forked from pemsley/coot
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathdnotes
8919 lines (5545 loc) · 227 KB
/
dnotes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
------
Wed May 9 13:54:04 BST 2007
Dirk Kostewa:
overblend for electron density?
-----
trying to run render without render in path:
rendering ray trace number: 0
rendering ray trace number: 1
rendering ray trace number: 2
rendering ray trace number: 3
done raytrace.
calling render...
calling display...
((safe_scheme_command) Error in proc: key: system-error args: (execlp ~A (No such file or directory) (..... scm_catch done
scm_catch returns: 20152
2)))
..... scm_catch done
scm_catch returns: #<unspecified>
Xlib: unexpected async reply (sequence 0xb9f30)!
Xlib: unexpected async reply (sequence 0xb9f4a)!
Xlib: unexpected async reply (sequence 0xb9f4b)!
Xlib: unexpected async reply (sequence 0xba0b6)!
Xlib: unexpected async reply (sequence 0xba0f1)!
Xlib: unexpected async reply (sequence 0xba0f3)!
lt-coot-real: Fatal IO error 14 (Bad address) on X server :0.0.
Some deprecated features have been used. Set the environment
variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
program to get more information. Set it to "no" to suppress
this message.
ObjectCache: Leaked 0002 refs to <P 31 2" Nuvw = ( 240, 240, 132)>
ObjectCache: Leaked 0002 refs to <P 31 2">
47.510u 14.504s 12:56.93 7.9% 0+0k 0+0io 160pf+0w
interesting!
-----
Wed May 16 09:27:21 BST 2007
User pickable atoms:
a function that registers interest in n atom selections and a
function to call when it has them. We test in
graphics-info-defines whether such a function exists and has
all the number of picks that it needs, if it does and it
doesn't then collect them and pass them on when it has all
it needs. When the function has been called delete it from
the queue/vector of such functions (umm, better do the
deletion just before the function call so that if there is an
error in the scm function we don't jump away from the function
deletion part).
----
Thu May 17 12:44:56 BST 2007
INFO::
use gtk_widget_get_name(widget) to find out about what the
name of the widget is.
-----
Fri Jun 15 13:09:53 BST 2007
In real space refinement, don't move the atoms with zero occ.
------
INFO::
old guile convert to string:
std::string name_target = SCM_STRING_CHARS(name_target_scm);
new guile convert to string:
std::string name_target = scm_to_locale_string(name_target_scm);
all guile convert from string:
SCM mess = scm_makfrom0str(a_string.c_str());
------
Fri Jul 6 13:24:43 BST 2007
compiling guile-1.8.1
prfx=$HOME/testg
./configure --prefix=$prfx LDFLAGS=-L$prfx/lib CFLAGS="-g -I$prfx/include"
./configure --prefix=/lmb/wear/emsley/testg LDFLAGS=-L/lmb/wear/emsley/testg/lib CFLAGS='-O -I/lmb/wear/emsley/testg/include'
i.e. NO DEBUGGING!
cycle ~/compile/g/guile-gtk-2.0> ./configure --prefix=/lmb/wear/emsley/guile-1.8.1 --without-gtkgl
make
make install
-
in guile-gtk-2.0's gdk-glue.c add
#define PANGO_PIXELS_CEIL(d) (((int)(d) + 1023) >> 10)
#define PANGO_PIXELS_FLOOR(d) (((int)(d)) >> 10)
-
also need goosh:
./configure --prefix=/lmb/wear/emsley/guile-1.8.1
make install
and guile-gui:
./configure --prefix=/lmb/wear/emsley/guile-1.8.1
make install
and net-http:
./configure --prefix=/lmb/wear/emsley/guile-1.8.1
make install
----
Mon Jul 16 13:09:11 BST 2007
if the first and last non-blank characters read from the scripting
window are not ( and ) then add them. So
read-pdb "test.pdb"
will "work".
-----
Here's a description of the PIR format:
http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
----
Tue Jul 17 13:11:20 BST 2007
Files that end in .fcf or .cif should not *first* be read as
MTZ files. Do the sensible thing first.
----
Mon Jul 16 23:18:03 BST 2007
in creating a GTK2 gl context:
> WARNING:: Can't enable stereo visual - falling back
> INFO:: Hardware stereo widget opened successfully
> INFO:: switch to hardware_stereo_mode succeeded
So in gl_extras():
We need a "stereo_successful" flag set before we get to saying
"Hardware stereo widget opened successfully"
-----
Wed Jul 18 09:09:16 BST 2007
Hydrogens naming problem with shelx.
Shelx calls hydrogens attached to ILE CG2 HG2A HG2B HG2C,
whereas refmac names are HG21 HG22 HG33.
There are lots of other problems like this.
----
Sat Jul 21 10:25:29 MDT 2007
problem with libcootaneer lib dependency when building in gtk1
version.
* Don't see it any more.
-----
Wed Aug 1 19:48:19 BST 2007
How about an Env Var to specify where to read and write
startup files (state, history etc) so that you can run coot
cleanly from the Desktop.
Good idea. Bit tedious though?
-----
Wed Aug 1 22:55:35 BST 2007
Add Chiral Volume Outliers to some validation graph. Geometry?
ie. make the blocks big and blue (c.f. missing atoms)
Priority Low, but cute and maybe useful.
-----
Thu Aug 2 03:20:36 BST 2007
add a test for overlap-ligands - quite tricky.
----
Thu Aug 2 14:43:06 BST 2007
unexpanded symmetry labels have 0-indexed symm labels. It
should be 1-indexed - Steven Sheriff
-----
Thu Aug 2 14:47:07 BST 2007
How about some flexibility in file name output?
How difficult is it to create (or, maybe, How would one go about
creating a) naming system for output PDB files that is consonant
with my usage? Currently COOT gives a default of
input_file_name-coot-0.pdb. I typically name my files
model_0i.pdb for the file out of refinement (before ligand, hence
the zero -- yes I do it too ;-) ) and my first output file as
model_0o1.pdb. If I do some "editing" outside of COOT, I might
then create model_0i2.pdb and if I make some changes inside COOT,
the output file would be model_0o2.pdb, etc. After the next
cycle of refinement, I would come in with model_1i.pdb, etc.
-- Steven Sheriff
-----
Sat Aug 4 14:36:06 BST 2007
how about adding assign-pir-sequence to the state file?
Problem is we don't store raw input, just the decoded sequence.
We need both.
something should be std::pair<std::string, std::string (orig, seq)
not just std::string
Hmm... perhaps a simple class then, because we need a flag to
say that this molecule has a sequence assigned to it.
------
Fri Aug 10 12:56:36 BST 2007
add a side chain flip test.
check that the OE1 was where the OE2 was
and vica versa.
also test torsions from running correct-nomenclature
-----
Mon Aug 13 15:43:54 BST 2007
Add a test
Use multiple wiggle ligands. Delete stuff and do it again.
-----
Mon Aug 13 16:52:03 BST 2007
fit SAH into 2an3.
It's really slow to converge. Why?
-------
Mon Aug 20 18:08:16 BST 2007
Add lots of tests for the space groups of shelx .res files
using show-spacegroup
----
Sun Aug 5 00:29:27 BST 2007
Revisit the --as-needed patch from Donnie Berkholz
Try to apply (bits of) it and see what happens - problems on
feisty, I guess
---
Sun Aug 5 00:30:26 BST 2007
The X11 libs dependencies need to be revisited - I had to install
some stuff to compile - they should be tested for in configure.
Try with a gutsy pre-release?
----
Sun Aug 5 00:32:03 BST 2007
The Coot FAQ should be written as a texi (article?) document, so
that it has an index and toc.
----
Sat Aug 11 13:15:35 BST 2007
Icons
http://jimmac.musichall.cz/icons.php
Think about icons for info dialog and the like.
----
Sat Aug 11 15:51:42 BST 2007
Open Clip Art Notes:
world in connect-to-world is "cartoon globe" by lunanaut
crispy computer mouse for scroll wheel.
-----
http://www.itbusiness.ca/it/client/en/home/News.asp?id=44529&cid=11
The Novell SUSE Linux subscription model is considerably less painful,
Chevalier argues, because it doesn't hit the capital expense budget
and it can often be considered an operational expense, which is better
from a tax perspective.
--------
Tue Aug 21 14:26:00 BST 2007
Thoughts for a tutorial or some such.
"Assessing structure quality with Coot"
(in response to EJD's comments on CCP4bb 2hr0)
Structure with 0 occupancy
What is a good (bad) Ramachandran?
What is a bad Kleywegt plot?
Good (bad) geometry graph.
Chiral volume outliers
Cis-peptides, planar peptide restraints
Good density fit graph (and how to scale it)
Nomenclature errors in rotamers - and how to fix them
Missing atoms
How to use with Molprobity (web output and local exes)
B-factor variance. What's good and bad.
Priority: Low
-----
Tue Aug 21 14:44:14 BST 2007
Note to self:
B factor average, variance vs resolution for each residue type.
Probably best to have a shell script to provide the pdb files
c++ program reads pdbs and does b-factor analysis,
on completion appends to files "ARG.tab" "ASP.tab" etc
with average and variance for each residue of that type in
that pdb file. Also the resolution.
only do 1 chain of each pdb file.
use Coot libs - make it a Coot program.
Priority: Low
-------
Tue Aug 21 16:50:52 BST 2007
ionic waters:
http://biochem.wustl.edu/~enrico/
e.g. WASP
Reference: Nayal, M., & Di Cera, E. (1996) J. Mol. Biol. 256: 228-234
Nayal M and Di Cera E. Valence screening of water in protein
crystals reveals potential Na+ binding sites. J Mol Biol 256:
228–234, 1996
Looks straightforward. Except symmetry must be used to find neighbours.
GSoC project?
-----
Tue Aug 21 18:15:47 BST 2007
blender's iksolver for inverse kinemetic (loop fitting).
Source code not obviously in 2.44.
But see this
http://www.koders.com/cpp/fid45A6AC666E04B001C8A397CC9CEA3A46D801EB30.aspx?s=cdef%3aparser
Hmm.
------
Fri Aug 24 15:40:17 BST 2007
electron_density_gradient_at_point() in simple-restraint.cc used
template type double. Would things be faster with a float?
clipper::Grad_orth<double>
coot::restraints_container_t::electron_density_gradient_at_point(const clipper::Coord_orth &ao);
----
Thu Aug 30 10:15:37 BST 2007
From reading JED mail
Do some speed tests on regularizing with and without peptide plane restraints.
Interface to change the weight of the peptide plane restraint
Interface to turn on peptide plane restraints for refinement (or regularizing) only?
Allow the display of anisotropic atoms per molecule - from the
scripting layer at least.
-----
Fri Aug 31 16:28:42 BST 2007
Do a NCS ghosts for a blue map,
Do it again for the difference map.
Does it recalculate the NCS operators?
It shouldn't.
------
Tue Aug 28 14:31:25 BST 2007
And if the display manager would automatically resize itself when
more objects are loaded, would be great.
Marko Hyvönen
Department of Biochemistry
University of Cambridge
Priority: Low, Difficulty: Medium.
A thing for GSoC.
-----
Tue Aug 28 14:48:50 BST 2007
http://blog.mithis.net/
lython and SchemePy
------
From: Matthew Wilce <[email protected]>
Subject: Coot and polynucleotide
Date: Tue, 17 May 2005 10:39:44 +1000 (01:39 BST)
Functionality for both RNA and DNA
the ability to change RNA into DNA and visa versa
mutation of bases
rotamer flipping (manual and automated)
fragment library for each nucleotide
a version of baton would be useful - either base to base and/or
phosphate to phosphate
o is that still needed?
insertion of nucleotides
addition of a nucleotide at 3' or 5' end of polynucleotide
o Done?
-----
Venki Ramakrishnan:
"CA mode" for nucleic acids should draw a P and C1' trace.
-----
Write a FAQ for sucking of metal ligands into metal density.
-----
make dist runs a scsh script. configure should check for scsh?
(not easy to convert to guile)
-----
Sun Sep 16 00:33:44 BST 2007
Suggestion on the coot list in the last week:
o Better algorithm to find picked atoms (prefer atoms at the front).
* Done.
o "Reverse" chi angle fragment tail/dog
* Done.
o Cache libcheck results for faster "Get Monomer"
* Done.
-----
Sun Sep 16 01:25:09 BST 2007
texi2html ../../coot/doc/user-manual.texi
*** Undefined node of menu_entry (Dictionary): * Dictionary::
*** Undefined node of menu_entry (Planar Peptide Restraints): * Planar Peptide Restraints::
*** Undefined node of menu_entry (The <TT>UNK</TT> residue type): * The @t{UNK} residue type::
Priority: Medium: Difficulty: Low
----
Sun Sep 16 12:31:03 BST 2007
refine-zone, regularize-zone, auto-refine-zone all ignore the
alt-conf specifier. They should not.
Priority: Medium.
------
Wed Sep 19 17:20:41 BST 2007
doing a flexible ligand fit in a ligands without flexible
bonds - e.g. SO4 gives non-optimal message ("Did you forget to
read the dictionary?").
-----
Tue Sep 18 12:01:13 BST 2007
Interesting/useful?
OpenBabel:
http://openbabel.sourceforge.net/wiki/Main_Page
pygtk-openbabel - A PyGTK frontend to OpenBabel A PyGTK
frontend to OpenBabel that utilizes the power of
python. Included is a graphical frontend to PubChem
PubChem:
http://pubchem.ncbi.nlm.nih.gov/
Priority: Medium: Difficulty: Low
----
Tue Sep 18 16:12:29 BST 2007
Mischa
if pick centering on an atom fails, can you fall back to test
against having clicked on the intermediate atoms?
Indeed. Why not.
-----
Fri Sep 21 18:17:52 BST 2007
When there is a sytax error in ~/.coot, is it obvious what has
happened?
-----
RSR when map is ambiguous cancels rsr. It should not.
----
Wed Sep 26 13:12:24 BST 2007
Regularize residue A 11, 2izq
Crashes in recently touched (well, the replace type has been
changed) replace_coords()
(gdb) where
#0 molecule_class_info_t::replace_coords (this=0x87bfc7c, asc=@0x866b518, change_altconf_occs_flag=false)
at ../../coot/src/molecule-class-info.cc:4564
#1 0x080c4a9f in graphics_info_t::accept_moving_atoms (this=0xbf8b8463) at ../../coot/src/graphics-info.cc:1364
#2 0x0815d612 in accept_regularizement () at ../../coot/src/c-interface-build.cc:5093
#3 0x08218ae2 in on_accept_reject_refinement_accept_button_clicked (button=0x90a88e8, user_data=0x0)
at ../../coot/src/callbacks.c:2283
#4 0xb6e009d9 in g_cclosure_marshal_VOID__VOID () from /usr/lib/libgobject-2.0.so.0
#5 0xb6df362b in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#6 0xb6e04103 in ?? () from /usr/lib/libgobject-2.0.so.0
----
Wed Sep 26 14:52:14 BST 2007
read junk*.pdb in order (starting at junk.pdb) and it crashes on junk2.
note that model 0 is not a valid model.
-------
A168 on 1A0F fails to properly find the right rotamer, even
though we select the rotamer by hand and do rigid body refine
it works fine.
Bug?
-------
Residue 13 of 1UBQ fails to Rigid body refine after chi1 was
rotated by 180.
Bug?
In fact, it looks like nothing with Rigid body refine. Hmmm!
------
What about interactions with PISA?
* Scheduled for 0.6.
------
Peter's talk:
need to set the ccp4 project from the start script.
- Done. Needs testing. Also, the correct ccp4 project should
selected on creation of file-selection. This may be a bit harder.
-----
Frank:
add test peptide flips cf a database
This is quite important.
-----
Sat Sep 29 20:04:56 BST 2007
Also, when I reverse direction of a chain, if I use Reverse
Direction followed by Ca Zone-> Mainchain, a few CAs will remain
without a chain. If I delete the preexisting residues and try to
Rotate/Translate them myself they are automatically reversed back
to their original direction once I try to Regularize Zone. Is
there a reason for this or a way to overwrite or go around this?
----
Thu Sep 27 09:27:26 BST 2007
Ramachandran plot from atom selection (no need for a gui for
this just yet).
---
Thu Sep 27 09:30:20 BST 2007
John Berrisford complains about OXT refinement.
Make sure Coot properly refines OXT at some stage (by
correctly handling modifications).
-----
Tue Oct 2 09:05:25 BST 2007
A must-do for 1.0:
*****
Put backrub into minimizer for auto-fit-rotamer - as an
alternative.
*****
----
Wed Oct 3 12:23:09 BST 2007
NCS Ligands
Make the NCS ghost matrices available at the scripting layer
(let ((rtop ((get-ncs-matrix imol "A" "B"))))
;; now apply rtop to the ligand "C" in the "A" pocket to
;; make "D" in the "B" pocket
----
Wed Oct 3 18:59:34 BST 2007
write a triv app with latest glade with icons and libglade
----
Sat Oct 6 08:04:36 BST 2007
pkg-config libglade-2.0 --cflags
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12
pkg-config libglade-2.0 --libs
-lglade-2.0 -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lm -lpangocairo-1.0 -lfontconfig -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXfixes -lpango-1.0 -lcairo -lX11 -lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0
----
Tue Oct 9 22:19:02 BST 2007
GSOC project?
nice graphic output of SSM results.
hari jayaram <[email protected]>
-----
Thu Oct 11 23:20:47 BST 2007
convert axes.scm to axes.py for Paolo.
----
Mon Oct 29 09:36:34 GMT 2007
Clemens:
Add function that does
copy_residue_range_from_ncs_master_to_others(int imol, const char *master_chain_id,
int residue_range_start, int residue_range_end)
but to a specific chain only:
i.e.:
copy_residue_range_from_ncs_master_to_chain(int imol, const char *target_chain_id,
int residue_range_start, int residue_range_end)
which looks up the master_chain_id from the ghost of the target_chain_id
------
I would like to report a bug in the 0.4 pre-release. In the clash
panel generated by probe, the vertical bar doesn't work anymore.
Could you fix it?n
Jianghai
------
I don't need anything, but it said I should send this to you.
Thanks,
Adam Okerlund
----------------------------------------------
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `/usr/local/coot/bin/coot-real'.
Program terminated with signal 11, Segmentation fault.
#0 0x081acbad in lookup_widget (widget=0x33203a66,
widget_name=0x84a151c "geometry_distance_togglebutton") at support.c:33
in support.c
#0 0x081acbad in lookup_widget (widget=0x33203a66,
widget_name=0x84a151c "geometry_distance_togglebutton") at support.c:33
#1 0x080d31ec in graphics_info_t::unset_geometry_dialog_distance_togglebutton
(this=0xffc0e7cb) at graphics-info.cc:5328
#2 0x0811fdda in graphics_info_t::check_if_in_geometry_range_defines (
this=0xffc0e7cb, event=0x8662118) at graphics-info-defines.cc:393
#3 0x081232c6 in graphics_info_t::check_if_in_range_defines (this=0xffc0e7cb,
event=0x8662118, state=@0xffc0e7bc) at graphics-info-defines.cc:201
#4 0x081aab02 in glarea_button_press (widget=0xab91428, event=0x8662118)
at globjects.cc:3344
#5 0x55f24f64 in gtk_marshal_BOOL__POINTER (object=0xab91428,
func=0x81aa812 ,
func_data=0x0, args=0xffc0e938) at gtkmarshal.c:28
#6 0x55f594d2 in gtk_handlers_run (handlers=0xc4cc200, signal=0xffc0e8b8,
object=0xab91428, params=0xffc0e938, after=0) at gtksignal.c:1917
#7 0x55f5bba3 in gtk_signal_real_emit (object=) at gtksignal.c:1477
#8 0x55f5c1e8 in gtk_signal_emit (object=) at gtksignal.c:552
#9 0x55f975a1 in gtk_widget_event (widget=0xab91428, event=0x8662118)
at gtkwidget.c:2864
#10 0x55f230b8 in gtk_propagate_event (widget=0xab91428, event=0x8662118)
at gtkmain.c:1378
#11 0x55f241ee in gtk_main_do_event (event=0x8662118) at gtkmain.c:803
#12 0x55fdf71b in gdk_event_dispatch (source_data=0x0,
current_time=0xffc0ed50, user_data=0x0) at gdkevents.c:2139
#13 0x56012bc9 in g_main_dispatch (dispatch_time=0xffc0ed50) at gmain.c:656
#14 0x5601345d in g_main_iterate (block=) at gmain.c:877
#15 0x5601365f in g_main_run (loop=0x8a054e0) at gmain.c:935
#16 0x55f2463f in gtk_main () at gtkmain.c:524
#17 0x080d233b in c_inner_main (closure=0x0, argc=1, argv=0xffc0f144)
at c-inner-main.c:217
#18 0x556258c0 in invoke_main_func () from /usr/local/coot/lib/libguile.so.12
#19 0x5562586d in scm_boot_guile_1 () from /usr/local/coot/lib/libguile.so.12
#20 0x5562556c in scm_boot_guile () from /usr/local/coot/lib/libguile.so.12
#21 0x080d2018 in c_wrapper_scm_boot_guile (argc=1, argv=0xffc0f144)
at c-inner-main.c:237
#22 0x080cd46e in main (argc=) at main.cc:402
Current language: auto; currently c
-----
Fri Oct 19 21:46:34 BST 2007
Message from EJD.
Check that the skeleton colour works correctly.
-----
Thu Oct 25 11:09:07 EDT 2007
reading in a minimal state file:
Bad view quaternion
----
Thu Oct 25 18:23:31 BST 2007
Can we fit the helix at residue 122 in the CSHL Au Lysozyme
dataset?
-----
Tue Oct 30 15:24:25 GMT 2007
crash from EJD, not much to report:
#4 0x089626e6 in gtk_canvas_re_unrealize (item=0x1b5ad798) at gtk-canvas-rect-ellipse.c:598
#5 0x0895a74d in gtk_canvas_group_unrealize (item=0x1a68e428) at gtk-canvas.c:1796
#6 0x0895bb39 in gtk_canvas_unrealize (widget=0x1b330028) at gtk-canvas.c:2568
validation graph open, then molecule closed?
validation graph open, and graph is updated? residue deleted?
residue generated (add terminal residue) then graph is asked to be
updated?
----
Tue Oct 30 15:49:12 GMT 2007
On starting up coot, if imol_refinement_map() is undefined, then
set insensitive the map fitting functions (e.g. refine zone,
autofit rotamer).
When it is set, we can activate those buttons (and menu items?).
----
Tue Oct 30 15:52:39 GMT 2007
CSHL CRASH:
on calculating a skeleton after deleting a map (and skeleton) and
reading in a new map.
----
Tue Oct 30 15:53:49 GMT 2007
Remove probability limit when using Richardson Rotamers.
* Done.
----
Tue Oct 30 15:54:27 GMT 2007
Editing chi angles on a reduced pdb file failed to rotate the
hydrogens (maybe a dictionary/version 3.0 problem).
Also (set-find-hydrogen-torsions 1) fails. Same cause?
---
Mon Nov 5 11:49:30 GMT 2007
Maria Solà Vilarrubias:
I want to display ILE, LEU, VAL residues with just sidechains (in a
different colour), the rest with Mainchain CAs.
----
Tue Nov 13 23:30:57 GMT 2007
what is read_number in cif reading for.
try to get rid of it.
examine read_number_in usage here:
coot::protein_geometry::init_refmac_mon_lib(std::string ciffilename, int read_number_in)
----
Tue Nov 13 23:42:21 GMT 2007
coot --recover
reads history file (history file needs to be written when commands
executed - not at exit time) to get maps.
reads most recent saved files in coot-backup.
recover those written < 5 mins ago (or some such).
----
Tue Nov 13 23:30:57 GMT 2007
Gregory C. Benison NMR program:
http://oregonstate.edu/~benisong/software/burrow-owl/
now at
http://sourceforge.net/projects/burrow-owl
-----
Fri Nov 16 20:23:19 GMT 2007
How do I change my residue to have insertion code and the following
residues to have -1 offset and it all to be joined up?
e.g.:
(change-residue-number 0 "C" 86 "" 85 "A")
Which is fine, execpt I can't then move C/85A to the A chain.
----
Sat Nov 17 12:14:46 GMT 2007
phosphorylate-active-residue:
what about phospholysine?
----
Sun Nov 18 16:47:57 GMT 2007
update Map Transformation example in user-manual
-----
Thu Nov 22 16:28:41 GMT 2007
EJD crash:
#0 0x0844eb3a in molecule_class_info_t::intelligent_this_residue_mmdb_atom ()
#1 0x0834be67 in graphics_info_t::on_go_to_atom_residue_tree_selection_changed_gtk1 ()
#2 0x0837f6c8 in on_go_to_atom_atom_list_selection_changed_gtk1 ()
#3 0x089d2c26 in gtk_marshal_NONE__POINTER_INT_INT ()
#4 0x08a0605b in gtk_handlers_run ()
#5 0x08a0520b in gtk_signal_real_emit ()
#6 0x08a02b07 in gtk_signal_emit ()
#7 0x089d2a80 in gtk_marshal_NONE ()
#8 0x08a05118 in gtk_signal_real_emit ()
#9 0x08a02b07 in gtk_signal_emit ()
#10 0x08a2dba0 in gtk_tree_select_item ()
#11 0x08a2c571 in gtk_tree_button_release ()
#12 0x0c520378 in ?? ()
#13 0x00000000 in ?? ()
------
texi2html ../../coot/doc/user-manual.texi
*** Undefined node of menu_entry (Dictionary): * Dictionary::
*** Undefined node of menu_entry (Planar Peptide Restraints): * Planar Peptide Restraints::
*** Undefined node of menu_entry (The <TT>UNK</TT> residue type): * The @t{UNK} residue type::