Twinning disorders solvent and hydrogen atoms position with adjustment of several factors, small molecules are no so complicated as macromolecules. Regards Umer
On Fri, Jun 4, 2021, 6:41 PM Phil Jeffrey <pjeff...@princeton.edu> wrote: > Unlike macromolecular crystallography, small molecule crystallography is > infrequently starved for data. So it makes no sense at all to extend > your data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1 > to be >10% for no good reason or utility, which is what was behind my > suggestion - test to see if the data cutoff is an issue. Also about the > fastest test you can do in SHELXL. > > > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - > with 0.8Å data most small molecule crystallographers would do this as a > first step after fitting all the non-H atoms. > > Actually, adding AnisoB's and hydrogens too soon will mess up your > disorder modeling, so blanket statements like that work for well-behaved > structures but not so much for more challenging ones. > > e.g. in one of the the four structures I've done this week, one had > significant main-molecule disorder so that comes ahead of adding > hydrogens, and refining unrestrained anisoB (as is the default) for > disordered atoms is asking for trouble. It's not as cookie-cutter as > you represent, and I stick to all my suggestions. > > Phil Jeffrey > Princeton > > On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote: > > Hi > > > > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with > 0.8Å data most small molecule crystallographers would do this as a first > step after fitting all the non-H atoms. > > > > One thing I can’t agree with is to cut the resolution of your data > _unless_ you have a very, very good reason to do so. Normal small molecule > refinements will use data to ~0.8Å and not use a cut-off based on > resolution or I/sig(I). A good dataset will often go to higher resolution > and small molecule crystallographers will be very happy to use these data > (unless, as I say, they have a very good reason not to), and would > certainly have to “explain to the referees” why they didn’t if they ignored > a systematic chunk. > > > > Something else that you might not have thought of - have you actually > told SHELXL what the reflection data are - i.e., are they F, F^2, > intensity? It’s perfectly possible to solve a small molecule structure by > e.g. telling the program you’re giving it F^2 but actually giving it F, but > refinement would be somewhat less straightforward. SHELXL normally uses F^2 > in refinement, macromolecular programs still normally use F (AFAIK). > > > > What programs did you use for processing the diffraction data? > > > > Of course, lowering the R factor is not the objective of the exercise - > a lower R-factor is a consequence of having a model that fits the data > better. > > > > I would be strongly inclined to ask a small molecule crystallographer > (or someone with a strong background in it) to have a look at your data & > model - they could probably give you a definitive answer by return of > e-mail. > > > > Just my two ha’porth > > > > Harry > > > >> On 4 Jun 2021, at 03:10, Jon Cooper < > 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > >> > >> Agreed, ANIS is the command to try. > >> > >> Sent from ProtonMail mobile > >> > >> > >> > >> -------- Original Message -------- > >> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> > wrote: > >> > >> R1 of 17% is bad for small molecule. > >> 0.8 Å is in the eye of the beholder - if you're using macromolecular > cutoffs then these might be too aggressive for small molecule-type > refinement stats - try a more conservative cutoff lie 0.9 and see how that > changes R1. However I suspect it's more to do with how your model is > fitting the data. > >> > >> Have you refined anisotropic Bfactors ? > >> Have you added hydrogens ? > >> > >> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the > interface for the refinements - I use the latter and it's somewhat Coot > like with useful features that are particular to small molecule. Also > PLATON has some things (like expand-to-P1 and Squeeze) that, respectively, > might be useful to explore space group issues and disordered solvent. > PLATON also has a means to check for some forms of twinning. > >> > >> Phil Jeffrey > >> Princeton > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jacob > Summers <000060a137e4bf3a-dmarc-requ...@jiscmail.ac.uk> > >> Sent: Thursday, June 3, 2021 2:49 PM > >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > >> Subject: [ccp4bb] Lowering R factor from small molecule structure > >> > >> Greetings! > >> > >> I am currently trying to reduce the R factor of a cyclic small molecule > peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. > The molecule itself fits the density very well, but there are a few > unexplained densities around the molecule which do not seem to be anything > in the crystallization conditions. The R1 factor of the refinement is > 17.07% but I am unsure how to lower this value. Any ideas on how to better > refine this molecule or fill densities to lower the R1 factor? I do not > have much experience working with small molecule refinement or with ShelX. > >> > >> Thanks so much, > >> Jacob Summers > >> > >> ######################################################################## > >> > >> 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/ > >> > >> 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 > > > > ######################################################################## > > > > 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/ > > > > ######################################################################## > > 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/ > ######################################################################## 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/
