Re: [ccp4bb] CCP4 Cloud structure determination help

It's actually easier than that these days. Merely centre on an atom in the symmetry-related position and use Calculate -> Modelling -> Symm Shift Reference Chain Here Paul. On 10/02/2025 13:47, Matthew Snee wrote: -- Hi Marco Is the N terminal part present in the correct place if you s

Re: [ccp4bb] access to the electron density maps of a PDB entry

denvercoder9 - not exactly the same, but similar. On 14/01/2025 22:09, Gerard Bricogne wrote: Dear Pavel, Your comment has been made many times, especially in discussions that eventually led to the official decision to make room for these coefficients in the mmCIF dictionary. The idea be

Re: [ccp4bb] replacing B-factor column and color accordingly

On 13/01/2025 16:43, Marcin Wojdyr wrote: Dear Yahui, I am looking for a PDB editing tool to replace the B-factors numbers with another column of numbers It depends where you get that new column of numbers from. Yes, this is most of the problem. Presuming, as did Clemens, that your input

Re: [ccp4bb] cif file uploading error

On 05/01/2025 16:02, Marcin Wojdyr wrote: I encountered an issue while uploading data (attached) to generate the validation report in Phenix. The error message states: "The PDB server reports a failure with your data. Please check that your input file follows the CIF specifications." That mes

Re: [ccp4bb] CryoEM map refinements in coot

On 18/12/2024 18:17, tim smith wrote: Hi all, Can you please advise once we fit the map and open in coot. What is next step to do in coot. I am somewhat confused. Once you have done the fitting then you're done. Right? You can run your model through (another) refinement program before you a

Re: [ccp4bb] Covalent ligand

On 13/12/2024 08:06, Nicolas Bocquet wrote: -- Dear community, I try to create a covalent bond between a nitrile warhead and a cysteine. Therefore, the final product should be S-C=NH2 (of course the C is also connected to the rest of my ligand). The triple bond between C and N of the ligan

Re: [ccp4bb] map in coot and chimera

On 05/12/2024 17:30, Vitali James wrote: I am visualizing the map in coot and chimera. How to view the map at the same unit or at the same contour  in coot and chimera. For example if a map viewed in coot at 2 rmsd, how to adjust or convert the same contour to chimera map level. As chimerax u

Re: [ccp4bb] depositing a posttranslational modification

On 15/10/2024 16:19, Palm, Gottfried wrote:   I have a couple of questions regarding deposition of a structure with a posttranslational modification. 1. I understand, that PCMs (protein chemical modifications) and PTMs are now handled in a standard way, but what is the standard way? Is th

Re: [ccp4bb] Resize Coot windows in Ubuntu 24.04 LTS

On 30/09/2024 10:20, Kolenko, Petr wrote: I have a fresh installation of Ubuntu 24.04 LTS and CCP4. In Coot 0.9, I cannot resize additional windows, e.g. check waters, distance measurement, residue info. The only thing I can resize is the main window.  Do I miss some library? I have not h

Re: [ccp4bb] Coot 1.* in CCP4 9

hings Serve the Beam  === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu ---- *From:* Paul Emsley *Sent:* Wednesda

Re: [ccp4bb] Coot 1.* in CCP4 9

On 8/28/24 21:53, David J. Schuller wrote: I installed CCP4 9 on Alma 9 Linux. I requested installation of both Coot-0.9.8.95 and Coot-1.1.08. How do I execute the latter? It's in the coot_py3 directory after installation. I believe that Charles has recently made a binary update to 1.1.10.

Re: [ccp4bb] CIF file Cannot Open by Coot

On 19/08/2024 14:42, Hu, Wenhao wrote: Dear Jon, Thank you so much for all your effort! I really appreciate it. I’ve just tried to load the files, but unfortunately, it still won’t open and continues to show the error message I’ve attached here. Martin, These are not restraints. They a

[ccp4bb] Coot keybinding [was Re: [ccp4bb] libcheck]

On 15/08/2024 17:14, Petr Pachl wrote: [And now this part] Also two off topic questions regarding coot-1 and coot. I tried to transfer some of my keybindings and settings to coot-1 "language". The language is Python (well, one of them is). Unfortunately, there is not a good web resource for

Re: [ccp4bb] libcheck

On 16/08/2024 09:06, Andrea Smith wrote: Dear Paul, Dear Andrea, my molecule can't be too big for libcheck as I used libcheck successfully for molecules of exactly the same size before. I said "too big" - what libcheck actually says is that your molecule is too _complex_ (particularly in

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 16:08, Hu, Wenhao wrote: Hi Paul, I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’

Re: [ccp4bb] libcheck

On 8/15/24 17:14, Petr Pachl wrote: Hi Paul, so there is not way how to generate cif file when we have precise ideal structure (given from quantum chemistry calculations)? [This part first] That's right (if by that you mean that you (only) have coordinates and elements) - not in the CCP4 Ec

Re: [ccp4bb] libcheck

On 8/15/24 09:01, Andrea Smith wrote: -- Dear all, Dear Andrea, I successfully used libcheck to generate libraries for my ligands a couple of months ago. Now I wanted to use it again and it is giving me an error. Moreover, even though I select COOR Y and LCOOR N, libcheck uses COOR N and

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 15:01, Tang, Jiazhi wrote: -- It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 14:44, Martin Hu wrote: Dear [Recipient's Name], Dear [Correspondent's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot

Re: [ccp4bb] Issue Aligning PanDDA Generated Map with PDB in PyMOL

On 23/07/2024 15:12, Aline Dias da Purificacao wrote -- Hello Thank you for your response. You’re right, I shouldn’t need to use |phenix.map_box|. I tried it as an attempt to make the map cover the selected region since the map’s origin does not cover the protein properly. The issue is tha

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

On 19/07/2024 09:11, Harry Powell wrote: Hi I was wondering if moorhen might be useful for this? Yes.., yes it might. (moorhen.org) If one is going down that particular road then I'd recommend the following Preferences -> Map Contouring Settings -> Map Sampling Rate to maybe 2.5 or so - o

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

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 printscreen from Coot my only option? Density figures from Coot 1 can look, if I may be so bold, pretty good.  See, for example Catapano

Re: [ccp4bb] COOT 1.1 and Symmetry

On 12/07/2024 13:12, Karol Woloszyn wrote: Hello, I’m a COOT 1.1.09 user on Fedora 40 as well as MacOS, working on DNA model refinement. I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no longer brings up any symmetry molecules. I remember in older versions (I was

Re: [ccp4bb] COOT 1.1 and Symmetry

On 12/07/2024 13:12, Karol Woloszyn wrote: Hello, Hello Karol, I’m a COOT 1.1.09 user exciting. on Fedora 40 as well as MacOS, a rare breed. working on DNA model refinement. OK... I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no longer brings up any s

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

that, I can proceed with density subtraction. I hope this clarifies my query. Sorry for any confusion. Thank you again. Regards Devbrat On Wed, Jun 5, 2024, 7:56 PM Paul Emsley wrote: On 05/06/2024 07:00, Devbrat Kumar wrote: -- Hello Everyone, Hello Devbrat, I

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

On 05/06/2024 07:00, Devbrat Kumar wrote: -- Hello Everyone, Hello Devbrat, I have a query regarding the resampling of cryoEM density to match crystal density to obtain a density difference map. Specifically, I am trying to determine if it is feasible to resample a cryoEM map with an X

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

On 01/06/2024 14:28, Jon Cooper wrote: It would be interesting to know if this will affect the the electron density maps which are downloadable from the EBI: PDBe is to RCSB as DVLA is to HMRC (surely?) To unsubscribe f

Re: [ccp4bb] CCP4i2 COOT no showing model or map?

On 31/05/2024 07:44, Marco Bravo wrote: Has anyone had the issue where they run coot from ccp4i2 on say a refmac5 job and when coot opens the model or even the map do not show up? its just empty? Does anyone know how to fix this and display the model and map? I like ccp4i2 so far more than cc

Re: [ccp4bb] Computational crystallography in 2024

On 16/05/2024 01:51, Lucas Bleicher wrote: -- Dear all, I've been outside of the field for a few years (I have very fond memories of the 2008 Crystallographic Computing School, but did a lot of different stuff since then), but I'd love to come back and figured this would be the best place to

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

On 15/05/2024 18:45, Filipe Maia wrote: CAUTION: This email originated from outside of the LMB: *.-owner-ccp...@jiscmail.ac.uk-.* Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to phi

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

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 you for the response. I am on Windows 11

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

On 15/05/2024 11:28, Harry Powell wrote: Hi folks [...] I noticed this because I was encouraged to try Moorhen and found that a HEM (apparently written by this module) did not have the atoms connected with bonds in the display. Q: Is it necessary to check columns 77-78 if I really want to be

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

On 13/05/2024 13:03, Otsile Mojanaga wrote: Dear All I have been using coot as part of my normal workflow but since last week I have been having issues with Coot after I built my own PC which contains the following Hardware: CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

On 13/05/2024 11:23, Laurent Maveyraud wrote: Hello, I like the function "update NCS ghosts with local match" found in the calculate/NCT tools menu. It's really helpful when NCS is not really strict. However, I find it clumsy that you have to go in a submenu to get it, so I would like to defin

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 26/04/2024 02:44, Paul Emsley wrote: On 25/04/2024 16:07, Simon Vecchioni wrote: Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA

Re: [ccp4bb] add ligand with AceDRG

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 25/04/2024 16:07, Simon Vecchioni wrote: -- Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA, I see what you mean. From the termina

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 04/04/2024 02:27, Simon Vecchioni wrote: Dear CCP4 Wizards, Hello Simon. I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model refinement. exciting. The current setup does not seem to let me sequence mutate (simple mutate or mutate residue range), as it's hard coded t

Re: [ccp4bb] Coot function - closest symmetry atom?

On 18/03/2024 10:26, Petr Pachl wrote: -- Does anybody know if there is a function (or procedure) how to get info about closest symmetry atom? For picking coot is performing something like "Model atom pick (if failed) -> Symmetry atom pick", then it returns to console and atom info at the botto

Re: [ccp4bb] EM maps

On 08/03/2024 10:47, Dean Derbyshire wrote: Hi, I’m almost certain this has been addressed before so apologies… but is there a trick to import EM map files into COOT, it keeps crashing when I’ve tried. My guess is that your computer is running out of memory. A pint into a quart port?

Re: [ccp4bb] Coot SSM Superpose Problem

On 16/02/2024 01:45, zx2...@connect.hku.hk wrote: Dear all, Hello Xin, I encountered an issue while attempting to calculate the RMSD between two PDB files (each containing 4 ASUs) do they really though? using the SSM Superpose tool in Coot. Unfortunately, the tool was unable to superpos

Re: [ccp4bb] program to complete (or to change) side chains to specific rotamers

I agree with James and for the record, the function that it seem to me that you want is set_residue_to_rotamer_name(imol, chain_id, res_no, ins_code, alt_conf, rotamer_name) Paul. To unsubscribe from the CCP4BB list, c

Re: [ccp4bb] low resolution data refinement

On 21/11/2023 12:02, Yahui Liu wrote: Dear all, I got a protein crystal dataset of 4.3 A and would like to some the structure with MR. Now I am suffering with the refinement. Just for the record, then intention of refinement is not to make you suffer. Paul. ##

Re: [ccp4bb] About model building

On 04/11/2023 14:04, Sam Tang wrote: Dear community, I am solving the structure of a complex between proteins A and B, where A is a protein with known homologs and B is a novel protein isolated from plant. The diffraction data was at 1.9 Ang collected in-house, indexed to P321. Using A as th

Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

On 19/09/2023 09:34, Deborah Harrus wrote: Dear all, Dear Deborah, wwPDB asks users and software developers to review code to remove any current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended CCD IDs are available via GitHub

Re: [ccp4bb] effect of torsion angle definition in cif file

On 17/08/2023 11:18, Palm, Gottfried wrote: > > I copied the EDO.cif from the library and changed the C1-C2 torsion > angle definition to > EDO sp3_sp3_4  O1  C1  C2  > O2 180.000    10.0 1 > > After loading EDO in coot via "import cif dictionary

Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: Tuesday, July 1

Re: [ccp4bb] problems starting pandda.inspect - maybe COOT / CCP4 related

On 08/08/2023 09:57, Schaefer, Martina wrote: > > Hello, > >   > > I have a problem running pandda.inspect after successful running > pandda.analyse with the newest ccp4 version of pandda. > >   > > What do we have: > > * We use Ubuntu as our Linux system > * We installed CCP4-8.0.012 > * Wh

Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

On 02/08/2023 13:53, Andrea Smith wrote: Dear all, I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can see different anomalous maps in Coot and Wincoot - see attached printscreen where on the left t

[ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

On 18/07/2023 03:55, Mark Saper wrote: I reported this problem to Paul and to the group at least 2-3 months ago. Your email didn't arrive. Just to be clear, Coot's real space refinement is not (was not) broken, the problem is that the version of Coot distributed by CCP4 and the version of th

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How to change keyboard shortcuts in Coot

seems fine. Maybe this is a bug in Coot 0.9.8.8 EL? I doubt that it's a bug in Coot. A bug in Ventura though... that does seem possible. Paul. Zhen *From: *Paul Emsley *Date: *Saturday, July 15, 2023 at 11:04 *To: *Gong, Zhen , CCP4BB@JISCMAIL.AC.UK *Subject: *Re: [EXTERNA

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How to change keyboard shortcuts in Coot

thing. Do you have any clue what could be the problem? Well, Shift G does a Reverse JED Flip (as does Ctrl Shift G) - that sounds similar to what you are seeing. Perhaps you have the Caps Lock key pressed? Paul. Zhen *From: *Paul Emsley *Date: *Saturday, July 15, 2023 at 02:40 *To

Re: [ccp4bb] How to change keyboard shortcuts in Coot

On 15/07/2023 03:22, Gong, Zhen wrote: Dear all, Can anyone kindly tell me how to change the keyboard shortcuts settings in Coot? My “control + g” did not go to the specified atoms anymore. I might have changed the shortcut settings by accident. Thank you very much for your help! Ctrl-G i

Re: [ccp4bb] Ligand superposition!

On 15/07/2023 03:49, Subramanian, Ramaswamy wrote: I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix).  The goal is for me to see how difference in ligand environmen

Re: [ccp4bb] O-glycans in coot and phenix/refmac

On 14/07/2023 08:52, Jonas Emsley wrote: Dear All We have a crystal structure with O-glycans for the first time attached to a Ser and a Thr sidechain If anyone can recommend the procedure for adding these in coot and refining them in phenix /refmac that would be greatly appreciated Hi J

Re: [ccp4bb] Coot query

On 06/07/2023 08:51, Tom Peat wrote: Hello All, I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy 7.81.0) and tried to start up Coot and received the following error message: It is my understanding that jammy jellyfish, by default, uses Wayland as the display

Re: [ccp4bb] Need suggestion

On 27/06/2023 15:01, Afshan Begum wrote: Dear expert, I am currently working on building my cryo-EM data using COOT. However, I have encountered an issue when trying to add monomers such as Glycerol or BCT using their letter code from the "Get monomer" option in COOT. Whenever I attempt to

Re: [ccp4bb] Script to refine water molecules - help

The Coot API is quite useful for this sort of thing imol = 0 # replace as needed residues = residues_matching_criteria(imol, lambda chain_id, res_no, ins_code, serial: residue_name(imol, chain_id, res_no, ins_code) == "HOH") refine_residues(0, residues) Regards, Paul. On 26/06/2023 22:14,

Re: [ccp4bb] Apple glasses

On 06/06/2023 08:19, Goldman, Adrian wrote: I’m hoping for a coot implementation that allows immersive stereo… Well, (a) you're in luck - Coot is Free Software and can develop it however you like. I am happy to collaborate and handle the technical details of integration and distribution. If

Re: [ccp4bb] Issue with CSO in Coot & Refmac

to "peptide" and press enter in the entry, then "Apply" Now you can refine your CSO in Coot. Paul. Best, Nick Clark On Fri, May 26, 2023 at 10:37 PM Paul Emsley wrote: On 27/05/2023 03:23, Nicholas Clark wrote: Hey Paul, I found the dictionary entry

Re: [ccp4bb] Issue with CSO in Coot & Refmac

On 27/05/2023 03:23, Nicholas Clark wrote: Hey Paul, I found the dictionary entry for CSO, it appears to be in the "peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif): "loop_ _chem_comp_alias.comp_id _chem_comp_alias.group _chem_comp_alias.atom_id _chem_comp_alias.atom_id_stand

Re: [ccp4bb] Issue with CSO in Coot & Refmac

On 27/05/2023 00:43, Nicholas Clark wrote: I have a cysteine residue that is oxidized and needs to be modeled as CSO. In the past, when "replace residue" was used to substitute for CSO, the CSO would "behave" during real-space refinement and essentially take the place of the Cys. However, when

Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

On 19/05/2023 10:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? Isn't this a bit of strange reques

Re: [ccp4bb] isopeptide bond and shelx topology file

On 28/04/2023 08:41, StrBio wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-ccp...@jiscmail.ac.uk-.* Hello, Can you suggest how to make isopeptide bond in coot and g

[ccp4bb] Coot Delete Item on MacOS Ventura

Last week I was using 13.2 and could reproduce the snap iconification on delete item. This morning I updated to 13.3 and the iconification problem is no more - so the update fixed it. Apple didn't mention XQuartz or Coot in the release notes (fwiw). Paul. ##

Re: [ccp4bb] Structural alignment and classification

On 06/03/2023 07:35, Armando Albert wrote: I want to align several structures we obtained from a fragment screening campaign and cluster them according to RMSD. To what end, may I ask? I would use LSQKAB, parse the log files for the RMSD and create an input file for R. (One cannot just do

Re: [ccp4bb] Coot on MacOS Ventura

Hello Elsa, On 30/12/2022 17:13, Elsa Garcin wrote: Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4? I believe so, but people have reported minimizing window when they try to do so. I tried installing coot with homebrew (instructions from Scottlab webpage), This is a qu

Re: [ccp4bb] Copying NCS chain to heteroligomer

On 17/11/2022 19:03, Alessandro S. Nascimento wrote: Dear all, We are refining a 24-mer complex composed of 12 copies of protein A and 12 copies of protein B. Since the resolution is not very high (~3.0 Ang), we will probably want to copy the modifications made in Coot for one chain to the ot

Re: [ccp4bb] Problem in generating restraint file for 5.2kDa ligand

On 09/11/2022 13:59, Deepak Deepak wrote: Dear CCP4 users, I am working towards solving a protein-ligand complex structure. The ligand is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive monomers. [...] I will happily provide more information if I am missing something here. You're

Re: [ccp4bb] mutate Methionine to Norleucine in Coot.

On 20/10/2022 02:06, Jiang Xu wrote: Hi Garib,    I deleted the Met residue and imported the nle.cif file Import the dictionary for NLE, make sure that the group is L-peptide, then centre on your Met and Calculate -> Modelling -> Replace Residue -> NLE Paul. ##

Re: [ccp4bb] Coot installation issue

Coot is not (yet) an official part of brewsci, so the goocanvas update bonked coot. This morning I uninstalled my coot and rebuilt it with YoshitakaMo's coot.rb. The second time it worked (i.e. build and installed just fine). You can see from the patch https://github.com/brewsci/homebrew-bio

Re: [ccp4bb] Help with isomer ligand from PDB database

On 17/09/2022 15:48, Marion Schuller wrote: > >   > > Dear CCP4bb community, > >   > > I am writing regarding a problem with the refinement of an isomer > ligand. I try to refine a structure which has the ligand “Carba-NAD” > (as beta isomer) bound. This ligand is already in the pdb database as >

Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot

Hopefully 0.9.8.4 should fix that. Paul. On 16/09/2022 13:54, Jan Dohnalek wrote: This has been quite variable in (several?) last versions of Coot. I have some three latest versions available and when one does not work I start another one. Sad but true. Jan On Thu, Sep 15, 2022 at 11:39 AM

[ccp4bb] PDBx-format utilities

A spectre is haunting structural biology - it is the spectre of the PDBx format. We at CCP4 are interested in providing tools that are equivalents of those that one might have trivially made with utilities such as grep or sed. For example:     delete the hydrogen atoms     extract the hydro

Re: [ccp4bb] Missing restrains for standard amino acid

On 07/08/2022 07:00, Cryo EM wrote: Hi everyone, I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey. The phenix version I am using is 1.20.1-4487. At the end of validation run or real space refinement for my cryo-EM map, I want to fix the problems in the model interactively

Re: [ccp4bb] Coot RNA bases Mutate

On 06/08/2022 09:08, Cryo EM wrote: Hi everyone, I am trying to mutate modified RNA nucleotide to standard nucleotide by coot using "Simple Mutate" button. But it is not working despite selecting the correct residue from the standard base list that pop up on clicking "simple mutate button". D

[ccp4bb] PDB to AlphaFold via Uniprot

I wonder if others are curious about (or know how to solve) the following problem: I am looking at a PDB file that I've downloaded from a wwPDB site and I would like to see the AlphaFold model(s) overlaid. What the best (or easiest) way of doing that? (let's imagine that I can do a bit of scr

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

On 27/07/2022 01:44, Dale C wrote: Hi all, I recently updated my ccp4 package to Program suite v8.0.002 and i have now run into a few issues with other programs. The issues are highlighted below... - When i click 'Open in Coot' on any output through Phenix (so far only tested phenix.refine an

Re: [ccp4bb] Modified nucleotides

On 18/07/2022 07:59, Cryo EM wrote: Hi all, I am working on a pdb of RNA where I intend to change the modified nucleotides to their parent unmodified original residues. For example, PSU to U, 1MG to G and so on. I was wondering if there is a better way to do that by either manually editing th

Re: [ccp4bb] Help with One dimensional electron density calculation

On 13/07/2022 19:18, Ravikumar wrote: I would like to calculate One-dimension electron density profiles of the different number of ions bound to an ion channel. Are there any programs in CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron density server) program to extract

Re: [ccp4bb] Phenix.refine sequence check equivalent in CCP4?

On 11/07/2022 12:36, Colin Levy wrote: Hi All, Is there an equivalent functionality to Phenix.refine Sequence check in CCP4?  A quick alignment tool of model sequence from pdb to the provided sequence? It seems to me there are a number of ways that one can check a model (and map) against

Re: [ccp4bb] Coot sporadically crashes

On 09/07/2022 12:36, Goldman, Adrian wrote: On a related theme, Paul, I often find that the undo button doesn’t work, but I can’t figure out why it sometimes does and sometimes doesn’t.  Is this something to do with how I open .pdb files - that somehow Coot can’t find the backup files, even tho

Re: [ccp4bb] Coot sporadically crashes

 Is there an option to save the session automatically every 10-15 minutes or so? And now to actually answer your question: yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default is 30 seconds)

Re: [ccp4bb] Coot sporadically crashes

On 08/07/2022 16:30, Oganesyan, Vaheh wrote: Hi All, Sorry for posting on CCP4BB. This is an appropriate venue for such a message. Coot installed together with latest CCP4 on Win10 crashes time to time with no messages/warnings. Is there an option to save the session automatically every

Re: [ccp4bb] Missing double bonds in the ligand

The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do your PDB atom names match the CCD? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED

Re: [ccp4bb] Easy/Silly question

On 01/07/2022 04:50, Joel Tyndall wrote: Hi folks, I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. Does any one have the code for the ligand? Surely its been used before. In Coot: File -> Search Monomer Library -> "maltose" -> Search -> MAL ##

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Although it may not be apparent, there has been a lot of work going on in Acedrg development regarding Boron. One cannot say the same for Coot though and I can reproduce the behaviour reported by Rafa Dolot. If/when I can fix it, it will be available in 0.9.8.4. Paul. On 06/06/2022 13:24

Re: [ccp4bb] coot 0.9.8.1 and phenix mtz files

On 27/05/2022 19:22, Jan Abendroth wrote: Hi all, not sure if this appropriate for this BB, since right at the interface between CCP4, Coot and Phenix. I wonder if someone else also experiences these issues after upgrading to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens b

Re: [ccp4bb] How to prevent acetate ion clash into ZN in refmac5 and COOT?

On 11/04/2022 15:55, Martin Moche wrote: Dear colleagues, We are refining a structure where an acetate ion (ACT) binds a zinc ion, Zn+2 (ZN), using an excellent quality 1.38Å dataset, [...] When doing COOT sphere refinement, the acetate ion moves on top of the ZN? like the ZN was not there

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

On 07/04/2022 09:24, Munoz.Ines wrote: Dear all, Is there any program or server that automatically assign the secondary structure elements into a pdb generated by alpha fold? If you are using Coot, you can use Calculate -> Scripting -> Python add_header_secondary_structure_info(imol) ###

Re: [ccp4bb] Coot and Pandda questions

On 06/04/2022 07:05, Laurent wrote: Good morning (French time…) Two unrelated questions… Using Coot, I would like to define some key binding… How can I find the command that is actually issued from an option in the « calculate » menu ? I would like to define a key binding for the function « N

Re: [ccp4bb] Coot 1

That, for the record, is more or less what Ralf said 18 years ago. On 01/04/2022 23:38, Pavel Afonine wrote: It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: Coot 1 18 years after the release of Coot 0 it's time that I actual

[ccp4bb] Coot 1

Coot 1 18 years after the release of Coot 0 it's time that I actually released Coot 1. Coot 1 is a major change beyond Coot 0. It has required a lot of writing and rewriting [1] and has been the preponderance of my work since 2017. I have had to learn how to program graphics from scratch usi

Re: [ccp4bb] Maps on mobile phones.

On 27/03/2022 00:17, Jon Cooper wrote: Hello, I have been trying to put together a thing for viewing small blocks of CCP4 electron density maps with a mobile web browser. If anyone is interested, the current state of it is here: http://ic50.org/jbctest14.html Have you seen/heard about ugly

Re: [ccp4bb] Cysteine-S-Iodine interaction

On 17/03/2022 17:37, Mohd Syed Ahangar wrote: I have been doing some protein crystal soaking with some covalently binding fragments and in one structure I have got an extra density on Cysteine but that density doesn't match with the expected fragment. The fragment was in the form of iodide s

Re: [ccp4bb] Adding hydrogens to a specific residue using Coot

On 13/03/2022 14:05, Tomas Malinauskas wrote: Dear All, Is it possible to add hydrogens to a specific residue using Coot? Something like Calculate -> Scripting -> Python -> coot_reduce(0) but targeting one residue only. sprout_hydrogens(0, "L", 101, "")  # or some such: molecule-number chain

Re: [ccp4bb] Coot on Mac OSX Monterey

On 11/02/2022 21:53, Laurence Pearl wrote: Does anyone know where I can download a pre-built Coot that will work on OS X Monterey  (12.2) on an iMac with an Intel i7 ? The packages I can find all fail at the File finder which comes up blank. X11 latest is installed. Not an answer to your que

Re: [ccp4bb] Make Ligand error

utput. Kindly let me know How I could fix this ligand. Thank you Regards Yuvara On Tue, Jan 25, 2022 at 12:03 AM Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 24/01/2022 11:11, YUVARAJ I wrote: Respected Prof. Paul, Thank you for your kind reply, After refinement u

Re: [ccp4bb] Make Ligand error

output and refmac log file with this mail. kindly let me know how I could fix this. Many thanks in advance. On Mon, Jan 24, 2022 at 12:39 PM Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 23/01/2022 09:56, YUVARAJ I wrote: Respected Prof. Paul, Thank you so mu

Re: [ccp4bb] Make Ligand error

nd another cif file for (HgI3-) as well and set of instructions, It will be very much helpful. Thank you in advance. Regards Yuvaraj On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 22/01/2022 22:10, Georg Mlynek wrote: Dear Paul,

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