Known Issues in 20180515 BUSTER release:


Introduction

Please also check the BUSTER home page and the news page for updates and snapshot releases. Issues mostly related to external programs can still be active: please check here.


AWK variants

Different operating systems (CentOS, Ubuntu, OpenSuSE, Fedora, Debian, Mac OsX etc) have different policies regarding the AWK version installed by default. It can range from nawk, mawk, gawk to plain awk.

We are aware of some issues that can easily be fixed by installing the GNU version (gawk) of AWK. To have the system use gawk by default, most Linux systems provide a mechanism ("update-alternatives" command) to select a specific version. One can also check for the currently used variant via

awk --version

We try to use AWK syntax that follows the lowest common denominator as far as possible, but since we can't test against all AWK variants on all OS systems, we recommend installing gawk by default.


Reporting of R-values

The reporting of R-values within BUSTER can be slightly out of sync: what is reported on standard output (or in the top part of the REMARK header of a resulting refine.pdb) can differ from the values within the REMARK 3 section. One is done on observational scale while the values in the REMARK 3 section are done on absolute scale as done by our rvalue tool.

This tool computes R-values in equal-observation-number binning (to be consistent with the handling of anisotropic data within STARANISO and autoPROC).

In order to be sure the reports of R-values are consistent you could switch off this feature with:

% refine autoBUSTER_Remark3EqualNumberBinning=no ...

(which could result in less than ideal binning for the REMARK 3 header when using highly anisotropic data as analysed by STARANISO).

This issue will be fixed in the next release making sure that R-values computed by the rvalue tool are in sync with the other computations in BUSTER.


Animated gifs in buster-report

You may observe an issue with the animated images of ligands and their density on the ligand tab, resulting in the density not refreshing correctly. This is due to a change in recent versions of ImageMagick.

A correction will appear in the next release of BUSTER.