[COOT] Does Coot 0.9.8.92 (CCP4 build) run on Sonoma

Colleagues, Before I install Sonoma on my intel-based MacBook Pro, would someone let me know if Coot 9.8.92 is compatible? Many thanks, Mark _ Mark A. Saper, Ph.D. sa...@umich.edu | +972 52 815-0480

[COOT] Bug in Pointer distances

For Paul, After enabling pointer distances, the distances don’t update (most of the time) when moving to a different place in the molecule. The Coot version is 0.9.8.92 running on macOS 13.6.1. Thanks, Mark _ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and

Re: [COOT] Release 0.9.8.9

Hi Paul, Does this new release address the problems with Real Space Refinement that I reported several months ago? Thanks, Mark _ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor

[COOT] Opening wincoot from phenix

What path do I use to open wincoot in phenix?  I configured the preferences in phenix to access the executable in /bin, but it doesn’t load any of the icons or load the molecule or map.  The wincoot version is 0.9.8 I think. The OS is windows but not sure what version.  I don’t know if the

[COOT] Coot version 0.9.8.7

ode found and loaded. Good morning Mark Saper. Welcome to Coot 0.9.8.7. (set-display-intro-string "Good morning Mark. Welcome to Coot 0.9.8.7") (set-display-lists-for-maps 0) load /Users/saper/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky

[COOT] Coot support for modeling DNA

I am having trouble fitting DNA structures to my map. Neither Real Space Refine or regularization seem to work with a DNA strand. I’m trying to insert a nucleotide in a strand where I have a gap. What am I missing?Thanks, Mark_Mark A. Saper, Ph.D.Visiting ProfessorFaculty of

[COOT] Closing generic display objects causes Coot to crash

t! Thanks, Mark Saper To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing li

[COOT] coot problems on Mac with external display

Ursula, I have the same problem when running Coot for Mac (0.9.6 from CCP4, XQuartz 2.8.1) on MacBook Pro (macOS 10.14.6) with an external monitor. I think this problem only occurs when you also have your laptop open. The Coot display window is not visible. I know the model window is

[COOT] Bug in Coot 0.9.6

Running 0.9.6 (CCP4 for Mac) If one is displaying structure as balls and sticks, or as sticks with waters as balls, then switching to stereo (wall-eye) causes all balls to become squares. Disabling stereo does not revert them back to balls. -Mark Powered by Mailbutler

[COOT] Reading .cif files from PDB

The sf-annotate_P1.cif file that I have generated for PDB submission contains the map coefficients along with the observed structure factors. _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT Is there any way that Coot can read these columns from a CIF file and

[COOT] Problem doing real-space refinement of MSE residue

I have a situation where I manually edited my PDB file to rename MET to MSE, then made the appropriate change to change all “ SD" atoms in MSE to “SE “. When I optimize the geometry with Real Space Refine Zone, the amide proton (H) moves several Å way, and the Torsions error goes to 2.24. Do

Re: [COOT] COOT Digest - 13 Sep 2014 to 14 Sep 2014 (#2014-117)

A 10.8 standalone would be helpful for me. I can't remember 10.6.8 but I would probably agree. Mark Saper 3040 3250 Chemistry Building Dept of Biological Chemistry sa...@umich.edu 734 764 3353 office 734 276 6505 mobile On Sep 14, 2014, at 7:01 PM, COOT automatic digest system lists