I’d have to say that Phil is possibly one of the small molecule crystallographers who could probably sort this out in a flash - hence my last suggestion…
Harry > On 4 Jun 2021, at 14:40, 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/
