Changes to RPluto

April 2002 version

January 2001 version

June 2000 version

December 1999 version


Changes to RPluto - April 2002

This summarises the changes to to the April 2002 RPluto version, since the January 2001 version.

New Features

ECAL THICK gives a new display with red lines in cylinder style: the stronger the interaction, the thicker the cylinder.

DELX atom-label. This completely removes the atom specified from the atom list, and this atom is not restored by Rset command. Useful sometimes to completely tidy up some disordered sites for certain display purposes.

REREAD This re-reads the current entry from the source data file. Useful if somehow a data entry has got corrupted or RPluto is confused as to settings of certain radii. Note this is the only way to undo the effect of DELX.

KEEP This has effect of keeping only those atoms with currently displayed labels. This has useful effect of isolating just a part of a complex structure so that one can examine interactions between only the selected atoms. For example, one might KEEP just water molecules in a strucutre, or just phenyl groups.

RELABEL This resets labels of atoms when desirable because of unexexpected effects from non-CSD data sets, e.g. pdb formats, mol2 formats.
e.g. RELABEL C15 Br1 to change C15 to Br1. Note this resets the atom type.
e.g. RELABEL SEQUENTIAL to relabel all sequentially as say C1 N2 C3 C4 O5 ...

REF new command meaning look for following reference code & plot
e.g. REF BENZEN02

VATM ALL acts on all atoms in the structure.
VATM H1 CRYST shows correct volume allowing for crystal neighbour atoms.
VATM H1 NOCRYST shows correct volume with no crystal (i.e. free molecule).

COOR button now offers more output formats. The full list is as follows:

Orthogonal
No unit cell just orthogonal angstrom coordinates
Fractional
Unit cell, symmetry, fractional atom coordinates
RASMOL
All coordinates on display in subset of .mol2 for RASMOL
For RASMOL display type rasmol -mol2 myfile.ras
MOL2
Tripos mol2 format as output from ConQuest
PAI
As Orthogonal but referred to principal axes of inertia, with origin at molecular centroid.
CEL
This format for powder pattern simulation program PCW
i.e. PowderCell available via website ccp14
CSP
This format used in workshop CSP2001 (also Pluto readable)
SHELX
Minimal SHELX input file - not complete but a starter file

Bug Fixes

Correct message no appears if no atom coordinates or no unit cell given.

COLOUR BOND lab1 lab2 Ncol now works correctly, e.g. COL BOND C5 N6 8
COLOUR BOND n1 n2 Ncol works with atom sequential numbers n1 n2

RAD BOND lab1 lab2 Brad Blines Nreaks now fixed.
This displays a bond for emphasis, with a larger radius Brad, more lines Blines and optionally broken lines with Nbreaks
e.g. RAD BOND C5 C6 0.20 15 5

ECAL fixed bug which ensures correct display of NTOP top energy interactions when NTOP < NINTER (the number of interactions selected stronger than a specified Elimit). Also now corrected handling of NTOP and ELIMIT as independent options for selection of displayed interactions.

ECAL bug fixed where certain O/N H-bond acceptors not recognised. In particular urea-type O now treated as amide-type. Also fixed recognition of H-bond for N-H...N and C-OH...O(amide)

ECAL ALL now uses the last selection value, either NTOP or ELIMIT.

ECAL option C or X. When displaying only centres of molecules in SOLID mode a radius 0.50 is now set, whereas previously was set to zero.

VATM fixed bug in scanning radius to detect atoms within range. Previously was adding the van der Waals atom radius twice. The correct action is now Rscan = Rvanderwaals + Rprobe + Rvdwmax where Rvdwmax is maximum van der Waals radius in the structure.

VATM fixed bug with NOCRYS option, for those structures having more than one independent molecule in the asymmetric unit.


Changes to RPluto - January 2001

This summarises the changes to to the January 2001 RPluto version, since the June 2000 version.

New Features

New typed command MVOL for calculating molecular volume and packing coefficient.

New typed command VATM for calculating accessible volume around a specified atom (command VATM at1) or atoms of a particular element (command VATM el1). Use option CRYS to take crystal environment into account (the default), NOCRYS to consider an isolated molecule.

Modifications

When reading free format input SPGP is accepted as a synonym of the SPAC instruction, and text after the REFC instruction is interpreted as a reference code.

In ECAL some extra H-bond recognition has been added for Gavezzotti potentials [C-OH...O=C (carboxylic), C-NH...O=C, C-OH...O=C (amide), C-OH...N (oxime), C-- NH ... O=S (treat as O=C amide), and C-- OH ... O=S (treat as carboxylic) ]. It is also possible to substitute Br by S for an approximate potential.

Display of dummy points has been added to indicate empty volume in cell in the VOIDS function.

Added new option 4 to COOR output, for orthogonal coordinates in mol2 format, for base molecules or a subset of the base molecules.

Added new option 5 to COOR output, for orthogonal coordinates with respect to the principal axes of inertia.

When reading mol2 files, recognise non-standard bond types 'dl' as CSD bt 7, 'pi' as CSD bt 9, and '4' as CSD bt 4.

Bug fixes

When reading SHELX input atoms were not read unless preceded by an FVAR line. The search for atoms now begins after LATT.

The crash in RingS, when checking for a doubled ring lying on mirror plane, is now fixed. The check is now only performed if actually adding a ring.

The bug where centroids were always named X1 has been fixed; these are now named X1, X2, X3... as intended.

The first 8 characters after TITL are now copied to REFCOD. Previously they were not copied.

COOR now operates correctly as a typed command, previously COOR was only available via the menu item

Fixed bug that intermolecular contacts were not visible after PICK.


Changes to RPluto - June 2000

This summarises the changes to to the June 2000 RPluto version, since the December 1999 version.

New Features

Symmetry Detection

The symmetry detection algorithm has been extended to detect (pseudo) symmetry elements between crystallographically independent but chemically similar molecules, with the new command TMSY.

Display of multiple structures

A new facility has been added for reading and displaying more than one structure simultaneously, with certain input formats. This allows structures to be overlaid and compared visually, with the new commands KSTR, CSTR, SSTR, COL STR

Unit cell transformations

A new command STDS has been added for performing unit cell transformations. The current cell can be transformed to the standard setting automatically for certain common space groups, or the desired transformation matrix entered explicitly.

Modifications

The maximum numbers of atoms and bonds which can be displayed in a packing/ expansion plot have been increased to 2500 and 3000 respectively. The limits on atoms and bonds in the base molecules remain unchanged at 1000 and 1500 respectively.

It is no longer necessary to use the Type button before typing commands. Commands can now be typed at any time instead of selecting a menu button.

Changes to prompts for HBond button. More default responses provided, number of prompts reduced, and facility added for changing the angular tolerance for all contacts globally. HBond now operates cumulatively, i.e. existing contacts are not deleted.

Unit cell corners may now be selected for performing geometric measurements, as for atoms or centroids.

Bug fixes

Molecular symmetry detection

Improve symmetry operator multiplication procedure, to minimise the number of structures which give the errors 'Too many matrices' or 'Problem with Nmat'.

Fix bug that T(h) symmetry was not identified and point group was given incorrectly as D(2h).

Improve position of vectors and planes in symmetry operator display by averaging equivalent vector directions rather than taking first vector found.

Ensure C(3), C(5) and C(7) symmetry assigned only when the appropriate n-fold axis is present. Previously, C(n) symmetry could be identified whenever n symmetry operations were found.

Other fixes

Fixed bug that UNIT, HKLF and SFAC commands appearing after FVAR in SHELX input files were incorrectly interpreted as ATOM instructions.


Changes to RPluto - December 1999

This summarises the changes to to the December 1999 RPluto version, since the June 1999 version.

New Features

Molecular Symmetry

The main new feature is the introduction of code for approximate molecular symmetry detection, and display of the point group symbol and symmetry operators as planes, vectors and centroids.

Input Formats

Added facility for reading molecule input in Tripos Inc. Sybyl MOL format.

Other Commands

New command EXCL THYD for hiding H atoms which have only one (intra or intermolecular) connection.

Modifications

Graph Sets

In graph set code, all intramolecular first-level simple motifs S are given, not just the shortest path involving one donor and one acceptor.

Geometric Objects

The maximum number of vectors and/or planes has been increased to 96.

Input Formats

When reading MOL2 input, CRYSIN line is now recognised and coordinates transformed to fractional if this is present in input file. This relies on orthogonal coordinates in MOL2 file being generated according to Tripos, Inc. algorithm. Multiple MOL2 entries can now be read from the same file.

PDB format reading fixed, atoms are now transformed from orthogonal to fractional coordinates correctly. CONECT record is now read, so bonds in PDB file are retained. Symmetry-generated atoms are recognised automatically.

Other Commands

Atm+/- buttons now scale the radii set with Adef or VdW buttons, rather than using uniform radii.

Bug Fixes

Graph Sets

Fixed bug that doubled graph set for a ring R could be given when atoms in ring lay on a mirror plane. Now such graph sets are omitted.

Fixed bug that second-level composite chain C patterns did not always display correctly. Now atoms appear in a connected sequence without spurious atoms at ends of chain.

Fixed bug that one extra donor and acceptor were counted in such second-level composite chain C patterns.

Fixed bug that shortest ring R not always included in the final graph set matrix.

Other fixes

Fixed bug that HOME command failed to move molecule into base unit cell if original position was too many lattice translations from base unit cell.

Fixed crash in HCAL when attempting to add Me hydrogens to atom only bonded to a terminal atom. Now no hydrogens are added.

Fixed bug that SCK command did not work with certain input formats (e.g. BCCAB, MOL2, PDB, CIF).