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

[Mark Saper]

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




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[COOT] Bug in Pointer distances

[Mark Saper]

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 Molecular Genetics
Hebrew University Faculty of Medicine

Associate Professor Emeritus of Biological Chemistry
University of Michigan Medical School

sa...@umich.edu   |  +972 52 815-0480




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Re: [COOT] Release 0.9.8.9

[Mark Saper]

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 Emeritus of Biological Chemistry
University of Michigan Medical School

sa...@umich.edu  |  +972 52 815-0480



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[COOT] Opening wincoot from phenix

[Mark Saper]

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 installed coot has python built in. Any help would be appreciated since all of my expertise is on Mac. Thanks,_Mark A. Saper, Ph.D.Visiting ProfessorFaculty of MedicineHebrew University of Jerusalem Associate Professor Emeritus of Biological ChemistryUniv of Michigan Medical Schoolsa...@umich.edu  |  +972 52-815-0480

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[COOT] Coot version 0.9.8.7

[Mark Saper]

ilenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Coot Scheme Scripting GUI code 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-sort-by-date)
(set-colour-map-rotation-on-read-pdb 21.00)
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)
(set-density-size 16.00)
(set-swap-difference-map-colours 0)
(set-colour-map-rotation-for-map 14.00)
(set-active-map-drag-flag 1)
(set-idle-function-rotate-angle 1.00)
load /Users/saper/.coot-preferences/curlew-refinement-tools.scm
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(filter-fileselection-filenames-state)
DEBUG:: filename: 
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
(handle-read-draw-molecule-with-recentre 
"/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb"
 1)
INFO:: Reading coordinate file: 
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
INFO:: file 
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12-coot-1.pdb
 has been read.
Spacegroup: P 41 21 2
INFO:: using standard CCP4 Refmac dictionary to search for "FE"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/f/FE.cif
INFO:: using standard CCP4 Refmac dictionary to search for "ZN"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/z/ZN.cif
INFO:: using standard CCP4 Refmac dictionary to search for "3DR"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/3/3DR.cif
INFO:: Found 1 models
   Model 1 had 2 links
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/299
INFO:: NCS chain comparison 0/5
INFO:: NCS chain comparison 0/5
INFO:: NCS chain comparison 0/7
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
debug:: g.safe_scheme_command() with command post-read-model-hook
INFO:: in run_post_read_model_hook() pFunc 0x107f5ca68 is not callable
INFO:: in run_post_read_model_hook() pDict 0x7fce8f297168 
INFO:: in run_post_read_model_hook() pModule 0x7fce8f282be8 
Molecule 0 read successfully
(filter-fileselection-filenames-state)
(filter-fileselection-filenames-state)
INFO:: making conventional map from MTZ filename 
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz
 using 2FOFCWT PH2FOFCWT
INFO:: Number of observed reflections: 21453
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 120, 120, 320)
Pre-filter Map statistics: mean: 5.42665e-08 st.d: 0.175245
Pre-filter Map statistics:  min: -0.563024 max: 1.24297
INFO:: n grid points: 576060
INFO:: mean before filtering: 5.42665e-08
INFO:: variance before filtering: 0.0307108
INFO:: filter by ignoring 413 of 576060 counts ( = 0.07169%) with values around 
-0.02655 bounds -0.02664 -0.02646 from bin-number 2970 of 1
Post-filter Map statistics: mean: 1.924e-05 st.d: 0.1753
Post-filter Map statistics: min: -0.563 max: 1.243
  Map extents: . 120 120 320 
  Map mean:  1.924e-05
  Map sigma: ... 0.1753
  Map maximum: . 1.243
  Map minimum: . -0.563
(make-and-draw-map-with-reso-with-refmac-params 
"/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz"
 "2FOFCWT" "PH2FOFCWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" 
"RFree:None-specified" 0 0 0 0.00 0.00)
INFO:: making difference map from MTZ filename 
/Users/saper/Research/SaNfo/230324_Diamond/Y33F_DNA_P023_X12/zn_above/xia2_3dii/phenix/Refine_12/Y33F_DNA_P023_X12_refine_12.mtz
 using FOFCWT PHFOFCWT
INFO:: Number of observed reflections: 21453
INFO:: finding ASU unique map points with sampling rate 1.8
INFO:: grid sampling...Nuvw = ( 120, 120, 320)
Pre-filter Map statistics: mean: 1.917e-06 st.d: 0.0796
Pre-filter Map statistics:  min: -0.4068 max: 0.661
INFO:: n grid points: 576060
INFO:: mean before filtering: 1.917e-06
INFO:: variance before filtering: 0.006337
INFO:: filter by ignoring 385 of 576060 counts ( = 0.06683%) with values around 
-0.01509 bounds -0.01515 -0.01504 from bin-number 3668 of 1
Post-filter Map statistics: mean: 1.203e-05 st.d: 0.07963
Post-filter Map statistics: min: -0.4068 max: 0.661
  Map extents: . 120 

[COOT] Coot support for modeling DNA

[Mark Saper]

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 MedicineHebrew University of Jerusalem Associate Professor Emeritus of Biological ChemistryUniv of Michigan Medical Schoolsa...@umich.edu  |  +972 52-815-0480On Feb 4, 2023, at 2:06 AM, COOT automatic digest system  wrote:There is 1 message totaling 147 lines in this issue.Topics of the day:  1. Strange coot crash on MacOS Ventura 13.1To unsubscribe from the COOT list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/--Date:    Fri, 3 Feb 2023 14:03:52 +0100From:    vincent Chaptal Subject: Strange coot crash on MacOS Ventura 13.1Hi,it's a weird behavior; after upgrading to Ventura 13.1, coot sometimes crashes without error message. (starting from the prompt)The crash usually happens when I save the molecule (the save is done correctly, so at least not all is lost).When I reopen coot, it behaves normally and after some time (say 5 minutes or so), a second coot window opens with the same display, pdb and map. So i'm getting confused on which one I was working on in the first place.I upgraded coot with the latest ccp4 package (v8.0), so it's coot 0.9.8.7. I was the same bug on a previous version but I forgot the number, perhaps 0.9.8.4 (?)Any idea of what's going on?ThanksVincent-- Vincent Chaptal, PhDDirector of GdR APPICOMDrug Resistance and Membrane Proteins LabMMSB -UMR50867 passage du Vercors69007 LYONFRANCE+33 4 37 65 29 01http://www.appicom.cnrs.frhttp://mmsb.cnrs.fr/en/To unsubscribe from the COOT list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/--End of COOT Digest - 27 Jan 2023 to 3 Feb 2023 (#2023-16)*

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[COOT] Closing generic display objects causes Coot to crash

[Mark Saper]

Hi all,

I am using macOS 10.14.6 and Coot 0.9.6 from ccp4.  After I open the "Generic 
Display Objects" dialog box, and then click Close, Coot crashes without a 
message.  I have the same behavior if I run Coot from within Phenix, or run it 
directly.  I can send you logfile upon request!

Thanks,
Mark Saper



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[COOT] coot problems on Mac with external display

[Mark Saper]

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 somewhere, because if I enter 
Mission Control (control-up-arrow or 3-finger swipe up on trackpad), it shows 
up.  To work around this problem, I enter Mission Control, then click and drag 
the Coot window to the Desktop corresponding to the laptop display.  Exiting 
Mission Control, will show the Coot window.  Unfortunately, the draggable top 
of the window is not visible.  To make it visible, just resize the window 
slightly.  The Coot window can now be dragged to the external monitor display.

I found another way to find the window.  If you go into system preferences 
Displays>Arrangement, you can move the laptop monitor icon to the other side of 
your external monitor icon.  

I think this may be a problem with XQuartz.  I have not had a problem when 
running ccp4i which also uses XQuartz. 

Hope this helps,
Mark

__
Mark A. Saper, Ph.D.
Visiting Professor at the Faculty of Medicine
Hebrew University of Jerusalem
Ein Kerem Jerusalem
ISRAEL

sa...@umich.edu mobile +972 52 815-0480‬


> Date:Tue, 2 Nov 2021 13:43:54 -0700
> From:Ursula Schulze-Gahmen  >
> Subject: coot problems on Mac with external display
> 
> I apologize if this question has been raised before. But I am still
> struggling with running Coot 0.95 on my mac laptop (Catalina) with an
> external display.
> Coot is functioning normal without the external display. But with external
> display, the window for displaying models doesn't open properly. Is there a
> fix for this situation?
> I am using the Coot version from sbgrid, ccp4 7.1. I am running XQuartz
> 2.8.1 for the graphics.
> 
> Thanks
> 
> Ursula
> 
> -- 
> Ursula Schulze-Gahmen, PhD
> Staff Research Scientist
> The J David Gladstone Institutes
> 1650 Owens St.
> San Francisco, CA 94158
> (415) 734 4835


 
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[COOT] Bug in Coot 0.9.6

[Mark Saper]

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


 
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> On Aug 21, 2021, at 2:03 AM, COOT automatic digest system 
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>  1. Grant Announcement for PhD Candidates- Open to Global Applications
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> 
> Date:Fri, 20 Aug 2021 12:05:28 +0100
> From:Ece Kural 
> Subject: Grant Announcement for PhD Candidates- Open to Global Applications
> 
> **Apologies for cross-posting**
> 
> I would like to circulate the message that Scrintal and PhDVoice sponsor a 
> US$500 grant to be awarded to one PhD student and the application period is 
> open. This grant is intended to support a PhD student financially for the 
> upcoming year. The grant is multi-purpose and can be used for any 
> study-related expense, including but not limited to conference or workshop 
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> October 1st (2021).
> 
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> affiliated institution. 
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[COOT] Reading .cif files from PDB

[Mark Saper]

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 calculate 
a map?

Thanks,
Mark
___
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III   sa...@umich.edu   +1 (734) 764-3353 mobile: (734) 
276-6505




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

[Mark Saper]

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 you have any idea what’s causing this?
_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI  48109-1055 U.S.A.
sa...@umich.edu phone (734) 764-3353fax (734) 763-4581

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

[Mark Saper]

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...@jiscmail.ac.uk wrote:
 
 There is 1 message totaling 36 lines in this issue.
 
 Topics of the day:
 
  1. Coot on OS X  10.6.X ?
 
 --
 
 Date:Sun, 14 Sep 2014 08:54:50 -0700
 From:William G. Scott wgsc...@ucsc.edu
 Subject: Coot on OS X  10.6.X ?
 
 Hi folks:
 
 Does anyone use my pre-compiled version of coot for OS X 10.6 anymore?  (This 
 would be either the 10.6 stand-alone or the fink debian distribution)?
 
 Fink has discontinued support for 10.6, and I only have the one mac mini in 
 my lab running it, so at some point the end is inevitable.
 
 (My personal, irrelevant opinion was that 10.6.8 was the best version of OS X 
 and it has been in decline ever since.)
 
 Also, we made a lot of small changes recently in the 10.7-10.9 coot fink dist 
 and the 10.9 stand-alone packages, so please let me know if there is any 
 weirdness.
 
 All the best,
 
 Bill
 
 
 
 
 William G. Scott
 
 http://scottlab.ucsc.edu/~wgscott
 
 --
 
 End of COOT Digest - 13 Sep 2014 to 14 Sep 2014 (#2014-117)
 ***