[ccp4bb] New version SHELXL 2016/6 and PDB2INS

SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very

Re: [ccp4bb] cif-file macro?

Edwin Pozharski writes: > I expect this not to exist, but is there a way to define a variable in > a cif-file (e.g. a global esd target for, say, angles)? No, I don’t think either CIF or CIF2 have such variables/macros, I’m afraid. -- Ian Clifton ⚗ ℡: +44

[ccp4bb] cif-file macro?

I expect this not to exist, but is there a way to define a variable in a cif-file (e.g. a global esd target for, say, angles)? I am certainly capable of putting together a bash script to emulate this, so please don't bother with suggesting a workaround unless you really enjoy that kind of thing

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

I'll also recommend Buccaneer. You might try using a combination of PARROT for density modification and NCS averaging followed by autobuilding with BUCCANEER using initial phases from your MR solution. You only have two copies of the protein in the ASU, so you only get a modest boost in

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

Hi Vikram, Try Buccaneer, it works much better at such resolution than Arp/Warp. Launch it several times with different parameters (e.g. use original structure as seed/initial/nothing), then open the results together and merge the pieces that look best and have lowest b-factors. Use Buster

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

Well - it sounds hopeful but still challenging.. First suggestion - are you SURE the SG is C2221 and not C222? If your two molecules are related by a NC translation of x_tran, y_tran, 1/2 then you will get the apparent absences along the 0 0 l axis which suggest SG C 2221 but the true SG could

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

Hi Vikram, lots of questions for you: - what do the images look like? Were there “contaminating” lattices? Did the spot shape look ok? Do they get worse later in the data collection, i.e. do you have radiation damage? Is the image quality regular or worse at certain angles? - how good is the

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal have a look at : https://doi.org/10.1107/S0907444910002763 Acta Cryst. (2010). D66, 514-521 Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions S. Trapani, G. Schoehn, J. Navaza and C. Abergel Best, --- Stefano Trapani Maître de

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

Hi everyone, We are trying to solve a protein structure of 2.6 A. We have processed it with HKL2000. We have even tried processing with mosflm and xia2. It is in C2221 space group (checked by pointless) and data is not twinned. It has 31% identical with a search model and has 57% sequence

[ccp4bb] suggestion for structure solution of a protein with low sequence identity

Hi everyone, We are trying to solve a protein structure of 2.6 A. We have processed it with HKL2000. We have even tried processing with mosflm and xia2. It is in C2221 space group (checked by pointless) and data is not twinned. It has 31% identical with a search model and has 57% sequence

Re: [ccp4bb] metal electron density detection

If figured out by yourself, this web page would help; http://tanna.bch.ed.ac.uk/ METAL COORDINATION SITES IN PROTEINS tanna.bch.ed.ac.uk METAL COORDINATION SITES IN PROTEINS (last updated August 2011) This website assembles information about the geometry and

Re: [ccp4bb] metal electron density detection

Hi Ansuman, Do you really want to do this in an automated way? Wouldn’t you rather figure it out for yourself? There is some automation in Phenix for ion building, but you still need to verify yourself. The CheckMyMetal server is quite good for that, but beware that to some extent you find

Re: [ccp4bb] metal electron density detection

Dear Ansuman, this could help you, it explain how it's working on Phenix.refine Echols, N., Morshed, N., Afonine, P.V., McCoy, A.J., Miller, M.D., Read, R.J., Richardson, J.S., Terwilliger, T.C., and Adams, P.D. (2014). Automated identification of elemental ions in macromolecular crystal

Re: [ccp4bb] metal electron density detection

Hi Ansuman, Phenix.refine* will place metal ions if you ask it to: - *Ion placement* extends solvent picking to build elemental ions such as calcium and zinc. To enable this option, simply enter a list of the elements to search for; this will also enable solvent picking as a first

[ccp4bb] metal electron density detection

Hi all, Is there any program (like ARP/wARP) available to locate the correct metal atom automatically in the electron density ? best, Ansuman

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal, the EM2DAM program from the ATSAS package for SAXS (https://www.embl-hamburg.de/biosaxs/manuals/em2dam.html ) can convert any EM envelope to a dummy-atom model in pdb format. Also, the recent SUPALM algorithm might provide

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal, A while ago when I did my tests on MR at a very low resolution, I did it both with “shaped” envelopes and with the “flat” ones. It did work for both (with simulated data, which is obviously not the same as the experimental), but MR with the “shaped” models was more robust. Some

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal, I'm assuming that you're talking about using the negative stain image as an MR model. I don't recall hearing of this having ever worked (though I would be very interested of course if anyone has managed to do this!), but my intuition is that it's not going to work. Negative

[ccp4bb] Postdoctoral positions at the University of Limerick

*Postdoctoral positions – Molecular Structural Biology at the University of Limerick, Ireland* Post-doctoral positions are available for highly motivated, hard-working candidates to join a research group interested in investigating the structure and function of selected membrane proteins. The