Re: [ccp4bb] Generating symmetry mates using python

Hi, Thank you all for your help! Of course coot works perfectly and also PISA is useful, not I am not sure both can be employed in a high-throuput manner for hundreds of structures. I looked at gemmi but am not familiar with python-mmdb, so I will take a look at that. Thank you Zhijie for the

Re: [ccp4bb] Generating symmetry mates using python

Hi Orly, REMARK 290 should be the easiest way for generating symmetry mates. Other routes are just going to give you the same results. As Jonathan already pointed out, the symm ops do not garantee that the symm copies are close to each other. The most simple-minded solution to this problem

Re: [ccp4bb] Generating symmetry mates using python

Happy New Year indeed. Thank you. If this is not just a personal programming exercise, Orly Avraham might also take a look at PISA, python-mmdb and/or gemmi. Paul. On 10/01/2020 21:48, Jonathan Cooper wrote: Hello, I am sure that you have found that if you apply the symmetry operations

Re: [ccp4bb] Generating symmetry mates using python

Hello, I am sure that you have found that if you apply the symmetry operations yourself, the resulting molecules can come out miles apart, so you need to find the right unit cell translations that bring them close together again to generate the real crystal packing. Coot does all this very

[ccp4bb] Generating symmetry mates using python

Hi all, I am a crystallographer currently employing computational methods as well as experimental crystallography. I am trying to generate symmetry mates in python (working with pandas dataframes), in order to analyze inter-sub-unit interactions. To do so I am trying to use the info in "REMARK

[ccp4bb] Postdoc position: cryo-EM project

The Kaguni lab in the Department of Biochemistry and Molecular Biology at Michigan State University seeks a talented and highly motivated postdoctoral researcher to determine the cryo-EM structure of a protein-DNA complex formed in the process of replication initiation using Escherichia coli as

[ccp4bb] Postdoc position: Computational Algorithms combining Crystallography and WAXS for Drug Discovery

Dear CCP4 Community, Please share this notice with potential candidates. A post-doctoral position is available immediately in the Grant Lab in the Department of Structural Biology at the University at Buffalo in Buffalo, NY, USA. Our group is

[ccp4bb] Save the date - CCP-EM Spring Symposium VI - 27-29th April 2020

Save the date - CCP-EM Spring Symposium - 27-29th April 2020 *** Registration will open soon *** CCP-EM are proud to announce the sixth annual 'CCP-EM Spring Symposium'. The conference aims to provide a forum to highlight state of the art developments in computational cryoEM and related

[ccp4bb] Postdoctoral position in time-resolved optical spectroscopy/crystallography at the ESRF

The European Synchrotron ESRF in Grenoble, France, will resume its activities this year after a complete machine upgrade, which will bring exciting new possibilities of experiments, in particular in time-resolved serial synchrotron crystallography (SSX). The Structural Biology Group is