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NEWS
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Interface
---------
right-mouse: zoom
key +/- map level changing
"l" or Shift + left-mouse atom labelling
Tue Feb 12 17:36:37 GMT 2002
10A box radius for a 1.5A map at 0.5e/A3.
with line elimination:
---------------------
Elapsed time: 622ms
over grid Nuvw = ( 128, 144, 240) at (10.812,29.349,57.11)
done 49770 lines, rejected 39525 lines
we returned 49770 map vectors
77 in 5.008 seconds = 15.3754 FPS
without line elimination:
-------------------------
Elapsed time: 516ms
over grid Nuvw = ( 128, 144, 240) at (10.812,29.349,57.11)
done 89295 lines, rejected 0 lines
we returned 89295 map vectors
47 in 5.05 seconds = 9.30693 FPS
i.e. for about 100ms extra time spent in contouring, you get much few
lines and therefore ~60% more frames per second -> smoother graphics.
Standard test:
---------------
Using 29nov 29nov01.cit.ref.pdb, m72.compl.freer.scaled_refmac1.mtz
maybelline ~/Projects/mapview/src> ./mapview
Gdk-WARNING **: locale not supported by C library
VENDOR : NVIDIA Corporation
VERSION : 1.2
EXTENSIONS : GLX_ARB_get_proc_address GLX_ARB_multisample GLX_EXT_visual_info GLX_EXT_visual_rating GLX_EXT_import_context GLX_SGI_video_sync GLX_SGIX_swap_group GLX_SGIX_swap_barrier GLX_SGIX_fbconfig GLX_SGIX_pbuffer
coords OK button clicked
Got filename /home/paule/Projects/mapview/src/29nov/29nov01.cit.ref.pdb
handle_read_draw_molecule: handling /home/paule/Projects/mapview/src/29nov/29nov01.cit.ref.pdb
Reading coordinate file: /home/paule/Projects/mapview/src/29nov/29nov01.cit.ref.pdb
PDB file /home/paule/Projects/mapview/src/29nov/29nov01.cit.ref.pdb has been read.
Spacegroup: P 21 21 21
Cell: 67.308 71.419 122.955
4214 atoms selected.
Cryst::GetTMatrix() is good in handle_read_draw_molecule
found 7784 contacts from 4214 selected atoms.
Found 1 disulfides
graphics_info_t::n_molecules is now 1
CG /1/chainid="A"/1251/TYR/ with B-factor: 19.76 at (10.455,26.245,59.917) : 0.117704
Elapsed time for map contouring: 0ms
dataset filename: /home/paule/Projects/mapview/src/29nov/m72.compl.freer.scaled_refmac1.mtz
There are 0 datasets
Making map from columns FWT and PHWT
using mtz filename: /home/paule/Projects/mapview/src/29nov/m72.compl.freer.scaled_refmac1.mtz
reading mtz file...
Number of reflections: 78888
making map...
Grid...Nuvw = ( 128, 144, 240)
doing fft...
done fft...
0 in 40.788 seconds = 0 FPS
143 in 5.001 seconds = 28.5943 FPS
143 in 5.031 seconds = 28.4238 FPS
142 in 5.024 seconds = 28.2643 FPS
39.230u 0.450s 1:27.34 45.4% 0+0k 0+0io 1975pf+0w
Using Mesa:
I got 9-10 FPS
-----------------------------
Mon Oct 21 17:47:44 BST 2002
Synched with clipper. Fixed up the clipper macro (clipper.m4)
and the include files.
Included the create_tree_node_map() call.
----
Sun Sep 21 07:34:10 BST 2003
Things Added since April:
The Coot User Manual
mutate-and-auto-fit
add OXT atom
Run refmac
Autofit best rotamer (script to run over residue range)
Residue look-ahead on "Fit Terminal Residue"
Save Coordinates
Baton Build
Mutations
Goto Atom ... much improved
Add Atom at Pointer (optionally add SO4, etc)
Backup/Undo system
history and state system
SGI build
Residue and atom delete
Symmetry as C-alphas
Flexible ligands search
Rotamers
Pepflip
Colour map rotation for maps
Colour map rotation for coordinates
----
Tue Sep 23 13:13:52 BST 2003
Things slated for after the initial release:
o Add multiple conformer to residue
refinement to "Do the Right Thing"
o Interactively change phi psi
o Interactively change chi angles of sidechains
---
Sun Nov 30 14:20:22 GMT 2003
New graphics card on home computer (geforce 4 mx440)
standard test:
Reading coordinate file: /home/paule/Projects/mapview-0.4.51-pre-1/src/data/29nov/29nov01.cit.ref.pdb
PDB file /home/paule/Projects/mapview-0.4.51-pre-1/src/data/29nov/29nov01.cit.ref.pdb has been read.
Spacegroup: P 21 21 21
Cell: 67.308 71.419 122.955 90 90 90
Symmetry available for this molecule
have 4214 non-Hydrogen_atoms
dataset filename: /home/paule/Projects/mapview-0.4.51-pre-1/src/data/29nov/m72.compl.freer.scaled_refmac1.mtz
There are 0 datasets
Making map from columns FWT and PHWT
making map from mtz filename /home/paule/Projects/mapview-0.4.51-pre-1/src/data/29nov/m72.compl.freer.scaled_refmac1.mtz
reading mtz file...
Number of reflections: 78888
finding ASU unique map points...
Grid...Nuvw = ( 128, 144, 240)
doing fft...
done fft...
204 in 5.022 seconds = 40.6213 FPS
206 in 5.019 seconds = 41.044 FPS
203 in 5.001 seconds = 40.5919 FPS
However, a BIG minus is the apparent display bug - depth cueing doesn't work.
---
Sun Nov 30 15:27:27 GMT 2003
Now I updated the XFree stuff to Xfree86-*4.2.1-15.73.23
231 in 5.021 seconds = 46.0068 FPS
232 in 5.018 seconds = 46.2336 FPS
231 in 5.004 seconds = 46.1631 FPS
234 in 5.014 seconds = 46.6693 FPS
which is a 63% performance improvement over last week.