refmac 5.5 bug removal and new features


1) Bug introduced in 5.5.0047 related with HKLOUT (output file would not be written if labout is not defined) has been removed

2) Inconsistency between document and refmac about alt codes in the external distances restraints removed. Now refmac can take ALTE and ALTC. Document is consistent with the program

3) More info about external restraints has been added (distance, angle, torsion, plane, chiral, interval restraints can be defined for any pair or triple etc atoms)


1) Several compatibility issues for irix and windows were resolved. Now it should compile on windows, however this website does not have makefiles for windows yet.

2) A bug of user output columns not working correctly under certain circumstances has been removed

3) A bug related to ANOM MAPOnly use possibly leading to crash has been fixed

4) Refmac can output F+,F-,SIGF+,SIGF- to the output mtz file optionally: those of these that appear in both LABI and LABO will appear in output mtz


Now unobserved reflections in the output mtz file also have free R flag (equal to zero). It should make programs using this output file happier


1) Ligands con, com, prn were broken. Now they should be ok.

2) Added a keyword: weight auto adjust <yes|no > If the value us yes then weight will be adjusted to make sure that rmsbonds are around 0.02 or so. 'yes' is default value.


1) Now the program can read intensities only (i.e. if sigmas for intensities are not available they may not be defined). This option should be avoided. However for some cases from pdb only intensities are available. This option has been added to deal with such cases.

Line minimisation temporary disabled


1) A bug related with FAN and DELFAN maps has been removed. Now the program produces anomalous and different anomalous maps if requested (ANOM MAPOnly) or SAD refinement is performed.

Now refmac with twin refinement prints out all equivalent twin operators. It should help comparing twin laws derived by different programs.

2) A keyword allowing refinement of occupancies of anomalous scatterers has been added. If the following keyword: REFINE OREFINE ANOMALOUS

then occupancies of anomalous scatterers will be refined

3) A keyword added that controls the level of small twin domains. The keyword TWIN FILTerlevel <value>

will give a signal to the program that all domains with twin fraction less than given value should be removed. After removal of these domain the program will make sure that twin and crystallographic symmetry operators together form a group. Default value is 0.05


1) A feature has been added: If the keyword ANOM MAPOnly

as well F+ and F- have been specified in the labin statement then refmac will produce anomalous difference as well as difference anomalous maps. Map coefficients are:

m DANO_o and m DANO_o - D DANO_c

DANO_o and DANO_c are observed and calculated anomolous differences. m is figure of merit (expected phase error) and D is the maximum likelihood scale parameter that is related with <(cos(2 π s Δ x) > (expectation value) with s a reciprocal space vector Δ x is error in positional parameters

These map coefficients are calculated by default if SAD refinement is performed, i.e. (i) F+ and F- have been given, (ii) coordinate file contains anomolous scatterers and (iii) wavelength (either in mtz file or using ANOM wave keyword) or ANOM FORM f' f'' statements have been defined.

2) TLS refinement has been stabilised further

3) If keyword TLSO ADDU keyword is given then the program output coordinate file will contain anisotropic U values calculated from TLS parameters and isotropic equivalent of TLS contribution will be added to B values. At this stage this keyword should be used for visualisation and analysis purposes. Output file file thus produced should not be used in the next stage of refinement

4) Bugs related with premature termination of refinement has been removed


An introduced bug affecting SAD refinement has been removed


A bug related with the high B values of non-tls groups has been removed

Automatic definition of domains as segments or chains sometimes had some problem

Stability of the multidimensional integration to derive the posterior expectation values for twin and intensity based maximum likelihood refinement has been improved


Bug related with addition of non-tls group to one of the groups has been removed


If auto weighting is specified (note that it is default) then the program will try to make sure that zbond is between 0.2 and 1.0.

If the input pdb file had anisou card and isotropic refinement is performed then the output file contained aniosu card with only the first element non-zero

Refinement exits if function value starts to increase.

Inaccuracy in mask based solvent contribution calculations has been corrected. Now R/Rfree should look better.

If ligands are close to one of the tls groups they are not included in these groups. Only metals and solvent molecules are added to TLS groups. Note that it is users' responsibility to make sure that all atoms in the asymmetric unit belong to one or another tls group.


For some groups small twin domains were not removed correctly. Now they are removed correctly. The program makes sure that space group symmetry together with twin symmetry form a group

An option added not to add waters to tls groups. New keyword is: tlsdetails waters exclude

A little bit better option for autoweighting

Garib Murshudov
Last modified: Sun Aug 7 23:14:54 BST 2008