HIC-Up

HIC-Up Release notes

Release notes are available for the folowing versions of HIC-Up:

  1. Release 12.1
  2. Release 11.2
  3. Release 11.1
  4. Release 10.2
  5. Release 10.1
  6. Release 9.1
  7. Release 8.2
  8. Release 8.1
  9. Release 7.3
  10. Release 7.2
  11. Release 7.1
  12. Release 6.1


Release 12.1 notes

Notes about release 12.1 on 1 March, 2008:

  1. This is the first HIC-Up version after the release of the remediated PDB. A few changes had to be made to the underlying scripts and programs, but hopefully everything has been ironed out now
  2. A number of new items have been added on the compound pages:
  3. Some minor changes:
  4. Statistics:
  5. Problem entries:


Release 11.2 notes

Notes about release 11.2 on 5 June, 2007:

  1. This is the last HIC-Up version prior to the release of the remediated PDB. Hopefully, the remediation will improve the quality of HIC-Up, but there could be unforeseen hiccups ...
  2. The lay-out of the compound pages has been changed slightly. Where available, the 2D structure diagram from MSDchem is now shown (in miniature) at the top of the page, and it functions as a link to the full-size diagram further down on the page.
  3. The section with "off-site" links has been changed. Links are now grouped in subsections called Validation, Description (dictionaries and formats), PDB entries, Structural biology and Miscellaneous.
  4. A number of new links have been added on the compound pages:
  5. Some minor changes:
  6. Statistics:


Release 11.1 notes

Notes about release 11.1 on 11 January, 2007:

  1. No major changes. HIC-Up now contains 7078 entries. For all but 219 of these ideal coordinates (taken from MSDchem) are available. EDS statistics are available for 4729 entries (of which 1598 have EDS stats for more than one resolution range).
  2. Errors encountered are essentially the same as in the previous version. Most of these will hopefully disappear when the remediated version of the PDB is released (later this year?).


Release 10.2 notes

Notes about release 10.2 on 26 July, 2006:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. Changed the lay-out of the compound pages a bit (in particular the off-site links)
  2. Added links in the compound pages to ChemDB at UC Irvine
  3. Added links in the compound pages to OCA at the Weizmann Institute
  4. Updated some links
  5. Ideal coordinates (from MSDchem) for more compounds (~5600, or 84%, of them)
  6. EDS statistics now for ~4250 (64%) of all compounds (of which almost 1500 have EDS stats for more than one resolution range)


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken (it is not clear to me why they did not give an error in the previous release):
    1. GFP 900 in 4GPB (see comment for release 7.3)
    2. MEC A194 in 1QNU (see comment for release 7.3)
    3. NYP A601 in 1GOS (see comment for release 7.3)
    4. VO3 A1001 in 1E59 (see comment for release 7.3)

  2. HETZE log file not created - this occurs for compounds that do not contain (any/enough) covalent bonds:
    1. 543 111 in 1EN8
    2. CYO 117 in 1LIC
    3. DML 1N in 132L
    4. MW3 A500 in 1F1R
    5. NA2 A275 in 2BMI
    6. NA5 17 in 292D
    7. NA6 17 in 293D
    8. OC7 112 in 1EN8
    9. OC8 304 in 1SK5
    10. OWQ L57 in 2BBK
    11. QTR L57 in 2MAD
    12. TML 72 in 1YCC

  3. bond distances shorter than 0.8 A - this occurs for the following compounds:
    1. 4PN 2001 in 1K4Y: Bond N7 - C4 = 0.771 A

  4. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. ARQ 401 in 3AID
    2. MON 101 in 1NDE
    3. ONM 100 in 1TL7
    4. PIS 301 in 1TUU
    5. TMA 950 in 1EK6
    6. U2P 400 in 1UCA


Release 10.1 notes

Notes about release 10.1 on 6 April, 2006:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. Added links in the compound pages to PubChem at NCBI
  2. Use canonical URLs to link to MSD Atlas pages
  3. Changed filename extension of the VRML files from .wrl.gz to .wrz
  4. Updated links to RCSB and MMDB
  5. Ideal coordinates (from MSDchem) for more compounds (~4900 of them)
  6. EDS statistics for more compounds (~4100 of them; all but ~400 of these have statistics for at least 7 of the 10 resolution ranges)


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. For the first time ever, all entities had a chemical formula in their parent entry ! Well done, wwPDB !

  2. HETZE log file not created - this occurs for compounds that do not contain (any/enough) covalent bonds:
    1. 543 111 in 1EN8
    2. CYO 117 in 1LIC
    3. DML 1N in 132L
    4. IHS 30 in 1LR8
    5. NH4 200 in 2PVB
    6. OC2 5008 in 1G8K
    7. OC7 112 in 1EN8
    8. OC8 304 in 1SK5
    9. OWQ L57 in 2BBK
    10. QTR L57 in 2MAD
    11. TML 72 in 1YCC
    12. UNL 1 in 2FCL (since it is an "UNKNOWN LIGAND" one assumes)

  3. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. 32T A57 in 1RMO
    2. ARQ 401 in 3AID
    3. MM2 500 in 1YIL
    4. TMA 950 in 1EK6
    5. UPF 300 in 1G9R


Release 9.1 notes

Notes about release 9.1 on 27 January, 2005:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. The most significant change is that from this version on, the "ideal" ChemPDB coordinates (generated with CORINA) are used for dictionary generation etc. (when they exist). Many thanks to Dimitris Dimitropoulos and Kim Henrick of MSD/EBI for making these available !
  2. Added 2D structure drawing from MSD ChemPDB
  3. For parent PDB entry, added links to OCA, IMB-Jena and PDBREPORT
  4. Added links to MSDsite for every entry
  5. Added links to PDB-Ligand for every entry
  6. Aatom names that have an embedded space (e.g., " N A") are modified so that the space is replace by an _underscore_ (e.g., " N_A")
  7. A bug in the writing of renumbered atom serial numbers has been fixed (this affected 334 compounds in the previous release, but is unlikely to have hurt anyone except the person who reported the problem)
  8. Updated links for PDBsum to point to new site at the EBI


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken:
    1. GFP 900 in 4GPB (see comment for release 7.3)
    2. MEC A194 in 1QNU (see comment for release 7.3)
    3. NYP A601 in 1GOS (see comment for release 7.3)
    4. UNL A601 in 1VP8 (since it is an "UNKNOWN LIGAND" one assumes)
    5. VO3 A1001 in 1E59 (see comment for release 7.3)

  2. HETZE log file not created - this occurs for compounds that do not contain (any/enough) covalent bonds:
    1. 543 111 in 1EN8
    2. CYO 117 in 1LIC
    3. DML 1N in 132L
    4. IHS 30 in 1LR8
    5. KO4 A549 in 1KP8
    6. MNQ 999 in 1D0X
    7. MW3 A500 in 1F1R
    8. NA2 A275 in 2BMI
    9. NA5 17 in 292D
    10. NA6 17 in 293D
    11. NAO B275 in 2BMI
    12. OC1 A151 in 1QTX
    13. OC2 5008 in 1G8K
    14. OC3 114 in 1ENE
    15. OC4 114 in 1EN8
    16. OC5 113 in 1EN8
    17. OC6 1113 in 1ENE
    18. OC7 112 in 1EN8
    19. OWQ L57 in 2BBK
    20. QTR L57 in 2MAD
    21. TML 72 in 1YCC
    22. UNL A601 in 1VP8 (since it is an "UNKNOWN LIGAND" one assumes)

  3. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. 165 1001 in 1SB1
    2. 32T A57 in 1RMO
    3. ARQ 401 in 3AID
    4. CUB B3921 in 1N62
    5. DND 502 in 1XQD
    6. EBS A1518 in 1OF0
    7. MON 101 in 1NDE
    8. ONM 100 in 1TL7
    9. TMA 950 in 1EK6
    10. TMH 450 in 1MPW
    11. U2P 400 in 1UCA
    12. UPF 300 in 1G9R


Release 8.2 notes

Notes about release 8.2 on 17 June, 2004:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. Used the latest version (3.2.2) of XPLO2D that omits the target values of the "torsion" definitions in the O dictionary


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken:
    1. GFP 900 in 4GPB (see comment for release 7.3)
    2. MEC A194 in 1QNU (see comment for release 7.3)
    3. NYP A601 in 1GOS (see comment for release 7.3)
    4. UNL 2 in 1VKE (since it is an "UNKNOWN LIGAND" one assumes)
    5. VO3 A1001 in 1E59 (see comment for release 7.3)

  2. HETZE log file not created - this occurs for compounds that do not contain (any/enough) covalent bonds:
    1. 543 111 in 1EN8
    2. BEF 1000 in 1LVK
    3. CUL 13 in 1D40
    4. CYO 117 in 1LIC
    5. DML 1N in 132L
    6. HGB 263 in 1BV3
    7. ICA 1 in 1AI2
    8. IHS 30 in 1LR8
    9. KO4 A549 in 1KP8
    10. MNQ 999 in 1D0X
    11. MW3 A500 in 1F1R
    12. NA2 A275 in 2BMI
    13. NA5 17 in 292D
    14. NA6 17 in 293D
    15. NAO B275 in 2BMI
    16. OC1 A151 in 1QTX
    17. OC2 5008 in 1G8K
    18. OC3 114 in 1ENE
    19. OC4 114 in 1EN8
    20. OC5 113 in 1EN8
    21. OC6 1113 in 1ENE
    22. OC7 112 in 1EN8
    23. OWQ L57 in 2BBK
    24. QTR L57 in 2MAD
    25. TML 72 in 1YCC

  3. bond distances shorter than 0.8 A - this occurs for the following compounds:
    1. 4PN 2001 in 1K4Y: Bond N7 - C4 = 0.771 A
    2. HXC 390 in 1CHW: Bond O32 - O33 = 0.222 A
    3. NGP 15 in 1L0R: atoms C12 and O2 have identical coordinates
    4. PPX 907 in 1QBV: Bond C4 - C9 = 0.046 A

  4. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. 165 1001 in 1SB1
    2. 32T A57 in 1RMO
    3. 3AT 1000 in 1F5A
    4. BBZ 25 in 447D
    5. CLP 498 in 1FP4
    6. CSU A1 in 1FB9
    7. CUB B3921 in 1N62
    8. DPO 414 in 1N5L
    9. EBS A1518 in 1OF0
    10. HXC 390 in 1CHW
    11. KTN 801 in 1JIP
    12. MON 101 in 1NDE
    13. PHW K1 in 1H8D
    14. RIT 301 in 1HXW
    15. T3P 600 in 1CY8
    16. TER 13 in 336D
    17. TMH 450 in 1MPW
    18. U2P 400 in 1UCA
    19. UPF 300 in 1G9R
    20. VIT 401 in 1KPM
    21. XYH 499 in 1EC9


Retired compounds

Hetero-compounds that have disappeared since the previous release:

  1. 3FQ (parent entry 1H06 now obsolete, replaced by 1V1K)


Release 8.1 notes

Notes about release 8.1 on 20 February, 2004:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. For every hetero-compound that occurs at least once in any entry in EDS (the Uppsala Electron Density Server), a separate page is generated with statistics concerning the real-space R-values (RSR), real-space correlation coefficients (RSCC), and occupancy-weighted average B-factors (OWAB) for that compound in a number of resolution shells. The average and standard deviation of these statistics are listed as well as the minimum and maximum observed values in each resolution shell, with pointers back to EDS. This information can be used, e.g.: Of course, many compounds only occur in one or two PDB entries, so the statistics are not much use, but as the PDB grows (and structure factors continue to be deposited) this facility will become more and more useful. At the moment, statistics for all resolution shells are available for the following compounds: ACT ADP FAD FS4 GLC GNP GOL HEC HEM MAN MES MSE NAD NAG NDP NH2 PCA PO4 SAH SO4 TRS CA CD CL CO FE HG MG MN NA ZN K
  2. The TNT dictionaries for every compound have been improved. They now contain BCORREL restraints, and problems with the CHIRAL restraints have been fixed
  3. For every entry, there is now a link to Google to search on the (first) name of the compound
  4. For every entry, there is now a link to the Ligand Depot at RCSB
  5. For every entry, there is now a link to KEGG-LIGAND to search on the (first) name of the compound
  6. If there are more than 15 PDB entries that contain a certain compound, the summary at the top of the page will contain a link to the PDB that will produce an up-to-date listing of all those entries
  7. The LIGPLOT figures are back
  8. The problems with the generation of the connection tables and listings of super-structures have been fixed
  9. All links related to EDS now point to the new home of the EDS server: http://eds.bmc.uu.se/


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken:
    1. GFP 900 in 4GPB (see comment for release 7.3)
    2. MEC A194 in 1QNU (see comment for release 7.3)
    3. NYP A601 in 1GOS (see comment for release 7.3)
    4. UNL 1 in 1VJ2 (since it is an "UNKNOWN LIGAND" one assumes)
    5. VO3 A1001 in 1E59 (see comment for release 7.3)

  2. HETZE log file not created - this occurs for compounds that do not contain (any/enough) covalent bonds:
    1. 543 111 in 1EN8
    2. BEF 1000 in 1LVK
    3. CUL 13 in 1D40
    4. CYO 117 in 1LIC
    5. DML 1N in 132L
    6. HGB 263 in 1BV3
    7. ICA 1 in 1AI2
    8. IHS 30 in 1LR8
    9. KO4 A549 in 1KP8
    10. MNQ 999 in 1D0X
    11. MW3 A500 in 1F1R
    12. NA2 A275 in 2BMI
    13. NA5 17 in 292D
    14. NA6 17 in 293D
    15. NAO B275 in 2BMI
    16. OC1 A151 in 1QTX
    17. OC2 5008 in 1G8K
    18. OC3 114 in 1ENE
    19. OC4 114 in 1EN8
    20. OC5 113 in 1EN8
    21. OC6 1113 in 1ENE
    22. OC7 112 in 1EN8
    23. OWQ L57 in 2BBK
    24. QTR L57 in 2MAD
    25. TML 72 in 1YCC
    26. UNL 1 in 1VJ2

  3. bond distances shorter than 0.8 A - this occurs for the following compounds:
    1. 4PN 2001 in 1K4Y: Bond N7 - C4 = 0.771 A
    2. HXC 390 in 1CHW: Bond O32 - O33 = 0.222 A
    3. NGP 15 in 1L0R: atoms C12 and O2 have identical coordinates
    4. PPX 907 in 1QBV: Bond C4 - C9 = 0.046 A

  4. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. 3AT 1000 in 1F5A
    2. BBZ 25 in 447D
    3. CLP 498 in 1FP4
    4. CSU A1 in 1FB9
    5. CUB B3921 in 1N62
    6. DPO 414 in 1N5L
    7. GTG 2137 in 1N52
    8. HXC 390 in 1CHW
    9. KTN 801 in 1JIP
    10. MON 101 in 1NDE
    11. PHW K1 in 1H8D
    12. RIT 301 in 1HXW
    13. T3P 600 in 1CY8
    14. TER 13 in 336D
    15. TMH 450 in 1MPW
    16. U2P 400 in 1UCA
    17. UPF 300 in 1G9R
    18. VIT 401 in 1KPM
    19. XYH 499 in 1EC9


Retired compounds

Hetero-compounds that have disappeared since the previous release:

  1. NRT (parent entry 1H0U now obsolete, not replaced by any new entry)


Release 7.3 notes

Notes about release 7.3 on 14 November, 2003:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. New version of XPLO2D has been used that produces stereochemistry entries suitable for use with O version 9.0 and later. Just add the entry for your compound to your .bonds_angles datablock (in stereo_chem.odb) and update the header of the datablock to contain the correct number of lines. You no longer need all the separate O stuff created by MOLEMAN2 and XPLO2D - just this entry suffices (providing you use O version 9.0 or later and no deprecated O commands).
  2. Due to a technical mishap, the LIGPLOT drawings of the compounds have not been created this time. Hopefully they will return with next release.


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken:
    1. GFP 900 in 4GPB (misspelled in the FORMUL record as "G1P" ?)
    2. MEC A194 in 1QNU (misspelled in the FORMUL record as "EMC" ?)
    3. NYP A601 in 1GOS (but there is a duplicate FORMUL record for "FAD")
    4. VO3 A1001 in 1E59 (misspelled in the FORMUL record as "V4O" ?)

  2. HETZE log file not created - this occurs for compounds that do not contain (enough) covalent bonds:
    1. 543 111 in 1EN8
    2. BEF 1000 in 1LVK
    3. CUL 13 in 1D40
    4. CYO 117 in 1LIC
    5. DML 1N in 132L
    6. HGB 263 in 1BV3
    7. ICA 1 in 1AI2
    8. IHS 30 in 1LR8
    9. KO4 A549 in 1KP8
    10. MNQ 999 in 1D0X
    11. MW3 A500 in 1F1R
    12. NA2 A275 in 2BMI
    13. NA5 17 in 292D
    14. NA6 17 in 293D
    15. NAO B275 in 2BMI
    16. OC1 A151 in 1QTX
    17. OC2 5008 in 1G8K
    18. OC3 114 in 1ENE
    19. OC4 114 in 1EN8
    20. OC5 113 in 1EN8
    21. OC6 1113 in 1ENE
    22. OC7 112 in 1EN8
    23. OWQ L57 in 2BBK
    24. QTR L57 in 2MAD
    25. TML 72 in 1YCC

  3. bond distances shorter than 0.8 A - this occurs for the following compounds:
    1. 4PN 2001 in 1K4Y: Bond N7 - C4 = 0.771 A
    2. HXC 390 in 1CHW: Bond O32 - O33 = 0.222 A
    3. NGP 15 in 1L0R: atoms C12 and O2 have identical coordinates
    4. PPX 907 in 1QBV: Bond C4 - C9 = 0.046 A

  4. bond angles of less than 80 degrees - this occurs for the following compounds (note that these may be genuine, e.g. in the case of three-membered rings):
    1. 3AT 1000 in 1F5A
    2. BBZ 25 in 447D
    3. CLP 498 in 1FP4
    4. CSU A1 in 1FB9
    5. CUB B3921 in 1N62
    6. DPO 414 in 1N5L
    7. GTG 2137 in 1N52
    8. HXC 390 in 1CHW
    9. KTN 801 in 1JIP
    10. MON 101 in 1NDE
    11. PHW K1 in 1H8D
    12. RIT 301 in 1HXW
    13. T3P 600 in 1CY8
    14. TER 13 in 336D
    15. TMH 450 in 1MPW
    16. U2P 400 in 1UCA
    17. UPF 300 in 1G9R
    18. VIT 401 in 1KPM
    19. XYH 499 in 1EC9


Retired compounds

Hetero-compounds that have disappeared since the previous release:

  1. 55C (renamed to 5CM)
  2. AMD (renamed to AMO ?)
  3. RAN (parent entry 1D9T now obsolete, replaced by 1NE7)
  4. TCS (renamed to TCL, triclosan)


Release 7.2 notes

Notes about release 7.2 on 17 April, 2003:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. Use links to ReLiBase at CCDC instead of EBI
  2. Added off-site link to list all entries with ligand at the RCSB-PDB site
  3. Added off-site link to list all entries with ligand at the IMB-Jena site
  4. Added PDB link for parent entry to MSD
  5. Added PDB link for parent entry to MMDB


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities (still ...)have no chemical formula in the PDB entry from which they were taken: MEC A194 in 1QNU ... NYP A601 in 1GOS ... VO3 A1001 in 1E59

  2. HETZE log file not created - this occurs for compounds that do not contain (enough) covalent bonds: 543 111 in 1EN8 ... BEF 1000 in 1LVK ... CUL 13 in 1D40 ... CYO 117 in 1LIC ... DML 1N in 132L ... HGB 263 in 1BV3 ... ICA 1 in 1AI2 ... KO4 A549 in 1KP8 ... MNQ 999 in 1D0X ... NA2 A275 in 2BMI ... NA5 17 in 292D ... NA6 17 in 293D ... NAO B275 in 2BMI ... OC1 A305 in 1CAQ ... OC2 5008 in 1G8K ... OC3 114 in 1ENE ... OC4 114 in 1EN8 ... OC5 113 in 1EN8 ... OC6 1113 in 1ENE ... OC7 112 in 1EN8 ... OWQ L57 in 2BBK ... QTR L57 in 2MAD ... TDX 3500 in 1KEP ... TML 72 in 1YCC ...

  3. bond distances shorter than 0.8 A - this occurs for 3 compounds (same as in the previous release) and all appear to be genuine errors (typos ?) in the parent PDB entry:
    1. 4PN 2001 in 1K4Y -> "Bond N7 - C4 = 0.771 A"
    2. HXC 390 in 1CHW -> "Bond O32 - O33 = 0.222 A"
    3. NGP 15 in 1L0R -> "Bond C12 - O2 = 0.000 A"
    4. PPU B76 in 1FG0 -> "Bond P - O5* = 0.715 A"
    5. PPX 907 in 1QBV -> "Bond C4 - C9 = 0.046 A"

  4. bond angles of less than 80 degrees - this occurs for the following compounds: MON 101 in 1NDE ... PHW K1 in 1H8D ... RIT 301 in 1HXW ... T3P 600 in 1CY8 ... TER 13 in 336D ... TMH 450 in 1MPW ... UPF 300 in 1G9R ... VIT 401 in 1KPM ... XYH 499 in 1EC9 ...


Retired compounds

No hetero-compounds have disappeared since the previous release.


Release 7.1 notes

Notes about release 7.1 on 15 January, 2003:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. Use newer EDS server at fsrv1.bmc.uu.se in links
  2. Replaced MSD ChemPDB links by simple GET syntax
  3. Prevent search engine indexing of super-structures pages with META tag
  4. Updated the list of links
  5. The HIC-Up server now uses same input parameters as are used in generating HIC-Up (in programs XPLO2D and HETZE)
  6. List warning when no chemical formula was found
  7. Changed maximum value of CUTBND in XPLO2D and HETZE to 0.5 Å
  8. Changed bad angles in HETZE to only include those for which the central atom is one of C, N, O, Si, P or S


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken: MEC A194 in 1QNU, NYP A601 in 1GOS, and VO3 A1001 in 1E59.

  2. HETZE log file not created - this occurs for compounds that do not contain (enough) covalent bonds. The increase in this number is due to a change in the parameters used in HETZE and XPLO2D: MNQ 999 in 1D0X, NA2 A275 in 2BMI, NA5 17 in 292D, NA6 17 in 293D, NAO B275 in 2BMI, OC1 A305 in 1CAQ, OC2 5008 in 1G8K, OC3 114 in 1ENE, OC4 114 in 1EN8, OC5 113 in 1EN8, OC6 1113 in 1ENE, OC7 112 in 1EN8, OWQ L57 in 2BBK, QTR L57 in 2MAD, TDX 3500 in 1KEP, and TML 72 in 1YCC.

  3. bond distances shorter than 0.8 A - this occurs for 3 compounds and all appear to be genuine errors (typos ?) in the parent PDB entry:
    1. NGP 15 in 1L0R -> "Bond C12 - O2 = 0.000 A"
    2. PPU B76 in 1FG0 -> "Bond P - O5* = 0.715 A"
    3. PPX 907 in 1QBV -> "Bond C4 - C9 = 0.046 A"

  4. bond angles of less than 80 degrees - this occurs for 10 compounds. Some are due to genuine errors, other a consequence of a bond-distance error perhaps, and yet others to HETZE not yet recognising special cases (such as a sodium ion with several waters - on the other hand, this is hardly a true "hetero-compound"): KTN 801 in 1JIP, MON 101 in 1NDE, PHW K1 in 1H8D, RIT 301 in 1HXW, T3P 600 in 1CY8, TER 13 in 336D, TMH 450 in 1MPW, UPF 300 in 1G9R, VIT 401 in 1KPM, and XYH 499 in 1EC9.


Retired compounds

Hetero-compounds that have disappeared since the previous release:

  1. EYS (parent compound 1QJ2 now obsolete, replaced by 1N5W)
  2. CA_ (renamed to _CA, i.e. with leading instead of trailing space)


Release 6.1 notes

Notes about release 6.1 on 9 July, 2002:

  1. Changes to the HIC-Up generation procedure and programs
  2. Errors encountered
  3. Hetero-compounds that have been retired since the previous release of HIC-Up


Changes

The following changes (among others) have been made for this release of HIC-Up:

  1. If a hetero-compound occurs in more than one PDB entry, their total number is now included in the header table on the compound page, together with the PDB IDs and links of (at most) the first 10 of these entries (sorted from highest to lowest resolution)
  2. More informative error messages
  3. Double quotes in atom names screwed up the PRODRG forms, so they are now automatically replaced by _underscores_
  4. XPLO2D and HETZE now explicitly ignore any and all hydrogen atoms encountered in a hetero-compound's PDB file to prevent spurious error messages
  5. The absence of a valid chemical formula is now handled (e.g. MEC and GFP)
  6. Reduced bond-length tolerance reduces number of spurious bonds generated by XPLO2D and HETZE
  7. Both XPLO2D and HETZE now consider a bond length 'bad' if it is less than 0.8 Å
  8. Both XPLO2D and HETZE now consider a bond angle 'bad' if it is less than 80 degrees, but only if not all three are bonded and the central atom has an atom nummer of 16 or less (i.e., up to and including sulfur)
  9. Every compound page now has a better standard footer
  10. Sethuraman Baranidharan has created JPEG images for the 3,416 compounds of release 5.3, which are now used in the headers of the corresponding compound pages
  11. In the "off-site" section of every compound page, a form link has been added to the EBI-MSD Ligand Chemistry service
  12. The list of compounds sorted by number of non-hydrogen atoms is now actually sorted numerically, rather than alphabetically
  13. Added a (very small !) FAQ
  14. In case of alternative conformations, only the first one is kept
  15. Lots of minor changes "under the hood"


Errors

Errors encountered, other than those involving multiple or inconsistent chemical formulas:

  1. The following entities have no chemical formula in the PDB entry from which they were taken: CA, GFP, MEC, NYP, UNK, VO3

  2. HETZE log file not created - this occurs for 4 compounds that do not contain any covalent bonds: DML, OWQ, QTR, TML

  3. bond distances shorter than 0.8 A - this occurs for 5 compounds and all appear to be genuine errors (typos ?) in the parent PDB entry:
    1. 4PN 2001 in 1K4Y -> "Bond N7 - C4 = 0.771 A"
    2. HXC 390 in 1CHW -> "Bond O32 - O33 = 0.222 A"
    3. NGP 15 in 1L0R -> "Bond C12 - O2 = 0.000 A"
    4. PPU B76 in 1FG0 -> "Bond P - O5* = 0.715 A"
    5. PPX 907 in 1QBV -> "Bond C4 - C9 = 0.046 A"

  4. bond angles of less than 80 degrees - this occurs for 15 compounds. Some are due to genuine errors, other a consequence of a bond-distance error (see above), and yet others to HETZE not yet recognising special cases (such as a sodium ion with several waters - on the other hand, this is hardly a true "hetero-compound"): 3AT, BBZ, HXC, ICA, KTN, NA5, NA6, NAW, PHW, RIT, T3P, TDX, TER, UPF, XYH. Some of the ones that appear to be genuine errors are:
    1. BBZ 25 in 447D -> "C21 - N6 - C24 : 78.84 degrees"
    2. HXC 390 in 1CHW -> "C2' - C3' - C4' : 76.77 degrees"
    3. KTN 801 in 1JIP -> "C7 - C6 - C14 : 73.86 degrees"
    4. TER 13 in 336D -> "C4 - C3 - C7 : 79.53 degrees"
    5. XYH 499 in 1EC9 -> "OH4 - C4 - C5 : 78.59 degrees"


Retired compounds

Hetero-compounds that have disappeared since the previous release (note: most of these are due to a change in PDB policy, namely not to include theoretical models in index lists any longer, and to keep them in a separate area of the ftp directory tree):

  1. ADG (came from a theoretical model, 1AUF)
  2. AVP (came from a theoretical model, 1B1F)
  3. BDR (came from a theoretical model, 1AT8)
  4. BPL (came from a theoretical model, 1EM4)
  5. BSU (came from a theoretical model, 1J8J)
  6. CCA (came from a theoretical model, 1EHO)
  7. CE9 (from entry 1FUM, replaced by 1L0V)
  8. CN_ (renamed to _CN, i.e. with leading instead of trailing space)
  9. CRE (came from a theoretical model, 1F1L)
  10. ECT (came from a theoretical model, 1EZ5)
  11. EUD (came from a theoretical model, 1F1N)
  12. FAN (came from a theoretical model, 1MIG)
  13. IIN (came from a theoretical model, 1RVN)
  14. ION (came from a theoretical model, 1F1K)
  15. KRA (came from a theoretical model, 2FTI)
  16. KRB (came from a theoretical model, 3FTI)
  17. NA_ (renamed to _NA, i.e. with leading instead of trailing space)
  18. NBZ (came from a theoretical model, 1MIG)
  19. NEC (came from a theoretical model, 1MMH)
  20. NIV (came from a theoretical model, 1RVO)
  21. NNS (came from a theoretical model, 1EFF)
  22. NSA (came from a theoretical model, 1DJJ)
  23. NTL (came from a theoretical model, 2CLN)
  24. ROL (came from a theoretical model, 1JP2)
  25. S01 (came from a theoretical model, 1FTI)
  26. THI (came from a theoretical model, 1RVP)
  27. TIB (came from a theoretical model, 1RVQ)
  28. TIO (came from a theoretical model, 1DL9)
  29. TPH (came from a theoretical model, 7TMN)
  30. UKC (came from a theoretical model, 1RVR)
  31. YYG (came from a theoretical model, 1K5X)
  32. Z23 (came from a theoretical model, 1CU8)
  33. ZK9 (came from a theoretical model, 1CU7)
  34. ZN_ (renamed to _ZN, i.e. with leading instead of trailing space)


Latest update at 3 March, 2008.