Auto functions have been merged and now applicable on a chosen part of a molecule or residue range.
The "FIX_GEOM" menu has been merged into the "AUTO_STUFF" (MAIN_MENU:auto_stuff.html)
Peptide bond orientations of the "active" residues are set based on non-bonding interactions, recognized secondary structure targets and a density map. Can instantaneously improve peptides on a whole protein molecule. See MAIN_MENU:auto_stuff.html.
> write file xx sele segm name WORK_SEGM end atom pdb chain
Writes out amino acids according to bonding connectivities along C-N bonds and thereby reorganizes your structure with no need for editor use and shifts of residues within a file.
The file should however be read without connectivity information. The bonds need to be calculated.
See MAIN_MENU:utils.html, MAIN_UTILS:re_order_chains.com and MAIN_COM:write.html.
Averaged kick and kicked omit maps
The "KICK_STUFF" menu block has been redesigned and includes now only items related to kick definition and map calculation. The kick maps (2FO-FC) and kick omit maps (FO-FC) can now be averaged. A user should specify the number of maps, which are calculated each from a different kick, added together and at the end rescaled to sigma units.
"KICK_ACT" has been moved to the minimization block ("DEPP_MINI", page 9) as the use of the "KICK_ACT" function actually makes sense in combination with the local geometry minimizer.
"KICK_ALL" has been moved to phasing and refinement menu block ("MAP_ATOM" page 10). It was mostly used before global refinement or map calculation.
See MAIN_MENU:kick_stuff.html.
The MAIN_MENU:map_mask.html menu block has been created to join scre map and skeleton routines. Skeleton can be with the help of "SELECT" menues edited and the current contens of the key "active" atoms displayed together with its symmetry mates.
The invert chain "INV_CHAIN" scripts (MAIN_MENU:xray_build.html) have been simplified and corrected.
The macros "MAIN_CONF:menu_refine.sh" and "MAIN_CONF:create_refine.sh" include now options for mutliple steps of refinement and kicking (cooling strategies) and a new target - a density map. See also MAIN_MENU:map_atom.html.
Phase combination scripts are now created with help of a macro "MAIN_CONF:create_phase_comb.sh" and require no more user editing.
Several bugs removed:
Further steps toward automatization
Menu page 10 menu blocks is increasing (MAIN_MENU:auto_stuff.html): peptide bond function "FIX_PEPT" got side chain functions to correct the current side chain conformation "FIX_SIDE" and extend the side chain conformation "EXT_SIDE". Most some rotamers need not to be corrected manually anymore.
A bug resulted from an error correction in reciprocal space generation. Manuel Than had a P3xxx group and the map did not look right, so I've fixed that, however, I've managed to lose symmetry operations in reciprocal space unit cell egneration of complex maps and the X-TARGET function resulted in a non refining algorithm.
The bug was introduced in April 99 release. For those having MAINs created between 1-april and 1-June, be aware that your X-TARGET function does not work, you can only refine your structures using DENS-TAR function - and of course get your new MAIN executable.
"main_config" scripts: a novel mean of user - MAIN interaction
"main_config" is the highest level of user and MAIN communication. The scripts configure MAIN macros based on user input, which consist of typed file names, resolutions limits, choice of methods and some other parameters. The "main_config" utility enables a user to know less about the program, and still be able to run it. An experienced user benifits from the speed of creating "error free" macros, which can be then edited.
"main_config" is number a Bourne shell macros. See MAIN_CONF:. "MAIN_CONF:main_config.sh is only the starting one. Some general description is available in MAIN_DOC:config/config.html). Details, will however be revealed through applications in other parts of the manual.
Not all "main_config" features work with old MAIN versions, so it is time to upgrade.
WARNING: Many descriptions of the MAIN macros have become obsolete. I haven't been able to adopt complete manual yet. The "A real case" chapter and the "2 molecules" chapters are, however, essentially rewritten. "A real case" contens has been moved into "1 molecule" chapter (MAIN_DOC:1mol/1mol.html), wheras the "2 molecules chapter got a general form in "N molecules" (MAIN_DOC:nmol/nmol.html).
Variables to shell environment
The "shell" command is an equivalent to a MAIN subroutine call ( "@" or "<" ), with a difference that MAIN subroutines are essentailly internal to MAIN, wheras the "shell" commands can invoke any UNIX command.
The commands
MAIN> set vari REAL = 1.3 MAIN> shell my_command REAL
result in UNIX system call:
> my_command 1.3
Ramachandran plot works now. Adding a new graph file format required to add the format into the MAIN_UTILS:rama.com. For OpenGL version I had to fix additional problem - no graph object could be seen due to some changes in projection matrices introduced in the previous release.