Load a PDB file

Note that there are several alternatives - the first one is the simplest, the second less, ...

Use "tk_main_config.pl"

"tk_main_config.pl" is a GUI to prepare your session. The second frame contains PDB import which you can doe either from a file or PDB

Use "create_auto_start.pl"

The use of "create_auto_config.pl" is the simplest approach intended for quick display of a single structure. It is confined to a single PDB file, which is on the other hand not constrained to the number of molecules and their position in space.

  -h|--help)     prints this message with available options and current status
  -c|--command)  define macro with MY COMMANDS [?MAIN_UTILS:my_commands.com]
  -i|--input)    set file name of the data input macro [read.com]
  -g|--groups)   define NCS groups by [NONE/CHAINS/SEGMENTS] [SEGMENTS]
  -o|--output)   set file name of the created macro [.main]
  -p|--pdb)      extract information from a PDB file []
  -x|--crystal)  PDB CRYSTAL record use [USE/IGNORE] [USE]
  -d|--depp)     depp pages [NEW/OLD] menu [NEW]
  -s|--display)  display position and sizes [0 0 1280 1024] menu []
     --doit)     create the macro

The "create_auto_start.pl" can accept a "pdb" file as an argument and extracts cell constants, space group, copies teh provided PDB file into SAVE_FILE.PDB for further work and creates the default "read.com" file.

 create_auto_start.pl -p 1CEW.pdb --doit
creating ".main"
reading PDB file "1CEW.pdb"
 UNIT CELL: 47.900 47.900 87.500 90.00 90.00 120.00
 SPACE GROUP: p31_2_1
creating "cell.dat"
creating "read.com"

Now you can start "mainps" and the model will be displayed.

This approach creates self sufficient working enviroment for molecule display and structure analysis and validation. Besides also default "re_image.cmds" macro is generated.

Use "create_re_image.cmds" to adopt display options or go to depp page "IMAGE" to do more.

Use depp page item IO_DATA

On the "Depp" on the main paga there is IO_DATA item. Configure it with the right mouse click and read PDB file.

This is meant to load additional files not your basic file.

Use command language

You have to type the complete command to read the atom coordinates:

> read file my_file.pdb atom pdb

Whereas the above approaches generated the connectivity table if not present, you should either read it or generate it.

> read file my_file.ctab ctab

if this is not the first file to read in, it makes sense to define a key to be able to deal with it:

> key old sele all end
> read file my_file.pdb atom pdb
> read file my_file.ctab ctab first sele .n old end

or generate connectivity list by

> calc bond sele .n old end neigh
> calc bond sele .n old end disu

Adapting residue and atom names

In order to enable energy minimization and refinement the coordinates must correspond to the topology libraries MAIN utilizes. You can also create your own ones, but before doing that it makes sense to use what is already offered. (For further reading see the chapter on topology and parameters: MAIN_DOC:top_par/top_par.html.)

If not read otherwise the "LIB_PROT", "LIB_DNA" and "LIB_CHO" load topology libraries and corresponding parameter files. The library items must be clicked in the order from the higher to the lower positioned one. "LIB_PROT" must be called first, "LIB_DNA" can be omitted. The "LIB_PROT" reads besides amino acid residues also ions.

A click on "DEFINE" (page 9) prepares the model for energy calculations. If "DEFINE" triggers warning and error messages something should be done about them. For proper use of energy calculations something should be done about it.

Most are usually a result of ATOM and RESIDUE naming in consistencies between the just read file and the MAIN libraries, whereas some may arise from wrong covalent bond connections. First take care for the unknown atom and residue names. "xpl2MAIN" menu item fixes most of them. For the rest residues and atoms should be renamed or additional libraries loaded.

Interactive tools MAIN_MENU:rename.html will help you to rename atom and residue names. You may chose also the manual way

 rename atom CD select atom name CD1 .and. residue name ILE end
 rename resi HISH sele resi name HIS end

Also the C-terminal atoms should be fixed:

 rename atom OT1 sele atom name O .and.  by resi atom name OT end
 rename atom OT2 sele atom name OT end

Wrong connectivities require some other actions. Usually they are result of too closely positioned atoms. In such cases covalent bond network should be edited. First center on the atom.

 image center atom 1265

and the by clicking atoms and items "DELE_BON" and "MAKE_BON" correct the bonds (MAIN_MENU:build_extend.html page 9). An alternative is also to use topology libaries to do the jobm, delete the connections between termini of different chains and add the disulfide bonds.

 make ctab sele segm name WORK_SEGM end init
 make ctab sele segm name WORK_SEGM end from topo
 dele bond sele bond range 4.0 1000.0 end
 calc bond sele segm name WORK_SEGM end disu

When atom or residue name start with spaces - they can not be changed with help of MAIN. In such a case modify the original file by using a text editor and shifting the blanks and start again with the modified file.

Include missing atoms

When there are some atoms missing, they should be inserted ("FILL_ATO"). Be careful with this step, since the non-matched atoms of a matched residue name will disappear. (for example C-terminals might be affected).

Missing atoms (for example missing hydrogens) inserted, according to their internal coordinates representation. First the Z-table is created from atom bonding connectivities. The internal coordinates are afterwards calculated according to their connectivities from atom coordinates. Missing atoms are inserted inside the BUILD module and their Cartesian coordinates calculated from internal afterwards.

Since new atoms have probably not been inserted with optimal geometry, it make sense to optimize their geometry by an quick energy minimization. First all energy terms have to be defined: Note that atom class of sulphur atoms included in disulfide bonds has to be modified after their assignment from topology residues. The same is true for C- and N-terminals. Usually it suffices to call the standard procedure (the file name variable DEF_ALL).


First energy calculation is checked and VDW and ELECTROSTATIC terms turned off:

 energy vdw off elec off
 energy sele .not old end sele all end

If the energy calculation has been successful, minimization may follow (maybe it should be repeated several times).

 minimize sele .not old end sele all end