Ov15 Notes (170118)

Always under construction

O-related Links


  1. A-Z of O

  2. How to O

  3. Ov15

O v15 (Strix nebulosa) release


What & Where

O version 15.0 is on my ov15 directory on our ftp server. Instructions for installing O are described elsewhere (in the new How to O). The O v15 distribution includes the following items:

* Zip and tar archives of the O data directory (with an appropriate date in the file name).
* Executable binary file for each OS that I support.

So far, I have only produced versions for Apple OS X (tested on El Capitan; I expect it to work on earlier releases of OS X that use Intel processors). A version will be available for Linux  (built on CentOS 6.3 but should work on all recent 64-bit versions of Linux) if requested.

I use OS X and do most of my testing on this platform. If you find a bug on any platform, please let me know.

The binary names are dated. When a program is run, it outputs a version number and date. The first release is 15.0, and any bug fixes will appear with release IDs 15.1 etc. The bug fixes may need changes in one or more files in the O data directory, and may put these separate files on the server rather than a complete new archives.

I have not seen much interest in the O-job submit system; contact me if you want the zipped directory (it remains unchanged since Ov14).

New Commands

  1. HKL_signal - this command shows the anisotropy present in a structure factor HKL project. The program can be started from the Terminal interface or via the ‘HKL signal’ blind, accessible from the Rebuild master menu.

  2. QDS_extract - this command allows you to use the stereo-chemistry of an existing residue to generate an initial QDS molecule. The QDS molecule can then be further extended to build a new ligand from the ‘Make a ligand (QDS)’ pull-down menu

  3. Auto_extend -- this command allows you to extend the results generated by Auto_2ry. I am still working on it but it works fine although there are no instructions on how to use it in ‘A-Z of O’. It is available from the ‘Auto build’ blind in the Skeleton master menu. If you use Auto_2ry, you might as well try it since it is instantaneous (despite the debug code).

  4. DB_average - this command allows you to average the values selected for an atom ODB.

New Functionality

  1. The default stereo-chemistry dictionary has been updated to allow the generation of classical secondary structures for DNA and RNA. The NDP dictionary has also been updated.

  2. QDS master menu and data ODB updated.

  3. Extensive bug fixes, everything is up-to-date as of 2017-01-17.

Updating Existing O User Files

For users who are updating from Ov12 and earlier, there are some issues to take into consideration. There are changes to the length of some ODB entries so that when Ov13, Ov14 or Ov145 reads in a user binary database created with older versions of the paper, the program will automatically take on my preferred defaults. However, there will be a breakdown in backwards compatibility in user binary databases once a user updates to the V13, V14 or V15 version. Version 13, 14 & 15 are fully compatible at the file level.

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 > read qds.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 ‘Master Menu’.