[COOT] molecule rubber banding not working in 8.1

After using 7.1 for a while, it was easy to 'real space refi zone' a amino acid. Pull on it and it will drag everything else with it. On 8.1 when I try this, it just rips an atom away from the residue and does not move the whole residue. There must be a parameter that is not set right. How do

[COOT] scroll wheel not working in 0.8.8

The density will not scroll in 0.8.8 when using the scroll wheel on my mouse. In v 0.7.1 it works find. How do I fix this? Linux dingo 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux thanks kas Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist,

[COOT] Water do not show up at all.

In 0.7.1 waters would display as a 3d cross. Symmetry related waters would not be represented at all. Now in 0.8.8 none of the waters show up. No cross, no star. They can be selected and labeled, but not represented. Am i not selecting the correct functions? thanks kas Linux dingo

Re: [COOT] Water do not show up at all.

, and the Carbone Cancer Center University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 From: Mailing list for users of COOT Crystallographic Software <COOT@JISCMAIL.AC.UK> on behalf of Kenneth Satyshur <kenneth.satys...@wisc.edu> Sent: Wedn

Re: [COOT] correct protonation state in His side chain

In fitting electron density of a His residue, the orientation should depend on the hydrogen bonding that can be assigned to the proton(s) on the His. If there is clear H bond acceptor, like a carboxylate, then it is likely that the proton is on this N in the ring and this is the correct

Re: [COOT] navigating back to the ligand

Thanks, this is great. Very helpful, but I tried to open the .scm in GIMP and it says unknown file type. kas Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry, Neuroscience, Oncology, and the Carbone Cancer Center University of

Re: [COOT] turn off auto recentring?

Mee too. But I can't read the reply because I don't know how to read a .scm file. Can you send as a pdf? thanks Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry, Neuroscience, Oncology, and the Carbone Cancer Center University of

Re: [COOT] set Coot download folder path in preferences

coot 0.8.9 crashes when reading cif file. I tried reading my G4P.cif file and coot crashed with the following output: ** (coot-bin:167556): WARNING **: Widget not found: cif_dictionary_file_selector_create_molecule_checkbutton /home/xray/ccp4/ccp4-7.0/ccp4-7.0/bin/coot: line 288: 167556

Re: [COOT] Carbohydrate torsion

Rinse, and repeat. Get Outlook for Android<https://aka.ms/ghei36> From: Kenneth Satyshur Sent: Thursday, May 9, 2019 8:06:45 AM To: Paul Emsley; COOT@JISCMAIL.AC.UK Subject: Re: Carbohydrate torsion Put structure in modeling program like Maestro or Sybyl,

Re: [COOT] Carbohydrate torsion

Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, generate restraints, refine. Get Outlook for Android From: Mailing list for users of COOT Crystallographic Software on behalf of Paul Emsley Sent:

Re: [COOT] Carbohydrate torsion

Center, and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 From: Bernhard Rupp Sent: Thursday, May 9, 2019 9:14:07 AM To: Kenneth Satyshur; COOT@JISCMAIL.AC.UK Subject: RE: Carbohydrate torsion Just a note to re

[COOT] Coot .9 pre does not display map in stereo

V 0.9 Pre drops the map out of display when going from mono to stereo. This does not happen in 0.8 V. I have enclosed the output of coot from the run in stereo. thanks kas Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences;

Re: [COOT] Where to find coot 0.9 and demos.

, 53706 608-215-5207 From: Mailing list for users of COOT Crystallographic Software on behalf of Kenneth Satyshur <302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk> Sent: Friday, April 3, 2020 6:18 PM To: COOT@JISCMAIL.AC.UK Subject: Re: Where to find co

[COOT] Where to find coot 0.9 and demos.

Thanks Paul for your tireless work on improving coot. It is a real gem of a graphics program! I went to your web site and I see 0.8.9.2 prerelease. Is there another place to get coot 0.9? I know that ccpem has 0.9 in it and this is the one I am using on Linux RHEL7. Works great (Except maps

Re: [COOT] Multithreading in 0.9

There is a difference between cores and threads. Think of cores as physical and threads, always 2x cores, as virtual. Some cores are not hyperthreading. Some linux report cores in use, not threads. 2400 x 2 is 48 threads. Get Outlook for Android

Re: [COOT] Nature this week

Hydrogen atoms should always be included in an X-ray model. They are half of the atoms in a protein. They are not refined except in a 'ridding' position, connected to the heavy atom. Molprobity will add hydrogens before any structural analysis and you can't do dynamics or MD without them. Only

[COOT] 0.9.5 crashes on RHEL7.9

Here is the error: Coot Scheme Scripting GUI code found and loaded. Good afternoon Ken Satyshur. Welcome to Coot 0.9.5. (set-display-intro-string "Good afternoon Ken. Welcome to Coot 0.9.5") (set-display-lists-for-maps 1)

Re: [COOT] 0.9.5 crashes on RHEL7.9

: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 From: Jason Key Sent: Friday, June 25, 2021 6:26 PM To: Kenneth

Re: [COOT] Current state of VR support

Thanks Paul for this information. I too am interested in VR. Our labs have Nvidia 3D stereo which we have used for a decade and we are happy with it. I have yet to be able to do any useful work with VR sets, but that may change. Chimera folks are also into VR. This is not their web site but

[COOT] coot crash.

I installed 0.9.5 on RHEL7.9 and it does not work. Just crashes. Enclosed is the txt file of the output. kas 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] on centos instll

Centos 8 is newer than what was used to compile coot. It will be missing some libraries that are installed with a a centos7 or 6 system. Usually, 8 has an upgraded version of a module and the compiled version is looking for the old one. You can install the older version and have then newer and

Re: [COOT] on centos instll

@jiscmail.ac.uk ; Kenneth Satyshur Subject: Re: on centos instll Dear All, Then is any way which can install coot 0.95 successfully in centos 8? And if there is the way, will you please share me with the step by step installation method? Best wishes, Smith On Saturday, April 10, 2021, 10:20:51 PM

Re: [COOT] removing dotted lines

users of COOT Crystallographic Software on behalf of pems...@mrc-lmb.cam.ac.uk Sent: Monday, November 8, 2021 3:47:37 PM To: COOT@JISCMAIL.AC.UK Subject: Re: removing dotted lines Did you read the blog post mentioned by Murpholino Peligro? Paul On 08/11/2021 19:16, Kenneth Satyshur

Re: [COOT] Centos issues

Already reported by Me. upgrade to 0.9.6 or 0.9.7. Although it still does not work correctly in 3D, since the windows are connected to 3D and the text is grabled. Centos 7 with Mate desktop works in 3D because stereo is associated with a window (stereo-in-a-window) which the Gnome desktop does

Re: [COOT] Recent communication

You deserve a medal, award, or something for the enormous effort in the programming. Without your effort I don't know where we would all be now. Thanks. kas p.s I have been working in this area for more than 50 years. Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life

Re: [COOT] Recent communication

dmarc-requ...@jiscmail.ac.uk>> wrote: Hear Hear - hard to remember life pre-COOT Eleanor On Tue, 12 Apr 2022 at 16:16, Kenneth Satyshur <302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk<mailto:302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk>> wrote: You deserve a medal, award, o

[COOT] H-bonding in sphere refine

I use the sphere refine in coot all the time. It's great. And when I turn on 'Environmental Distances'. I can see the H-bonding to the residue. Great. I have recently been using Isolde in ChimeraX to fit 3 A CryoEM density. When I select a residue, turn on H-bonding, it shows all the nearest

[COOT] disulfide bond breaks in coot 0.9.6

I have a disulfide bond defined in the pdb as SSBOND. It shows up in coot as a link between the sulfur atoms. But when I use 'sphere refine' the link is broken and there is no disulfide bond. The same happens for my CYS to ZN ligands. They are defined with a 'LINK' line in the pdb. How do I

Re: [COOT] Missing Restrains for standard amino acids

You can tell phenix where to find coot. Point coot to the ccp4 version, which has the libs. The stand alone version may not have the link to the lib that is maintained by ccp4. kas Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Retired From: College of Ag and Life Sciences: Department

[COOT] coot does not save hydrogens.

I added H atoms in coot and they appear in the list of atoms, but when coordinates are saved, they are not saved with the rest of the atoms. Is there a way of saving them or is this not advised? I can put them on during refinement and they are just ridding anyway. kas 0.9.6 version. Kenneth

Re: [COOT] stero/Mono

Harware stereo. A complicated issue. I have been using it for a long time. The SGI computers used crystal eyes glasses and was displaying fine for the 90's, but went away with the end of SGI. So we switched to linux. For a while (2000's) 3D stereo was not useable, except on old SGI. Then Nvidia

Re: [COOT] stero/Mono

sometimes flickering background. And you don't need to disable composite, neither in the xorg.conf file nor in the desktop settings. Best, Dirk On 25.05.23 17:49, Kenneth Satyshur wrote: Harware stereo. A complicated issue. I have been using it for a long time. The SGI computers used cr