4.1 Reading coordinates

The format of coordinates that can be read by coot is either PDB or mmCIF. To read coordinates, choose File -> Read Coordinates from the menu-bar. Immediately after the coordinates have been read, the view is (by default) recentred to the centre of this new molecule and the molecule is displayed. The recentring of the view after the coordinates have been read can be turned off by unclicking the "Recentre?" radio-button.

To disable the recentring of the view on reading a coordinates file via scripting, use: (set-recentre-on-read-pdb 0). However, when reading a coordinates file from a script it is just as good (if not better) to use (handle-read-draw-molecule-with-recentre filename 0) - the additional 0 means “don't recentre”. And that affects just the reading of filename and not subsequent files.

Note that as of version 0.6.2 Coot can read MDL mol/mol2 files (the atom names are not unique (of course), but at least you can see the coordinates).

4.1.1 A Note on Space Groups Names

Coot uses the space group on the “CRYST1” line of the pdb file. The space group should be one of the xHM symbols listed (for example) in the CCP4 dictionary file syminfo.lib. So, for example, "R 3 2 :H" should be used in preference to "H32".

4.1.2 Read multiple coordinate files

The reading multiple files using the GUI is not available (at the moment). However the following scripting functions are available:

(read-pdb-all)

which reads all the “*.pdb” files in the current directory

(multi-read-pdb glob-pattern dir)

which reads all the files matching glob-pattern in directory dir. Typical usage of this might be:

(multi-read-pdb "a*.pdb" ".")

Alternatively you can specify the files to be opened on the command line when you start coot (see Section Command Line Arguments).

4.1.3 SHELX .ins/.res files

SHELX ".res" (and ".ins" of course) files can be read into Coot, either using the GUI File -> Open Coordinates... or by the scripting function:

(read-shelx-ins-file file-name)

where file-name is quoted, such as "thox.ins".

Although Coot should be able to read any SHELX ".res" file, it may currently have trouble displaying the bonds for centro-symmetric structures.

ShelxL atoms with negative PART numbers are given alternative configuration identifiers in lower case.

To write a SHELX ".ins" file:

(write-shelx-ins-file imol file-name)

where imol is the number of the molecule you wish to export.

This will be a rudimentary file if the coordinates were initially from a "PDB" file, but will contain substantial SHELX commands if the coordinates were initially generated from a SHELX ins file.