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Automated ligand identification
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PurposePurpose of the Resolve_ligand_identification taskThe Resolve_ligand_identification task carries out fitting of a library of 200 most frequently observed ligands in the PDB to a given electron density map. The program also conducts the analysis and ranking of the ligand fitting results. The current Resolve_ligand_identification task work with the ligand library provided with the Phenix program by default. It is also capable of fitting and ranking ligands in a custom PDB library provided by the users. UsageThe Resolve_ligand_identification task can be run from the PHENIX GUI as a stand-alone strategy, or as a task in a multi-task strategy. How the Resolve_ligand_identification task works:The Resolve_ligand_identification task provides a graphical user interface allowing the user to select either (1) a datafile containing crystallographic structure factor information and a PDB file with a partial model of the structure without the ligand, or (2) an mtz file containing the information of an electron density map of the potential ligand to be identified. The ligand fitting routine is done by RESOLVE as described in the LigandFit wizard documentation. The Resolve_ligand_identification task carries out this fitting process for a library of 200 most frequently observed ligands in the Protein Data Bank, ranks and analyzes the overall fitting results. The output of the task consists of a list of the best fitted ligands from the library. The task display provides options to view the top ranked ligand in Pymol with or without the electron density. How to run the Resolve_ligand_identification taskAn example 'ligand identification' strategy is located in the 'ligands' section in the Phenix strategy menu. Follow the directions and helps in the GUI. What the Resolve_ligand_identification task needs to run:The Resolve_ligand_identification task needs:
ExamplesAn example 'ligand identification' strategy is located in the 'ligands' section of the Phenix strategy menu. Possible ProblemsSpecific limitations and problems:
LiteratureAdditional informationList of ligands in the PHENIX ligand identification library--------------------------------------------------------------- PDB #ATOM LIG_ID 103m 6 NBN 1a99 6 PUT 1bio 6 GOL 1dc1 6 DIO 1dwk 6 OXL 1g29 6 DOX 1g8t 6 MO5 1h16 6 PYR 1k26 6 CRY 1fc5 7 MO6 1gaj 7 PEG 1l5j 7 F3S 1ad2 8 MPD 1b6i 8 HED 1cpf 8 TRS 1e42 8 DTT 1gth 8 URA 1jll 8 COA 1knp 8 SIN 1m6z 8 TMN 1nhz 8 HEZ 1o94 8 SF4 1s8l 8 LI1 1a0j 9 BEN 1amk 9 PGA 1bzy 9 POP 1d0v 9 NIO 1djr 9 BEZ 1f4l 9 MET 1gck 9 ASP 1bf3 10 PHB 1bjq 10 ADE 1dan 10 FUC 1e1d 10 FSO 1e1o 10 LYS 1e7f 10 DAO 1e7h 10 PLM 1ewk 10 GLU 1fwn 10 PEP 1i0i 10 7HP 1kjp 10 PHQ 1kwn 10 TAR 1lrj 10 PGE 1os7 10 AKG 1akd 11 CAM 1d3g 11 ORO 1f98 11 HC4 10gs 12 MES 1amu 12 PHE 1e7e 12 DKA 1f7u 12 ARG 1bj5 13 MYR 1bxh 13 AMG 1f07 13 MPO 1gcz 13 CIT 1gni 13 OLA 1h9x 13 NHE 1j4u 13 MMA 1p0z 13 FLC 1e6r 14 NAA 1gkl 14 FER 1o7v 14 NDG 1rff 14 SPM 1a5a 15 PLP 1afb 15 NGA 1ajk 15 EPE 1c9s 15 TRP 1avd 16 BTN 1bg3 16 G6P 1cnq 16 F6P 1f7s 16 LDA 1fi1 16 FTT 1jsl 16 1PE 1d1v 17 BH4 1d7c 17 1PG 1e2j 17 THM 1n2n 17 H4B 1ho5 19 ADN 1o57 19 P6G 1b4w 20 BOG 1brr 20 RET 1dnc 20 GTT 1dug 20 GSH 1ere 20 EST 1fkp 20 NVP 1hvy 20 UMP 1ldn 20 FBP 1ldn 20 OXM 1bh3 21 C8E 1d2s 21 DHT 1e2d 21 TMP 1h7f 21 C5P 1o28 21 UFP 1c3m 22 MAN-MAN 1cx4 22 CMP 1fsg 22 PRP 1gz1 22 BGC-BGC 1l4f 22 NCN 1ocj 22 BGC 1a0f 23 GTS 1aer 23 AMP 1cdg 23 MAL 1ex2 23 SUC 1gim 23 IMP 1gwv 23 LAT 1a97 24 5GP 1bir 24 2GP 1cq1 24 PQQ 1goy 24 3GP 1hk3 24 T44 1jcq 24 FPP 1ay2 25 GAL-NAG 1c3j 25 UDP 1h7l 25 TYD 1af7 26 SAH 1bfd 26 TPP 1k3l 26 GTX 1mcz 26 TDP 1ao0 27 ADP 1ao0 27 FS4 1cg1 27 IMO 1efh 27 A3P 1fpx 27 SAM 1a4r 28 GDP 1ao5 28 NAG-NAG 1b30 28 XYS-XYS-XYS 1b3v 28 XYS 1lv5 28 DCP 1opx 28 2PE 1cjk 29 FOK 1cjv 29 DAD 1g2v 29 TTP 1i52 29 CTP 1cr2 30 DTP 1ag9 31 FMN 1aq2 31 ATP 1aux 31 SAP 1b63 31 ANP 1f9h 31 APC 1gll 31 ACP 1r3k 31 DGA 1a2b 32 GSP 1b23 32 CYS 1b23 32 GNP 1ckm 32 GTP 1pj6 32 FOL 1d1g 33 MTX 1bos 34 GAL 1bos 34 GAL-GAL-GLC 1bwu 34 MAN 1byh 34 GLC-GLC 1bzw 34 GAL-GLC 1cvn 34 MAN-MAN-MAN 1e40 34 GLC-GLC-GLC 1kzj 35 CB3 1n9b 35 MA4 1ek6 36 UPG 1b0f 38 NAG-FUC-NAG 1fuj 38 NAG-FUC 1g82 38 NAG-NAG-FUC 1d7d 39 NAG-NAG-MAN 1foa 39 UD1 1nb3 39 NAG-NAG-BMA 1kby 42 SPO 106m 43 HEM 1at5 43 NAG-NAG-NAG 1e85 43 HEC 1ek6 44 NAI 1esw 44 ACR 1p9l 44 NAD 1ece 45 GLC-GLC-GLC-GLC 1c3v 48 NDP 1c3v 48 PG4 1r2c 48 7MQ 1ti7 48 NAP 1aof 49 DHE 1gsl 49 NAG-NAG-MAN-FUC 1jnd 50 NAG-NAG-MAN-MAN 1dv3 51 BCL 1dv3 51 BPH 1dv3 51 U10 1p0h 51 ACO 1fnd 53 FAD 1lsh 53 PLD 1lsh 53 UPL 1f0y 54 CAA 1okc 54 PC2 1a65 56 NAG 1bdg 56 GLC 1en2 56 NAG-NAG-NAG-NAG 1f9d 56 GLC-GLC-GLC-GLC-GLC 1aky 57 AP5 1myr 58 NAG-FUC-NAG-MAN-XYS 1fq8 61 NAG-NAG-MAN-MAN-MAN 1prc 65 BPB 1cxp 71 NAG-NAG-MAN-MAN-MAN-FUC 1deo 72 NAG-NAG-MAN-MAN-MAN-MAN 1ax0 80 NAG-FUC-NAG-MAN-XYS-MAN-MAN 1kby 81 CDL 1dio 91 B12 | |