Re: [ccp4bb] solvent mask for partial ligands, addendum
Hi Gottfried, I was wondering what happens if you make a Polder omit map for the HEPES? I am also curious, if the extra positive density is for missing bulk solvent with ligand of occupany 0.5, do you observe the density with ligand present at 0.5 occupancy to be more diffuse than with no ligand present? If we take the example of amino acid side chains modeled with dual conformations, generally an abundance of extra positive density is not observed due to side-chains having partial occupancy and missing bulk solvent. Regards, John On Thursday, December 14, 2023 at 01:55:20 PM CST, James Holton wrote: You guessed right. Bulk solvent does not get a localized "occupancy". It is set to "0" anywhere near modeled atoms, even if those atoms have an occupancy of 0.01. Yes, it might seem sensible to do "occupancy" for the bulk, but in practice it is tricky. I tried my hand at a "fuzzy" bulk solvent mask, which can be read in by refmac. It tends to perform better than the default masks, but is rather computationally intensive to make. Script here: https://github.com/bl831/fuzzymask This is perhaps a closer approximation to what you are thinking a bulk solvent mask should be? You might also want to try the Babinet inverse type of bulk solvent model. refmac supports this if you use "scale type bulk". -James Holton MAD Scientist On 12/14/2023 2:40 AM, Palm, Gottfried wrote: > I can only guess that the solvent at the place of the EPE is set to 0 > (instead of 0.5) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution
Hi Devbrat, here are a couple of other things to try: - When screening crystals use rastering to find regions of the sample where multiple lattices may be less problematic. If multiple lattices are observed, often regions on the crystal(s) close to the edge will not be as affected by twinning/multiple lattices. Also try using fine slicing if you are not already. - Try using AlphaFold to generate a model for the MR template. All the best,John On Wednesday, November 15, 2023 at 06:10:06 AM CST, Phil Evans wrote: Is the space group really P2? P21 is MUCH more common Phil > On 14 Nov 2023, at 15:55, Devbrat Kumar wrote: > > sed data were integrated with the data reduction tool AIMLESS in the CCP4i2 > suite. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] DEADLINE EXTENDED: CALL FOR PROPOSALS: neutron beam time at the Protein Crystallography Station at LANL
Dear Colleagues, The Protein Crystallography Station (PCS) is a high performance neutron beamline located at the spallation neutron source at the Los Alamos Neutron Science Center at Los Alamos National Laboratory. The PCS has a long-standing history of serving the neutron crystallographic community. The PCS is equipped with a 3He detector, offering high sensitivity and an adjustable 2-theta arm, allowing for collection of ultra-high resolution data (up to 1.1 Å data has been collected) using crystals as small as 0.3 mm3. This is an excellent opportunity for traditional X-ray crystallographers interested in diverse aspects of structural biology such as enzyme mechanisms, protein dynamics, hydrogen bonding networks, and protonation states, to determine neutron derived structures of their target proteins. We also offer mail-in services for your protein crystals and routinely screen crystals using our in-house X-ray diffractometer. Full support for protein expression, purification, deuteration, and crystallization is also available, housed in a new laboratory space. We are accepting proposals for our upcoming neutron beam run cycle starting 7 October 2014 and running until 26 February 2015. The deadline for receipt of proposals has been extended to 13 June 2014. Proposals may be submitted by clicking on the “Apply for Beamtime” link in the left column of the Lujan home page: http://lansce.lanl.gov/lujan. Additional information about the PCS can be found at http://lansce.lanl.gov/lujan/instruments/PCS.shtml. We strongly encourage you to contact us for questions concerning sample preparation, instrument capabilities, sample environments, and/or proposal preparation. Julian Chen, che...@lanl.gov John Bacik, jba...@lanl.gov Clifford Unkefer, c...@lanl.gov
