Imported Upstream version 0.7pre1+svn3470

parents
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Paul Emsley
Kevin Cowtan
Bernhard Lohkamp
Additional code:
[mgtree] from Stuart McNicholas
[isosurface] Raghavendra Chandrashekara
Paul Bourke and Cory Gene Bloyd
[font and trackball] Silicon Graphics, Inc.
[comap dir] Free Software Foundation, Inc.
Additional data:
[Ramachandran data] in rama-data the tables are from the
Richardson's group in Duke University.
Reading Non-CCP4 maps cause a crash.
Refining, Regularizing and Geometry validation with insertion codes
often crash.
----
I got this confusing message:
g++ -DHAVE_CONFIG_H -I. -I../../coot/src -I.. -I../../coot/compat -I../../coot/ccp4mg-utils -I../../coot/coot-utils -I../../coot/intl -I../../coot/mmtz-extras -I../../coot/coords -I../../coot/skeleton -I../../coot/angles -I../../coot/atom-utils -I../../coot/db-main -I../../coot/mini-mol -I../../coot/ligand -I../../coot/sequence-view -I../../coot/geometry -I../../coot/ideal -I../../coot/coot-surface -I../../coot/surface -I../../coot/density-contour -I../../coot/build -I../../coot/high-res -I../../coot/analysis -DHAVE_SSMLIB -I/h/paule/mapview/include -I/h/paule/mapview/include -I/h/paule/mapview/src -I/y/people/emsley/coot/Linux/include -I/h/paule/mapview/mccp4 -I/h/paule/mapview/fftw/include -I/h/paule/mapview/boost -I/h/paule/mapview/include -I/y/people/emsley/coot/Linux/include -DHAVE_GTK_CANVAS -I/h/paule/build/include -I/usr/include/gtk-1.2 -I/usr/include/glib-1.2 -I/usr/lib/glib/include -I/usr/X11R6/include -I/h/paule/build/include -DPKGDATADIR='"/y/people/emsley/coot/Linux/share/coot"' -DDATADIR='"/y/people/emsley/coot/Linux/share"' -DUSE_GUILE -I/h/paule/build/include -g -O -c -o graphics-info-graphs.o `test -f '../../coot/src/graphics-info-graphs.cc' || echo '../../coot/src/'`../../coot/src/graphics-info-graphs.cc
../../coot/src/graphics-info-graphs.cc:749: `geometry_graph_block_info_generic'
undeclared in namespace `coot'
../../coot/src/graphics-info-graphs.cc:750: template argument 1 is invalid
../../coot/src/graphics-info-graphs.cc:750: template argument 2 is invalid
../../coot/src/graphics-info-graphs.cc:752: ISO C++ forbids declaration of `
density_fit_from_residues' with no type
../../coot/src/graphics-info-graphs.cc:752: no `int
graphics_info_t::density_fit_from_residues(CResidue**, int, int, int) const'
member function declared in class `graphics_info_t'
../../coot/src/graphics-info-graphs.cc: In member function `int
graphics_info_t::density_fit_from_residues(CResidue**, int, int, int)
const':
../../coot/src/graphics-info-graphs.cc:754: `geometry_graph_block_info_generic'
undeclared in namespace `coot'
../../coot/src/graphics-info-graphs.cc:754: template argument 1 is invalid
../../coot/src/graphics-info-graphs.cc:754: template argument 2 is invalid
../../coot/src/graphics-info-graphs.cc:754: ISO C++ forbids declaration of `v'
with no type
../../coot/src/graphics-info-graphs.cc:793: `geometry_graph_block_info_generic'
undeclared in namespace `coot'
make[2]: *** [graphics-info-graphs.o] Error 1
but it worked fine on Paris and svn was up to date.
Why was it happening?
Because coot on bubbles strangely did not have GSL
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# Makefile.am
#
# Copyright 2001, 2002, 2003, 2004, 2005, 2006, 2007 The University of York
# Author: Paul Emsley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
## Process this file with automake to produce Makefile.in
# Tell autoreconf where to find macros
ACLOCAL_AMFLAGS=-I macros
# see configure.in for po intl
#
# coot-utils depends on mini-mol.
# geometry depends on utils
#
SUBDIRS = auxil scheme python macros compat utils protein_db geometry mini-mol \
coot-utils surface coot-surface lidia-core \
coords angles skeleton ccp4mg-utils density-contour \
db-main ideal ligand high-res build greg-tests python-tests \
analysis tw lbg cootaneer src data rama-data doc
# po, no po today.
cootrc: $(top_srcdir)/cootrc.template
$(MAKE_COOTRC_CMD) $(top_srcdir)/cootrc.template > $@
EXTRA_DIST = \
autogen.sh \
make-scheme-tar \
mapview.glade \
cootrc.template \
standard-residues.pdb \
BUGS \
depcomp \
libtool \
config.sub \
config.guess \
install-sh \
missing \
TODO \
count-loc \
syminfo.lib \
colours.def \
function-notes \
my.supp \
guile.supp \
make-patches \
windows/syminfo.lib \
fix-cif-loops.awk \
ifdef-for-create-aboutdialog.awk \
mtrix-to-ncs-matrix.awk \
theor-helix-70.pdb \
RELEASE-NOTES \
copyright-disclaimer.txt \
intltool-extract.in \
intltool-merge.in \
intltool-update.in
install-data-local:
@$(NORMAL_INSTALL)
if test -d $(srcdir)/pixmaps; then \
$(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/pixmaps; \
for pixmap in $(srcdir)/pixmaps/*; do \
if test -f $$pixmap; then \
$(INSTALL_DATA) $$pixmap $(DESTDIR)$(pkgdatadir)/pixmaps; \
fi \
done \
fi
if test -z "$(COOT_WINDOWS_CFLAGS)" ; then \
$(INSTALL_DATA) $(srcdir)/syminfo.lib $(DESTDIR)$(pkgdatadir); \
else \
$(INSTALL_DATA) $(srcdir)/windows/syminfo.lib $(DESTDIR)$(pkgdatadir); \
fi
dist-hook:
if test -d $(srcdir)/pixmaps; then \
mkdir $(distdir)/pixmaps; \
for pixmap in $(srcdir)/pixmaps/*; do \
if test -f $$pixmap; then \
cp -p $$pixmap $(distdir)/pixmaps; \
fi \
done \
fi
subpkgdatadir = $(pkgdatadir)
subpkgdata_DATA = cootrc standard-residues.pdb colours.def \
mtrix-to-ncs-matrix.awk theor-helix-70.pdb
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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.