Hi Phil, yes, you are right. I mixed up the occupancy number with the part number.
I find these things easier in front of the res-file. Thanks a lot for correcting this. Best, Tim On Thursday, February 6, 2020 10:26:51 PM CET Phil Jeffrey wrote: > That doesn't sound right re: PART numbers > > classically: > > PART 1 > majority disordered atoms with FVAR/occupancy of e.g. "21.0000" instead > of usual "11.0000" > PART 2 > minority disordered atoms with FVAR/occupancy of e.g. "-21.0000" > PART 0 > The 21.000/-21.000 pairs makes the sum of occupancies add to 1.0, but > the actual value of each group is defined by the second free variable. > > See: http://shelx.uni-goettingen.de/shelxl_html.php#PART > The "PART 1" atoms would not interact with the "PART 2" atoms. > There's even an example for a disordered SER in the documentation. > > PART -n is used for disorders that overlap on themselves on symmetry > axes. "If n is negative, the generation of special position constraints > is suppressed and bonds to symmetry generated atoms with the same or a > different non-zero PART number are excluded; this is suitable for a > solvent molecule disordered on a special position of higher symmetry > than the molecule can take". > > I use PART 1/PART 2/PART 0 all the time in "small molecule world" but > I've used PART -1 precisely once. > > Phil Jeffrey > Princeton > > On 2/6/20 4:15 PM, Tim Gruene wrote: > > Dear Matthias, > > > > > > some developers introduce new features of their refinement programs with > > the words " ... which has been there in SHELXL since the beginning of > > time". > > > > If you are only looking for two conformations, you are looking for the > > combination of free variable number N with part N and part -N. In case you > > deal with more than two conformations, take a look at SUMP (as Jon > > suggested). > > > > The use of free variables is easier to explain right at the computer, so > > please ask a colleague near you office, who is familiar with SHELXL for > > the > > details. > > > > Best, > > Tim > > > > On Thursday, February 6, 2020 8:10:01 PM CET Barone, Matthias wrote: > >> Sorry if the mail was not clear. I figured that out now yes. As I wrote > >> in > >> the update, I found this stupid error I made and now everything looks > >> good. > >> > >> Now that I got the feeling of how shelxl works, I miss one of it's > >> features > >> in the pdb format, namely the possibility to link occupancies of a double > >> confirmation to another moiety, say a water or a double confirmation of > >> the > >> ligand. It's there a way to use something similar like FVAR in a pdb > >> file? > >> > >> > >> > >> > >> Dr. Matthias Barone > >> > >> AG Kuehne, Rational Drug Design > >> > >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > >> Robert-Rössle-Strasse 10 > >> 13125 Berlin > >> > >> Germany > >> Phone: +49 (0)30 94793-284 > >> > >> ________________________________ > >> From: bogba...@yahoo.co.uk <bogba...@yahoo.co.uk> > >> Sent: Thursday, February 6, 2020 5:01:14 PM > >> To: Barone, Matthias > >> Cc: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl > >> > >> > >> Hello, hope I can help. > >> > >> > >> OK, so here is the disp table... > >> > >> SFAC C H CL N O > >> > >> DISP $C 0.00510 0.00239 15.73708 > >> > >> DISP $H -0.00002 0.00000 0.66954 > >> > >> DISP $CL 0.18845 0.21747 1035.16450 > >> > >> DISP $N 0.00954 0.00480 28.16118 > >> > >> DISP $O 0.01605 0.00875 47.79242 > >> > >> > >> If we take these coordinates... > >> > >> N 3 0.414964 -0.147635 0.116896 11.00000 0.19533 > >> 0.44341 = > >> > >> H0A 2 0.427823 -0.138656 0.123256 11.00000 -1.50000 > >> > >> C 1 0.348035 -0.160776 0.110979 11.00000 0.20723 > >> 0.28451 = > >> > >> O 4 0.363785 -0.174154 0.102906 11.00000 0.21226 > >> 0.22954 = > >> > >> SG 5 0.177303 0.101267 0.040572 10.04000 0.06849 > >> 0.03024 = > >> > >> O 4 0.241304 0.071735 0.038567 10.96000 0.14982 > >> 0.12755 = > >> > >> ... the first N (followed by 3) is being assigned the scattering factors > >> of > >> chlorine because this element is 3rd in the SFAC list. The SG (followed > >> by > >> 5) is being assigned the scattering factors of O because the latter is > >> 5th > >> in the SFAC list. > >> > >> I think you need to check these assignments and the chlorine occupancy > >> are > >> Ok. > >> > >> Jon Cooper > >> > >> On 6 Feb 2020 11:13, "Barone, Matthias" <bar...@fmp-berlin.de> wrote: > >> > >> Dear community > >> here is an update of my shelxl problem. I solved it after an epiphany > >> last > >> night in bed... I tried countless things to get the postive density on > >> the > >> Cl under control. Markus suggested that the density came from a > >> radiolysed > >> chloride, so I tried to superimpose chlorinated and radiolysed ligands. > >> However that did not lead to anything fruitful. > >> > >> Remember that I tried to incorporate DISP of Cl into the .ins file: > >> This is the original of the protein .ins, chloride just pasted as last > >> element: SFAC C H N O S CL > >> DISP $C 0.00510 0.00239 15.73708 > >> DISP $H -0.00002 0.00000 0.66954 > >> DISP $N 0.00954 0.00480 28.16118 > >> DISP $O 0.01605 0.00875 47.79242 > >> DISP $S 0.15995 0.16998 812.87489 > >> DISP $CL 0.18845 0.21747 1035.16450 > >> > >> The upper list only creates postive density on the Chloride, the rest of > >> the map is clean and looks the same as if you would omit the DISP line > >> of Cl alltogether. The following list is coming from the .ins file of > >> the converted prodrg file: > >> > >> SFAC C H CL N O > >> DISP $C 0.00510 0.00239 15.73708 > >> DISP $H -0.00002 0.00000 0.66954 > >> DISP $CL 0.18845 0.21747 1035.16450 > >> DISP $N 0.00954 0.00480 28.16118 > >> DISP $O 0.01605 0.00875 47.79242 > >> UNIT 38 48 1 5 7 > >> > >> Pasting CL as third element in the .ins file, however, created these > >> weird > >> difference signals on the backbone O and N that I mentioned. You can > >> probably see where this is going. Here are some atoms of the protein in > >> the > >> .ins file: > >> > >> N 3 0.414964 -0.147635 0.116896 11.00000 0.19533 > >> 0.44341 = H0A 2 0.427823 -0.138656 0.123256 11.00000 > >> -1.50000 C 1 0.348035 -0.160776 0.110979 11.00000 > >> 0.20723 > >> > >> 0.28451 = O 4 0.363785 -0.174154 0.102906 11.00000 > >> > >> 0.21226 0.22954 = SG 5 0.177303 0.101267 0.040572 > >> 10.04000 0.06849 0.03024 = O 4 0.241304 0.071735 > >> 0.038567 10.96000 0.14982 0.12755 = > >> > >> And here are some atoms of the inhibitor: > >> > >> OBM 5 0.325170 0.441790 0.181777 11.00000 0.42576 > >> 0.30731 = <- oxygen CE1 1 -0.036497 0.262177 0.187030 > >> 11.00000 0.12056 0.22455 = <- carbon HE1 2 -0.028898 > >> 0.247344 > >> > >> 0.187663 11.00000 -1.20000 <- proton NAY 4 0.107745 > >> > >> 0.387704 0.210972 11.00000 0.16719 0.14264 = <- nitrogen CLAA > >> 3 0.028744999 0.271200001 0.199305996 0.500000000 <- Chloride > >> > >> Turned out that Jon had a good feeling about the swapping of the lines > >> and I did not understand Tim's comment "The scattering factor is derived > >> from the number next to the name." Once I adjusted the numbers in the > >> second column of my inhibitors to match the DISP list numbering, Rfree > >> dropped to 16.96% and the map looks notably better (see attached snap > >> shot). > >> > >> > >> Again, thank you very much for such an incredible feedback. > >> > >> Best, Matthias > >> > >> > >> > >> > >> > >> Dr. Matthias Barone > >> > >> AG Kuehne, Rational Drug Design > >> > >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > >> Robert-Rössle-Strasse 10 > >> 13125 Berlin > >> > >> Germany > >> Phone: +49 (0)30 94793-284 > >> > >> ________________________________ > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tim Gruene > >> <tim.gru...@univie.ac.at> Sent: Tuesday, February 4, 2020 9:24:24 AM > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl > >> > >> Dear Jon, > >> > >> in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you > >> like. The scattering factor is derived from the number next to the name. > >> The name is just that, and identifier. > >> > >> Best, > >> Tim > >> > >> On Monday, February 3, 2020 9:20:03 PM CET 00000c2488af9525-dmarc- > >> > >> requ...@jiscmail.ac.uk wrote: > >>> Remembered earlier that if the "CL" is not shifted one place to the > >>> left, > >>> Shelx and probably most other programs treat it as carbon, i.e. its > >>> assumed > >>> to have 6 rather than 17 electrons. Trust occupancies OK, too ;-? > >>> > >>> > >>> Jon Cooper > >>> > >>> > >>> On 3 Feb 2020 18:26, "Barone, Matthias" <bar...@fmp-berlin.de> wrote: > >>> > >>> > >>> Hi Pavel > >>> > >>> glad you write me. I was hoping you would read my post. > >>> > >>> - Yes, protons are added, both on the protein as well as on the molecule > >>> > >>> - I initially only refined protein and ligand anisotropically, now Im > >>> running a refinement with all atoms anisotrp except Hs. This would then > >>> also be the same as shelxl is doing. > >>> > >>> - Alternate conformations are modeled, also on the ligand. There are > >>> plenty, sure, but I think I got most of them. > >>> > >>> - I already used Water update during refine, there are some NO3s in the > >>> structure. I got them in. There is a second ligand somewhere as > >>> artifact. > >>> its density is not well defined, so I hope to get that in once the map > >>> clears up more. > >>> > >>> - I let phenix.refine optimize adp and chemisty weights, but as Petri > >>> suggested, Im manually increasing the scale factors to match the ones > >>> from > >>> shelxl (just to compare them properly). Im aiming for an rsmd of > >>> 0.02-0.03A > >>> like Petri suggested and keep an eye on how tight the structure is > >>> refined > >>> in shelxl. > >>> > >>> > >>> > >>> > >>> About the Rfact and the gap. Yes, thats what I was expecting. I hope if > >>> I > >>> add more anisotropic B fact, the Rfacts should go down to at least what > >>> shelxl yielded. > >>> > >>> > >>> > >>> > >>> thank you all again for the massive feedback, ideas and help. > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> Dr. Matthias Barone > >>> > >>> AG Kuehne, Rational Drug Design > >>> > >>> > >>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > >>> Robert-Rössle-Strasse 10 > >>> 13125 Berlin > >>> > >>> Germany > >>> Phone: +49 (0)30 94793-284 > >>> > >>> > >>> From:Pavel Afonine <pafon...@gmail.com> > >>> Sent:Monday, February 3, 2020 7:14:25 PM > >>> To:Barone, Matthias > >>> Cc:CCP4BB@JISCMAIL.AC.UK > >>> Subject:Re: [ccp4bb] refinement of 0.73A data in shelxl > >>> > >>> Hi Matthias, > >>> > >>> > >>> did you use correct model parameterization and optimal refinement > >>> strategy > >>> for the resolution? Such as: - Add H atoms; > >>> - Refine all but H atoms with anisotropic ADPs; > >>> - Model alternative conformations (that one'd expect many at this > >>> resolution); - Add solvent (water, crystallization cocktail components > >>> if > >>> you see any); - Relax restraints on geometry and ADPs; > >>> .... long list! > >>> > >>> > >>> If not, then what you have in terms of R factors is more or less what > >>> I'd > >>> expect. > >>> > >>> > >>> In the absence of obvious data pathologies, I'd expect Rwork/Rfree in > >>> 10-15% range, and the Rfree-Rwork gap around 1-2% or less. > >>> > >>> > >>> Since you mentioned Phenix refinement, I am happy to help you with > >>> details > >>> etc off-list. > >>> > >>> > >>> Pavel > >>> > >>> > >>> On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias <bar...@fmp-berlin.de> > >>> wrote: > >>> > >>> > >>> Dear ccp4 community > >>> > >>> Im having some problems solving a 0.73A structure. Spacegroup seems to > >>> be > >>> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. > >>> Outer > >>> shell CC1/2 24% and 90.4% complete. > >>> > >>> The model is nearly fully built, there is no remaining unmodelled areas. > >>> However, Rfactisstuck 27% in phenix, with a very distinct artifact in > >>> the > >>> electron map (see phenix.jpg). You can see difference density on various > >>> well defined sidechain atoms. Notably, they seem to follow a pattern: > >>> Nearly all Val CG have difference signal, as well as many backbone > >>> NH. Hence, I suspected that it might be a problem with the SF, since we > >>> recorded the DS at 0.86A. > >>> > >>> > >>> > >>> > >>> Hence I gave shelxl a shot: > >>> > >>> I used the refined model from phenix, converted it via pdb2ins and > >>> pasted > >>> the restraints created by prodrg. > >>> > >>> The shelxl hkl was produced by xdsconv, using the freeR flagging of the > >>> mtz > >>> used by phenix (no merge, friedel false). > >>> > >>> Interestingly, shelxl can bring Rfree down to 16% and almost all of > >>> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg). > >>> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand > >>> 2L5) which now shows massive difference density for Cl. > >>> > >>> I therefore suggested that I might deal with a wrong SF for Cl. Funny > >>> enough, pdb2ins does not produce a DISP line for Cl if converting the > >>> pdb > >>> that contains the inhibitor. Hence, I used pdb2ins and the pdb from > >>> PRODRG > >>> to produce SFAC for the inhibitor Cloride. I then pasted this line > >>> > >>> > >>> DISP $CL 0.18845 0.21747 1035.16450 > >>> > >>> > >>> > >>> into the .res file and updated the UNIT line. Shelxl runs through, and > >>> the > >>> density looks ok on the Chloride now. However Rfree is back up at 24% > >>> and > >>> the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now, > >>> very distincitvly, backbone carbonyls and NHs show difference density. > >>> > >>> Am I right in my assumption, that the SFAC of Cloride is not properly > >>> calculated at the given wavelenght? And if so, how do I guess it > >>> correctly? > >>> > >>> > >>> > >>> > >>> > >>> Thank you very much for your help! > >>> > >>> Best, matthias > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> Dr. Matthias Barone > >>> > >>> AG Kuehne, Rational Drug Design > >>> > >>> > >>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > >>> Robert-Rössle-Strasse 10 > >>> 13125 Berlin > >>> > >>> Germany > >>> Phone: +49 (0)30 94793-284 > >>> > >>> > >>> > >>> > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >>> > >>> > >>> > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >>> > >>> > >>> > >>> > >>> > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> -- > >> -- > >> Tim Gruene > >> Head of the Centre for X-ray Structure Analysis > >> Faculty of Chemistry > >> University of Vienna > >> > >> Phone: +43-1-4277-70202 > >> > >> GPG Key ID = A46BEE1A > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> ________________________________ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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