MakeTNT-toolkit User Documentation To MakeTNT-manual
MakeTNT Evaluation

MakeTNT Test Runs

Evaluation :  Generation of TNT-Restraints by MakeTNT

No. Comp. Restraint Type Restraint Source Successful Conversion Conversion Failed Reason for Failure Remarks
49967 XPLOR_CORINA NCI open source database (249071 3D structures) / Corina [1] 49967 - - -
2426 REFMAC Refmac standard library [2] 2426 - - -
3289 XPLOR_XPLO2D NCI open source database / xplo2d  [3] 3288 1 input: 2 molecules [4]
1000 REFMAC (written by Corina) NCI open source database / Corina [5] 1000 - - -
[1] From the first 50000 compounds of the NCI open source database, 49967 structures with 3D coordinates have been selected. 10 of the structures have kindly been provided by Dr. Armin Ruf, Roche, Basel. XPLOR-type *.top and *.par files have been obtained from Corina.
[2] All 2457 cif monomer descriptions (ccp4-4.2.2) have been run through Libcheck, Vers 4.0.1. 2426 lib-files could be obtained. For 31 files Libcheck failed.
[3] From the first 20000 compounds of the NCI open source database, 3289 compounds have been selected if they had 3D coordinates and fulfilled at least one of the following criteria: > 1 4-atom ring, > 2 5-atom rings, > 2 6-atom rings, > 4 (4-6)-atom rings.
[4] Compounds including metal atoms can cause trouble, as metal coordination is treated as a covalent bond by xplo2d, which increases the number of ring systems to be processed by MakeTNT. In order to cope with this problem, MakeTNT has been configured to process generous numbers of ring systems. In case of problems, please make sure, that the metal coordination listed in the *.top files generated by xplo2d is correct. If it still does not work, let us know.
[5] The test was run on Refmac-dictionaries generated by Corina for the first 1000 coordinates of the NCI-dataset.

Evaluation :  Small Molecule Refinements Using Corina-Derived Restraints Converted to TNT-Format by MakeTNT

Each cell in the table below represents one optimisation run, using the TNT-GEOM module without X-ray terms and a fast optimization routine kindly provided by Dr. Oliver Smart, Globalphasing. Corina generated coordinates have been randomized to a RMS deviations of 0.25, 0.5 and 1.0 Ångstrøms and optimized with TNT-dictionaries, sizes s, m and l. Different coordinates have been generated for each run. Each resulting structure has been manually inspected for integrity. Optimizations producing apparent errors in the geometry have been marked in red. The results indicate that:

compound
number of atoms
structure optimisation: jiggle[Å]/Size of MakeTNT-Restraint file
no. refinement cycles/successful?
0.25/s 0.25/m 0.25/l 0.5/s 0.5/m 0.5/l 1.0/s 1.0/m 1.0/l
NCI124652/28 126
yes[a]
57
yes[a]
74
yes[a]
49
yes[a]
45
yes[a]
167
yes[a]
73
yes[a]
108
yes[a]
55
no
NIST04051410392D/10 16
yes
36
yes
17
yes
17
yes
81
yes
14
yes
36
yes
32
yes
29
yes
NCI16498/25 13
yes
16
yes
184
yes
17
yes
25
yes
86
yes
60
yes
88
yes
114
yes
NCI367798/48 116
yes
231
yes
494
yes
284
yes
219
yes
>2001
no
98
yes
416
no
415
no
NCI376722/29 26
yes[a]
21
yes[a]
144
yes[a]
18
yes[a]
26
yes[a]
62
yes[a]
158
yes[a]
205
yes[a]
415
no
NCI46/20 46
yes
21
yes
21
yes
59
yes
117
yes
215
yes
72
yes
136
yes
243
yes
NCI56940/28 21
yes
134
yes
173
yes
21
yes
74
yes
173
yes
73
yes
258
yes
115
yes
NCI628503/58 147
yes
127
yes
140
yes
190
yes
151
yes
396
no
238
yes
223
no
624
no
NCI631303/29 21
yes
46
yes
88
yes
199
yes
25
yes
189
no
35
yes
131
yes
303
no
NCI640266/26 61
yes
72
yes
157
yes
31
yes
75
yes
125
yes
112
yes
127
yes
266
yes

[a]: structure of good quality, except for positioning of metal ions(e.g. Cu, Co), where currently no parameters for non-bonded interactions are available in Buster/TNT

 

Evaluation :  Small Molecule Refinements Using Refmac-Derived Restraints Converted to TNT-Format by MakeTNT

Each cell in the table below represents one optimisation run, using the TNT-GEOM module as described in the previous section. 10 structures have been chosen from the Refmac (ccp4-5.0.2) standard library. Starting coordinates and library description files have been obtained by Libcheck (Vers 4.1.3). The coordinates have been randomized to RMS deviations of 0.25, 0.5 and 1.0 Ångstrøms and optimized with TNT-dictionaries, sizes s and l. Different coordinates have been generated for each run. Each resulting structure has been manually inspected for integrity. Optimizations producing apparent errors in the geometry have been marked in red. We observed that:

compound
number of atoms
structure optimisation: jiggle [Å] / Size of MakeTNT-Restraint file
no. refinement cycles / successful?
0.25/s 0.25/l 0.5/s 0.5/l 1.0/s 1.0/l
AQS
28
16
yes
13
yes
30
yes
40
yes
30
yes
46
yes
BRL
25
28
yes
55
yes
36
yes
34
yes
45
yes
36
yes
DPS
36
55
yes
93
yes
24
yes
106
yes
100
yes
291
yes
EST
20
36
yes
24
yes
53
yes
29
yes
90
no
86
yes
GR3
39
73
no
96
no
73
no
294
no
169
no
529
no
MTB
22
no
atom labels in Refmac input (e.g.: 'C5'')
currently not recognized by TNT
NEV
20
80
yes
34
yes
102
yes
71
yes
106
yes
29
yes
TMF
33
40
yes
105
yes
72
no
56
yes
99
yes
136
no
TXL
58
225
yes
257
yes
206
yes
155
no
395
yes
273
no
ZYA
28
56
yes
22
yes
95
yes
44
yes
61
yes
71
yes

Maria Brandl,<buster-develop@GlobalPhasing.com>
Last modification: 13.12.05