News
20.03.05 BLANC - new version
21.12.04 MOLREP - new version 9.0 (see documentation)
SFCHECK - new version 7.0 (see documentation)
. . . . . . . . .
01.07.02 MOLREP - new version 7.3.02
* pure rigid body refinement (in patterson or real space)
This possibility is useful in the last stage of MR.
For example after fitting the model into EM map.
You can use multi-domain Rigid body refinement.
* find HA positions by MR solution
* Self RF for HA position and
Heavy atom search (experimental version)
* Binaries (executable files) are available:
molrep_sgi.gz
molrep_alpha.gz
molrep_linux.gz
SFCHECK -
* Binaries (executable files) are available:
sfcheck_sgi.gz
sfcheck_alpha.gz
sfcheck_linux.gz
26.02.02 MOLREP - new version 7.2.0
* Search model orientation in electron density map
for particular position by phased RF.
* New possibility for 'Search model in electron density map'
With keyword PRF= 'S':
1.SAPTF (Spherically averaged phased translation function).
2.For current point of SAPTF solution input map is modified,
i.e program sets 0 the density outside of sphere with
radius = twice radius of model and with the centre in
current point.
3.usual Rotation function for this modified map.
4.Phased Translation functions
26.11.01 SFCHECK - new version 6.0.2
No more directory 'dic' and any dictionaries. Now all
dictionaries are inside of program.
* Partial twinning test.
Can create output file with untwinned data.
(CIF or MTZ)
* for omit procedure can create output file
with omit phases (CIF or MTZ)
* psedo-translation check
15.07.01 MOLREP - new version 7.1.0
Main difference from previous version 7.0 /28.02.2001/:
No more directory 'dic' and any dictionaries. Now all
dictionaries are inside of program.
28.02.01 MOLREP - new version 7.0.0. (beta-release)
* five times faster
* can use EM or electron density map as model or
as Fobs (BLANC or CCP4 format)
* Locked cross rotation function
BLANC:
Total improvement and correction.
New programs:
ROTDNS density map rotation
CCP42DNS convert CCP4 density map to BLANC density map
DNS2CCP4 converts density map to CCP4 format
06.11.00 MOLREP - new version 6.2.5.
* diad search for two different monomers.
* NMR model can be used.
- 14.06.00
- Home page was created
02.06.00 MOLREP - version 6.0.4. Correction for Linux.
14.04.00 Corrected version 6.0.1 of program MOLREP
10.04.00 New version 6.0 of program MOLREP
* diad (or just dimer) search
* model correction by sequence alignement
New version of program ALIGN
19.12.99
MOLREP - version 5.4
* new keyword NOSG - number of new space group if you want
to change space group of file of structure factors.
new program BLANC_HELP - gives list of blanc's programs with short
description.
11.11.99
MOLREP - version 5.3
* can just rotate and position the model and compute R-factor,CC
Use keyword FUN = 'S' and define two files: model
( keyword FILE_M ) and file of structure factors
( keyword FILE_F ). Program will rotate ( keyword ANGLES )
and position( keyword VPST ) the model and write to output
coordinate file. Also compute R-factor and Correlation
Coefficient.
TRANS - ortogonal transformation of atomic coordinates.
new keyword SMODE
SMODE: <O>/F - O - shifts in orthogonal system
F - shifts in fractional
24.10.99
MOLREP - version 5.2
* new keyword FILE_T. Program creates file of list of peaks
of rotation function or reads this file. File name is
defined by keyword FILE_T. Default is 'molrep_rf.tab'
* new style of output of RF and TF, like:
Sol_RF 36 89.82 66 ......
Sol_TF_4 1 0.00 180......
useful for grep command. See ../molrep/doc/test.doc
MIR version 4.1
* if input file was MTZ program creates new MTZ file
* with Fobs and phases.
New program BLANC2MTZ:
* writes a contents of internal BLANC files: Fobs, Fcalc,
* Phases to new MTZ file. The exit from program suite BLANC.
04.09.99 New version of program ALIGN
alignes optimally 2 aminoacid sequences. Two files can be
PDB or BLANC coordinate file or just ASCII file of sequence.
Program writes output file which is poly-alanine
model for first file with coordinates from second according
to the alignement.
File with sequence is ASCII file:
!
!# sequence
!SVIGSDDRTRVTNTTAYPYRAIVHISSSIGSCTGWMIGPKTVATAGHCIY
!# this is comment
! DTSSG--SFAGTATVSP GRNGTSYPYG
!NRGTRITKEVFDNLTNWKNSAQ
If first symbol in the line is "#" it means the line is comments
Blancs are ignored.
New program TWIN
*perfect and partial hemihedral twinning test
*can create output file with detwined data
18.07.99 New program SFVSUM
sum two vectors of structure factors: (F1 + scale*F2)
or convolution: F1(h)*scale*F2(-h)
MOLREP - version 5.1
new possibilities for keyword SURF:
SURF: <N>,Y,A,O - means to do the model correction.
O - only shift to the origin.
A - polyalanine model and all B = 20, remove from model
water molecules, H atoms, atoms with alternative
position (except first), atoms with occupacy = 0,
shift to the origin.
Y - remove from model water molecules, H atoms, atoms
with alternative position (except first), atoms
atoms with occupacy = 0 , shift to the origin,
to compute atomic accessible surface area and
replace atomic B to
B = 15.0 + SURFACE_AREA*10.0
21.06.99 New program F2CIF
writes a contents of internal BLANC files: Fobs, Fcalc, Phases
to one output formatted CIFile. The exit from program
suite BLANC.
MOLREP - new version 5.0
* Spherically averaged phased translation function.
* Phased Rotation and Phased Translation functions.
* fitting two models.
SFCHECK
* perfect twinning test
10.04.99 Modified files blanc_descr.txt and README
New program CONSEQ - converts sequence to coordinate file
which can be used for ALIGN.
New version and arragement of MIR, TRAHALO, MIR_II:
* independent from BLANC version of MIR
Now MIR is main program, others can be used only if their
input files are in BLANC format. We can have it after MIR.
TRAHALO has a lot of possibilities.
* all program are in unique tar file: mir.tar.gz
* MIR has ccp4 version which uses MTZ file
* more peaks to check, up to 20
* can take into account pseudo-translation
* three times faster
* MIR , TRAHALO can be used for SAD case
* more in blanc/mir/README
13.03.99 New version of MOLREP /Vers 4.1; 09.03.99/
* If keywords FUN = 'R' and LIST = 'L' program computes and
writes to molrep.doc all symmetry realated peaks of Rotation
Function.
* If keywords FUN = 'R' and LIST = 'L' program computes list
of peaks of Patterson and writes to molrep.doc. It may be useful
to detect pseudo-translation.
* New keyword LMIN ( see README )
09.12.98 New version of MOLREP /Vers 4.0; 09.12.98/
New feature:
* can check and manage pseudo-translation.
* check more peaks of rotation and translation function, up to 50.
* default MODE='F' is three times faster
* after Rotation Function program creats file "molrep_rf.tab"
with list of peaks of RF. You can edit and use this file
instead of compute RF again.
* can do the model correction. Correction means to remove
from model water molecul, H atoms, atoms with alternative
position (except first), atoms with occupacy = 0 , to compute
atomic accessible surface area and replace atomic B to
B = 15.0 + SURFACE_AREA*10.0
new README file
01.09.98 TRAHALO, SIR - correction for SAD case.
26.08.98 Improvement and correction in example programs
New file blanc/prog/README - how to use BLANC subroutines to
write program.
New program "fminusf" - computes ! !F1! - scale * !F2! !
MOLREP - new keyword "P2" - experimental option, if P2 (percent of
model_2) > 0 than program uses
!!Fobs!-!Fmod2!*(P2/100)! instead of !Fobs! for RF
13.08.98 Improvement and correction:
align - writes two output files which are suitable
for FIT program.
fit - can use files from ALIGN program
rotlsq - computes Rfree
angsum - correction
readPDB - now use insertion code correctly.
04.08.98 Some bugs removed.
Improvement programs:
makecif, libcheck, emin, modcheck
sfcheck
mir,sir,trahalo
New version: SFCHECK see README
02.06.98 New method of the getting BLANC. Now there is only one tar-file
for getting BLANC. See README
Much more improvements in makecif, libcheck, emin, modcheck
Correct TRPACK for Phased translation function.
Phased Fast Rotation function was reconstructed.
28.04.98 New order of messages. Now new message will be first.
Check all program for linux system. A lot of correction (small)
in all programs. New makefiles.
Please replace old version of BLANC.
13.03.98
1. New programs:
ROTFFT rigid body refinement by FFT.
2. New version:
SFCHECK see README
MOLREP see README, can create PostScript file with
CROSSROT a picture of self or cross rotation function.
SELFROT
TRFUN
19.12.97
1. New programs:
SF_CALC computes Structure factors by formula for
atomic model, can use atomic aniso B factors.
ANISOSCL calculates anisothermal scaling of two files.
completely new correct version.
GENDEN_ANISO generates electron density for atomic
model with aniso B factors.
DNS2CCP4 converts density map to CCP4 format
2. SFCHECK new version with anisothermal scaling.
Can use atomic aniso B factors.
3. more blanc_descr.txt
11.09.97
1. Correction and improvement in:
libsubr.ftn:
libutils.ftn:
in programs :
peaksrch.f
concrd.f
in superprograms :
trahalo.f (new name instead of pattsrch.f)
molrep - ccp4 version which can read MTZ file.
sfcheck - ccp4 version which can read MTZ file.
2. New programs:
risoline
angsum
mtz2cif - reads MTZ file and writes CIFile.
3. Dictionary correction:
ener_lib.cif
mon_lib.cif
symlib.blc for space group F432 and F4132
4. more blanc_descr.txt
--- change location to YORK ---
14.02.97
Global improvement and correction for all programs.
Now you can use BLANC for DEC alpha computer.
New versions of superprograms: SFCHECK, MMM, MOLREP, MIR, SIR,
PATTSRCH, MAKECIF, MODCHECK, LIBCHECK, EMIN, DENMOD
CONTACT.
New versions of programs: PSCALE, HISTOGRM, WATPEAKS
12.01.97
1. Correction in:
libsubr.ftn:
in programs :
readPDB.f
lookfl.f
in superprograms :
molrep
MIR
denmod
2. New version / "ver. 1.0 12.01.97" / :
makecif
modcheck
libcheck
emin
3. Dictionary correction:
ener_lib.cif
mon_lib.cif
4. more blanc_descr.txt
30.12.96
more blanc_descr.txt
new file: blanc/README
24.11.96
a lot of improvements and corrections and new possibilities
in programs :
makecif - see README file in blanc/make
libcheck
new programs :
MIR - atomatical heavy atom solution. Now is completely new.
computes the phases of native structure factors by use
information of several derivatives. Can use the phases
from other sources. Can use anomalous scattering,
refines phases by modification density /solvent flattening/
EMIN - energy minimization / or B_factor regularization /
minimizes the energy of structure using the restraints files
from program MAKECIF. see README file in blanc/make
MMM - Macro Molecular Minimization.
Minimizes difference between observed electron density map
and map of atomic model. Uses the restrains files from
program MAKECIF.
Program runs good enouph but this is just preliminary
version. I am going to completely change X_ray part.
20.10.96
a lot of improvements and corrections and new possibilities
in programs :
makecif - see README file in blanc/make
modcheck
libcheck
sfcheck - now can read blanc-system files.
Program "checksf" for blanc-system files is deleted.
denmod - new version which uses packing function when create
envelope.
a lot of small correction in the other programs.
06.10.96
Correction and improvement in:
libutils.ftn
libsubr.ftn
pattsrch
sir
isoline
Library mon_lib.cif was corrected for latest proposal mmCIF.
sfcheck and checksf - new possibility:
you can have local estimation
for map calculated with omit refinement
phases, i.e phases calculeted from
total omit map (see program "omit")
New parameter NOMIT - number of
cycles omit_procedure. 0 - means without
this posibility, 2 - is good.
new programs : makecif - see README file in blanc/make
modcheck
libcheck
contact - see README file in blanc/contact
the same program as "contact" in
blanc/for , but reads PDB_file and
writes to PDB_file instead of
blanc_crd files.
16.09.96
New program CONDEN - converts XY_map to YZ_map or XZ_map.
Correction in ISOLINE.
14.09.96
All programs and libraries was corrected for latest proposal
mmCIF.
Correction and improvement in:
libutils.ftn
libsubr.ftn
toblanc
readPDB
writePDB
contact - two times faster
peaksrch
pattsrch
sir
concrd - new possibility: convert ort. coords to fract.
and fract.coord to ort.
New program ISOLINE (draft) - creates PostScript file of electron
density map.
22.08.96
Now SFCHECK and CHECKSF create PostScript file.
ftp_anonymous_user contains compressed files. Use command
"uncompress".
Change file: ftp.bat. Now ftp.bat creates subdirectories,
copies files from ftp_anonymous_user and uncompresses all files.
23.06.96
All programs and libraries was corrected for latest proposal
mmCIF.
Correction:
programs: TOBLANC
A little more in blanc_descr.txt about input and output CIFiles.
12.06.96
remove program: PATT_SCALE , use now only PSCALE
Correction:
all super_program.
program: COPYFL, PSCALE
Rename "symlib.sym" to "symlib.blc"
07.06.96 total revision all programs.
Now all files of sructure factors, phase, coefficients, density
have file extension "dat". So when you tape file name for program
request you need not tape the extention. Program add the extention
automatically.
New super_program CHECKSF - as SFCHECK only for BLANC_coordinates file
and internal BLANC structure factors file. Now SFCHECK - checks
agreement PDB coordinates file and PDB structure factors file.
New program CHECK_CRD - gets information about file "crd".
This possibility was removed from readPDB.
Correction:
super_programs: PATTSRCH, SIR, MIR
programs: CONTACT, readPDB, writePDB, SORTMRG, PEAKSRCH
21.05.96
improve pattsrch
sir
new program: CONTACT - computes inter or/and intra molecular contacts.
12.05.96
correction:
libutils.ftn
libsubr.ftn:
refine
06.05.96 new version: sir
mir
pattsrch
correction:
libutils.ftn
libsubr.ftn:
phase
abcdph
phabcd
more blanc_descr.txt
24.04.96 correction:
libsubr.ftn:
peaksrch
phase
super_programs:
sfcheck
denmod
sir
pattsrch
molrep
17.04.96 new program: pscale
improve libsubr.ftn
super_programs:
denmod
omit
omit_map
sir
pattsrch
more blanc_descr.txt
15.04.96 - libutils.ftn: new subroutine GET_NSYMZ.
libsubr.ftn: a lot of corrections.
Improvement programs:
molrep
crossrot
trfun
trpack
selfrot
sfcheck - add distribution of B-factor per residue
new programs:
writePDB - instead of this possibility in program CONCRD
copyold - instead of this possibility in program CONCRD
rfadd
rfrot
surface
blanc_descr.txt - a little more.
23.03.96 - create this file.
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