MakeTNT-toolkit User Documentation | previous next |
PDB2TNT |
Copyright © 2004-2008 Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the
Author: (2004-2008) M. Brandl
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% PDB2TNT -i <input-file> [-n <tag>]
[-o <filename>] \ [-noB] [-FLEXTOR] [-size <length of output>]\ [-HPOS][-NOMDL][-ccp4][-ccp4_tnt][-Odict][-ODB <O-database>][-OnoH][-notor][-TightRestraints] |
Switch | Argument | Description | Possible Values | Compulsory | Note | ||||||||||
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-i | <input-file> | name of PDB-file submitted | no format restrictions, any extension | yes | |||||||||||
-n | <tag> | 3-Letter code to be used in TNT-dictionary file | e.g.: ATP,GMP,ANY,THI,NGY,OUL,IKE | no |
default = 3-letter ID from PDB-file if absent: UNK Use your own! |
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-o | <filename> | unique filename for TNT-dictionaries | e.g.: kinase_inhibitor986B, ... | no |
default = 3-letter code defined by -outname Choose something unique! |
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-noB | flag to suppress default BCORREL restraints | no | |||||||||||||
-FLEXTOR | output of default parameters for non-planar torsion angles | no | |||||||||||||
-size | <length of output> | defines the overall size of the resulting dictionary |
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no |
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-HPOS | Switch to ignore H-atom positions | no | Not recommended ! Use only if H-atoms are unreliable | ||||||||||||
-NOMDL | Switch off generation of pseudo-MDL file | no | Recommended if the quality of your PDB-file is good | ||||||||||||
-ccp4 | flag to generate CCP4-restraints instead of TNT-restraints | no | |||||||||||||
-ccp4_tnt | flag to generate CCP4-restraints AND TNT-restraints | no | |||||||||||||
-Odict | flag to generate dictionaries for O instead of TNT-restraints | no | |||||||||||||
-ODB | <O-database> | append non-redundant O-dicionaries to existing O-database | no | only relevant to the generation of O-dictionaries | |||||||||||
-OnoH | exclude hydrogen atoms from O-dictionary entries | no | only relevant to the generation of O-dictionaries | ||||||||||||
-notor | flag to suppress torsion restraints for non-planar groups in O-dictionaries | no | only relevant in combination with -Odict | ||||||||||||
-TightRestraints | sigma for bond lengths: 0.020Å, sigma for bond angles: 2.0deg | no | default: 0.040Å, 5.0deg |
If an atom has three neighbours bonded to it, an improper torsion is measured between those four atoms and if its value is close to 0 or 180 degrees a TRIGONAL restraint is created, otherwise an IMPROPER torsion restraint is generated. IMPROPER torsion restraints are also generated for atoms surrounded by four (or more) neighbours.
Planar torsion restraints are put out if two bonded atoms (of elements with double/triple bond potential) are in planar coordination (based on their bond angles) and all torsion angles around this bond are planar as well. If the bonded atoms are in planar conformation, but at least one torsion angle is not, no restraints are not formed and a message to the user is written instead.
The different options for the -size argument are:
Overlapping planes will produce one single TNT-PLANE restraints; produces large, rigid planes; recommended for visualization; if necessary planes can be broken down to smaller fragments using size m(default);
Planar 5/6-membered rings give one PLANE restraint each. Recommended for large planar systems and in structures of high resolution.
Each planar torsion angle will result in a separate PLANE restraint.
To produce a TNT-dictionary file taxotere.dic, run:
% PDB2TNT -i TXL_tnt.pdb -n TXL -o taxotere |
To test this functionality, run PDB2TNT on TXL.pdb :
% PDB2TNT -i TXL.pdb -n TXL -o taxotere |
Please use taxotere_tnt.pdb for further refinement in BUSTER-TNT.
% PDB2TNT -i TXL_tnt.pdb -n TXL -o taxotere -ccp4 |
% PDB2TNT -i TXL_tnt.pdb -n TXL -Odict -ODB stereo_chem.odb |
% PDB2TNT -i TXL_tnt.pdb -n TXL -Odict -ODB stereo_chem.odb -notor |