990423
Set 'iskip' default to 1 in DISTANCE command.
990413
Fixed a problem that makes the orthorization matrix in the header
created by x-plor unreadable.
990322
Fixed a bug that aborlishes inputting molecular weight to VM command.
990210
Fixed a bug that caused MKFILE command fail on a unix computer.
990108
Add MW command to caculate the molecular weight of a selected
part of the structure.
980610
Fix a problem in the main program; now the unix edpdb can read a
file with a filename containing catital letters.
980407
Add 'angle' option in 'X,Y,Z,W and B' so that the values at these
columm can be judged as "periodical" angles.
980402
Fix a bug which cause "from-phrase" dysfunctional since 970421.
980115
Modify the "get_command" subroutine so that the end of the PDB output
file will be marked with "END" if the CLOSE or EXIT command is used.
980101
Change the SORT command such that the options (W,-W,B and -B) now
work on the ON atoms only.
971229
Add "MKFILE" command which can be used to define a macro within
another macro.
971214
Fix a bug in the subroutines read_ar and read_ai, which causes
unexpected input if a comma is used to indicate a default value.
971203
Modify READF subroutine. If multiple chain markers are given when
reading a PDB file, the chain markers change at positions where
a residue id number becomes smaller than the previous one.
971119
Add VM command -- given molecular weight calculating possible
Vm (Matthews coef.).
971014
Start working on V97C. Make COS as the default of the WRITE command.
UNIX will overwrite existing files with the WRITE command.
Modify CLIQUE such that two atoms will not match if they share the same
entry number.
971010
rename MOVE_ALL option in MMIG as PUNCH_ALL.
fix a bug in piping -- now {a command} should work.
970523
fix one bug in RTN which causes a problem when the option keyword
SYMMETRY is spelled completely, (pointed out by Dr. S.J. Remington.)
970421
*start working on v97b version.
*build pipe (unix-like) command interpretor. Characters
'|' (vertical line) and '\' (backslash) are used for logical
'and' and 'or'. Hopefully this method may eventually replace
the "from" sub-selection, which uses recursion of subroutine
calling and is inconsistent when used for different commands.
*delete the 'recall' command whose function has been replaced
by the arrow keys.
970418
add 'if ()' statement.
970325
add 'match3d' macro in the library.
fix a bug in the subroutine 'dfgroup', which causes problem in the
unix version of edpdb when a previous command contains '/'.
delete 'monitor' subroutine which is not useful any more
for a fast modern computer.
970227
The unix version gets the window size (ie.
the number of lines in the x-window) from the system.
970214
fix a bug in CLIQUE that may make a result non-reproducible.
970211
started a new version of edpdb (v97a).
added commands ALIGN3D, PATTERN.
modified MATCH3D.
made macro overlay.edp for homologous structural overlay.
961231
The unix version sometimes has problems in defining a GROUP.
The reason is unknown yet.
960822
Mr. Ben Goodsteen wrote a subroutine for unix EDPDB, so that now on
an SGI computer one can use the up/down arrows to recall a typed-in
command and edit it.
960716
fix a bug in setw.
960712
start a new version of edpdb (v96a). all the difference in the code
between the vms and unix versions have been move to one file. in
vms it is called vms_subrtn.for; in unix, it is called unixsubrtn.f.
960701
problem: multiple selection does not work correctly
if the first command is longer than 16 characters.
fix: change the string length of txt_s in get_zone from 16
to 'max_num_chars'.
960123
problem: a bug in the unix version which occurs when the
program code is converted from VMS to unix. one problem
that this bug causes is that the symmetry card would not
work properly when a translational component was given.
fix: the edit command (s/'+/' /w) has been changed to (s/'+/' /all ">").
new code is needed to recompile the program.
951116
fix a bug in rtn.for (edp_rtn subroutine) which affects some
unix version of v95a.
950616
fix a bug in readf.for for alpha-version "exit , " command.
950615
fix a bug in "setc" command for "a1" like residue.
950610
merge sys$input and .edp command interperation so that parameter substitution
can be used for sys$input too.
950504
add MATCH3D command: Yes, for structure homology search.
950501
fix a bug in sett. now "sett i0 i1 ' '" should work.
950420
add wildcard % in ATOM command.
950418
parameterize the length of the input line.
950414
use a generic open_file statement, so that unix
system can use a file type suffix (such as .pdb).
950406
generalize the vector names.
create a "VECTOR" command that combines the old commands VV, VP, and PV.
950405
fix a bug in "subroutine root", which may affect commands
"momentuminertia" and "overlay" in the unix version.
950404
add a selection command "text".
950330
add "polar srf_red" to analyze the rotation function.
convert the online help to HTML file to be read with mosaic/www.
promote the program to version v95a.
950320
modify subroutine "monitor" to show % completeness of input for a large
PDB file.
Bug: for very large pdb file (eg. B-gal), sometimes MMIG
does not work symmetrically. (unsolve).
950301
add "update t" option.
950105
fix a potential bug in read_txt subroutine. Now the "tolower" option of setenv command should work more reliably.
941127
fix a bug in "axis file_name Vn".
^^
941114
fix delimiter problem in code files "pair","readf"
fix wildcard problem in code files "get_command"
941111
change "polar" and "euler" commands, using "TO_POLAR", "TO_EULER"
"SYMMETRY", "ASYMM" and "MOVE_TO_O" options.
941108
Fix a bug in syntax "exclude 'command' from { ... }"
941101
*Add "polar move " and "euler move" options.
940922
*modify "main_chain" subroutine -- ca, main, side commands, to fix the
problem like " main 1-162 from { residue met}". Now the program will expend
it to " main from {zone 1-162 from { residue met}}"
940811
Bug:
exit file_name cos (in case of no cell parameters defined)
940726
* add chain mark abbreviation, eg. 'a-d' stands for 'abcd' for the "chain"
command
940721
* add chain mark abbreviation, eg. 'a-d' stands for 'abcd' for the "read"
command
* modify 'correlation' command, now it calculates correlation between
specified column of the ON atoms and a given group.
940714
fix a bug in "rtn ... mult file1 file2 " command
add "verbose" env_option
add "tolower" env_option, to replace "" quatation.
ignor starting * characters
940504
1) user-definable variables
2) define parameter from the records in a group, add character increament/
decreament in parameter command.
3) delete igroupa(2,,), add sequence() array
4) add looped "goto"
5) change "type" to "write(6, )"
6) add log file
94022
1) modify euler and polar. If is there is only ON record, all its symmetry
mates will be listed.
2) Adjustable delimiter, wildcard.
3) rename the unnamed group as SCR.
4) fix a reading problem in read_ar, which may effect nayb.
940106
add "goto" "return" and label_statement.
change "command ?" to "command /?"
931108
add "command ?" HELP
add mutiple chain markers.
change :Pn to $(Pn)
add symmcheck subroutine.
930701
create edpdb_v93b,
generallize group names, (user definable)
vms commanderize EDPDB.
930630
modify edpdb.inc and some subroutines to include adjustable groups.
the current version will accept a-z 26 groups.
930622
add SORT SWAP option.
930617
fix a bug in MXINV subroutine.
930615
modify RTN to accept (RTN 2 -'#symm' fx, fy,fz)
930606
fix MMIG, a bigbig problem that may cause lost of neighboring atoms.
modify (RTN 2 0 fx, fy,fz)
930604
fix CHAIN, and EDPDB_V93A, ' ' ==> :px
fix MMIG (in DIST), a bigbig problem that may cause lost of neighboring atoms.
930602
bgt ==> b_gt, b_lt, b_btw, b_not_bwt, ....
920528
CHAIN A B
CHAIN A FROM ...
NAYB Dmax ;
B max from ...
930524
weighted OVERLAY.
930524
unitary operator in MMIG.
930415
creat v93a version
change to lower case.
930126
modify AXISDIST, ROTOUT, EDPDB_V92E to accept axis id for axis command.
930114
fix the coupling of DFGROUP and DFGROUPR in ATOM.FOR.
921215
fix DIST problem: group A can not include ON atoms.
921111
1) modify DIST to fix phi-acc plot.
2) modify FIND to accept default.
921012
1) modify DIST to output phi-acc plot
2) modify RTN 8 to transform the coordinate to "standard orientation".
920903
1) modify MORE to have from option
2) modify DFGROUP subroutine (from option) to accept {} sub-command
920832
modify edpdb_v92d.for to call smg$ system service (recall input line)
920827
1) send a tape of edpdb_v92d, edpdb_u92d to
Dr. Jung-Ja Kim
Department of Biochemistry
Medical College of Wisconsin
Milwaukee, WI 53226
2) modify edpdb_x92d.for to report fetal when a new file can not be opened.
920823
add W option in SETW command.
920821
add UDK.for
920820
1) change "exit(16**7*4)" to "exit( 4)".
2) modify readp.for to allow incomplete input.
920808
change the command name DCL to SYSTEM to make it more general.
920804
do not change the letter case in the input PDB file text (e.g. ca is
now different from CA).
920803
1) the case of text string within "" will not be change.
2) new function for FILE option.
3) add `edp_file.inc', and `edp_data.inc' files.
Rename `edpdb.cmm' to `edpdb.inc'.
920801
1) change ENCODE to WRITE, DECODE to READ
2) modify write(...'(...)') and read(....'(...)') statements
3) file name set to UPCASE.
4) delete DEFAULTFILE option in OPEN statements.
5) modify some of the 'NEW' file status in OPEN statements.
920707
1)modify order.for (SORT DFRES)
2)send Jeff Bell edpdb_v92c
3) modify brg.for, to include the iskip option.
920625
To be done:
1) modify SWITCH command
2) stop (%abort) , done
3) corrolation WB
NBE option is deleted.
920619
modify EXCLUDE command. now it can works just for one selecting command.
Add NO_CELL() function to read cell parameters from the input PDB file.
920617
modify the zone selection so that A1-A2, A1:A2, A1 to A2 works in the same way.
920512
add ROTMOMENTUM command to calculate the rotation momentum of the ON
aotms about the x,y and z axisis, the priciple rotation momentum and
the matrix which brings the principle axisis to coincide with
the x,y and z axisis.
FORMAT:
ROTMOMENTUM
EXAMPLE:
ZONE 1 - 162 ; select the ragion
ROTMOMENTUM ; calculate the momentum and the matrix
RTN 1 RTN.DAT ; apply the matrix
ROTMOMENTUM ; to check the effect of the rotation/translation
920507
add PREKIN option in DIST command to create KINEMAGE vector list.
920430
modify the blinking errror message.
920408
fix a problem in RTNOUT.FOR.
920401
add FROM option to ATOM,RESIDUE,ZONE,MATCH,BGT commands
add RECALL, EXTRACT commands
edit EDPDB.HLP with help of Dirk.
920318
modify MMI.FOR, initializing NUM_SYMM=-1.
920207
Add EULAR and POALR commands. modify MMI,EDPDB,AXISDIST to make EULAR/POLAR
work.
920201
Add HARKER command.
920128
Add MULT option for RTN output.
modify POLAR.FOR, AXISDIST.FOR
920117
Add eulerian (Z,Y*,Z**) angle in AXISDIST.FOR.
911227
Add chain selection (CHAIN.FOR)
Add warning output in RTN (RTN.FOR) whenever there is no ON atom.
change max_symm from 12 to 18.
911223
modify DFCELL (in MMI.FOR). If cell(4)=90./cell(5)=90./cell(6)=90.
there is no need to check the alignment rule.
911213
Add MOVE-O entry in MMI.FOR. The MOVE-O command will
move the molecule close to a specified point by symmetry
operators.
911210
noninteractive RTN mode will create RTN.DAT (matrix or its inverse)
as an option.
If (,/Y/SAVE) is used as the last word, the matrix will be written to
RTN.DAT. If INVE is used as the last word, the inverse matrix will
be written to a new version of RTN.DAT.
911206
noninteractive RTN mode will create RTN.DAT automatically.
911126
RTN 9 .... command does not work sometimes (unitary matrix)
Add polar angle subroutine (POLAR.FOR) to AXISDIST.FOR
modify READP.FOR
911115
Add conversion between R space group and Cardition coordinates.
(CHK_LIB:TRNSLNBx, MMI.FOR)
911114
fix a bug in volume.for, which may cause sqrt(-x).
911029
add ruler to PERMUT command
911021
RTN 7 .... command does not work sometimes
911016
change logical name pdb$data to edp_data
911010
Change the symmetry contact rearch from (-1,1;-1,1;-1,1) to (-2,2;-2,2;-2,2).
Subroutines modified are MMI(MMI,MMIR), DIST(MMIG).
Copyright 1995, Cai X.-J. Zhang. All Rights Reserved.