| DATE OF BUG REPORT | BUG EXPLANATION | QUERY TYPE | STATUS | FIXED AT |
|---|---|---|---|---|
| Aug. 24, 2023 | It seems like almost all metals in all pdb files now give very poor scores, 6 or lower, even ones that performed much better a week ago. Dear User, Thank you for providing your feedback. In comparing metal ions, an approximate ranking can be established by considering the metal in the position of the current one. This comparison involves three parameters that may vary: Atomic contacts Valence Geometry Each of these parameters contributes a maximum of 2 points, resulting in a total potential score of 6 in the current version. In previous versions, the remaining parameters were remaining constant. E.g. Parameters such as B-factor (env) are not taken into consideration due to the requirement of approximately 3 cycles of refinement for each metal ion to attain accurate results. Such process would demand a significant amount of time. We can implement choosing scooring approach (old/new) in upcoming ~2 weeks. Best regards, Minor Lab | bug | Partially fixed | Aug. 26, 2023 |
| May 24, 2023 | cmm soes not draw distances to sulfurs | bug | Fixed | Aug. 24, 2023 |
| May 20, 2023 | 3wax doe snot work | bug | Not fixed | None |
| April 13, 2023 | fix pymol_select line 94 | bug | Not fixed | None |
| Feb. 7, 2023 | In the pdb 1IHH, the platinum center is correctly assigned having the oxidation state (II) and a square planar geometry. However the geometry field is highlighted in yellow, which I do not understand. See also (4) Kuppuraj G, Dudev M, Lim C (2009) J. Phys. Chem. B, 113, 2952-2960. Thanks for checking! Best regards Bernhard | bug | Fixed | Aug. 22, 2023 |
| Jan. 26, 2023 | Distances when using cif file are not shown | bug | Not fixed | None |
| Nov. 21, 2022 | 8EW4 shows wrong diff map | bug | Not fixed | None |
| Nov. 18, 2022 | Zn square plannar is now in both version as dubious | suggestion | Fixed | Nov. 18, 2022 |
| Nov. 15, 2022 | Install pymol module in django version | bug | Fixed | Nov. 18, 2022 |
| Nov. 4, 2022 | precalculated dirs should be deleted if there is modification to display fresh ones | suggestion | Not implemented | None |
| Nov. 3, 2022 | 1a2p contact.pdb file is not generetaed (listsite route) | bug | Fixed | Nov. 3, 2022 |
| Oct. 24, 2022 | add diffrences during ref to Fe(III) and Fe(II) | bug | Not fixed | None |
| Oct. 17, 2022 | /home/michal_g/Documents/cmm/fix1/pdb.cif does not work | bug | Not fixed | None |
| Oct. 17, 2022 | if DELFWT PHDELWT and FOFCWT PHFOFCWT do it in pairs not mix | bug | Not fixed | None |
| Oct. 17, 2022 | write new faster neighborhood | bug | Not fixed | None |
| Oct. 14, 2022 | 7LVK don't work | bug | Not fixed | None |
| Oct. 13, 2022 | Change acceptable (upload) to automatically used | suggestion | Not implemented | None |
| Sept. 30, 2022 | Update REFMAC version, please. | suggestion | Not implemented | None |
| Sept. 27, 2022 | 4ab2 dows not work | bug | Not fixed | None |
| Sept. 23, 2022 | 1ppx in cif format does not work (NH does not work) | bug | Not fixed | None |
| Sept. 23, 2022 | test 1ppx on cif if correct distances | question | Not fixed | None |
| Sept. 22, 2022 | Refine pipline should have option to refine with anomalous signal | suggestion | Not implemented | None |
| Sept. 22, 2022 | Brief description of CMM parameters, change ligand to atomic contacts | bug | Fixed | Sept. 23, 2022 |
| Sept. 22, 2022 | Do description that right now mtz can produce maps | suggestion | Implemented | Sept. 22, 2022 |
| Sept. 22, 2022 | Maps are now generated from mtz. Uploading mtz file is now enough to generate maps. | suggestion | Implemented | Sept. 22, 2022 |
| Sept. 22, 2022 | 2fna shows two sites at once | bug | Fixed | Sept. 23, 2022 |
| Sept. 22, 2022 | Inform that after substitution withour ref maps are old and b fact also | suggestion | Not implemented | None |
| Sept. 21, 2022 | CHnge acceptable -sf.cif to .cif | bug | Fixed | Sept. 26, 2022 |
| Sept. 19, 2022 | 4MDG is listing only 2 sites out of 11. | bug | Not fixed | None |
| Sept. 19, 2022 | 4p3q does not work | bug | Not fixed | None |
| Sept. 19, 2022 | Display only model 0/1 1PPX | bug | Fixed | Sept. 23, 2022 |
| Sept. 19, 2022 | Show only bonds for N/O not C | bug | Fixed | Sept. 23, 2022 |
| Sept. 19, 2022 | When no mtz/-sf.cif hide the list of ref | bug | Fixed | Sept. 26, 2022 |
| Sept. 13, 2022 | Report bug is not working on validation page | bug | Fixed | Sept. 14, 2022 |
| Sept. 13, 2022 | Maps should be available if an MTZ file is submitted. Maps should not have to be uploaded. | suggestion | Implemented | Jan. 24, 2023 |
| Feb. 18, 2022 | Toggle spin with button instead of checkbox | suggestion | Fixed | None |
| Feb. 11, 2022 | time out 504, fix apache config file | bug | Fixed | Feb. 11, 2022 |
| Jan. 13, 2022 | 4ins.cif problem debug errors | bug | Fixed | Sept. 19, 2022 |
| Jan. 13, 2022 | cif format does not produce neeighbor unit atoms | suggestion | Not implemented | None |
| Jan. 13, 2022 | pdb format does not produce neeighbor unit atoms | bug | Fixed | Jan. 13, 2022 |
| Jan. 7, 2022 | showing statistics on homepage | bug | Fixed | Jan. 7, 2022 |
| Dec. 21, 2021 | 5t6l strange name of residues | bug | Fixed | Sept. 19, 2022 |
| Dec. 16, 2021 | site is crushed when pdb have no metals | bug | Fixed | Dec. 17, 2021 |
| Dec. 16, 2021 | funcion model_pdb only can do pdb not cif files, review it | bug | Fixed | None |
| Dec. 16, 2021 | refmac works only for residues 801, and it should work on A:801 | bug | Fixed | Dec. 17, 2021 |
| Dec. 15, 2021 | CMM does not read crystallization conditions from cif file. | bug | Fixed | Dec. 15, 2021 |
| Dec. 15, 2021 | CMM needs also to read mtz file not only -sf.cif. | bug | Fixed | Dec. 17, 2021 |