Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Thank you Pavel for your input. Venkat On Wed, Apr 10, 2024 at 1:44 AM Pavel Afonine wrote: > Hi, > every time you run phenix.refine it may exclude some reflections from > refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the > number of reflections omitted ranges from

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi, every time you run phenix.refine it may exclude some reflections from refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the number of reflections omitted ranges from none to just a few, however, this may be just enough to make the resolution statistics look slightly differe

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Thank you very much Garib. Venkat On Sat, Apr 6, 2024 at 1:12 AM Garib Murshudov wrote: > Unless you are confident that twin exists you should not use twin > refinement (Occam’s razor) > > > > On 5 Apr 2024, at 17:24, venkatareddy dadireddy > wrote: > > CAUTION: This email originated from outs

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Unless you are confident that twin exists you should not use twin refinement (Occam’s razor) > On 5 Apr 2024, at 17:24, venkatareddy dadireddy wrote: > > CAUTION: This email originated from outside of the LMB: > .-owner-ccp...@jiscmail.ac.uk -. > Do not cli

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Kay and Garib, Thank you for your input. It is actually the twin refinement that gave rise to resolution discrepancy. For what reason I don't remember that I have turned the twin refinement ON and the same job was cloned again and again. With the twin refinement OFF, it gave rise to resolution

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Did you use twin refinement (is it really twin if you used that). If twin refinement was used then twin related intensities might have different resolution, in case when your crystal are pseudomerohedral twinned. Regards Garib > On 4 Apr 2024, at 18:40, venkatareddy dadireddy wrote: > > CAUT

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Venkat, so what I suggested is not the real problem. To get to the bottom of this, I suggest you show the logfiles from REFMAC5 and phenix.refine, and the output of the following command: mtzdmp experimental_data.mtz >& mtzdmp.log run on the command line. Please upload the files to some clou

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Kay, Thank you very much for your insights. Following are the cell parameters from mtz and pdb header. *MTZ: 117.8560 66.1700 70.9040 90. 91.4240 90.000* *CRYST1 117.856 66.170 70.904 90.00 91.42 90.00 C 1 2 1* The only difference is in the 3rd decimal point. Thank you

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Venkatareddy Dadireddy, do the unit cell parameters of your MTZ file and PDB file agree exactly ? Take for example a cell of (100,110,120,90,90,90) in the header of the MTZ file, and (97,110,120,90,90,90) in the CRYST1 line of the PDB file. In this example, the (50,0,0) reflection would be

[ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi, The resolution range in my MTZ file is 70.88 - 2.0 A. When I refined my structure using REFMAC5, the resolution that it gives is 70.88 - 1.94 A, the difference of 0.04 A. I also used Phenix.refine which gives the resolution output as it is in the MTZ file. Again, EDS (validation report) gives

Re: [ccp4bb] Resolution Discrepancy in Data Set

o somewhere around >>> 1.9Å >>> >>> The program Pairef can help inform your choice of high-resolution cutoff. >>> >>> This can be run from CCP4cloud, but is also available for Phenix, I believe. >>> >>> See https://www.ncbi.nlm.n

Re: [ccp4bb] Resolution Discrepancy in Data Set

This can be run from CCP4cloud, but is also available for Phenix, I > > believe. > > > > See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248825/ > > > > Hope this helps, > > > > Dave > > > > > > Dr David C. Briggs CSci MRSB > > Princi

Re: [ccp4bb] Resolution Discrepancy in Data Set

gt; about.me/david_briggs > -- > *From:* CCP4 bulletin board on behalf of Liliana > Margent > *Sent:* Wednesday, January 17, 2024 9:19:36 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Resolution Discrepancy in Data Set > > > Exte

Re: [ccp4bb] Resolution Discrepancy in Data Set

/david_briggs> From: CCP4 bulletin board on behalf of Liliana Margent Sent: Wednesday, January 17, 2024 9:19:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Resolution Discrepancy in Data Set External Sender: Use caution. Hello all, I hope this message finds you well. In my curren

[ccp4bb] Resolution Discrepancy in Data Set

Hello all, I hope this message finds you well. In my current data set, I’ve encountered a discrepancy between the completeness in the high-resolution shells in merged statistics vs the refinement statistics. For example, when I look at my merged statistics file, output by Xia2 dials, the compl

Re: [ccp4bb] Resolution cutoff in CCP4

rsday, September 24, 2020 5:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Resolution cutoff in CCP4 Hi everyone, I’ve been having an issue with the CCP4 program scatomtz to convert .sca generated from HKL2000 into .mtz. While my resolution cutoff in HKL2000 is higher (~ 2.0 A), this program cu

[ccp4bb] Resolution cutoff in CCP4

Hi everyone, I’ve been having an issue with the CCP4 program scatomtz to convert .sca generated from HKL2000 into .mtz. While my resolution cutoff in HKL2000 is higher (~ 2.0 A), this program cuts it off at 2.2 A even if I set a higher resolution limit in this program. Has anyone else experienc

Re: [ccp4bb] resolution

Last time I checked phenix.refine did not use sig(F) nor sig(I) in its likelihood calculation.  Refmac does, but for a long time it was not the default.  You can turn it off with the WEIGHT NOEXP command, or you can even run with no "SIGx" at all in your mtz file.  You do this by leaving SIGFP

Re: [ccp4bb] resolution

Dear Sam, If you have a P1 space group and your dataset was collected in a single orientation, you will have a great big gaping cusp in it. I would suggest that you submit your full dataset to the STARANISO server at http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi

Re: [ccp4bb] resolution

Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Sam Tang > Sent: Friday, July 05, 2019 15:49 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] resolution > > Dear all > > Hello again > > Thanks a lot for the numerous i

Re: [ccp4bb] resolution

looks like a case of the "if Rfree is lower than 0.300 the structure is perfect, if Rfree is higher than 0.300 your structure is completely rubbish" police striking again (some reviewers are like this). A bit like if p is smaller than 0.05 the effect is definitely real and if p is just about 0.0

Re: [ccp4bb] resolution

Well - i would always do the final refinement to the highest resolution with CC1/2 > 0.5 There may be other problems with the data - completeness low for current standards .. Does multiplicity fall off with resolution etc? Is there considerable anisotropy? both sets of R factors look surprisingl

Re: [ccp4bb] resolution

Dear all Hello again Thanks a lot for the numerous input. I received a dataset which was processed to 2.4A but refined to 3A -- this was the background I raised this question in the first place. Then I looked at the aimless statistics. At 2.4A the high resolution bin CC1/2 0.626, I/sigI 2.0, Com

Re: [ccp4bb] resolution

Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Alexandre Ourjoumtsev > Sent: Friday, July 05, 2019 09:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] resolution > > Dear Graeme, > > > Right, but you are talking about

Re: [ccp4bb] resolution

Dear Graeme, Right, but you are talking about weights that reflect the data quality and say nothing about that of the starting model ; however refinement is a comparison of a model with data. The higher resolution of the data, the more sensitive they to model imperfections. Refinement targe

Re: [ccp4bb] resolution

Pavel, Please correct if wrong, but I thought most refinement programs used the weights e.g. sig(I/F) with I/F so would not really have a hard cut off anyway? You’re just making the stats worse but the model should stay ~ the same (unless you have outliers in there) Clearly there will be a poi

Re: [ccp4bb] resolution

Hi Sam Tang, Sorry for a naive question. Is there any circumstances where one may wish > to refine to a lower resolution? For example if one has a dataset processed > to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A? > yes, certainly. For example, when information content

Re: [ccp4bb] resolution

Hi Sam, If you have good data to 2A, then I cannot imagine throwing away a significant fraction of it (there are lot of spots from 2.5-2A) will make your model better Suggest reading http://scripts.iucr.org/cgi-bin/paper?S0907444913001121 All best Graeme On 5 Jul 2019, at 06:43, Sam Tang mai

[ccp4bb] resolution

Hello everyone Sorry for a naive question. Is there any circumstances where one may wish to refine to a lower resolution? For example if one has a dataset processed to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A? Thanks! Sam Tang ##

[ccp4bb] FW: [ccp4bb] Resolution mismatch aimless/refmac

AC.UK> Subject: Re: [ccp4bb] Resolution mismatch aimless/refmac On 18 Mar 2018, at 16:02, Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> wrote: Does it matter? The refinement will only use observed reflections. It should not matter for refinement and map calculations (needs to be chec

Re: [ccp4bb] Resolution mismatch aimless/refmac

On 18 Mar 2018, at 16:02, Eleanor Dodson wrote: > Does it matter? The refinement will only use observed reflections. It should not matter for refinement and map calculations (needs to be checked carefully). However it does matter for deposition when multiple entries are analysed and the PDB d

Re: [ccp4bb] Resolution mismatch aimless/refmac

Does it matter? The refinement will only use observed reflections. As Andrew says your output from dataprocessing includes a complete list of all possible* indices* to the upper resolution limit with a Free R flag assigned to the indices. This makes it easier to keep the same FreeR assignments for

Re: [ccp4bb] Resolution mismatch aimless/refmac

Dear All, As far as I know it could happen when you are using i2. We are working to fix this problem. At the moment the best solution is to use advanced options in the refmac interface and define resolution limits explicitly. For example you can add in the advanced options: resolution 37 2.5

Re: [ccp4bb] Resolution mismatch aimless/refmac

Hi Orru, If you have used the normal CCP4 processing pipeline, the data from AIMLESS will go into the “uniqueifyy” script that adds all possible reflections to the MTZ file (down to the lowest possible resolution for your unit cell dimensions), so that might explain why the low resol

[ccp4bb] Resolution mismatch aimless/refmac

Dear All, I am noticing that the low resolution in the reflections files after scaling with aimless and after refinement with refmac does not coincide. In a case I have 37A with aimless but for some reason refmac is 67A. Any idea? All the best, R.

Re: [ccp4bb] Resolution cut off

into > doing paired refinement by forging the header of your pdb file. > > > > HTH, > > Robbie > > > > Sent from my Windows 10 phone > > > > *From: *Graeme Winter > *Sent: *maandag 12 februari 2018 20:48 > *To: *CCP4BB@JISCMAIL.AC.UK > *Subject:

Re: [ccp4bb] Resolution cut off

<mailto:graeme.win...@diamond.ac.uk> Sent: maandag 12 februari 2018 20:48 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Resolution cut off The most useful information for this can come from paired refinement, which will tell you if the data in outer shell is improvi

Re: [ccp4bb] Resolution cut off

... Best wishes Graeme From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vands [vanx...@gmail.com] Sent: 12 February 2018 19:27 To: ccp4bb Subject: [ccp4bb] Resolution cut off Hi, I solved a crystal structure at 1.69 A resolution with R /R

[ccp4bb] Resolution cut off

Hi, I solved a crystal structure at 1.69 A resolution with R /R free 18 / 20 i used 1.69 A data. Data completeness is 100 % and for the outer shell, it's 50 %. for i /Sig I > 1. Do I need to cut resolution in refinement?? Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry a

Re: [ccp4bb] resolution limits

Andrew, phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you have a good reason to disable this, then use xray_data.outliers_rejection=false. P.S.: There is Phenix mailing list for Phenix-related question

Re: [ccp4bb] resolution limits

Hi Eleanor, what you say is of course true, particularly in the case of the 1st dataset where probably the indices go down to 52 Ang. but the measurements only start at 36 Ang. But still it's hard to see how for the 2nd dataset, if the low res cut-off of the indices and/or measurements is 57 Ang.,

Re: [ccp4bb] resolution limits

The resolution limits of the measured data are not changed but your output file must contain all possible h k l even if there is no observations for the lowest resolution ones.. dont worry about it! Eleanor On 26 July 2017 at 08:36, Andrew Marshall wrote: > Dear crystallographers, > > I have t

[ccp4bb] resolution limits

Dear crystallographers, I have two datasets that were merged/scaled using ccp4's aimless, with resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for the other. 1) Why does phenix.refine change the low resoluti

Re: [ccp4bb] Resolution, R factors and data quality

Hi Frank and Ian, We struggled with the small changes in free R-factors when we implementing the paired refinement for resolution cut-offs in PDB_REDO. It's not just the lack of a proper test of significance for (weighted) R-factor changes, it's also a more philosophical problem. When should you r

Re: [ccp4bb] Resolution, R factors and data quality

On 1 September 2013 11:31, Frank von Delft wrote: > >> 2. >> I'm struck by how small the improvements in R/Rfree are in Diederichs & >> Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/); >> the authors don't discuss it, but what's current thinking on how to >> estimate the

Re: [ccp4bb] Resolution, R factors and data quality

On 1 September 2013 11:31, Frank von Delft wrote: > > 2. > I'm struck by how small the improvements in R/Rfree are in Diederichs & > Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/); > the authors don't discuss it, but what's current thinking on how to > estimate the expe

Re: [ccp4bb] Resolution, R factors and data quality

chakrabort...@gmail.com <mailto:arko.chakrabort...@gmail.com>] *Sent:* Tuesday, August 27, 2013 7:45 AM *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* Re: [ccp4bb] Resolution, R factors and data quality Hi all, does this not again bring up the still prevailing adhe

Re: [ccp4bb] Resolution, R factors and data quality

Hi Bernhard, > But the real objective is – where do data stop making an improvement to the > model. The categorical statement that all data is good > > is simply not true in practice. It is probably specific to each data set & > refinement, and as long as we do not always run paired refinement a

Re: [ccp4bb] Resolution, R factors and data quality

Jim, This is coming from someone who just got enlightened a few weeks ago on resolution cut-offs. >>I am asked often: What value of CC1/2 should I cut my resolution at? << The K&D paper mentioned that the CC(1/2) criterion loses its significance at ~9 according to student test. I doubt that

Re: [ccp4bb] Resolution, R factors and data quality

> what if the reviewer has no clue of these things we call structures ? I think > for those people table 1 might still provide some justification. Someone who knows little about structures probably won’t appreciate the technical details in Table 1 either J rgen Sent from my iPad On Aug

Re: [ccp4bb] Resolution, R factors and data quality

Hi, a random thought: the data resolution, d_min_actual, can be thought of as such that maximizes the correlation (*) between the synthesis calculated using your data and an equivalent Fmodel synthesis calculated using complete set of Miller indices in d_min_actual-inf resolution range, where d_mi

Re: [ccp4bb] Resolution, R factors and data quality

What a statement ! Give reviewers maps, I agree however, what if the reviewer has no clue of these things we call structures ? I think for those people table 1 might still provide some justification. I would argue it should go into the supplement at least. Jürgen Sent from my iPad On Aug 28,

Re: [ccp4bb] Resolution, R factors and data quality

> We don't currently have a really good measure of that point where adding the extra shell of data adds "significant" information > so it probably isn't something to agonise over too much. K & D's paired refinement may be useful though. That seems to be a correct assessment of the situation and

Re: [ccp4bb] Resolution, R factors and data quality

with an arbitrary resolution cut-off based on a value of Rmeas already? And > now we are going to replace that with an arbitrary resolution cut-off based > on a value of CC* or is it CC1/2? > > > > I am asked often: What value of CC1/2 should I cut my resolution at? What

Re: [ccp4bb] Resolution, R factors and data quality

off based on a value of CC* or is it CC1/2? > > ** ** > > I am asked often: What value of CC1/2 should I cut my resolution at? > What should I tell my students? I've got a course coming up and I am sure > they will ask me again. > > ** ** > > Jim**** >

Re: [ccp4bb] Resolution, R factors and data quality

tell my students? I've got a course coming up and I am sure they > will ask me again. > > Jim > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka > Chakraborty [arko.chakrabort...@gmail.com] > Sent: Tuesday, August 27, 2013 7:45 AM > To: CCP

Re: [ccp4bb] Resolution, R factors and data quality

got a course coming up and I am sure they will ask me again. Jim _ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka Chakraborty [arko.chakrabort...@gmail.com] Sent: Tuesday, August 27, 2013 7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution, R fact

Re: [ccp4bb] Resolution, R factors and data quality

and I am sure they > will ask me again. > > Jim > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka > Chakraborty [arko.chakrabort...@gmail.com] > Sent: Tuesday, August 27, 2013 7:45 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Resolution

Re: [ccp4bb] Resolution, R factors and data quality

K<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf of Arka Chakraborty [arko.chakrabort...@gmail.com<mailto:arko.chakrabort...@gmail.com>] Sent: Tuesday, August 27, 2013 7:45 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Resolution, R factors and data quality

Re: [ccp4bb] Resolution, R factors and data quality

lf of Arka Chakraborty [arko.chakrabort...@gmail.com] Sent: Tuesday, August 27, 2013 7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution, R factors and data quality Hi all, does this not again bring up the still prevailing adherence to R factors and not a shift to correl

Re: [ccp4bb] Resolution, R factors and data quality

Hi all, does this not again bring up the still prevailing adherence to R factors and not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. Phil Evans has indicated).? The way we look at data quality ( by "we" I mean the end users ) needs to be altered, I guess. best, Arka Chakrabort

Re: [ccp4bb] Resolution, R factors and data quality

The question you should ask yourself is "why would omitting data improve my model?" Phil On 27 Aug 2013, at 02:49, Emily Golden <10417...@student.uwa.edu.au> wrote: > Hi All, > > I have collected diffraction images to 1 Angstrom resolution to the edge of > the detector and 0.9A to the corne

Re: [ccp4bb] Resolution, R factors and data quality

off of (reasonably complete) high resolution shells. LG, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Emily Golden Sent: Dienstag, 27. August 2013 07:48 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution, R factors and data quality Thanks Yuriy and

Re: [ccp4bb] Resolution, R factors and data quality

Excellent point about R-factors. Indeed, at this resolution they should be quite lower than what you have. Did you: - model solvent? - use anisotropic ADPs? - add H (this alone can drop R by 1-2%)? - model alternative conformations? - How R-factors (Rwork) look in resolution? Pavel On Mon, Aug 26

Re: [ccp4bb] Resolution, R factors and data quality

Thanks Yuriy and Pavel, at this resolution one would expect R/Rfree to be ~ 10-11%/12-13% assuming you applied anisotropic B-factor refinement ( and probably having a low symmetry SG). R merge of 80% may be OK if I/sig for high res shell is >2. Yes, I used anisotropic Bfactors and the space grou

Re: [ccp4bb] Resolution, R factors and data quality

Hi Emily, I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A > shell. > > However, my Rmerge in the highest shelll is not good, ~80%. > > The Rfree is 0.17 and Rwork is 0.16 but the maps look very good. If I > cut the data to 1 Angstrom the R factors improve but I feel the

[ccp4bb] Resolution, R factors and data quality

Hi All, I have collected diffraction images to 1 Angstrom resolution to the edge of the detector and 0.9A to the corner.I collected two sets, one for low resolution reflections and one for high resolution reflections. I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A shel

Re: [ccp4bb] Resolution limit of index in XDS

Behalf Of Kay Diederichs Sent: Thursday, March 21, 2013 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote: >Dear Tim, > >It could be that COLSPOT does not rely on experimen

Re: [ccp4bb] Resolution limit of index in XDS

N_RANGE . best, Kay > >Best regards, >Herman > > > >-Original Message- >From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] >Sent: Wednesday, March 20, 2013 11:17 PM >To: Schreuder, Herman R&D/DE >Cc: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit o

Re: [ccp4bb] Resolution limit of index in XDS

o:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim >Gruene >Sent: Tuesday, March 19, 2013 11:06 PM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit of index in XDS > >-BEGIN PGP SIGNED MESSAGE- >Hash: SHA1 > >Dear Niu, > >indexing relies on strong reflect

Re: [ccp4bb] Resolution limit of index in XDS

March 20, 2013 11:17 PM To: Schreuder, Herman R&D/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, the short answer might be that at the stage of COLSPOT the term 'resolution' has a limi

Re: [ccp4bb] Resolution limit of index in XDS

solution cutoff for COLSPOT as > well. > > Best, Herman > > > -Original Message- From: CCP4 bulletin board > [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: > Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: > Re: [ccp4bb] Reso

Re: [ccp4bb] Resolution limit of index in XDS

, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, indexing relies on strong reflections only, that is (in very brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections

Re: [ccp4bb] Resolution limit of index in XDS

Hello, The way I do it is by manually editing the SPOT.XDS file (generated by the COLSPOT step). Spots are arranged by order of decreasing intensity in that file. So if you do down the file, select an appropriate intensity cutoff and then remove all spots below that value, it will have the ef

Re: [ccp4bb] Resolution limit of index in XDS

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, indexing relies on strong reflections only, that is (in very brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in COLSPOT which in turn are used by IDXREF. You can work around this, however, by making use o

[ccp4bb] Resolution limit of index in XDS

Dear All, Is there any command can set the resolution limit for index step in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a definition of resolution range after index step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Than

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Dear Dr Zhu, I hope the following might make things easier to grasp. The 3.0Angstrom diffraction resolution is basically required to resolve a protein polypeptide chain whether your protein is in an 80% solvent content unit cell or a 50% solvent content unit cell. You will have more observations

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

s everything is ideal. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guangyu Zhu Sent: 15 March 2013 00:28 To: ccp4bb Subject: [ccp4bb] Resolution and data/parameter ratio, which one is more important? I have this question. For exmaple, a protein could be crystallized

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Well, when it comes to observations/parameters, it is important to remember that not all observations are created equal. 10,000 "observations" with I/sigma = 1 are definitely not as desirable as 10,000 observations with I/sigma = 10. Not all parameters are created equal either. Yes, you ma

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Dear Guangyu Zhu, if this is not a hypothetical case you can refine both structures in each crystal form separately using whatever software and compare them later. The structure can be refined also in both crystal forms simultaneously using the multi crystal NCS refinement as implemented in MAIN

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

ngyu From: Ian Tickle mailto:ianj...@gmail.com>> Date: Friday, March 15, 2013 6:33 AM To: System Administrator mailto:g...@hwi.buffalo.edu>> Cc: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" mailto:CCP4BB@jiscmail.ac.uk>> Subject: Re: [ccp4bb] Resolution

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

uangyu > > From: Ian Tickle > Date: Friday, March 15, 2013 6:33 AM > To: System Administrator > Cc: "CCP4BB@JISCMAIL.AC.UK" > Subject: Re: [ccp4bb] Resolution and data/parameter ratio, which one is > more important? > > > Hi Guangyu, > > I think

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

! Guangyu From: Ian Tickle mailto:ianj...@gmail.com>> Date: Friday, March 15, 2013 6:33 AM To: System Administrator mailto:g...@hwi.buffalo.edu>> Cc: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" mailto:CCP4BB@jiscmail.ac.uk>> Subject: Re: [ccp4bb] Resoluti

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Hi Guangyu, I think it's not as straightforward as comparing d/p ratios, that is only one of several factors that influences precision. Another important factor would be the overall level of thermal motion & disorder which will most likely be significantly higher in the 3.6A 80% case; after all t

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Zhu Sent: Friday, March 15, 2013 1:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Resolution and data/parameter ratio, which one is more important? I have this question. For exmaple, a protein could be crystallized in two crystal forms. Two crystal form have same space group, and 1 molecule/a

[ccp4bb] Resolution and data/parameter ratio, which one is more important?

I have this question. For exmaple, a protein could be crystallized in two crystal forms. Two crystal form have same space group, and 1 molecule/asymm. One crystal form diffracts to 3A with 50% solvent; and the other diffracts to 3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=

Re: [ccp4bb] resolution limit

Hi Narayan, there's nothing wrong with using data with I/sigmaI 2.5, Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. However, when you discarded frames you might have made the data worse - one should only reject data if they deviate systematically (e.g. from radiation damage). Weak

Re: [ccp4bb] resolution limit

I was [too] obliquely alluding to this thread... http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html JPK On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski wrote: > http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html > > > > > Rsym...what's that? > > > > JPK > > > > On Wed, Jul 18

Re: [ccp4bb] resolution limit

http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html > Rsym...what's that? > > JPK > > On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski > wrote: > >> As has been shown recently (and discussed on this board), Rsym is not >> the >> best measure of data quality (if any measure at all): >> >> ht

Re: [ccp4bb] resolution limit

Rsym...what's that? JPK On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski wrote: > As has been shown recently (and discussed on this board), Rsym is not the > best measure of data quality (if any measure at all): > > http://www.sciencemag.org/content/336/6084/1030.abstract > > > > > narayan viswa

Re: [ccp4bb] resolution limit

As has been shown recently (and discussed on this board), Rsym is not the best measure of data quality (if any measure at all): http://www.sciencemag.org/content/336/6084/1030.abstract > narayan viswam wrote: >> Hello CCP4ers, >> In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI

Re: [ccp4bb] resolution limit

narayan viswam wrote: Hello CCP4ers, In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. The

Re: [ccp4bb] resolution limit

Hi Narayan My only comment would be that P622 is a fairly uncommon space group (currently 43 PDB entries excl homologs), but obviously that doesn't mean it's wrong - just worth double-checking! Just out of interest what's the CC(1/2) statistic for your highest shell? Personally I specify more bi

[ccp4bb] resolution limit

Hello CCP4ers, In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. The water content is 68%. I low

Re: [ccp4bb] "resolution" on PDB web page

I had heard that there was a world-wide Tungsten shortage, but this is ridiculous! JPK On Wed, Apr 25, 2012 at 1:29 PM, H. Raaijmakers wrote: > That's nothing. Once someone wrote me because the tungsten atom of my > "Tungsten containing formate dehydrogenase" had dissapeared. > Lost in translati

Re: [ccp4bb] "resolution" on PDB web page

That's nothing. Once someone wrote me because the tungsten atom of my "Tungsten containing formate dehydrogenase" had dissapeared. Lost in translation during some autoscripted conversion. It was corrected soon enough.:) Cheers, Hans Jan Dohnalek schreef: > There have been other manipulations

Re: [ccp4bb] "resolution" on PDB web page

. Berry Sent: Wednesday, April 25, 2012 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] "resolution" on PDB web page We also use the US portal. Can't speak to the solvent content as we never had a value much over 70%. As for the resolution range, I never saw any place to ente

Re: [ccp4bb] "resolution" on PDB web page

Original message >Date: Wed, 25 Apr 2012 11:08:52 -0400 >From: CCP4 bulletin board (on behalf of "Edward A. >Berry" ) >Subject: Re: [ccp4bb] "resolution" on PDB web page >To: CCP4BB@JISCMAIL.AC.UK > >My apologies, I guess there is a separate en

Re: [ccp4bb] "resolution" on PDB web page

Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Wednesday, April 25, 2012 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] "resolution" on PDB web page We also use the US portal. Can't speak t

Re: [ccp4bb] "resolution" on PDB web page

b/explore/explore.do?structureId=1vkk Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Wednesday, April 25, 2012 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] "resolution" on PDB web page We

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