Re: [COOT] examples of simple coot scripts

On 19/12/2020 21:53, Guenter Fritz wrote: Dear all, dear Paul, I want to prepare scripts to run coot functions like water picking or rotamer fitting  in command line. I checked the manual and the wiki hosted by Kay, so I got the basic idea but I have failed so far. Therefore I am looking for

Re: [COOT] Holiday season

On 22/12/2020 17:15, Eleanor Dodson wrote: Very festive! Your work paul? No. I am bemused and amused. I do have a "holidays" project simmering. More on that in a bit. Happy Xmas everyone Indeed. To unsubscribe

Re: [COOT] latest osx version of coot

0.9.2 is out now. 0.9.3 will be out within the week. They will be picked up by CCP4 and CCPEM soon(ish). Paul. On 11/11/2020 16:07, Marian Vogt wrote: Hi Len, assuming you are talking about the coot v0.9 Marina Bay, upgrading to the latest ccp4i2 version did the job for me

Re: [COOT] homology model in coot

On 16/11/2020 16:26, Moustafa, Ibrahim M. wrote: Hi all,   I'd like to build a C-alpha model to fit a low-res cryoEM map based on a homologous C-alpha model template. I tried to use coot "use clustal for alignment then mutate", the alignment is generated but when I try to mutate listed

Re: [COOT] How to import KCR molecule in Coot

On 19/11/2020 02:54, 任祥乐 wrote: Dear Coot team, I am refining a coordinate using Coot software, and molecules with three-letter codes of KCR and LBZ need to be imported into Coot. I could normally search for LBZ molecule, but it did not work to KCR molecule (see the attachment). Could you

[COOT] Release 0.9.3

Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.3.tar.gz Binaries https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.3-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz Release Notes:   o BUG-FIX: Colour-by-chain

Re: [COOT] homology model in coot

On 16/11/2020 18:18, Moustafa, Ibrahim M. wrote: Another question:   I am not able to change the color of atoms when it displays C-alpha atoms/backbone, always shown in brown color. Is there a command to change the C-atom color? (I have coot-0.9.1 EL ccp4 running) Hmm. I see what you

Re: [COOT] Coot scripting get imol number

On 12/11/2020 11:16, Luise Kandler wrote: Dear Coot Users, I was wondering if there is a python/scheme scripting command to catch/get the imol number of a certain map, that was opened in Coot. So far I could not find a suitable command in the Coot User Manual... imol =

[COOT] Release 0.9.2

Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.2.tar.gz Binaries: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.2-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz   Release 0.9.2   o BUG-FIX: Fix crash in

Re: [COOT] Script for making DED maps in Coot

On 01/11/2020 01:49, A. H. Zadeh wrote: Dear Coot Users, I do have around 1000 difference electron density maps and need to display them in Coot and take screenshots to make a movie out of them at the end. But I do not intend to do this procedure, manually! So is there any script to

Re: [COOT] Coot Ligand-library not found

https://pemsley.github.io/coot/blog/2020/09/21/how-to-make-a-bug-report.html On 02/11/2020 11:11, Ferdinand Kirsten wrote: Dear Coot users, I have a current problem with adding ligands to my structure. When i try to add the ligand  via SMILES the error: WARNING: in init_refmac_mon_lib, file

[COOT] Release 0.9.1

Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.1.tar.gz Binaries (currently only Scientific Linux 7.6): https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.1.Linux-x86_64-scientific-linux-7.6-gtk2-python.tar.gz Paul.  

[COOT] Nature this week

Hi, My colleagues recently published a paper (Nakane et al. (2020) "Single Particle cryo-EM at atomic resolution") and asked me to make a figure. I did so and it is this week's front cover image. https://www.nature.com/nature/volumes/587/issues/7832 I wrote a short blog post with high

Re: [COOT] Nature this week

They are indeed in the direct map. Yes, you are right, hydrogen atoms are more readily seen in a cryo-EM reconstruction than a map from x-ray data (given the same resolution of the data). "Atomic resolution" of course doesn't refer the the data resolution required to resolve a hydrogen atom and

Re: [COOT] install/run coot on Ubuntu 20.04 : lost

Hello Bryan, On 05/01/2021 22:31, Bryan Lepore wrote: Greetings - I am lost getting coot to run (see below the signature for fine details).  I have started `apt install` in piecemeal fashion and am getting nowhere (also see below for details), e.g. installing libguile-3.0 but it is already

Re: [COOT] install/run coot on Ubuntu 20.04 : lost

On 06/01/2021 00:37, Bryan Lepore wrote: a short update: On Tue, Jan 5, 2021 at 6:02 PM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: Coot on ubuntu links the system png library libpng12-0:amd64: /lib/x86_64-linux-gnu/libpng12.so.0 I guess you need to install

Re: [COOT] install/run coot on Ubuntu 20.04 : lost

On 06/01/2021 16:11, Bryan Lepore wrote: Before I forget - I'll post this because it was not obvious : libpng12 is apparently frowned upon by apt - whatever the case, I found this page : https://askubuntu.com/questions/1194386/how-to-correctly-install-libpng12-0-on-the-ubuntu-19-10#1194489

Re: [COOT] Coot Speed Run, Map 1

With this setup and my preliminary route I have tried perhaps a dozen times seriously and gotten varying results. Initially times would hover around 3 minutes and then steadily decrease as I made fewer mistakes. So far my fastest times are; *Time (fastest accepted): 2 min

Re: [COOT] Building N-glycan chains in coot

On 23/01/2021 17:36, Ahmad Khalifa wrote: Hi, I followed this tutorial to add a NAG to my structure http://legacy.ccp4.ac.uk/tutorials/tutorial_files/jligand/1_glycan.html . My question is, how can I add another NAG to

Re: [COOT] Coot Speed Run, Map 1

On 04/01/2021 10:42, Victor Tobiasson wrote: Time to join the party, a bit late perhaps but christmas got in the way! I will mention the speedrun in my presentation tomorrow and hopefully that may spark a bit of interest. So there are a few days left. I haven't set a date, maybe 14 Jan.

Re: [COOT] coot library path issue

On 07/01/2021 17:26, Brian Cuttler wrote: New install of coot on an Ubuntu 20.04 system. From the scripts I expected coot to set the load library path to find the coot /lib directory, this does not seem to be occurring. Unclear if I am misunderstanding, or need to set it from the command line

Re: [COOT] build-it

On 07/01/2021 14:55, Bryan Lepore wrote: Greetings - I noticed the last copyright in the build-it script is 2016 - is there any current guidance for this script (before I get carried away with it)? I'm not on top of the license and copyright notices. But I suppose now is the time to update

[COOT] Release 0.9.4.1

Coot 0.9.4.1 is released: source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.4.1.tar.gz binaries https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ I spotted a bug shortly after making the 0.9.4 release and before I made the

Re: [COOT] Release 0.9.4.1

Dear Erwin, Bernhard will announce the new WinCoot release when he has done it. Paul. On 04/02/2021 07:34, Erwin Pannecoucke wrote: Dear Paul, Could you (again, unfortunately) point us towards the location of the Windows installer?

Re: [COOT] WSL2 installation

On 30/01/2021 17:17, Jan Gebauer wrote: I am running WSL with xds also for my normal work. Your descriptions is very good. The trick to get shelx running was new to me - thank you for that! However, on my AMD / Win 10 machine coot is not running with your instructions. It only shows a

Re: [COOT] Ramachandran Refinement goes wrong in Coot

On Mon, 2021-06-14 at 15:51 +0100, Phong Nguyen wrote: > Hello, > > I am using Coot 0.9.5, installed from CCP4 package. It was working well until > today I decided to install ccp4 again > because I have some trouble of trying to install ARP package. So I guess that > Coot also get reinstall

Re: [COOT] Ramachandran Refinement goes wrong in Coot

On Mon, 2021-06-21 at 12:13 +0100, Phong Nguyen wrote: > Hello again, > > Thanks for your answer but it didn´t work in my case so I have downgrade to > coot 0.9.4.1 and it works perfectly again. > I don´t know what is the problem or where it comes from but it is only in the > new version 0.9.5.

Re: [COOT] accept with space bar and dynamic validation

On 22/06/2021 07:08, Frank von Delft wrote: Am I really the one that gets to post this?  Yay! https://xkcd.com/1172/ :-) Paul:  can I suggest hot-keys?  To save people tabbing around dialogs... Not being one for tabing in dialogs myself, please do so - itemized

Re: [COOT] accept with space bar and dynamic validation

On Mon, 2021-06-21 at 23:33 +0100, Georg Mlynek wrote: > Dear Paul, dear all, > I am running coot on Windows10 (I guess on linux and mac it works). Hmm... > > in past versions pressing the space bar after the Accept refinement? window > appeared, accepted the refinement, If the dialog has

Re: [COOT] Ramachandran Refinement goes wrong in Coot

On Tue, 2021-06-15 at 11:07 +0100, Phong Nguyen wrote: > > Upping the weight on the Rama restraints doesn´t help in my case. I think the > problem come from the interface because > if I turn on the validation ramachandran, it shows that the outliers come in > favoured regions after refinement

Re: [COOT] Feature suggestion: Check/Delete Waters, toggle hydrogens on/off

On Fri, 2021-06-04 at 18:45 +, CRAIG A BINGMAN wrote: > The "Check/Delete Water" function under “Validate" would be more useful to me > if it were possible to ignore hydrogen > atoms in the distance calculations. There seems to be no distance window that > works simultaneously for water O-O

Re: [COOT] OneDrive synchronisation

On 14/05/2021 16:55, Sebastiano Pasqualato wrote: Hi Paul, guys, I have a question regarding file sync and backup. As many, I am forced to use Microsoft OneDrive as cloud sync option, working on a Mac. Problem is, OneDrive for Mac does not allow synchronisation of files with “special

Re: [COOT] Undisplay ligand distortions

On Tue, 2021-05-18 at 18:24 +, André Graça wrote: > > I like to use the nice ligand validation tool ‘Display Ligand Distortions’ > from the Ligand menu. This uses Mogul to > assesses the geometry of chirals, for instance. Possibly not. If it takes about a minute, it's using Mogul, if it

Re: [COOT] Another keybinding question

On 20/05/2021 20:45, David M Dranow wrote: Thank you so much, that fixed the problem! Yay for keyboard shortcut refinement! Good. Yes, although I rarely use, t or r now. Of course now that this is fixed, I find another problem I wonder if you could help with. I noticed that I can't

Re: [COOT] Another keybinding question

On Wed, 2021-05-19 at 22:00 +0100, David M Dranow wrote: > I just upgraded to 0.9.5 in WSL (Ubuntu) and I noticed that three of my > keybindings for refinement no longer work (t, > T, r). When I run those commands I see the following messaged in the > terminal: > >

Re: [COOT] key binding question

On Mon, 2021-05-03 at 23:17 +0100, Paul Emsley wrote: > On Fri, 2021-04-30 at 14:04 +0200, Alastair McEwen wrote: > > We have just updated COOT from 0.9.4.1 EL to 0.9.5 EL on Ubuntu, and I have > > noticed a change in the function of the > > 'r' and 'x' key bindings. When

Re: [COOT] key binding question

On Mon, 2021-05-10 at 16:48 +, Hruza, Alan wrote: > We have also run into a key binding issue with coot(0.9.4.1 EL) bundled with > ccp4 for windows and stand alone for > Linux. > I would routinely use the "w" key to add waters and it no longer works in > either OS. I have found that if I

Re: [COOT] Another keybinding question

On Thu, 2021-05-20 at 17:04 +0100, David M Dranow wrote: > Hi Paul, > > I'm not familiar with fitting.scm. It's in xxx/share/coot/scheme, possibly, in your case /usr/local/ccp4/ccp4-7.1/share/coot/scheme/fitting.scm Copy that to you ~/.coot-preferences directory. And let's see if it executes

Re: [COOT] Wild refinement of waters

On Tue, 2021-06-01 at 20:45 +0100, David M Dranow wrote: > > Does anyone have a decent set of refinement parameters for Coot 0.9.5 in > linux? My colleagues and I find that using > the "r" shortcut causes most waters to fly off and center on carbons, > sometimes as far away as 45 Å! I've

Re: [COOT] Wild refinement of waters

On Wed, 2021-06-02 at 10:44 +0100, Eleanor Dodson wrote: > I think it is a sphere refine problem. Just use the old real space refine.. > sphere refine hates clashes, It's not "sphere refine" that hates clashes, it's that the non-bonded contact interactions have a new model. > so before you

Re: [COOT] Wild refinement of waters

> between the maps. I imagine that you can create a custom toggle button in a few lines of python to do this switching. Paul. > On Wed, Jun 2, 2021 at 8:03 AM Paul Emsley wrote: > > On Wed, 2021-06-02 at 10:44 +0100, Eleanor Dodson wrote: > > > > > I think it is a sphere refi

Re: [COOT] Feature suggestion: Check/Delete Waters, toggle hydrogens on/off

On Fri, 2021-06-04 at 18:45 +, CRAIG A BINGMAN wrote: > The "Check/Delete Water" function under “Validate" would be more useful to me > if it were possible to ignore hydrogen > atoms in the distance calculations. There seems to be no distance window that > works simultaneously for water O-O

Re: [COOT] Wild refinement of waters

On Wed, 2021-06-02 at 15:56 +0100, Paul Emsley wrote: > On Tue, 2021-06-01 at 20:45 +0100, David M Dranow wrote: > > Does anyone have a decent set of refinement parameters for Coot 0.9.5 in > > linux? My colleagues and I find that using > > the "r" shortcu

Re: [COOT] Wild refinement of waters

After more off-list correspondence, I further investigated the water refinement issue. I now think that the problem isn't what I thought it was. A few months ago, I had noticed how frustratingly long it took for Coot to start moving the atoms when RSRing a fragment into a cryo-EM map. I

Re: [COOT] Wild refinement of waters

On Thu, 2021-06-03 at 09:02 -0700, Philip Kiser wrote: > Thank you for spotting the problem and introducing the new restraint. I have > to say that it was easy to get in the > habit of creating poorly placed water molecules when filling difference map > peaks as the prior refinement method for >

[COOT] Release 0.9.6

Coot-0.9.6 has been released. source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.6.tar.gz binaries: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ Bernhard will announce the schedule for WinCoot 0.9.6 shortly. Paul. Release 0.9.6

Re: [COOT] auto_fit_best_rotamer, residue range / all residues

On Wed, 2021-06-23 at 16:24 +0200, Guenter Fritz wrote: > > I am running a very short python script in coot to do some automatic > fitting. So far I used the fit_protein option. I want to have a try on > auto_fit_best_rotamer. If possible I would like to fit sidechains of all > residues or a

Re: [COOT] on centos instll

On Sat, 2021-04-10 at 08:45 +, Smith Lee wrote: > Dear All, > > In Centos 8 system I have downloaded > "coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ". By > "tar -xzvf > coot-0.9.5-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz ", in > the

Re: [COOT] Coot crash on CentOS 7

On Wed, 2021-04-21 at 16:48 +0100, DougB wrote: > Hello. > > I'm attempting to run coot on CentOS 7 using > "coot-Linux-x86_64-scientific-linux-7.6-gtk2-python" binaries > > I'm getting the splash screen, but then coot crashes. I appreciate any help! > It would be better if Coot could exit

Re: [COOT] on centos instll

CentOS 8 binaries will probably need to be compiled. The build-it script will try to do that. It may fail. The build logs will, by default, be in ~/public_html/build-logs. I am being pulled in 15 ways at the moment and the time I have to spend on making Coot compile new operating systems on

Re: [COOT] key binding question

On Fri, 2021-04-30 at 14:04 +0200, Alastair McEwen wrote: > > We have just updated COOT from 0.9.4.1 EL to 0.9.5 EL on Ubuntu, and I have > noticed a change in the function of the > 'r' and 'x' key bindings. When centred on a residue with and alternative > conformations, when I use 'r' or 'x'

Re: [COOT] Bug report - change chain ID crashes when model =2

On 03/05/2021 14:07, vincent Chaptal wrote: > A small bug report and the fix. > > I've been trying to apply/change chain IDs using coot for a pdb containing a > series of models from a MD > trajectory. > The pdb has been separated into individual models for individual chain > renaming. > For

Re: [COOT] Coot NaN issue

On Mon, 2021-05-03 at 17:49 +0200, Victor Tobiasson wrote: > Has anyone else encountered a refinement/regularisation issue in coot where > refinement produces a phi NaN? It seems to > be fairly new and specific to 0.9.5 and will completely freeze the coot > process. Unfortunately the only info I

Re: [COOT] Mutating DNA residues with mutate-residue-range

Hi Ming, One Uses "DT" in DNA. One doesn't use "T" in RNA, one uses methyl-uridine, specifically 5MU. Poor old Coot gets confused if you try to insert an RNA base into a DNA strand. And doubly so for thymine. > I have a similar error on MacOS Coot 0.8.9.3 EL That's an Old Coot. Maybe

Re: [COOT] Mutating DNA residues with mutate-residue-range

On 09/02/2021 16:04, Ming Sun wrote: Thanks for the information. I did give another several try. However, I got the same error messages. using the GUI, mutating A --> T; not working; (but could do it from A to U) For me, it was the other way around. using the python script, mutate

[COOT] Coot Speed Run, Map 1 Winner + Next Challenge: Map 2

The Winner of the Coot Speed Run, Map 1 Challenge, with a time of 2:29 is Victor Tobiasson. Yay. Victor has asked for a more difficult challenge for the next map and I agree. I have selected EMD-22898/7kjr which is SARS-CoV2 ORF 3a - an ion channel and potential therapeutic and vaccine

Re: [COOT] XQuartz 2.8.0_beta1 is not compatible with COOT

I take it to mean the XQuartz 2.8.0 doesn't distribute the library against which Coot (0.9.x) is linked by CCP4 and CCPEM. At some stage CCP4 will drop the hammer and update to 2.8.0 and build Coot against that - at which stage (of course) the Coot of all 2.7.x users will stop working. Paul

Re: [COOT] Current state of VR support

On 23/03/2021 04:18, G ökhan Tolun wrote: Dear COOT developers and experts, Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I hope that the molecular visualization and modelling software will

Re: [COOT] Jigglefit

On Thu, 2021-04-01 at 15:26 -0700, Bernhard Rupp wrote: > where do I find the jigglefit in wincoot 9.4.1? You mean 0.9.4.1 - Coot hasn't got to version 1.0 yet. 2 years ago I had planned that for today, but there was so much to learn and to do that I didn't manage it. Jiggle fit tools are in

Re: [COOT] Link residues in different chains

On 31/03/2021 22:08, Bernhard Rupp wrote: I spectacularly fail trying to link for real space refine 2 different chains with the modelling/make link command. The bonding in Coot's RSR only works within the chain - including links. (You can make links between chains, but RSR won't use them.)

Re: [COOT] Link residues in different chains

; > -- > Kevin Jude, PhD (he/him/his) > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > > On Wed, Mar 31

[COOT] Release 0.9.5

I am pleased to announce the release of Coot 0.9.5 I am releasing it now in the hope that someone will use it for the 2021 EM Validation Challenge. The most important new feature of 0.9.5 is bringing control of the weights to the user-level. The Refinement and Regularization Control widget now

Re: [COOT] Release 0.9.5

I meant to add that I have written a couple of related blog posts: https://pemsley.github.io/coot/blog/2021/03/11/coot-goes-nuclear.html https://pemsley.github.io/coot/blog/2021/03/11/dynamic-weights.html Paul. To

Re: [COOT] Coot - ibreadline.so error

On 17/03/2021 11:16, Michael Weyand wrote: Hi, with the recent Coot (0.9.4.2) from CCP4i I receive an error message when I try to use the "undo" button. In the Coot terminal I receive the following error. > SNIP INFO:: backup file name

Re: [COOT] RNA Model Building

On 19/03/2021 15:27, M.S. Islam wrote: I have done rigid body fitting of a couple of chains of "A form RNA" into an EM map using Chimera. Why not do it in Coot? Or, put it another way: what does Chimera give you for rigid body fitting that Coot does not? Now I intend to join the chains

Re: [COOT] RNA Model Building

On 19/03/2021 17:18, M.S. Islam wrote: Hi Paul Thanks a lot. Yes, I could have done the fitting on COOT :-) OK. I can see these options under "Edit". But I am still struggling. Let me clarify, I have modelled 10 A-form RNA chains, chain A, B, ... Now I want to merge all chains

Re: [COOT] add_module_for cryo() ?

On 20/03/2021 20:28, Bernhard Rupp wrote: could someone please share what’s the secret handshake to get the Cryo-EM module up into the menu bar? Such as add_module_carbohydrate() for the Glyco would be add_module_?() for the Cryo-EM ? add_module_cryo_em() Where does one find

Re: [COOT] Copy fragment with instertion

On 16/03/2021 22:03, Bernhard Rupp wrote: Hi Fellows, wincoot 9.4.1 when I try to copy a fragment with insertions, say 855 to 855M, only the first residue gets copied Is there a different copy option I could/should use? For now, use //A/855-856 and delete 856 if you don't need it.

Re: [COOT] Acknowledge Your Appraisal

On 25/02/2021 12:00, David Briggs wrote: This looks awfully like a phishing scam. Agreed. I'll see if I can remember how to ban someone. Usually, jiscmail are quite good at filtering out this sort of thing. Paul.

Re: [COOT] coot 0.9.4.1 installation on centos 8

Hello Ming, OK, So the coot build doesn't build everything it needs from scratch - it relies on the system for some libraries. One of those libraries is libpng. Tell us about the version of libpng that you have installed. $ rpm -q libpng Now do a rpm -ql on the result, something like: $

Re: [COOT] display EMDB map in coot 0.9.4.1

On 05/03/2021 17:38, Tong wrote: I installed the newest coot from binary: coot 0.9.4.1. I download maps from EMDB and open the map in this new coot. I did not see any map. Display Manager indicate the map is displayed. I am able to view this map in the old version 0.8.9.2-pre. Does anyone

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

On 23/02/2021 13:42, Pedro Matias wrote: I tried both ways (coot.py and .coot) and only the latter worked for me. that should be .coot.py - presumably that's what you meant (but if not, it would explain why it didn't work) .coot-preferences is a directory and its contents should not be

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

So, let me be clear. The bug is: "I get lots of annoying error messages on starting stereo. If I set_display_lists_for_maps(0) then it's OK and the messages go away. I want Coot to start up in a way where I don't have to type set_display_lists_for_maps(0)" Is that right? I don't have access

Re: [COOT] Coot 0.9.4.1 3D Hardware Stereo still does not work properly

programs on Linux now seem to follow this convention, and it’s actually nice to have one’s home directory more cleanly organized. Guillaume On 23 Feb 2021, at 14:53, Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 23/02/2021 13:42, Pedro Matias wrote: I tried both ways

Re: [COOT] hardware stereo

On 27/02/2021 10:01, Andrea wrote: My structure and map is stereo, but my mouse (the cross) is mono - see the picture I attach. Any idea how to fix this? It's "mono" I think because the pick cursor only exists in the same plane as the rotation centre - and on that plane, the left eye and

Re: [COOT] coot symbolic link

On Tue, 2015-10-06 at 03:14 +0100, Lu Zuokun wrote: > On installating coot, I make a symbolic link between coot sources > coot/bin/coot and /usr/local/bin/coot. > When opening coot in the /usr/local/bin directory with command: ./coot , I > got the error message: > > lu@ubuntu:/usr/local/bin$

Re: [COOT] coot error on mac osx Big Sur

Hi Paula, On 19/04/2021 10:08, Paula Salgado wrote: I'm trying to run Coot on MacOs Big Sur (v. 11.2.3) That is not something that I've tried. via ccp4i2 and get this error: -ERROR- Ccoot_rebuild:56 Error in wrapper coot_rebuild 0.0:: External process exited with exit code != 0 Process:

Re: [COOT] How to build alternate water cluster

On 17/04/2021 00:17, Mitchell D. Miller wrote:   I am building a high resolution structure (1.2A) with alternate side-chain positions that show evidence of nearby waters that move with the side chain. E.g. I see what needs to be an alt-B water to H-bond with the alt-B side chain. It also

Re: [COOT] large non-native peptide .cif restraints

On Wed, 2021-09-01 at 16:55 -0700, Seth Harris wrote: > Hi all, Hi Seth, > I am increasingly dealing with large macrocycles or cyclized peptides that > include unnatural amino acids or > modifications. Early on my approach was to treat most of it as the native > peptide scaffold, then add a

Re: [COOT] Applying NCS edits - heterotrimer complex

On 08/09/2021 17:38, Jose Artur Brito wrote: I apologise in advance if this is in the documentation (or if it was answered before), but I honestly couldn't find it. I have 8 copies of a heterotrimer in the asymmetric unit (24 chains). At this (very initial) stage, I am focusing on chains A,

Re: [COOT] Mac OS and Coot Update from CCP4

On 17/09/2021 09:17, Xavier Brazzolotto wrote: I am using Coot on a Mac (Big Sur) I’ve lately updated my CCP4 (7.1.016) which includes the latest Coot version, but after this update Coot systematically crashes (From Phenix or directly from my terminal). I’ve downgraded to CCP4 7.1.015, to get

Re: [COOT] Mac OS and Coot Update from CCP4

ing Le 18 sept. 2021 à 03:22, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> a écrit : On 17/09/2021 09:17, Xavier Brazzolotto wrote: I am using Coot on a Mac (Big Sur) I’ve lately updated my CCP4 (7.1.016) which includes the latest Coot version, but after this update Coot systematica

Re: [COOT] python scripting commands

On Thu, 2021-07-15 at 10:53 +0530, manikandank wrote: > > I would like to find the descriptions of list of python functions/commands on > how should be used (please see the > attached image). > > For example, How to use 'change_chain_id' in python scripting ? > > change_chain_id(imol,

Re: [COOT] Glyco module going off script at the B1-4 BMA?

On Tue, 2021-07-13 at 23:59 -0700, Seth Harris wrote: > > I have some good resolution (~1.3 A) data with glycosylation that can pretty > clear describe the expected N-linked tree > of Asn-NAG-NAG-BMA with two MAN off the end and a FUC at the base NAG (plus > something on the other side of the

Re: [COOT] Compiling COOT 0.9.5.0 for RHEL7

On Mon, 2021-08-02 at 21:53 +, Gordon Madise wrote: > What is the configure command line to drive the compile process? I have used > the following but it errors out. > > I had to do a complete build of COOT from scratch. I seem to have all > prerequisites installed and the configure >

Re: [COOT] RSR of tRNA with nascent chain

On Tue, 2021-07-27 at 15:20 +0100, Helge Paternoga wrote: > Dear all, > > I have what feels like a trivial question about modelling in coot, but > unfortunately I have not managed to solve it > myself. > > I would like to create a bond between a P-tRNA and nascent chain and then > subsequently

Re: [COOT] cannot open coot on Ubuntu 20

On 20/10/2021 07:56, 陈喆 wrote: Hello, my ubuntu system has coot software installed. It has been running normally for a long time, but the coot can’t be opened a few days ago. I pasted the error message below. I don’t know if other additional information is needed. I don't know what the

Re: [COOT] Place Atom at Pointer

On 01/10/2021 11:57, Becker, Stefan wrote: placing water with "place atom at pointer" in coot doesn’t work for me with up to date Coot 0.9.6, running on Ubuntu 16.04 LTS. No water appears. Is this a known bug? Can you tell me (us) how to reproduce what you are seeing using the built-in

Re: [COOT] Place Atom at Pointer

On 01/10/2021 11:57, Becker, Stefan wrote: placing water with "place atom at pointer" in coot doesn’t work for me with up to date Coot 0.9.6, running on Ubuntu 16.04 LTS. No water appears. Is this a known bug? IIRC, I prevented Coot from adding a water at  the position of another atom (so

Re: [COOT] How to reset occupancy from 2 or 3 to 1?

On 04/12/2021 08:29, Yuqi Zhang wrote: Hi, all! I met a problem when I upload the PDB file to wwPDB. There is an error about the occupancy was larger than 1. So I checked the model in COOT. There are many atoms whose occupancy was 2 or 3. How to reset occupancy from 2 or 3 to 1? Can someone

Re: [COOT] How to turn off prompt for nomenclature errors?

On 22/12/2021 15:37, Frank von Delft wrote: Hello - when I drag a bunch of files onto my wincoot, I end up with a long slew of dialogues, asking me if I wan to fix nomenclature errors. I've just realised I find it irritating, because I just want to look, not build. How do I turn it off by

Re: [COOT] coot scripting question

On 23/11/2021 20:03, Artem Evdokimov wrote: Dear Cooters! I am new to this list, but would love to get a little bit of help scripting Coot to do something for me, like this: 1. read one PDB and one MTZ file 2. center on a particular location (ideally defined as e.g. a residue) 3. orient in a

Re: [COOT] coot scripting question

, 10:01 AM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 23/11/2021 20:03, Artem Evdokimov wrote: > Dear Cooters! > > I am new to this list, but would love to get a little bit of help > scripting Coot to do something for me, like this: &g

Re: [COOT] Build-it cannot find self-build guile

On 20/10/2021 14:12, Jan Stransky wrote: Update, no-guile build version passed, but I dont see the icons :-) I don't think that those things are related. I don't know much about icons, maybe there something of interest in the console output. Jan On 10/20/21 14:04, Jan Stransky wrote:

Re: [COOT] Map contour level

On 26/10/2021 10:32, Holton, Simon wrote: When running Coot v 0.9.6 (revision-count 10625, standalone installation as a precompiled binary), we observe that no map contour levels are displayed. In contrast, when we run Coot 0.9.5 (revision-count 10365) that comes as part of the CCP4

Re: [COOT] removing dotted lines

Did you read the blog post mentioned by Murpholino Peligro? Paul On 08/11/2021 19:16, Kenneth Satyshur wrote: Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular

Re: [COOT] Coot and D-amino acids

work = Success On Wed, Nov 3, 2021 at 10:41 PM Paul Emsley wrote: On 03/11/2021 22:28, prasun kumar wrote: > > > I have a structure that has a lot of D-amino acids. When I open the > mtz and pdb open it in Coot you mean? > it shows me C-beta outli

Re: [COOT] Coot and D-amino acids

On 03/11/2021 22:28, prasun kumar wrote: I have a structure that has a lot of D-amino acids. When I open the mtz and pdb open it in Coot you mean? it shows me C-beta outlier warning (Molprobity Warnig). Coot doesn't do that. Are you talking about some other program? I have also downloaded

Re: [COOT] removing dotted lines

On 10/12/2021 17:16, Thomas, Leonard M. wrote: It appears that the command does not work at least on my Mac with v0.9.5 from CCP4.  I did have to redirect my command line version to get an the lasted, I think, version running when I wanted it. Hmm... Did the command complete? What does it

Re: [COOT] Coot 0.9.6 unstable?

On 16/12/2021 14:43, Jan Gebauer wrote: > Hi everyone, > > I currently giving a course for students in XTAL crystallography and > bravely installed the newest version of Phenix for it. > It is bundled with the 0.9.6 version of COOT, which now in multiple > instances crashed for my students. I

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