oops, sorry, have to correct the smiles string... (O)[Al](F)(F)F
Cheers Jeroen -- Dr. math. et dis. nat. Jeroen R. Mesters https://orcid.org/0000-0001-8532-6699  University of Lübeck Institute of Biochemistry https://www.biochem.uni-luebeck.de phone: +49-451-3101-3105 Ratzeburger Allee 160 23562 Lübeck Germany -- > Am 15.08.2023 um 16:27 schrieb jeroen.mesters@uni > <jeroen.mest...@uni-luebeck.de>: > > Hello Jinyu, > > one way to go is to use the grade web server at > https://grade.globalphasing.org <https://grade.globalphasing.org/> > > As input use the „string" for AlF3(OH) which equals (OH)[Al]F)(F)F if I am > not mistaken. > > This will give you a „starting" cif file that under circumstance may need > fine-tuning concerning the angles and bond length…... > > Cheers, > > Jeroen > -- > Dr. math. et dis. nat. Jeroen R. Mesters > https://orcid.org/0000-0001-8532-6699 > > <logo_biochem.png> > > University of Lübeck > Institute of Biochemistry > https://www.biochem.uni-luebeck.de > phone: +49-451-3101-3105 > Ratzeburger Allee 160 > 23562 Lübeck > Germany > -- > >> Am 15.08.2023 um 15:38 schrieb Friday <jlliu20022...@gmail.com>: >> >> Hi Jeroen, >> >> Thank you so much for your reply! >> >> 2fofc density is almost the same the force density shown in the email, also >> seen slightly negative density as you noticed. >> >> My question is how to get a corrective cif file for this AlF3(OH) for >> refinement. AlF3 does not need a cif file, but it apparently is not correct >> for the refinement of AlF3(OH) since the transition state of AlF3 is in the >> same plate, but the AlF3(OH) is a tetrahedron. Do you know how to generate a >> cif file for the refinement of this AlF3(OH). >> >> Thanks again for your help! >> >> Jinyu >> >> On Tue, Aug 15, 2023 at 1:08 AM jeroen.mesters@uni >> <jeroen.mest...@uni-luebeck.de <mailto:jeroen.mest...@uni-luebeck.de>> wrote: >>> Dear Jinyu, >>> >>> it is not a water attacking the AlF3 but rather, by adding/mixing AlCl3 and >>> NaF you first get Al(OH)3 and over time different Al species appear >>> depending on the fluoride-ion concentration in solution. One of those >>> species can be the ALF3(OH) anion, see JBC 267(10) 6710-6718. >>> >>> The picture is not that clear/informative as to the direct surroundings and >>> constellation of the AlF species: Where is the GDP terminal phosphate >>> located and which side-chain N- and O-atoms are involved coordinating the >>> F3(OH) group? Since the picture shows negative Fo-Fc density around the >>> Al-ion, first refine the Al-ion anisotropically if not already done so. >>> Does AlF4 give you positive Fo-Fc around the putative OH? A 2Fo-Fc >>> map.would be helpful. >>> >>> J. >>> >>> >>>> Am 15.08.2023 um 02:31 schrieb Friday <jlliu20022...@gmail.com >>>> <mailto:jlliu20022...@gmail.com>>: >>>> >>> >>> >>>> Dear CCP4 community, >>>> >>>> I have a question for how to generate the correct cif file for a chemical >>>> that I can't find the correct geometry for. Basically we used ALF3 for >>>> mimicking the 3rd phosphate of a nucleotide and the water molecule is >>>> clearly attacking the 3rd phosphate (ALF3) and formed a covalent bond to >>>> the ALF3 (basically we have a leaving group of ALF3O. How do I make the >>>> correct cif for this compound, I can't find this kind of compound anyway. >>>> Please see the density of the CF3O in below. >>>> >>>> Your suggestions are highly appreciated. >>>> >>>> Jinyu >>>> <image.png> >>>> >>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> >>> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
