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

2022-04-12 Thread Paul Emsley
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

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

2022-04-07 Thread Paul Emsley
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

2022-04-06 Thread Paul Emsley
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 « 

Re: [ccp4bb] Coot 1

2022-04-01 Thread Paul Emsley
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 actually released

[ccp4bb] Coot 1

2022-04-01 Thread Paul Emsley
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

Re: [ccp4bb] Maps on mobile phones.

2022-03-27 Thread Paul Emsley
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: Have you seen/heard about

Re: [ccp4bb] Cysteine-S-Iodine interaction

2022-03-18 Thread Paul Emsley
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

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

2022-03-13 Thread Paul Emsley
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

Re: [ccp4bb] Coot on Mac OSX Monterey

2022-02-11 Thread Paul Emsley
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

Re: [ccp4bb] Make Ligand error

2022-01-24 Thread Paul Emsley
. 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>> wrote: On 24/01/2022 11:11, YUVARAJ I wrote: Respected Prof. Paul, Thank you for your kind reply, After refinement using

Re: [ccp4bb] Make Ligand error

2022-01-24 Thread Paul Emsley
the 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>> wrote: On 23/01/2022 09:56, YUVARAJ I wrote: Respected Prof. Paul, Thank you s

Re: [ccp4bb] Make Ligand error

2022-01-23 Thread Paul Emsley
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 <>> wrote: On 22/01/2022 22:10, Georg Mlynek wrote: Dear Paul,

Re: [ccp4bb] Make Ligand error

2022-01-22 Thread Paul Emsley
, before I tried now.) Many thanks, br Georg. Am 22.01.2022 um 22:51 schrieb Paul Emsley: On 22/01/2022 21:47, Paul Emsley wrote: On 22/01/2022 17:34, YUVARAJ I wrote: I have solved a protein structure using anomalous signal using mercury(II)potassium Iodide(K2HgI4). I wanted

Re: [ccp4bb] Make Ligand error

2022-01-22 Thread Paul Emsley
On 22/01/2022 21:47, Paul Emsley wrote: On 22/01/2022 17:34, YUVARAJ I wrote: I have solved a protein structure using anomalous signal using mercury(II)potassium Iodide(K2HgI4). I wanted to submit the structure of the protein with mercury(II) potassium iodide to PDB. I am facing

Re: [ccp4bb] Make Ligand error

2022-01-22 Thread Paul Emsley
On 22/01/2022 17:34, YUVARAJ I wrote: I have solved a protein structure using anomalous signal using mercury(II)potassium Iodide(K2HgI4). I wanted to submit the structure of the protein with mercury(II) potassium iodide to PDB. I am facing problems while making the ligand (HGI4) . HGI4

Re: [ccp4bb] AW: [ccp4bb] COOT RSR

2021-11-22 Thread Paul Emsley
What's the difference between a dummy water and a real one? Paul On 22/11/2021 14:34, Schreuder, Herman /DE wrote: Dear Paul, I agree with Oliver and Norbert, in the early phases of refinement, when a lot of rebuilding has to be done, the coot RSR is not very helpful and in general I

Re: [ccp4bb] COOT RSR

2021-11-20 Thread Paul Emsley
ere extensive rebuilding is required. Best regards Oliver From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley [] Sent: 20 November 2021 11:37 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] COOT RSR On 20/11/2021 09

Re: [ccp4bb] COOT RSR

2021-11-20 Thread Paul Emsley
On 20/11/2021 09:42, Matthew Snee wrote: I had a bit of trouble getting used to the new COOT real space refine... it took me an embarrassingly long time to work out that there is nothing wrong with the fitting/restraints.. You are not alone in finding Coot's RSR unintuitive (at least

Re: [ccp4bb] update 7.1.016, very poor pyrogen restraints

2021-11-09 Thread Paul Emsley
On 08/11/2021 08:55, Guenter Fritz wrote: Dear all, with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision 10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing. Yes, it's the default now (i.e. without mogul). I

Re: [ccp4bb] Add hydrogens

2021-09-29 Thread Paul Emsley
On 29/09/2021 12:03, Sam Tang wrote: This may appear to be a silly question -- I am trying to add hydrogens to the structure in PDB 1CDW. My initial thought is to run a single run of refinement with a refinement program.[...] So... is there an easy way to do what I want in this case?

Re: [ccp4bb] COOT running on Macbook Pro M1 chip

2021-09-16 Thread Paul Emsley
On 16/09/2021 08:40, WENHE ZHONG wrote: Dear CCP4 community, The COOT is not running smoothly on my M1 chip Macbook. For example, when both model and the electron density map are displayed, the moving from one residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only happened

Re: [ccp4bb] Specifying achiral residue as D-amino acid

2021-07-31 Thread Paul Emsley
On Sun, 2021-08-01 at 00:54 +, Prasun Kumar wrote: > Hi All: > > I am trying to solve a structure that has got D-amino acids. The sequence has > also got few achiral residues but is > mentioned as a part of L-peptide in the monomer library. For example GLY or > AIB. Since my sequence has

Re: [ccp4bb] sphere refine radius in coot

2021-07-13 Thread Paul Emsley
On Fri, 2021-07-09 at 13:49 -0400, Ashok Nayak wrote: > > Is it possible to increase the radius of real space refinement Yes. Use sphere_refine with an argument, e.g. sphere_refine(8.5) You can add your own button to do this using Right Mouse on the Tool bar and selecting "Add a User-defined

Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-22 Thread Paul Emsley
On 22/06/2021 06:47, Jiang Xu wrote:    I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain

Re: [ccp4bb] Non-standard amino acids in Coot

2021-06-14 Thread Paul Emsley
On Mon, 2021-06-14 at 10:42 -0400, Cheng Zhang wrote: > I had this issue before and tried several ways to fix it. The best way that > works for me is to edit the PDB and cif > files of this unnatural amino acid for Coot or Phenix. I am already furrowing my brow... > The goal is to allow COOT

Re: [ccp4bb] Topology diagrams software

2021-06-10 Thread Paul Emsley
On 10/06/2021 12:14, Gambelli, Lavinia wrote: I'm looking for a software to make topology diagrams of proteins. Ideally, I'd like to submit a pdb file and obtain the topology model. Do you know what alternatives are out there? So far I'm only aware of PDBsum that can do this, but I was

Re: [ccp4bb] Coot shortcut key for Mutate

2021-06-09 Thread Paul Emsley
On Wed, 2021-06-09 at 20:44 +0100, Paul Emsley wrote: > On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote: > > Hello everyone > > > > Can anybody tell me the Coot shortcut key for mutate or mutate and refine. > > Is there any way to turn it on or to >

Re: [ccp4bb] Coot shortcut key for Mutate

2021-06-09 Thread Paul Emsley
On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote: > Hello everyone > > Can anybody tell me the Coot shortcut key for mutate or mutate and refine. Is > there any way to turn it on or to assign > a particular key if it is disabled ? > "Keyboard mutate" Curlew. You will have to remember

Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Paul Emsley
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote: > > I am trying to get the peak values from omit maps. The peakmax from the GUI > works fine. However, I tried to run > peakmax from the terminal, and it stuck when returning P1. Same map file > works fine, when I use the GUI. Any ideas,

Re: [ccp4bb] H-bond modelling

2021-06-07 Thread Paul Emsley
On Mon, 2021-06-07 at 01:35 +0530, vivek sharma wrote: > > How does one validate if 2 atoms (non-hydrogen) which are close enough, > actually participate in H-bonding? > I have a recent data that i am currently working on, the NH2 of ARG is at > 2.61A from ligand's oxygen atom (refer to >

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Paul Emsley
On Tue, 2021-05-25 at 20:04 +, Frank Von Delft wrote: > Yes I thought so too, but discovered I am too stupid to decode the highly > parsimonious manual on the ccp4 pages. > The first thing that I'd try (using Coot) is Calculate -> PISA -> Assemblies...

Re: [ccp4bb] Omit maps in phenix and ccp4

2021-04-07 Thread Paul Emsley
On 07/04/2021 07:46, Hari shankar wrote: I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have tried phenix

Re: [ccp4bb] coot & other graphics programs draw too many bonds

2021-04-01 Thread Paul Emsley
On Thu, 2021-04-01 at 15:02 +0200, Fred Vellieux wrote: > Hello there, > > After running autodock vina on certain small molecules, the graphics > software I am using (e.g. Pymol, Coot) draws far too many bonds on the > docked small molecule. See enclosed screen capture. > > Is there any way to

Re: [ccp4bb] Why do large blobs show up in the pores of my crystal when I do refinement?

2021-04-01 Thread Paul Emsley
On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote: > > I once again am asking for your advice. ☺ I am trying to solve the > structure of an RBD:Fab complex. > > After molecular replacement, the density fits the model very well. > Looking at the overall crystal structure (by applying

Re: [ccp4bb] phaser-MR warning

2021-03-30 Thread Paul Emsley
On 31/03/2021 04:37, rohit kumar wrote: I tried to remove H atoms in pdbcur in ccp4 but still there are lots of HD and HH atoms present in the pdb. Could anyone please suggest how to fix this problem. PDBCUR would want to use the element column in order to identify that the atom is a Hydrogen

Re: [ccp4bb] phenix refinement for bent DNA

2021-03-29 Thread Paul Emsley
On 30/03/2021 02:52, Srivastava, Dhiraj wrote: I am sorry about phenix related question. But since the question was refinement related I thought it will be ok to ask on ccp4bb. For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and timely

Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

2021-03-18 Thread Paul Emsley
The geometry targets for protein are well established (by which I mean "agreed upon") and so the distribution On 18/03/2021 07:19, Cyril Hamiaux wrote: Dear Jasmine (and all), Many thanks for the article. I have a question regarding the Z cutoffs used to flag geometry outliers in the PDB

Re: [ccp4bb] Chiral center R/S labels in Coot

2021-03-10 Thread Paul Emsley
On 11/03/2021 01:12, Weston Lane wrote: Does anyone know if there is a way of showing if a chiral compound is R or S configuration in Coot?  It would be nice to not resort to thumbs while modelling! Coot does not show you if your chiral compound is R or S. The closest it gets is the

Re: [ccp4bb] all of a sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac laptop

2021-03-09 Thread Paul Emsley
On 09/03/2021 17:04, Roversi, Pietro (Dr.) wrote: Dear all, sorry to bother you all with such mundane headaches - but all of a sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac laptop (running MacOS Mojave): [bioch3242-596:~] pietro% coot(coot-bin:15697): (Coot does not

Re: [ccp4bb] Ice ring data issue

2021-03-05 Thread Paul Emsley
It might just be possible that background modelling of diffraction data in the presence of ice rings is better done in more modern software. Paul. On 06/03/2021 00:10, Edward A. Berry wrote: (Obviously this is for culling the bad data after data reduction is complete- doesn't do anything to

Re: [ccp4bb] Pymol Map range

2021-02-26 Thread Paul Emsley
On 26/02/2021 16:07, Horrell, Sam (DLSLtd,RAL,LSCI) wrote: Hello BB, I’m trying to make an image of some electron density in pymol but am running into a problem, my atoms are half in and half out of the unit cell so I only get half the density. Has anyone ran into this problem previously,

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

2021-02-20 Thread Paul Emsley
FWIW, looks like somebody at ETH Zurich is (or had been) trying to bring Coot into the OS: Hello! Let me know if I can help. Paul. On 20/02/2021 15:35, Tim Gruene wrote: Hi Matthias, I have been using Debian for more than a decade. Every

[ccp4bb] RS refinement of cyclic peptides

2021-02-19 Thread Paul Emsley
Jan Abendroth wrote: does anyone have any hints on how to real space refine cyclic peptides with unusual amino acids in Coot? A good example are DNA-sliding clamp proteins in complex with the cyclic peptide Griselimycin, eg. PDB code 6PTV. In Coot I load the ligand description cif files for

Re: [ccp4bb] Coot/Phenix.refine C-terminus issue

2021-02-18 Thread Paul Emsley
On 18/02/2021 15:21, Neno Vuksanovic wrote: I've been having an issue when manually adding C-terminal residue in Coot (I add a terminal residue, then add OXT atom, and perform real space refinement). The residue links the previous one properly and the density matches it well, but after

Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

2021-02-09 Thread Paul Emsley
On 09/02/2021 13:33, Eleanor Dodson wrote: Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E Yeah, I never liked that colour scheme either. Maybe this is a job for Super-Gemmi! Paul. To

Re: [ccp4bb] RCrane in Coot for Mac

2021-02-09 Thread Paul Emsley
On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote: I have Coot installed on macOS Catalina. I would like to launch RCrane, but I can't find it under "Extensions". Does anybody know whether there is a way I can make it work on the version of Coot, or should I rather uninstall it

Re: [ccp4bb] Fixing Modified residue

2021-02-09 Thread Paul Emsley
On 09/02/2021 07:10, Arunabh Athreya wrote: Hi I have been facing a similar problem with a backbone thiocarbonylated L-serine residue (here's the SMILES: N[C@@H](CO)C(O)=S  ) This residue was not present in the pre-existing library, so I did the following: 1. Used AceDRG to draw the

Re: [ccp4bb] Fixing Modified residue

2021-02-08 Thread Paul Emsley
On 08/02/2021 13:45, Afshan Begum wrote: I have a trouble to fix the lysin modified residue in to the PDB coordinate. what i did, I get the KCX(Modified lysin) coordinate from monomer library in COOT (0.9) , merge in to the coordinate file , its listed into position 193 lysin then  run rafmac

Re: [ccp4bb] coot is drawing the unit cell away from the modelled molecule

2021-02-01 Thread Paul Emsley
On 01/02/2021 13:23, leo john wrote: I am sure this issue might have addressed before, Correct. but somehow I am not able to find it. That's because email is a terrible system for archiving structural biology information. An that goes doubly so for the Jiscmail archive. We should use

Re: [ccp4bb] Modeling sugars with Coot and Phenix

2021-01-05 Thread Paul Emsley
On 03/01/2021 01:50, Emilia C. Arturo (Emily) wrote: Hello all, Hello Emily, I suspect that there were no replies to these questions because those no-one has a sufficiently rounded experience. I know something about Coot and can make guesses about OneDep. More details are required.

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Paul Emsley
On 04/01/2021 14:38, Silvia Napolitano wrote: Dear CCP4 Community, I am currently working on the structure of a monomeric protein of 23KDa. The protein is generally quite "loopy" and I think I am mid-way refinement. At the moment I am struggling, among other things, with an extremely high

Re: [ccp4bb] Up-to-date 3D stereo solution

2020-12-16 Thread Paul Emsley
On 16/12/2020 16:09, Wimberly-Gard, Gina wrote: We just set up our new linux machine using the older Nvdia set up as given on Coot and PyMol. We managed to get hold of all the various components some second hand (the stereo glasses were pre used). PyMol worked fine immediately. We ran into

Re: [ccp4bb] Wincoot labels.

2020-12-15 Thread Paul Emsley
On 15/12/2020 17:41, Jon Cooper wrote: Just received a query from someone: "Can you tell me when working with Coot maps how to make the atom names and numbers more prominent." Sorry, I've not looked at manual yet but, being idle, I thought someone might just know the answer instantly ;-)

Re: [ccp4bb] how to swap chain IDs

2020-12-07 Thread Paul Emsley
Maybe sort_chains(imol) is what you want. Additionally or alternatively, change the order or the SSBOND or LINK header records. HTH. Paul. On 07/12/2020 18:59, Christian GALICIA wrote: Dear Folmer, Thank you for your answer. Only one out several chains is bound to a ligand in the

Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

2020-11-25 Thread Paul Emsley
On 23/11/2020 15:21, Pedro Matias wrote: In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo doesn't seem to work. The NVIDIA emitter turns on but the stereo picture does not appear when the glasses are turned on. Strangely enough, the only coot update I can find in the

Re: [ccp4bb] Refine modified residues based on cryo-EM maps

2020-11-24 Thread Paul Emsley
On 25/11/2020 03:24, Cheng Zhang wrote: This question must have been asked before Correct. but I couldn't find a good answer online. the jiscmail archive is a terrible system for archiving our collective knowledge. There should be a better way. I work on a cryo-EM structure with one

Re: [ccp4bb] defining chiral center in .cif file for ligand atom linked to amino acid side chain

2020-11-05 Thread Paul Emsley
On 05/11/2020 20:26, George Lountos wrote: I wanted to check to see what the proper way to include a chiral center definition to the .cif file. I have a ligand that is covalently attached to a cys side chain and I wanted to adjust the chirality of the atom of the ligand attached to the

Re: [ccp4bb] Install coot in linux

2020-10-21 Thread Paul Emsley
On 21/10/2020 17:40, Doo Nam Kim wrote: Since I can't access That link was extant 2004-2007. I installed coot by installing ccp4. OK - watch out for 0.9.1 though - it's the chicken's elbows! However, I

Re: [ccp4bb] Tyr pushed out during refinement

2020-10-19 Thread Paul Emsley
On 19/10/2020 19:52, Boniecki, Michal wrote: I have a problem during refining with one of the Tyr residues. It is constantly pushed out of the position during refinement in all 4 chains in ASU. I have tried to exclude it from refinement in phenix but it is refined anyway out of the position

Re: [ccp4bb] Error shows in Ligand file by using PyRx

2020-10-15 Thread Paul Emsley
On 14/10/2020 13:38, Abhilasha Thakur wrote: I have a query related to PyRx Virtual Screening Software, Some of my ligands files are not read by PyRx. I downloaded the SDF format and then SDF to PDB conversion by Open Bable, then uploaded the ligand library into the PyRx and then set as

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-11 Thread Paul Emsley
Maybe because I've never attended a Coot course? And maybe because, I've even never searched for Coot tutorials because the usage of Coot was (almost) always very intuitive? I am open for any new developments OK "Pro Tip of the Day!" then... Edit -> Settings -> Install Template Key Bindings

Re: [ccp4bb] Relion's own implementation of motioncorr2 on gpu cluster

2020-09-10 Thread Paul Emsley
On 11/09/2020 00:18, Lora Sinha wrote: In the Relion 3.1 tutorial, the job is submitted to a local machine, but I wonder if I can submit the job to a GPU cluster? What MPI configuration should I use? Is this the mailing list you're looking for?

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-10 Thread Paul Emsley
t as excellent as the dealer but you might not. From my point of view it's the lack of choice that personally I do not like so much, especially if there is no other coffee dealer around... Nevertheless, I'm aware and fully respect all the effort you put in the development of coot and I'm really grat

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-08 Thread Paul Emsley
On 08/09/2020 16:25, Georg Zocher wrote: we have the same experience in our lab. What experience is that? I am still in the dark about you think is now worse. Personally, I did would not like to judge here, as so far, I did not have had enough time to get into the new RSR of coot 0.9.x

Re: [ccp4bb] Going back to Coot 0.8

2020-09-08 Thread Paul Emsley
Dear Veronica, Sorry to re-open old thread (staycatation...) I don't think that it's old - just slow. glad for you listening to the feedback - much appreciated. Thank you, fellow in-liner. All that top posting was causing me mental anguish. I think the situation has arisen because

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-07 Thread Paul Emsley
e in the new version. Since I am not convinced - why should I switch ? Best regards, Eike * thanks to Bill Scott for the pre-compiled mac-binaries -Original Message- From: CCP4 bulletin board on behalf of Paul Emsley R

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-04 Thread Paul Emsley
planation. I will try to adapt my way of working to the new coot. Best, Herman -----Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Paul Emsley Gesendet: Freitag, 4. September 2020 13:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-04 Thread Paul Emsley
Dear Frustrated Coot 0.9 Users, I'd like to let you know that you I have heard similar reports in the recent past (including, as you can see, from EJD). I have taken what I believe to be remedial action to address the most pressing issue. I think the situation has arisen because Coot users

Re: [ccp4bb] Stuck with Refinement

2020-08-06 Thread Paul Emsley
On 06/08/2020 16:39, Silvia Napolitano wrote: Dear CCP4BB community, Dear Silvia, I am working on a crystal structure and I am a bit stuck with the refinement. To build the model I use Coot and to refine I use Phenix. I may be able to offer some insight about the first part. First,

Re: [ccp4bb] real real-space-refinement

2020-08-01 Thread Paul Emsley
On 31/07/2020 20:33, James Holton wrote: But, if you real really want to do real real-space, then I suppose coot is doing that?  I'm actually not sure. If by "real-space refinement" you mean the same thing as described by Bob Diamond [1], then no, the sum of the squared difference

Re: [ccp4bb] adding external planar restraint in refmac5

2020-07-08 Thread Paul Emsley
On 08/07/2020 12:39, Laurent wrote: I am currently refinining an enzyme structure obtained in the presence of a substrate analog : the catalytic serine is acylated and form an ester bond with the ligand. I have added a LINK record in the PDB file to specify the newly created covalent bond

Re: [ccp4bb] insertion of a chemical

2020-06-30 Thread Paul Emsley
On 30/06/2020 10:51, Daniele Veggi wrote: Dear CCP4bb, I'm trying to insert an Acetone molecule between two cysteine residues in coot or modifying the pdb. I'm working on this modified molecule where the disulfide bridge was chemichally opened and inserted an acetone molecule between the two

Re: [ccp4bb] COOT crash

2020-06-29 Thread Paul Emsley
On 29/06/2020 14:52, Denis Rousseau wrote: When I try to merge a ligand obtained from the library into my pdb file COOT shuts down. I am using COOT downloaded with the latest CCP4. Is there an easy fix? Coot is not part of the latest CCP4 (unless you're running

Re: [ccp4bb] COOT 0.9 cuts pdb header

2020-06-16 Thread Paul Emsley
On 16/06/2020 11:17, Dirk Maurer wrote: Hi, Hi. I noticed that, while saving my pdb model in COOT 0.9, sometimes a big part of the header (compared to the originally loaded file) is just left out in the new pdb-file. This results in that COOT cannot reopen this file at another time. Any

Re: [ccp4bb] Coot labels

2020-06-15 Thread Paul Emsley
On 15/06/2020 22:06, Cygler, Miroslaw wrote: Hi Hi. I just started using coot 0.9 and see some differences in behaviour from version 0.8. When I move to the next residue using space bar the residue name of the residue does not appear. How can I make appear automatically? Wow, 0.8 and

Re: [ccp4bb] Ligand building

2020-06-13 Thread Paul Emsley
On 13/06/2020 18:16, Paul Emsley wrote: On 13/06/2020 17:50, Hari shankar wrote: I want to build a ligand that does not exist in reality (or be able to modify an existing ligand as per choice). 1. JLigand in the ccp4 suite seems to work only on java and gives me an “configuration problem

Re: [ccp4bb] Ligand building

2020-06-13 Thread Paul Emsley
On 13/06/2020 17:50, Hari shankar wrote: I want to build a ligand that does not exist in reality (or be able to modify an existing ligand as per choice). 1. JLigand in the ccp4 suite seems to work only on java and gives me an “configuration problem” as an error message on my Windows. I am

Re: [ccp4bb] Lost extension bar in Coot

2020-06-11 Thread Paul Emsley
On 11/06/2020 13:26, Firdous Tarique wrote: Just downloaded the new CCP4-7.1. Wondering where the extension bar in Coot 0.9 has gone. Please help me to find it. I think it is hidden somewhere. "Menu items shall neither be created nor destroyed but transformed from one menu into another"

Re: [ccp4bb] COOT download site

2020-06-04 Thread Paul Emsley
On 04/06/2020 15:41, Clemens Grimm wrote: Dear All, accessing the COOT download pages at gives me an "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was not found on this server." error

Re: [ccp4bb] How to fix: residues with missing atoms

2020-05-23 Thread Paul Emsley
On 23/05/2020 20:18, Yong Tang wrote: Dear all, is there a way to "automatically" patch up the missing atoms in the residues that otherwise are properly defined in a PDB entry. For example, an Arginine is defined as Arginine but only has the beta carbon on the side chain. In Coot I could use

Re: [ccp4bb] QTMG font too small

2020-05-20 Thread Paul Emsley
On 21/05/2020 01:00, Khushboo Patel wrote: Hi Everyone, This is rather a silly question but the font of my QTMG is too small, screenshot attached. I have tried everything from changing display settings on my mac to looking in preferences in QTMG software but cant seem to fix the problem. Did

Re: [ccp4bb] Ligand Refinement in coot

2020-04-30 Thread Paul Emsley
On 30/04/2020 21:55, Muhammad Bashir Khan wrote: I want to ask about the ligand refinement in coot. Earlier I was able to refine the ligand in the coot using real space refine zone but now by some reason when I want to refine the ligand in coot it asks me "Refinement setup failure failed to

Re: [ccp4bb] Ligand Refinement in coot

2020-04-30 Thread Paul Emsley
On 30/04/2020 21:55, Muhammad Bashir Khan wrote: I want to ask about the ligand refinement in coot. Earlier I was able to refine the ligand in the coot using real space refine zone but now by some reason when I want to refine the ligand in coot it asks me "Refinement setup failure failed to

Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

2020-04-26 Thread Paul Emsley
On 26/04/2020 16:21, Abhishek Anan wrote: Dear all, I have a peptide crystal structure at 0.97 Å that contains two surface exposed Methionine. The CE atoms of both MET have a suspiciously high b-factor >40 and a positive density. In addition, the sulfur atom SD has a large negative density

Re: [ccp4bb] placing and refining IOD Coot & refmac

2020-04-24 Thread Paul Emsley
On 24/04/2020 15:16, Sebastian Falk wrote: Dear CCP44bb community! I am currently building and refining a structure and want to place several iodines (IOD). However, both COOT( does not refine IOD by real space refinement after placing it as it misses the restraints. Placing

Re: [ccp4bb] CCP4 7.1 problems

2020-04-24 Thread Paul Emsley
On 24/04/2020 14:01, Robert S Phillips wrote: I installed CCP4 7.1 yesterday, and I have problems.  On an Ubuntu 18.04 LTS system, I get the following: Similarly, with COOT: rob@rob-SA76R4:~$ coot INFO:: Reading coordinate file: /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb

Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Paul Emsley
. Paul. On 24/04/2020 13:33, Tim Gruene wrote: Hallo Fred, lsqman (Uppsala software factory) is another option. With lsqman you can give explicit atom names, so that it works e.g. even for small molecule structures that do not follow PDB conventions. @Paul Emsley: a graphical option that let's you

Re: [ccp4bb] Coot download dir

2020-04-22 Thread Paul Emsley
On 22/04/2020 14:43, Eugene Osipov wrote: is there a way to specify Coot download directory, like the way I can specify backup dir by COOT_BACKUP_DIR? I did not find any guidelines in the Coot User Manual. No, but that would be just as useful, it seems to me. You can semi-fake it for

Re: [ccp4bb] Methods to improve ligand density of a homodimer?

2020-04-20 Thread Paul Emsley
On 20/04/2020 20:23, Kyle Gregory wrote: I am assessing ligand binding and each of the monomers display density at the site but it is not as clear as I would like. [] I was wondering if it is feasible, or if there are any tools, that can be used to improve density based of the fact there are

Re: [ccp4bb] Coot 0.9 Released

2020-04-02 Thread Paul Emsley
On 02/04/2020 16:59, Aleksandr Sverzhinsky wrote: This is great! Yes it is. It is a big change from the 0.8 series. Do you have an idea when this version will be available for WinCoot? This is a frequently asked question, more so recently - perhaps because many people are working at

[ccp4bb] Coot 0.9 Released

2020-04-01 Thread Paul Emsley
 Coot 0.9 is released.   This release has been a long-term effort (4 years according to my notes). It is powerful but not as   clean and stable as I would have liked, but I don't want to delay any longer. Many of the additions   and updates have been focused on the problems posed by cryo-EM

Re: [ccp4bb] Covalent Cysteine Aduct

2020-03-27 Thread Paul Emsley
I see. Might there be some discrepancy between best practice and what actually happened? ? On 27/03/2020 21:38, Cowan, Richard H. (Dr.) wrote: The Fab constructs have a c-terminal cysteines on both the heavy and light chains, which should form a disulphide. Adding reducing agent to the

Re: [ccp4bb] Covalent Cysteine Aduct

2020-03-27 Thread Paul Emsley
On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote: although [BME] seems unlikely, since the crystallized protein is a Fab. I don't follow. To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] text color in coot buttons

2020-03-26 Thread Paul Emsley
On 26/03/2020 16:46, Palm, Gottfried wrote:   I have problems reading some of the text in coot. Example situation: I open the Ramachandran Dynarama. The I hover with the mouse over one of the dots for a residue. A small box appears, but the text is white on very light grey background. Most

Re: [ccp4bb] Wincoot middle-mouse button does not work

2020-03-23 Thread Paul Emsley
On 23/03/2020 14:47, Schreuder, Herman /DE wrote: Courtesy to the Corona crisis, I am now separated from my Linux workstation and I am trying to get everything working from home. Running coot remotely via a low-speed internet connection was no option so I had Wincoot installed on my

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

2020-03-22 Thread Paul Emsley
On 23/03/2020 03:05, Jacob Wong wrote: I love the ccp4 suite. I'm interested in knowing if there is any other solution out there that may be more economical in licensing, especially if I only go as far as coot as a "commercial user". Are you suggesting that coot may not be a freeware anymore

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

2020-03-22 Thread Paul Emsley
Just would love to know what else is out there in addition to ELBOW in Phenix? Acedrg is the modern dictionary generator distributed by CCP4. My utility is to generate the .pdb and .cif files from a SMILES string that would allow me to do compound fitting and real-space refinement in coot,

Re: [ccp4bb] Coot under WSL2

2020-03-19 Thread Paul Emsley
On 19/03/2020 12:43, Clement Degut wrote: I have been recently trying to use ccp4 in windows subsystem for Linux 2 (Ubuntu distribution), everything i tried run perfectly smoothly, including graphical interfaces. I am pleasantly surprised - when I tried that (some time ago) the graphics

Re: [ccp4bb] Red trapezoids in Coot

2020-03-12 Thread Paul Emsley
On 12/03/2020 09:14, Joël Bloch wrote: Is there any way in Coot to remove/hide the red trapezoids that are indicating planar bonds? I couldn’t find anything on that, neither in the manual nor FAQ. (Good for you for reading the documentation) The red trapezoids represent cis

Re: [ccp4bb] Generating symmetry mates using python

2020-01-10 Thread Paul Emsley
Happy New Year indeed. Thank you. If this is not just a personal programming exercise, Orly Avraham might also take a look at PISA, python-mmdb and/or gemmi. Paul. On 10/01/2020 21:48, Jonathan Cooper wrote: Hello, I am sure that you have found that if you apply the symmetry operations

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