ReliaSolve Molprobity2 issues

ReliaSolve / Molprobity2

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Complete unit tests for Reduce2

#177 russell-taylor closed 1 year ago
1
Fix the placed-hydrogen distance behavior

#176 russell-taylor closed 2 years ago
1
Consider augmenting the mainchain selection in CCTBX to include bonded hydrogens

#175 russell-taylor opened 2 years ago
0
Reduce2 input file telling what flips to make and which way to make them

#174 russell-taylor closed 1 year ago
3
Write a final report on the supplement and the additional work that is happening to finalize everything

#173 russell-taylor closed 2 years ago
1
Send Jane a list of what small snippets we would need to test each of the Movers and Probe

#172 russell-taylor closed 1 year ago
3
Behavior of polar and non-polar Hydrogen addition checks.

#171 russell-taylor opened 2 years ago
0
Behavior of polar and non-polar Hydrogen addition checks

#170 russell-taylor opened 3 years ago
0
Check both orientations and lock the non-Nitrogen atom towards a +ion of there is one near either atom.

#169 russell-taylor opened 3 years ago
0
Add a debugging feature in Probe to keep the phantom hydrogen markers for those that end up actually making contacts

#168 russell-taylor opened 3 years ago
0
Add a description of the 4 not working unless there is a hydrogen (based on the other parameter) and clarify in -4H

#167 russell-taylor closed 3 years ago
1
Make Histidine behave like it used to, checking double deprotenation with a -1 bias

#166 russell-taylor closed 3 years ago
1
Running reduce2 on 4fen.pdb has errors during optimization.

#165 russell-taylor closed 2 years ago
2
Reduce on neutron structures with some known hydrogens

#164 russell-taylor opened 3 years ago
1
Regression-test Reduce2

#163 russell-taylor closed 1 year ago
3
Implement Reduce2

#162 russell-taylor closed 1 year ago
15
Update the metallic/ionic nomenclature to get things correct

#161 russell-taylor closed 3 years ago
3
Compare hydrogen placement between old and new probe

#160 russell-taylor closed 1 year ago
2
Oxygens in waters as acceptors

#159 russell-taylor closed 3 years ago
1
SuiteName Python 2.7 regression tests fail to run

#158 russell-taylor opened 3 years ago
6
Different numbers of suites for 3cma in -report format

#157 russell-taylor closed 3 years ago
1
Error computing suiteness on 4qln for any output type

#156 russell-taylor closed 3 years ago
8
Differences in 6hhq

#155 russell-taylor closed 3 years ago
1
Move covalent and ionic tests for Movers inside Reduce

#154 russell-taylor opened 3 years ago
0
Verify that current Reduce only removes both Histidine Hydrogens for two ionic bonds

#153 russell-taylor closed 3 years ago
1
Metallic atoms in Probe and Reduce have incorrect radii

#152 russell-taylor closed 3 years ago
5
Report incorrect DT C7 radius to CCTBX

#151 russell-taylor closed 3 years ago
4
Run SuiteName against the PDB and compare suiteness

#150 russell-taylor opened 3 years ago
19
Updates to how SuiteName handles 1-letter codes for Thymine and Y

#149 russell-taylor closed 3 years ago
0
Spell arsenic correctly in ElementInfo.cpp and the new Reduce (and Probe)

#148 russell-taylor closed 3 years ago
1
Think about how to handle the coming 4-letter residue names in input files for Probe, Reduce, SuiteName

#147 russell-taylor opened 3 years ago
0
Avoiding 'Sorry' messages and continuing to parse the files

#146 russell-taylor closed 3 years ago
1
Enable the user to specify restraints (ligand) files for Probe and Reduce

#145 russell-taylor closed 1 year ago
1
Add command-line argument so that probe and reduce can be stricter for Phenix case

#144 russell-taylor closed 1 year ago
1
Reduce/CCTBX: Consider keeping unexpected hydrogens

#143 russell-taylor closed 1 year ago
0
Make a dihedral calculator that bases things on atom names within a residue

#142 russell-taylor closed 3 years ago
3
PDB + CCTBX/SuiteName avoiding Dangle

#141 russell-taylor closed 3 years ago
3
Suiteness should be highest closest to the center and zero at the edge; verify this

#140 russell-taylor closed 3 years ago
1
Bring up what happened to some of dihedral angles in the PDB files with Christopher

#139 russell-taylor closed 3 years ago
1
Find the heavy-atom tables in CCTBX and see whether their X-ray and nuclear distances matches Probe

#138 russell-taylor closed 3 years ago
1
Check on the number of point ID fields in your test cases; some seem to have 6 and others 7

#137 russell-taylor closed 3 years ago
2
1Q9A needs to be parsed to see if SuiteName is able to handle alternate conformations

#136 russell-taylor closed 3 years ago
1
Consider selecting only the standard bases in protein and RNA and then doing restraints only on that subset

#135 russell-taylor closed 3 years ago
3
Rename neutron to nuclear

#134 russell-taylor closed 3 years ago
1
SuiteName must run on all PDB entries

#133 russell-taylor closed 3 years ago
4
Learn to produce the "RNA backbone" number on the PDB page for a molecule

#132 russell-taylor closed 3 years ago
4
Load 4rby.pdb to see if I can load it into my CCTBX programs; let Ken know

#131 russell-taylor closed 3 years ago
1
Consider including CH..O bond-scale factor

#130 russell-taylor opened 3 years ago
2
Determine what radius to use for C=O (carbonyl) atoms

#129 russell-taylor closed 3 years ago
4
Find out how to determine which atoms are mainchain (including hydrogens)

#128 russell-taylor closed 3 years ago
0