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: [log in to unmask] <[log in to unmask]>
>> Sent: Thursday, February 6, 2020 5:01:14 PM
>> To: Barone, Matthias
>> Cc: [log in to unmask]
>> 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" <[log in to unmask]> 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 <[log in to unmask]> on behalf of Tim Gruene
>> <[log in to unmask]> Sent: Tuesday, February 4, 2020 9:24:24 AM
>> To: [log in to unmask]
>> 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-
>>
>> [log in to unmask] 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" <[log in to unmask]> 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 <[log in to unmask]>
>>> Sent:Monday, February 3, 2020 7:14:25 PM
>>> To:Barone, Matthias
>>> Cc:[log in to unmask]
>>> 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 <[log in to unmask]>
>>> 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
>>>
>>>
>>>
>>>
>>>
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>>
>> --
>> --
>> 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
>>
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>>
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