Hi Paul,
I am referring to the map contour levels that are located in the top right hand
side of the display window and that can be scrolled with the mouse wheel. In
our CentOS 7 installation these levels are not displayed with any map generated
by coot from mtz files that we have tested. We can reproduce this with
following example files
https://edmaps.rcsb.org/coefficients/7l3c.mtz
https://files.rcsb.org/download/7L3C.pdb
I have copied the associated saved state file below.
Are there any further files that would help to understand /debug this?
Best wishes,
Simon
; These commands are the saved state of coot. You can evaluate them
; using "Calculate->Run Script...".
;;molecule-info: 7l3c.pdb
;;molecule-info: 7l3c_phases.mtz FWT PHWT
;;molecule-info: 7l3c_phases.mtz DELFWT PHDELWT
(set-graphics-window-size 1110 786)
(set-graphics-window-position 2515 80)
(vt-surface 2)
(set-clipping-front 0.00)
(set-clipping-back 0.00)
(set-map-radius 16.00)
(set-iso-level-increment 0.0500)
(set-diff-map-iso-level-increment 0.0050)
(set-colour-map-rotation-on-read-pdb 21.00)
(set-colour-map-rotation-on-read-pdb-flag 1)
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)
(set-swap-difference-map-colours 0)
(set-background-colour 0.00 0.00 0.00)
(set-symmetry-size 13.00)
(set-symmetry-colour-merge 0.50)
(set-symmetry-colour 0.10 0.20 0.80)
(set-symmetry-atom-labels-expanded 0)
(set-active-map-drag-flag 1)
(set-show-aniso 0)
(set-aniso-probability 50.00)
(set-smooth-scroll-steps 40)
(set-smooth-scroll-limit 10.00)
(set-font-size 2)
(set-rotation-centre-size 0.10)
(set-do-anti-aliasing 1)
(set-default-bond-thickness 5)
(set-map-sampling-rate 1.80)
(handle-read-draw-molecule "Downloads/7l3c.pdb")
(set-molecule-bonds-colour-map-rotation 0 21.00)
(set-draw-hydrogens 0 1)
(make-and-draw-map "Downloads/7l3c_phases.mtz" "FWT" "PHWT" "" 0 0)
(set-solid-density-surface-opacity 1 0.50)
(set-last-map-colour 0.20 0.38 0.70)
(set-last-map-contour-level 5.444917e-01)
(set-last-map-sigma-step 0.10)
(make-and-draw-map "Downloads/7l3c_phases.mtz" "DELFWT" "PHDELWT" "" 0 1)
(set-solid-density-surface-opacity 2 0.50)
(set-last-map-colour 0.20 0.60 0.20)
(set-last-map-contour-level 3.00e-01)
(set-last-map-sigma-step 0.10)
(set-scroll-wheel-map 1)
(set-matrix 60.00)
(set-show-symmetry-master 0)
(set-go-to-atom-molecule 0)
(scale-zoom 1.00)
(set-rotation-centre 26.17 -11.52 9.71)
(set-view-quaternion 0.40689 0.48495 0.04784 0.77264)
From: Mailing list for users of COOT Crystallographic Software
On Behalf Of Paul Emsley
Sent: Tuesday, 26 October 2021 16:43
To: COOT@JISCMAIL.AC.UK
Subject: Re: 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 installation, contour levels are displayed.
Does anyone have the same issue and any tips how to fix this?
I am afraid that I can't help. I don't recognise the problem and can't
reproduce it (not that I tried hard, I am a bit busy with other things).
It would help if you made it apparent how to reproduce the problem.
Paul.
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
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 list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
