sayan > > If you have multiple lattices showing in your diffraction pattern, it may be > wo

  1   2   3   4   5   >