Dear Eike, we have a simple automation exactly for this problem: a pipeline called DIMPLE. In Diamond it's run automatically after data collection, if the user provided pdb file.
If you have CCP4 installed try: dimple file.mtz file.pdb output_dir The last arg is a directory where you want results to be put. The results include pictures of blobs of el. density not accounted for by the model -- places where a ligand is suspected. Best, Marcin On Tue, Feb 03, 2015 at 12:00:20PM +0100, Eike Schulz wrote: > Dear all, > > I am looking for a way to automate molecular replacement and refinement > runs. > > From ligand / fragment screening trials we have many datasets of the same > protein with various resolutions (2.8 – 1.2Å). The apo-structure is known > and well refined. The cell constants are fairly similar but not in all > cases identical, hence I would prefer a MR run prior to the refinement. > > I am sure this can somehow be realised with some shell-script but maybe > there is some more sophisticated way of realising this? > > I would also be happy for partial solutions or general advise to the > problem. > > Best regards > > Eike -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
