How to install arp warp in ccp4i

A number of new projects are currently being planned, some of which are described briefly on a separate CCP4i Projects page. Please report bugs and problems with CCP4i to ccp4 ccp4.

We will initially try to run the task with the same parameters as you but with our own data, however this may not always be possible. If you are concerned about confidentiality: the def file does not tell us anything about your data except the file names - if you like then you can edit the def file to change the name of the files do not delete them completely as this will make it more difficult to solve the problem.

Sometimes it can also be useful to examine the "session log" that CCP4i generates while it is running. This is a text file which is created in the user's CCP4 directory. Zanuda Space group and crystallographic origin validation jsPISA on another server Calculation and analysis of macromolecular surfaces and interfaces AMPLE Automated ab initio search model generation for molecular replacement. CRANK2 Automated structure solution pipeline for experimental phasing using maximum likelihood methods.

MoRDa MoRDa is a pipeline for molecular replacement protein structure solution based on its own domain database. Models relevant to the target sequence are further adjusted before molecular replacement search.

A replacement hgen. The dispatchers should take this version in preference to the system version whilst not effecting any other components on the system.

On systems without the file tcl. As a result idiffdisp fails to run. If this file is missing, rebuild DiffractionImage explicitly specifying the location of the tcl. There is a serious error in all the 1. The wrong 1. However I know that people have installed 1. Available from ccp4 ftp for linux , os x and windows.

Also a source can be used in ccp The bug may scramble the order of symmetry operators relative to the ISYM flags on each observation see below, technicalities , leading to an incorrect reconstruction of the original hkl indices in Scala or Aimless. This happens for MTZ input files usually from Mosflm integrated is the highest point group in higher symmetry lattices, specifically tetragonal , hexagonal , rhombohedral R32 and cubic , when the output file is also in the same point group.

Files with scrambled symmetry operators will lead to wrong reconstruction of the original indices which are used in Scala or Aimless to generate beam directions for the SECONDARY absorption correction. Thus the error will have the biggest effect on long wavelength data with substantial absorption, and have much less effect on typical short wavelength data.

High multiplicity will also tend to average out the errors. This information can then be used to reconstruct the original hkl indices measured. Thanks to Phil Evans. The input fixed model mode of molrep fails with the message linux version Fortran runtime error: End of record For binary distributions replace the molrep binary with the appropriate file for linux , os x or windows. Available from ccp4 ftp for linux , os x. A fixed version is available from the ftp site.

This version also replaces the distributed binary in automated downloads from this point onwards. Thanks to Raj Pannu. Thanks to Airlie McCoy. Thanks to Martyn Winn.

View files in coot The dictionary files are not transfered to coot. ProDrg - restraints preparation. The cprodrg executable was not recognising the title keyword. We recommend updating to the latest ligand dictionary, available here.

Replacement files for ctruncate are available for various platforms and the source bundle. These should replace the existing ones. The bundles for linux and i OS X have also been updated. Thanks to Jeff Headd. A patch is provided that can be untarred over an exisiting distribution. A replacement file is provided that replaces the check. Running through CCP4i it all works fine but outside CCP4i it causes a segmentation fault when it can't find a particular environment setting that it requires.

A fixed Linux executable is available: pisa. Under some circumstances, most likely the presence of ice rings in the data, Ctruncate may fail to give amplitude data in its output mtz file and attempting to view the Wilson plot with loggraph will result in an error.

The following patch to ctruncate. This replacement file corrects the problem using an updated ccp4i file refmac5. This is because changes have been made to the Refmac interface in CCP A workaround and fix using replacement files is given.

Either: use Run and View Com to add the correct form name project crystal dataset Or: scalepack2mtz. The solution is to manually copy the file. Using the "Analyse Protein Interfaces" task under "Structure Analysis" will give rise to the error message "cannot load assembly analysis parameters". The error is due to path variables in the pisa. This requires the user to have write permissions in the CCP4 installation area.

Note that on Mac OSX systems the user will need to use " sudo -s " to run the script. There is a minor formatting bug in the acorn. This results in failure of the program but only in the unusual case when the user has selected to use one of the more obscure options in acorn. The link below is to a patch file which will fix the source code file. Patch file for acorn. This problem occurs when trying to start iMosflm from the CCP4 interface without having set up a project and project directory in CCP4i.

This problem usually only occurs after a new installation of the suite has been performed. This is a side effect of a fix of different problem. There are 2 updated ccp4i files which should fix both problems:.

The fix is to reduce optimisation to -O1. The fix is available as a patch configure-r1. Note that compilation using Intel 9. Compilation of Refmac5. The idea was that this was a template for the required foo. However, this is not convenient and has been removed. This has now been applied to intensity output as well. This is now fixed. The documentation refers to a "configure" subdirectory that should be created as part of the installation process, and which should contain the setup files e. The phaser 2.