Did not design compound strings for some time, the atom O should be without brackets…
O[Al](F)(F)F works 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 20:28 schrieb Friday <jlliu20022...@gmail.com>: > > Hi Jeroen, > > Here is what I get from running Grade using the string you sent kindly: > (O)[Al](F)(F)F > >  > > Jinyu > > On Tue, Aug 15, 2023 at 7:32 AM jeroen.mesters@uni > <jeroen.mest...@uni-luebeck.de <mailto:jeroen.mest...@uni-luebeck.de>> wrote: >> 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 <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 <mailto: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 <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 >>>> <mailto: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/
