GettingStarted

Content:

Introduction

Here we will show only the most basic initial steps you might want to work through, if this is the first time you come across autoPROC. If you are responsible for installation of the software, please check the GettingStartedAdmin page too.

In the examples below we use % to symbolise the command prompt (to show that this needs to be typed in a terminal) and it should not be typed as such.

Using autoPROC

To use autoPROC, some environmental variables need setting. For that, two files (setup.sh and setup.csh) are created during installation. Depending on the shell used, a user needs to execute one of the following commands (with the correct installation path instead of /where/ever/autoPROC):

% . /where/ever/autoPROC/setup.sh           # bash/zsh/ksh/sh
 - or -
% source /where/ever/autoPROC/setup.csh     # csh/tcsh

One can check the current shell using eg.

% echo $SHELL
% ps

So if you are using "bash" and the software was installed in /home/software/autoPROC/20200206, the relevant command would be

% . /home/software/autoPROC/20200206/setup.sh

Some sites/labs will use a different system for setting up programs and environments: please ask your local IT management. If the setup of crystallographic software is not handled automatically, you might want to add any necessary commands to your ~/.bashrc or ~/.cshrc file (note: differnet shells and differnet operating systems might use differnet files during shell startup).

Please note that all external programs used by autoPROC (CCP4, XDS) are expected to be in the users PATH and set-up correctly.

More details about those setup scripts above (and what they intend do achieve) can be found here.

Simple run

If you are desperate to get started quickly:

change into the directory with your images
just run the process command:

      % process -d 01 | tee 01.lis

if processing data in HDF5 format (e.g. from Eiger detectors):

      % process -h5 /where/ever/some_master.h5 -d 01 | tee 01.lis

That wasn't that difficult, right? However, there are various rather common issues that could prevent this simple command from performing as expected or hoped. So it might be a good idea to look at some of the other topics on this Wiki and to read the online documentation (also available locally in your installation - see process -h output for a pointer). It is also a good idea to have a printout of the autoPROC reference card: the most up-to-date version will be available in your local installation at

$autoPROC_home/docs/autoproc/manual/autoproc_reference_card.pdf

Some common next steps

Options and steps to try next - either because the simple run didn't work or you think it could be better:

Ensure that the direct beam position in the image header is correctly defined (see also BeamlineSettings for a more detailed discussion). Data from some beamlines requires additional settings (e.g. if the rotation axis runs in the opposite sense you will need to add ReverseRotationAxis=yes to the command-line).

Always look at the output messages, e.g. the "summary.html" file produced - and compare it with the manual. They give a lot of additional information and detailed analysis.

We provide a macro ("-M LowResOrTricky") for more complicated cases: this can especially stabilise parameter refinement.

If you prefer using CC1/2 as a high-resolution criteria: "-M HighResCutOnCChalf".

To use XSCALE for scaling/merging of data (instead of AIMLESS), use "-M ScalingX"). For an AIMLESS-only scaling path use "-M ScalingA3".

Consider using some manual beamstop masking to get the best (especially low-resolution) data.

this might require using XDS keywords via the autoPROC_XdsKeyword_UNTRUSTED_RECTANGLE, autoPROC_XdsKeyword_UNTRUSTED_QUADRILATERAL or autoPROC_XdsKeyword_UNTRUSTED_ELLIPSE parameters

Be careful when multiple indexing solutions where found: how are they related and where do they occur?

Try to avoid ice-rings if at all possible.

Hopefully the detector is well calibrated (all problem pixels are masked), hte meta-data in the image header is correct and any beamline/instrument-specific data handling avoids some common pitfalls (regarding masking and countrate cutoff).

Additional information can be found at: