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 >> is the best option to do this? >> >> [...] >> >> Is pri

Re: [ccp4bb] Error in mosaicity estimation by iMOSFLM

Hi The simple answer is to estimate your own value (as we always used to do before I coded this up about 20 years ago…) by overlaying a prediction over the images and determining what value of mosaicity gives the best coverage. It may also be worthwhile changing the “mosaic block size” in the “

Re: [ccp4bb] message yesterday on the CCP4BB

Hi Pandora’s box comes to mind… Harry > On 10 Jul 2024, at 07:14, Grant Hansman > wrote: > > Hi, > > I sent a message yesterday on the CCP4BB (below). I received so many > enquires. Can I edit or stop this message as I no longer need help. The

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&A=1 This message was

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

Hi You probably need to try again later... It looks to me as if the CCP4 Cloud server (for “remote”) is down for some reason - I just tried to run it and I get a pop-up that says “CCP4 Cloud Maintenance”, that includes the text “failed to connect”. I think that the “structure prediction” task

[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

do-main development by creating an account on GitHub. > github.com > > From: CCP4 bulletin board on behalf of Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> > Sent: Monday, June 24, 2024 2:03 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] List of

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

Hi An internet search doesn’t yield an obvious list of these (I did find a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included appears to be dead - http://deposit.pdb.org/hetdictionary.txt). I’m almost convinced that this has been asked here previously (if not r

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 rescued. I preferred this websi

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 Bleicher

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

n the CCD are correct, but > they are much more reliable. If you find errors, please report them to the > proper authority. See it, say it, sorted. > > Cheers, > Robbie > > On 15 May 2024 14:41, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: &

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

Hi This is very, very useful and hits on the four-letter name problem that I am encountering - thank you. Saves me trying to produce a new design for a circular object with an axle… For the files that I am trying to use, columns 77-78 are present (actually, columns 79-80 are there so I can rea

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

mbol comes from the chemical component dictionary. > > > Ezra > > > > On 5/15/24 6:28 AM, Harry Powell wrote: >> Hi folks >> >> I’m sure that this has been answered many times before (I’m sure that when I >> was young I even read it here…),

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

Hi folks I’m sure that this has been answered many times before (I’m sure that when I was young I even read it here…), and I *know* that we should all be using mmCIF, but I’m using PDB format files generated by a popular Python module and I wanted to check the output against a definitive format

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

t Outlook for Android >>>> 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 Reproducibil

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, Randy John

[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 ; Pedro Beltrao > ;

[ccp4bb] replacement for Scientific Linux

Hi folks For many years I’ve been using Scientific Linux as my OS of choice (when not using my Mac) - but it’s been discontinued. SL was based on RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler than that released by RH. What do people here recommend as a replacement? Harr

Re: [ccp4bb] Microscope camera

Hi Pat Depends on how much you want to spend. I’d start with a web search for “webcam astrophotography”, which should show options on how to remove a webcam’s lens and mount the cam (not the kens, of course!) on another optical instrument. Back in the day, I had a Philips webcam that had a scr

Re: [ccp4bb] Rescale merged data?

” surprised, read “you could have knocked me down with a feather”. > On Thu, Apr 18, 2024 at 09:22:04AM +0100, Harry Powell wrote: >> Only comment is that (surely) any decent refinement program these days >> would down-weight any reflections with negligible I/sig(I) (for example,

Re: [ccp4bb] Rescale merged data?

Hi Only comment is that (surely) any decent refinement program these days would down-weight any reflections with negligible I/sig(I) (for example, those in the “unobserved” high resolution regions) so that they do not contribute (significantly) to the refinement. Or am I wrong (I don’t mind bei

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

Hi Fred There *used* to be CCP14 (for small molecules and powders), but this lost funding many years ago. In the UK, I’d contact the National Crystallography Service at Southampton to see if they have any pointers to bulletin boards - I have a vague recollection of one but can’t remember the d

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 chimerax session as a

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

Hi folks I’ve made considerable progress in getting to the bottom of this problem. From what I can gather, AlphaFold writes “modelCIF”, which is not quite the same as “mmCIF”, and just saying “CIF” is not unambiguous. So I guess I should have been more aware of this when posting my original que

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

gt; > Nick > > > > -- Forwarded message - > From: Nicholas Clark > Date: Fri, Feb 23, 2024 at 8:03 AM > Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill > To: Harry Powell > Cc: Harry Powell > > > Hi Harry, > > M

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

at Buffalo >> Department of Structural Biology >> Jacob's School of Medicine & Biomedical Sciences >> 955 Main Street, RM 5130 >> Buffalo, NY 14203 >> >> Cell: 716-830-1908 >> >> >> On Fri, Feb 23, 2024 at 7:36 AM Harry Powell >> <

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

Hi Martin, Marcin, Arturo, Avinash First off, I’m **NOT** saying that there’s anything wrong with the CIF files produced by these routes - just that AlphaFill doesn’t like them (it *does* like CIFs from AlphaFold - > alphafill process alphafold.cif filled.cif > 1DKE =-

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

> to convert pdb to mmCIF . Hope, it was usuful for your modelled coodinates. > > Regards > > Marta > > > > El 2024-02-23 12:32, Harry Powell escribió: > >> Hi folks >> >> I am in the situation of having coordinates of apoproteins (i.e. polypep

[ccp4bb] mmCIF files from PDB format for AlphaFill

Hi folks I am in the situation of having coordinates of apoproteins (i.e. polypeptide chains without prosthetic groups) in PDB format - but I need them in mmCIF format so I can run them through a locally built copy of AlphaFill. I need something I can install locally, so web services are a no-n

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

Hi Graeme (I may well have mentioned this when we shared an office) et al I’ll add something from my small-molecule crystallography days, when we used point detectors - so this would be pre-1996 which was the last time I used one of these machines. I don’t remember which structure it was (feel

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

Hi Marco Further to Pedro’s comment, one way to avoid missing data in cusps is to use a multi-sweep strategy for data collection (as championed by the good folk at Global Phasing over many years). Many of the problems encountered in structure solution can be traced back to a sub-optimal data co

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 PyMOL, each representing > d

Re: [ccp4bb] what is isomorphous?

Hi Didn’t Francis Crick have something to say about this in the early 1950s? I’m sure it was published but off the top of my mind I can’t think where (one of the more “established” members of this community will be able to give chapter and verse)! If you want to read something a little more de

Re: [ccp4bb] RMSF calculation in pymol

Hi Not PyMol, but relevant to the ccp4BB - why not try “gesamt” for this? e.g. for the nmr structure 1q01 - > gesamt pdb1q01.ent -s '/1/A' pdb1q01.ent -s '/2/A' pdb1q01.ent -s '/3/A' > -r0=1.5 -sigma=1.0 -o 1q01_cluster.cif -o-cf -a align.seq gives me an alignment of the first three models in

Re: [ccp4bb] What could these crystals be?

Hi I can’t see any (obvious) suggestions in the current list of answers to try room temperature diffraction before introducing cryoprotectants and cryocooling your crystals (but I might just have missed it). Often, just the act of changing the conditions that your crystals sit in will destroy

Re: [ccp4bb] Fragile Crystals

Hi Well worth contacting your favourite (or favorite…) synchrotron about in-plate data collection - I’d imagine that APS has something in-place (there was a report way back in the depths of time [2015, when I still worked in the field…] about a prototype on ID-19?), and that might be easier to

[ccp4bb] HH-Suite, HHBLits, HHSearch query

Hi folks I was wondering if anyone on ccp4bb could give me a hand with some queries I have about HHBlits and HHSearch? The “issues” page on github (https://github.com/soedinglab/hh-suite/issues) seems to be completely moribund and no-one has answered any queries for quite some time - this may

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, Jon Coo

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 Iulek wrot

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

On the general topic of tenure, I read an interesting article in the news organ of the American Chemical Society (Chemical and Engineering News) about the future of tenure in the US recently - it’s available free-to-view (C&EN allows viewing one article a month without being a paid subscriber) -

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

Hi If you’re not in a hurry, I should be able to take a look and see what needs to be done (I’m a little busy right now, but I do know more than a ittle about Mosflm and image formats). Otherwise I’d contact Mathias Meyer directly at Rigaku Oxford Diffraction, who should be able to point you in

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

Good idea, but amazon.com.be tells me - "Actuellement indisponible. Nous ne savons pas quand cet article sera de nouveau approvisionné ni s'il le sera.” and amazon.co.uk - "Currently unavailable. We don't know when or if this item will be back in stock.” and amazon.com - "This item canno

Re: [ccp4bb] naturally obsessed - the movie

Hi Chris I seem to remember arranging a showing or two of it at the 2011 IUCr meeting in Madrid (Frances Bernstein asked my about doing this, to give credit where it’s due). I have a vague memory of having obtained the DVD but couldn’t swear to it now. I’ll have a look through my bits and bobs

Re: [ccp4bb] Intractable outliers in wwPDB validation report

Hi I think It may be worthwhile submitting your model and data to PDB-REDO to see if (inter alia) you have applied any unconscious bias to your building that has resulted in these outliers, or over- or under-interpreted the data. It’s quick and easy to submit and requires remarkably little effo

Re: [ccp4bb] the structures of Nucleic acid

Hi I am also reminded that I was involved in the data collection but not structure solution of a DNA cyclic octamer from a single wavelength dataset collected to atomic resolution (on image plate…), which was solved after locating a Ba (which turned out to be one of several with partial occupan

Re: [ccp4bb] the structures of Nucleic acid

Hi folks just my two ha’porth. Back in the mid 1990s, when MAD was becoming common and tunable beamlines were being installed at every synchrotron you could shake a stick at, I was involved in several successful projects involving 5-Br-U in oligo-DNA crystallography. In my (very, very) naïve h

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 there > are one or two

Re: [ccp4bb] mmciif pdb file editor.

Hi There is no particular special editor from PDB (or from anywhere else, as far as I know) for doing this - mmCIF is basically a simple text file with a defined set of contents. It frees you from the tyranny of fixed-width columns that your have in the historic PDB file. I’d just use whatever

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 > wrote: > > Th

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: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC

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

Apropos Phil’s last point - > > 4. On the model front, go find an AlphaFold model, they have worked for me > multiple times in molecular replacement so far. If there is no extant Alphafold model, it may be worthwhile creating your own via colabfold (duckduckgo it like I did…). Only takes a s

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

Hi folks I note that the installation pages for ccp4i2 tell me that I need _exactly_ version 2.8.0 of XQuartz so that things like Coot, iMosflm, etc will work. The problem with that is that my TrueType fonts seem to have disappeared from XEmacs and I’m left with the spidery bit-mapped fonts (I

Re: [ccp4bb] Patenting ligand binding?

I’m left wondering which aspects of the patent application are novel and haven’t already been published elsewhere in the list of references (which include a number of Tamir’s other papers). Others will know - can you patent something that you have already published in a paper? I try to steer cl

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

Hi Armando At the risk of appearing flippant, why not submit the sequence of the full-length protein to something like Alphafold (readily available to all via ColabFold (see https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)? I suspect that each of the t

Re: [ccp4bb] 1990s-style stereo viewer

hand drew each vectors line by line - and my god that >> flickered awfully with “complex” objects. >> >> Adrian >> >> Sent from my iPhone >> >>> On 24 Jul 2023, at 18:53, Harry Powell >>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wro

Re: [ccp4bb] 1990s-style stereo viewer

gt; IGBMC > 1 rue Laurent Fries > 67404 ILLKIRCH - FRANCE > tel: +33 (0)3 69 48 52 82 > From: CCP4 bulletin board on behalf of Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> > Sent: 24 July 2023 16:58:26 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] 1990s-

Re: [ccp4bb] 1990s-style stereo viewer

y used LCD-based shutter glasses connected with a wire > although awfully flickering with a switching frequency in the 8 Hz range! > Wim > > - Mail original - > De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk> > À: "CCP4BB" >

[ccp4bb] 1990s-style stereo viewer

Hi folks I was wondering if anyone has a photo of the old-style head-mounted stereo viewers that used to be used to see 3D images from wall-eyed stereo pairs? I don’t mean the ones that were used to view the side-by-side stereo images that once appeared in printed journals, but the ones that we

Re: [ccp4bb] PDB, mmCIF, chain ID

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

Hi One small issue with Aaron’s answer - the alert specifically says “Not (SHELXL) Weight”, so I suspect that you may not be using SHELXL for your refinement, in which case the “OMIT” instructions may not be available or may take a slightly different form. There’s an open-access IUCr paper wri

[ccp4bb] PDB, mmCIF, chain ID

Hi folks I’ve noticed that for some structures, the PDB file seems to have the mmCIF entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB files it has the “_atom_site.label_entity_id”. e.g. for 4bpq, for ATOM 1 I see - > CIF: ATOM 1N N . UNK A 1 1 ? 14.187 19.54

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

Hi David This is *exactly* what I did when implementing iMosflm’s double-clickable icons for Mac, Windows (“proper” Windows, not WSL, CygWin or MSYS) and Linux, many years ago… Since MacOS is based on (may well actually be, I can’t remember…) BSD UNIX, loads of shell things (nearly but not qui

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 surname (in two > places)? Or

Re: [ccp4bb] British X-ray Crystallographers

t; On 24 May 2023, at 10:17, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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: >> &

Re: [ccp4bb] British X-ray Crystallographers

gt; Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On May 24, 2023 11:26, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Jon > > “Preaching to the choir”! > > Harry >

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-crystallographers > > Best wishes, Jo

Re: [ccp4bb] choosing an NMR structure from PDB

straints > per residue were used and if high-resolution restraints as RDCs had been used. > Recall that NMR structures are build using monomer libraries that are > seriously different from the x-ray ones. > > Best, > > > E. > > >> On 3 May 2023, at 1

[ccp4bb] choosing an NMR structure from PDB

Hi folks I was wondering. If there is a UniProt entry (for example, P01132, but there are plenty of others) for which I want the “best” (whatever that might mean) representative _experimental_ structure (i.e. not one of these new-fangled predicted models that some folk say have removed the nee

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: > > Dear BB, > Quite a few o

[ccp4bb] Fwd: Crystallographic Computing School

Dear all Those of you who are travelling to Melbourne for the IUCr Congress and General Assembly in August may be interested in this (which finishes in time to get to the opening ceremony of the main Congress). To get an idea of the content of the workshop, you may wish to look at tetails of

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 2023, a

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

10 Mar 2023, at 16:58, Jurgen Bosch wrote: > > Going back to RIP phasing methods :-) > So Harry in your particular case occupancy of zero would actually reflect > reality for those “combusted” atoms. > > Jürgen > >> On Mar 10, 2023, at 11:56 AM, Harry Powell &

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

Hi folks One other thing that I haven’t noticed anyone mentioning yet (sorry to those who have mentioned it!!) is that you may not see your sidechain atoms in density because they are not there at all, in spite of what you may have had in the original protein, or even if the atoms were really t

Re: [ccp4bb] Structural alignment and classification

ry > On 6 Mar 2023, at 14:55, Eleanor Dodson wrote: > > Does Superpose or GESAMT align multiple structures? > And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 > etc? > Eleanor > > On Mon, 6 Mar 2023 at 14:53, Harry Powell > <193323b1

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 different ways. USalign is ve

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: > > Dear

[ccp4bb] Bioinformatics post

Hi folks Please let anyone know who may be interested in working in the heart of South Kensington, funded by the Wellcome Trust. Job Opportunity for Experienced Bioinformatics Software Developer (Phyre and Missense3D) See: https://www.jobs.ac.uk/job/CXG066/bioinformatics-software-developer-i

Re: [ccp4bb] Future Diffraction Methods

My (limited) experience of the Diffraction Methods GRC suggests that the most valuable part of these meetings is when people get together outside the talks - so independent of the session chairs (apart from the people that they invite) and of any instructions given to speakers. Just my two ha’p

Re: [ccp4bb] binding pockets...

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...

occasionally split a larger pocket into smaller ones, similar to the fpocket > behavior, but perhaps not quite as frequent. > > -Mike > > On Wed, Jan 4, 2023 at 6:31 AM Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > THX for the replies - > > &

Re: [ccp4bb] binding pockets...

THX for the replies - > On 3 Jan 2023, at 22:56, Bernhard Rupp wrote: > > 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

[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 the fo

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) for d

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

.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519 > > > Provides a SDF file. > > Hope this helps > > Oliver > > p.s. I you are stuck with ChEBI identifiers it would be possible

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

fiers it would be possible to > programatically find the equivalent PubChem CID. > > > > >> On 6 Dec 2022, at 11:31, Harry Powell >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hi folks >> >> Can anyone help with t

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...

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 seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now since I solved any s

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

Hi MIke Beyond the obvious that they should sum to no more than unity, if they are similar to or not hugely greater than other temperature factors in your structure, they are probably okay. People often apply restraints or constraints to keep the temperature factors similar for equivalent atom

Re: [ccp4bb] ChEBI and SMILES

tps://www.ebi.ac.uk/unichem/compoundsources?type=sourceID&compound=BNZ&sourceID=3 > searches for the compound we know as BNZ in the PDB. > > Hope this helps, > > --Gerard > > > > > On Fri, 7 Oct 2022, Harry Powell wrote: > >> Hi Jeet

Re: [ccp4bb] ChEBI and SMILES

ach SMILES string. > Note: you have to first convert each SMILES in the database to canonical form. > I hope this helps. > Thanks > Jitendra Kuldeep > Postdoc researcher > Machine learning and precision oncology group > Cancer research center of marseille, INSERM > France 1300

[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 the f

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

cross this > number of data sets at non-cryo temperatures > > Best wishes Graeme > >> On 8 Sep 2022, at 10:21, Harry Powell >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> hi folks >> >> I’ve been away from data processing for a

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 wrote: > >

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 example of a crystal structu

Re: [ccp4bb] scitbx issue....

for conda-forge that does not have those changes, but I can make a > point release if it is helpful. > > If the PAE code or your installation still does not work, please create an > issue on GitHub and we can sort it out. > > -- > Billy K. Poon > Research Scientist, Molec

[ccp4bb] scitbx issue....

Hi folks No doubt someone will tell me that I should be posting this on the Phenix BB, but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach the right audience anyway! Two Qs - (1) most important - scitbx.array_family seems to have disappeared (see stuff below Q2). (2)

  1   2   3   4   5   >