O 12 Release Notes

O 12.0.0 (080226)

Instructions for installing O are described elsewhere.
The O v12 distribution includes the following items:

* Zip archive of the O data directory (with an appropriate date in the file name).
* Zip archive of the O job directory (with an appropriate date in the file name).
* Zip compressed executive, binary file for each OS that I support. These are:

osx - PowerPC version for Apple Macintosh.
osx86 - Intel version for Apple Macintosh.
lin - Linux version on Intel/AMD processors.
sun86 - Sun Solaris version on AMD processors.
win - Microsoft Windows version on Intel/AMD processors.
sg_X - Silicon Graphics version, via X-windows.

The binary names are not dated. When a program is run, it outputs a version number and date. The first release is 12.0.0, then bug fixes will appear with release IDs 12.0.1 etc. The bug fixes may need changes in one or more files, and usually I will put these files on the server rather than new archives.

In this release, I am using zip files rather then unix compress’ed files. If this causes a problem, please let me know!

Ov12 has the following new functionality:
* Improvements in how waters are added to a model during crystallographic refinement. This makes use of a new qualitative indicator for deciding what is or isn’t a water molecule.
* Explicit structure factor and Fourier calculations that allow rapid so-called chop Fourier calculations and water evaluation.
* Improvements in how models with strict NCS are handled. O will now make better use of PDB MTRIX records, including structure factor calculations, NCS averaging, the generation of NCS-related molecules and instanced objects. If you load a model generated with NCS-restraints, O can now easily generate the LSQ operators, and allow you to create a new PDB file with the constrained model. The latter is particularly useful for REFMAC users since this program does not allow one to refine with strict NCS-constraints.
* A new set of commands (QDS) to interactively generate small molecule coordinates, stereo-chemical restraints and torsion information. This can be done with a point-and-click interface as part of the master menu system.
* Master-menu system attempts to provide a user menu that covers the most frequently needed commands in O, some of which the novice user might not know but which are useful.
* A major overhaul of the menu system, including interactions with the keyboard arrow keys, dials info, object on/off menu, widths, fonts.... The user menu can now contain ‘blinds’ that may be expanded or compressed as needed.
* FastMap sliders now uses absolute density values instead of the cursed ‘sigma’ that I foolishly introduced long ago. You can set something in the ODB to keep using sigmas if you really want to.
* A user can now do logical AND/OR operators on ODB entries.
* Atomic properties can now be averaged to make residue-based properties.
* The user can backup and restore model data as part of a multi-level undo system. At the moment, only the QDS commands implicitly make use of this system. The user is free to activate a pair of commands to force backups and restores. I plan to retrofit some commands that could make good use of this system.
* A new, database driven grab function.
* Expanded symbol handling.
* Improved REFMAC refinement templates for the JOB system
* New environment variable to allow the running of O without a graphics system.

Ov12 has these new commands (alphabetical order):
Db_and
Db_a2r_average
Db_or
Grab_guide
HKL_chop_Fourier
HKL_upd_Fourier
Job_reset
Lsq_chain_ops
NCS_instance
NCS_sphere
QDS_atom
QDS_extend
QDS_ring
QDS_setup
QDS_undo
QDS_write
Symbol_define
Symbol_delete
Symbol_increment
Symbol_list
Undo_read
Undo_write
Water_add
Water_electrons
Water_profile

The following commands have changed names:
Fm_water_peak -> Water_peaks
Symm_object -> Symm_instance
Water_bsort -> Water_sort

The following commands have major/important changes:
NCS_average
Pdb_read
Pdb_write
Water_sort

Graph pull-down
User-menu pull-down.
Major-menu system.

New commands are described in detail elsewhere, as are bug fixes, and changes to existing commands.

There are changes to the length of the OGL ODB entries that automatically take on my preferred defaults. If you use Ov12, save or create a user dataset and then read this with version 10 or older, the image displayed in the old version of O will have the wrong fogging value (‘db_kill *ogl*’ to restore defaults).

To update a file created with an older version of O, set up the new data directory as usual, start the new O release, read in your old file, and then do the following:

O > db_kill *ogl*
O > read menu.odb
O > read stereo_chem.odb
O > save

After reading menu.odb into the database, the user menu will change to the following:

This easily allows the user to activate the new master-menu system by clicking on the text.

Menu-related
O v12 requires that the latest menu.odb is read into the user’s database. It is safest to pick up the whole data directory. If I make any later changes, separate files will be on placed on the server as may be appropriate later.

I have started master-menu system that contain User Menu entries appropriate for particular activities. So if one does the following

O > read menu_master.odb

one gets a user menu from which one can select a sub-menu devoted to a particular function. I’m planning to expand on this as I get some spare time. From today’s master-menu, you can access sub-menus that are designed for:
Rebuilding a model
Working with skeletons
Creating a small molecule, such as a ligand, with QDS.
Selecting fonts for the menu system.

Other menu’s will certainly follow. Users are welcome to modify these as they think appropriate.

Changes in stereo_chem.odb
The most important news concerns the PDB attempts at bringing some sense to the naming convention used to describe atoms in their databases. O uses atom names for all sorts of things, connectivity, stereo-chemical restraints, torsion angles etc etc, so if the names in the dictionary do not match the names in the model, there is the potential for trouble. Amino-acid atom names are unchanged (thank goodness) but RNA, DNA, very common ligands (NADP, NAD...) are affected. For example, if you download coordinates for our recent DXR structure 2JCZ (Henriksson et al., JBC 2007, 282, 19905) and look at it with the Ov11 stereo_chem.odb, you will not see the NADPH molecule that is present in the file. The Ov12 distribution, therefore, contains 2 versions of the dictionary file:
stereo_chem.odb follows the new naming convention
stereo_chem_old.odb follows the old convention.

I have no idea how long it will take for the new names to be the standard in all programs, but for now at least, I’ll keep updating both files.

Changes in menu.odb
Changes reflect the new commands, renaming a few of the old commands, the addition of Forsyth & Wells scattering factors for all elements up to uranium. The user menu ODB entry (.menu) has been changed to allow easy access to the master-menu system.

O v12 requires that the latest menu.odb is read into the user’s database if you wish to use any of these changes. The user will be warned if the version number ODB entry that is embedded in the menu.odb differs from the running program

There are no changes to the startup.odb file.

Changes in the data and job directories
There is a new file in the O data directory, menu_master.odb for use with the master-menu system. If you read this file into O, the other files used by the system will get read in as they are needed.

The job templates for refmac and refmac_chop have been updated.

Remediated Stereo-chemical dictionary
Here is a list of residues contained in the remediated stereo-chemistry dictionary stereo_chem_new.odb :

residue GLC - glucose
residue GAL - galactose
residue XYL -xylose
residue PEP - used by O
residue DIP - used by O
residue ALA
residue ARG
residue ASN
residue ASP
residue CYH
residue CYS
residue GLN
residue GLU
residue GLY
residue HIS
residue ILE
residue LEU
residue LYS
residue MET
residue MSE
residue PHE
residue PRO
residue SER
residue THR
residue TRP
residue TYR
residue PHY - phosphorylated TYR
residue PHS - phosphorylated SER
residue PHT - phosphorylated THR
residue VAL
residue A - RNA nucleotide
residue G - RNA nucleotide
residue C - RNA nucleotide
residue U - RNA nucleotide
residue DA - DNA nucleotide
residue DG - DNA nucleotide
residue DC - DNA nucleotide
residue DT - DNA nucleotide
residue AMP - adenosyl mono-phosphate
residue ADP - adenosyl di-phosphate
residue ATP - adenosyl tri-phosphate
residue SAM S-adenosyl methionine
residue NDP - NADPH
residue HOH - water, atom name O
residue SOL - water, atom name OHH
residue MG
residue CL
residue SO4 - sulphate
residue DXP - DXR substrate
residue MEP -DXR product
residue MSP - MetSox, a potent glutamine synthetase inhibitor

I began by downloading so-called ‘ideal’ model coordinates for the nucleotides, NADPH, SAM from the PDB and adopted their stereo-chemistry. It turns out that the phosphate stereo-chemistry definitions for some residues (such as NADPHs) do not follow IUPAC recommendations. I’m not sure if the necessary improper torsion angles at these phosphates are checked at the PDB. This is not a serious problem,and just corresponds to swapping the names of the branching oxygen atoms.

IUPAC recommends this naming convention:

and that is what I’ve followed. This could cause problems with dictionaries in refinement programs when they eventually follow the PDB’s lead. I have not found any problems with RNA nor DNA models.