Re: [ccp4bb] Bad density for chains

gt; Pointless and Ctruncate analyses didn't show twinning or NCS. I have > checked the space group using Zanuda. We are stuck at a free value of 32. > > On Thu, Jan 26, 2017 at 4:47 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk > > wrote: > >> This is a bit too vague t

Re: [ccp4bb] Glass etching of structure

I would ask Steve Gamblin or Phil Walker - they had some done last year. philip.wal...@crick.ac.uk or steve.gamb...@crick.ac.uk On 28 January 2017 at 15:26, Nicholas Larsen < nicholas_lar...@h3biomedicine.com> wrote: > Dear All, > I'm sorry if this is off topic, but it might be of interest to

Re: [ccp4bb] excluding residues from NCS

Could you rename it for the time being - ASN or LEU for ASP or some such cheat? Not sure whether local NCS requires identical residue names as well as conformations.. Eleanor On 21 February 2017 at 10:39, Alice Dawson (Staff) wrote: > Dear all > > I am working on a

Re: [ccp4bb] AW: [ccp4bb] Problem with MolRep

Check solvent % - as suggested low solvent content means tight packing means poor signal. Check matthews coefficient ? Do you expect several molecules? As suggested - does the model form an oligamer? ( You need to be careful with these - sometimes you generate thm using both crystal and

Re: [ccp4bb] POINTLESS error: "NormaliseInRuns::apply Unused run 0"

can you send the whole log file? Somehow the XDS input isnt agreeing with pointless expectations, so I suspect no reflections have been read Eleanor On 20 January 2017 at 23:41, Joseph Brock wrote: > Dear ccp4 experts, > > I am trying to use the ccp4i Pointless, Aimless,

Re: [ccp4bb] AW: [ccp4bb] output directory

You must all be very well organised, and have a very good memory for where you ran that tidy-up job for some alternative project! Eleanor On 28 September 2016 at 07:51, wrote: > I fully agree. It would be great to be able to use the current working > directory

Re: [ccp4bb] ligand binding and crystal form

Are your 3 crystals isomorphous, and do they all refine well? I guess you struck lucky with DS3 - as suggested it could be a different soaking, different crystal size, etc, etc.. If isomorphous I would compare all 3 structures in COOT and look for subtle differences.. Your C222 and C2221 cells

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

Well - it sounds hopeful but still challenging.. First suggestion - are you SURE the SG is C2221 and not C222? If your two molecules are related by a NC translation of x_tran, y_tran, 1/2 then you will get the apparent absences along the 0 0 l axis which suggest SG C 2221 but the true SG could

Re: [ccp4bb] Problem with twin refinement, refmac suddenly adds data?

Hmm - what is your space group, cell, and twin law? The mtz file output from REFMAC contains detwinned data - ie the column labelled as F is NOT the measured amplitude derived from the measured twinned intensities. So in some SGs it is conceivable that an index has been generated.. This shouldnt

Re: [ccp4bb] Problem with twin refinement, refmac suddenly adds data?

Robert Gustafsson > PhD Student > Department of Biochemistry and Biophysics > Stockholm University > 106 91 Stockholm, Sweden > > e-mail: robert.gustafs...@dbb.su.se > > > > On 21 Oct 2016, at 11:54, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: &

Re: [ccp4bb] Problems finding the correct Cif file of a crystal structure

There is a data bae - cambridge Structural Data Base with most crystal structures coordinates and measure data in it. if your university subscribes you should be able to acess it. Eleanor dodson On 26 November 2016 at 21:00, Bianca Valdes <bianca.valdes...@gmail.com> wrote: > Hello

Re: [ccp4bb] Phaser: tNCS present but correction not applied

That is a very high nTCS vector (78% of the origin. Are you sure your unit cell isny doubled ie cell is not 94.2073 148.003 72.9967 90 97.6686 90 But 47.136 148 7390 98 90 What does pointless suggest for theSG Eleanor On 26 November 2016 at 18:56, KAUSHIK H.S. <

Re: [ccp4bb] intrasubunit rotation axis

Wont PISA do it? It sorts out the most likely biological unit for you after applying symmetry operators. Either submit your coordinates to the EBI PDB server or use the version in CCP4 Eleanor On 17 November 2016 at 19:57, chemocev marker wrote: > Hi All > > I am

Re: [ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

With such a lot of molecules, I would check for oligamers. Look at the MOLREP self rotation - is there anything obvious? Send the*.ps if you like and I can comment. And do the models form oligimers? If so search with that.. Eleanor And as Randy says - try PHASER .. On 31 October 2016 at

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

That must mean there is a bug in the reindexing to I2 Eleanor On 4 November 2016 at 12:00, Paul Paukstelis wrote: > Thanks to all that responded. I sorted this out. > > It all appears to stem from the C2->I2 conversion. Forcing everything in > processing to stick with

Re: [ccp4bb] Conversion from PDB-downloaded structure factors to mtz

Got to GUI and it will call the appropriate program.. Eleanor On 4 November 2016 at 15:55, Ian Tickle wrote: > cif2mtz > > Cheers > > -- Ian > > > > On 4 November 2016 at 15:34, Keller, Jacob > wrote: > >> Dear crystallographers, >> >> >> >> What

Re: [ccp4bb] AW: [ccp4bb] Why Does Detwinning Not Work?

Search for: "experimental phasing with detwinned data" and you will find some hits. You need a low degree of twinning, and a strong sub-structure signal.. Re MR solutions - it is usually possible to solve the structure providing you get the space group right, but in my experience the maps are

Re: [ccp4bb] Choosing test set for twin refinement, with multiple operators

The twinning factors all about 0.25 do point to a higher symmetry than P21. As others say - I would be very surprised (and would question result as a referee) if your FreeR was not >> 30% for such low resolution data Is the data anisotropic - often is with such a long cell edge.. If so do process

Re: [ccp4bb] R/Rfree values

es - look carefully at your data quality indicators - batch scales, Wilson plot - moments etc.. tHese can show up if there is a problem with ice rings or crystal decay or whatever. Then I always look at the REFMAC plot of v If they overlap well - good - but problems with scaling will show up

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Thank you Uppsala lot - it has been a great service and taught a lot of people that "The map is the Message" Eleanor Dodson On 14 December 2016 at 12:54, Daniel Picot <daniel.pi...@ibpc.fr> wrote: > Veni vidi > I wil have to change my advices and lectures: go and look at

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

This isnt the sort of thing a refinement program does. Refinement starts from the model you provide - uses that to generate phases and the appropriately weighted difference map to alter the input coordinates. So that map is used in the close environment of a the model, so solvent flattening is not

Re: [ccp4bb] To win or not twinning?

First - there is a useful document about possible twin laws in the CCP4 documentation. It references the SHELX description of twinning for small molecules. http://www.ccp4.ac.uk/html/twinning.html It is possible in a trigonal system that you could have two twin operators but the twinning stats

Re: [ccp4bb] visible side-chains but breaks in main-chain

What is the resolution? Breaks can be caused by anisotropic data - but that map does not look right. Is that picture taken from COOT ? Eleanor On 1 December 2016 at 14:37, Reza Khayat wrote: > I would have to agree with Tim. I'm a little surprised that your R/Rf is >

Re: [ccp4bb] To win or not twinning?

n might just be wrong. > > Thank you all for the help! > > I'm still looking for references that can teach me how to look at protein > diffraction images and understand what I am seeing. The basics like > recognizing bad data and what usually leads to deformity in the spots (for > exampl

Re: [ccp4bb] Merging MAD wavelengths together?

Yes - but isnt that common practice? Eleanor On 2 December 2016 at 18:11, Keller, Jacob wrote: > Dear Crystallographers, > > > > Although it seems common practice to use just one wavelength/sweep for the > refinement of the final model, wouldn’t it make much better

Re: [ccp4bb] ccp4i2 errors

It could be, but could you attach the whole REFMAC log file ? ( you can find that in the CCP4_JOBS/job_n/ directory) Maybe there are no atoms in your COOT output.pdb? If so REFMAC does fail rather ungracefully! Eleanor On 29 December 2016 at 12:45, Alun R Coker wrote:

Re: [ccp4bb] Large number of outliers in the dataset

If you have outliers - worry about why? (By the way - what is the multiplicity?} Look at the AIMLESS list of rejections/ the scale factor for different batches/ reports of ice rings/ etc There has to be a reason, and with snsible reprocessing you can probably but much better resolution data

Re: [ccp4bb] Estimate NCS copies

No - not completely. Better to at least start from matthews_coeff and get a guestimate of the expected number of copies. Presumably you know the sequence of your crystal. A native patterson can show a non-crystallographic translation. A self-rotaton may suggest something, but best to start from

Re: [ccp4bb] No improvement in R-factor after Refmac.

You dont say whether there is Non cryst translation - that will be reported at various stages - the pointless/aimless/ctruncate task gives it. But if it exists and the translation ihas a component of .5 along any axis, that makes the SG estimate a bit uncertain - the absences could be due to the

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

I think CCP4MG does this very selectively? Eleanor Dodson On 17 March 2017 at 17:03, Xiao Lei <xiaolei...@gmail.com> wrote: > Dear All, > > Thanks for the information. > I tried the way suggested by pymol wiki, but pymol fail to display the > map. > This is what I

[ccp4bb] anomalous difference fourier

I suppose I should have expected this, but I still was led astray.. Ir atom - strong anomalous signal.. Good peak in anom diff fourier phased from protein. So I add it to the model with occ = 1.00 and refine.. The B factor is very high and it seems clear that the occupancy should be <<1.0 And

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

HOW sure are you of the spacegroup? The only difference between I4 ans I41 absences is that l=2n is absent for I4, l=4n for I 41. If you have the wrong choice half your symmetry equiv molecules will be corret but not the others.. Getting the screw axis wrong is a good way to get a reasonable but

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

> > 0.30 -34009.00 -33478.99 -33493.97 > > 0.33 -38707.08 -37931.58 -37972.35 > > 0.35 -43982.57 -42782.44 -42863.82 > > 0.38 -49953.87 -47966.38 -48105.22 > > 0.40 -56711.13 -53196.56 -53411.44 > > 0.42 -64141.85 -57712.76

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

Twin refinement cannot be compared directly to untwinned - the R factors are between different parameters - without twinning it is assumed you have an amplitude obtained more or less from sqrt(I But for a twinned data set that I is actually [ I1 + twin_factor I2 ] so the amplitude is not really

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

What was the refined twin fraction after Refmac? It’s much more accurate > than initial tests. Also, how many twin domains do you have? If you have > many, it might be a higher space group but with less twinning. I recently > had a case in which apparent tetartohedral (four-domain) twinn

Re: [ccp4bb] ADD sulfinic-cysteine to protein aa-chain

Is there a dictionary entry for your sulfinic cisteine? And is it part of the aa chain with a sequential numbering? I f so check it is labelled peptide in the dictionary (look at the dictionary for any amino acid tto check the format..] If so it should be linked properly. Or attach the

Re: [ccp4bb] How the IMEAN is calculated in scalepack2mtz

thing to do? Not sure! Eleanor Dodson On 11 March 2017 at 15:18, Karthikeyan Subramanian <skarthi...@gmail.com> wrote: > Dear CCP4bb, > > How IMEAN and SIGIMEAN is calculated in scalepack2mtz if the input is with > anomalous intensity (obtained from HKL2000). Any guide/r

Re: [ccp4bb] How the IMEAN is calculated in scalepack2mtz

sd(I-), which is obviously not very > common. > > Cheers > > -- Ian > > > > On 12 March 2017 at 17:58, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > >> You read: >> h k l IPLUS SIGIPLUS INEG SIGINEG >> Then program calc

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

at 14:16, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > TLSANL? > Eleanor > > On 8 March 2017 at 14:08, Nicholas Keep <n.k...@mail.cryst.bbk.ac.uk> > wrote: > >> It would be nice to be able to run zero cycles of refmac to get a map etc >> direct

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

TLSANL? Eleanor On 8 March 2017 at 14:08, Nicholas Keep wrote: > It would be nice to be able to run zero cycles of refmac to get a map etc > direct from a PDB file. > > However due the PDB requiring the TLS component of B factor to be included > this does not work.

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

SOLU SPAC P 32 1 2 > > > > SG P32 > > SOLU SET RFZ=7.4 TFZ=10.4 PAK=0 LLG=187 TFZ==10.7 RF++ TFZ=17.0 PAK=0 > LLG=436 TFZ==17.8 LLG=1715 TFZ==34.3 PAK=0 > > LLG=1715 TFZ==34.3 > > SOLU SPAC P 32 > > > > Based on TFZ and LLG, the P32 seems to be b

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

maybe attach your data processing log file.. e On 14 April 2017 at 20:10, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > That twin factor list means the apparent crystal symmetry must be P6/mmm. > > You say you only have 2 molecules in the asymmetric unit of P32,therefor &g

Re: [ccp4bb] Problem with a cell content

This is very strange . If you have a large non- crystallographic translation vector you would expect either to have two molecules in the asymmetric unit or your one molecule must have two very similar domains? What is the n-c translation vector? Could you have assigned too high symmetry ? SG

Re: [ccp4bb] Problem with a cell content

vent cell content was similarly high. > > Within a protein monomer there are no similar domains. > > > > Best regards, > > Anna > > > > > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor > Dodson <eleanor.dod...

Re: [ccp4bb] Problem with a cell content

Best regards, > > > > Anna > > > > > > > > Dr. Anna Koromyslova, Postdoctoral researcher > > German Cancer Research Center (DKFZ), F150 > > Im Neuenheimer Feld 242 > > D-69120 Heidelberg > > Germany > > > > > > *From: *Elean

Re: [ccp4bb] How to determine Quaternary symmetry

Hard to comment without more detail. What is your cell and point group symmetry? Do you know space group? What is likely asymmetric unit content? Is there a non-crystallographic translation and if so what is it? All this information given in GUI2 data processing report. Eleanor On 10 July 2017

Re: [ccp4bb] high Rfree

Have you looked for other possible models in the PDB? Eleanor On 21 July 2017 at 02:16, 张士军 <21620150150...@stu.xmu.edu.cn> wrote: > Hi everyone > >I have got a anti-parallel coiled-coil structure in a short fragment > recently, then I want to solve a longer fragment structure with phenix-MR

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: >

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

Or use PISA to position bits sensibly.. Eleanor On 24 July 2017 at 10:35, Jon Agirre wrote: > Dear Alice, > > there's an option in both ccp4i and ccp4i2 interfaces that lets you tell > Buccaneer that you want to build the new model in the same place as the > partial model

Re: [ccp4bb] Problem with a cell content

t; > > > Dr. Anna Koromyslova, Postdoctoral researcher > > German Cancer Research Center (DKFZ), F150 > > Im Neuenheimer Feld 242 > > D-69120 Heidelberg > > Germany > > > > > > *From: *Eleanor Dodson <eleanor.dod...@york.ac.uk> > *Date: *Tuesd

Re: [ccp4bb] Rmergicide Through Programming

Agree although i usually look to CC1/2. Rmeas makes more sense than Rmerge but- most software reports both, so cant you just provide Rmeas yourself Probably simpler to persuade journals to alter the Table 1 requirements than get all developers to comment those lines out! Eleanor On 4 July

Re: [ccp4bb] Antw: Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

ng. > > At 2.76A resolution, hydrogen bonds would be difficult to visulize. > > I found phenix.refine more user friendly. You may too find it useful. > > Vipul Panchal, > Ph.D. student > CSIR-IGIB > (M)- 091 7678617949 > > On 02-Jul-2017 9:14 PM, "Eleanor Dodson&quo

Re: [ccp4bb] RMSD between unaligned structures

amond.ac.uk alternative email: j.fo...@imperial.ac.uk > personal web page: http://www.jfoadi.me.uk > > > On Monday, 3 July 2017, 11:59, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > > > Dont understand your Q James.. > You have to make sort of alignment to get

Re: [ccp4bb] RMSD between unaligned structures

Dont understand your Q James.. You have to make sort of alignment to get the RMSD surely? And csymmatch will just apply the symmetry and origin shifts needed for any comparisonn? E On 3 July 2017 at 11:32, Stéphane Duquerroy wrote: > Hi James > LSQMAN can calculate

Re: [ccp4bb] large number in ASU

Have you looked at a self rotation function? Is there a clear 3-fold axis perhaps? Eleanor On 27 April 2017 at 10:45, Mark J van Raaij wrote: > Does the self-rotation function suggest presence of NCS axes? If so, this > may help you figure out the symmetry inside the

Re: [ccp4bb] doubt regarding setting resolution cutoff

e your thoughts as to how I should proceed. > > > > Thanks, > > Satvik > > On Tue, Aug 8, 2017 at 11:47 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk > > wrote: > >> You have some horrible ice rings - some data processing software may be >> able to cut them

Re: [ccp4bb] pseudo-centering or twinning problem in P3

Sudipta Bhattacharyya, > Postdoctoral fellow > Department of Molecular Biosciences > University of Texas at Austin > Texas, USA. > > > On Tue, Aug 8, 2017 at 8:27 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > >> First of all - check whether your crystal da

Re: [ccp4bb] doubt regarding setting resolution cutoff

You have some horrible ice rings - some data processing software may be able to cut them out.. how are you processing it? Eleanor On 8 August 2017 at 15:43, Christian Roth wrote: > Your plots look strangely different to the old Scala output you posted > before, but

Re: [ccp4bb] pseudo-centering or twinning problem in P3

First of all - check whether your crystal data shows twinning - thee is an L-test plot which usually gives a clear indication and if you are using GUI2 the report suggests if this is so. If you have twinning the most likely SG is P31 (or P32 ) - you cant tell the difference till the structure is

Re: [ccp4bb] refmac output

the CCP4 gui does just that - provides map coeffs by default.. You can seek out the full REFMAC output if needed but it is not there by default. Eleanor On 3 August 2017 at 02:04, Pavel Afonine wrote: > Hi Ed, > > your suggestion makes perfect sense to me, and it's trivial

Re: [ccp4bb] Some TLS issues in REFMAC5

Oh dear - TLS transformations are a bag of worms! I usually start all over again if I want TLS .. SET all Bs to B_wilson Run 10 cycles of TLS with the groups listed in the PDB header. That is boring but comparatively safe! Eleanor On 6 August 2017 at 15:36, Stefano Trapani

Re: [ccp4bb] doubt regarding setting resolution cutoff

First comment - your data looks excelent - even to 1.8A. Second - look also at the wilson plot and second moment plots - these should not be jerky - wilson plot falling off smoothly, 2nd moment pretty constant to the good resolution limit.. Thirdly - just use all your data and check the

Re: [ccp4bb] Refienmnet

There is a REFMAC plot of Rfactor v resolution, and of v v resolution. These can show if there is some resolution dependent spike - e.g. one due to ice rings or saturated low resin data. Look at those I suggest Eleanor On 17 August 2017 at 18:38, Kay Diederichs

Re: [ccp4bb] Poor density fit.

It sometimes help to use the coot tool NCS ghost control to fit the good chain over the weak. Obviously you must work at a lower contour level than for the good chain.. Of course be careful about the basics.. Is the space group right? is there twinning? Check data quality - anisotropy - tc..

Re: [ccp4bb] Different loop conformations

well - Q1. I think you can observe it.. And there is no format problems in modelling several residues as conformation A and B Eleanor On 16 May 2017 at 19:33, Sam Tang wrote: > Dear all > > Sorry for the slightly off-topic thread. > > We are lucky enough to have recently

Re: [ccp4bb] AIMLESS unmerged MTZ output

I believe so! Eleanor On 22 June 2017 at 17:04, wtempel wrote: > Hello all, > > Are the following statements regarding AIMLESS unmerged mtz output > accurate? > - the H, K, L, M/ISYM columns are sufficient to recover the "original" H K > L indices. > - a combination of

Re: [ccp4bb] AIMLESS unmerged MTZ output

This reminds me - one of the sensible things in SCALEPACK unmerged is it lists explicitly: (h k l) unique followed by (h' k' l') measured. I think the M/ISYM was introduced to save file space but it is kind of redundant now! and a bit flawed, as it depends on assigned symop numbering , Is it

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

the information.. Eleanor Dodson On 18 May 2017 at 15:22, Jasmine Young <jas...@rcsb.rutgers.edu> wrote: > Hi Ed, > > The PDB accession code will be based on the primary data stored in the > PDB. Therefore depositors will need to make a new deposition with new PDB > accession code

Re: [ccp4bb] ctruncate user problem

I never use it except through te GUI but I thought the default was to output Fs and Is What happens if you try: .. ctruncate -mtzin X6_3_aimless.mtz -mtzout X6_3_ctrunc.mtz - wrote: > I am using CCP4

Re: [ccp4bb] Positive density of H2O at symmetry axis

I presume you set te occupancy to 0.5? if it is a 2fold.. eleanor On 26 May 2017 at 19:35, jeorgemarley thomas wrote: > Dear all, > I encountered a positive density of water molecule (probably) at the > symmetry axis of the protein molecule (resolution 1.75 Ang) . After

Re: [ccp4bb] Conserved water

Many years ago I wrote code to label waters with a code related to the residue/atom they were Hbonded to , so then you could check whether all OH TYR 227 in each chain had an associated water.. But it used non-standard water naming .. Easiest way is to line up molecule pairs or chain pairs in

Re: [ccp4bb] Refining a crystal structure with (very) high solvent content

ny times. > > The problem is that this confusion is enshrined in the default values > of certain parameters in display programs and scripts, that are assumed > (not by their authors, but by almost everybody else) to embody all the > common sense we need :-) . > > > With bes

Re: [ccp4bb] Refining a crystal structure with (very) high solvent content

Thank you Dale! You talk so much common sense.. Eleanor On 2 June 2017 at 23:30, Dale Tronrud wrote: > On 6/2/2017 1:42 PM, wtempel wrote: > > Hello all, > > crystals with high solvent content tend to diffract poorly, at least > > according to intuition. Several years ago

Re: [ccp4bb] similar unit cell

10:52, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > The cell dimensions are very suspicious, but try merging the two sets of > data to see if they really are the same - you can do that best from the > integrated data sets, or just compare the Riso between the two sets of &g

Re: [ccp4bb] similar unit cell

The cell dimensions are very suspicious, but try merging the two sets of data to see if they really are the same - you can do that best from the integrated data sets, or just compare the Riso between the two sets of amplitudes. I think there is a web server at CCP4 SIMBAD which searches to see if

Re: [ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

The R factors may be high because the structure is imperfect - almost inevitable at that resolution - but also there are often serious difficulties with scaling at this resolution . If you are using REFMAC look at the v wrt resolution plot at the end of refinement (follows R and Rfree plot v

Re: [ccp4bb] Unknown Ligand Density

First thing to check - is there any anomalous scatterer peak in the density? Easy to do an anom diff map from GUI2 - choose REFMAC and add - do anom diff fourier, then follow with a diff peak search in COOT . Eleanor On 14 June 2017 at 18:04, Sanishvili, Ruslan wrote: >

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

As others point out, anisotropy is endemic in protein crystals, and severe cases make the single number score for Rmerge, CC1/2 etc pretty meaningless for the outer shell. But do not throw out the meaningful data at your higher resolution because of single number stats- first LOOK at your images

[ccp4bb] REFMAC? COOT? and TER records

These do seem to multiply wonderfully in the PDB output files and sometimees to have have strange effects/ affects in COOT? As I understand there should be a TER record after a protein chain? but not after a ligand. Dont know about carbohydrate chains. Eleanor The correspondence about N linked

Re: [ccp4bb] REFMAC? COOT? and TER records

t are not > amino acids. This indeed causes side effects. I also noticed that COOT > leaves TER records if you add C-terminal residues. This can cause Refmac to > think that the residues should not be connected. > > Cheers, > Robbie > > > > -----Original Message- > &g

Re: [ccp4bb] how to run shelx C/D/E using CCP4 GUI on windows

I cant say anything about Windowssystems - jobs are MEANT to run on either. But re Intensities - you will have intensities in an mtz file somewhere - all data processing outputs both amplitudes and intensities.. As a rule the conversion for I to F and back does not change the stronger

Re: [ccp4bb] discriminate between solutions from phaser

Well - I am not very familiar with helical collagens, but a partial solution could match several different helical turns.. Your resolution seems high and the LLGsare very good. Why dont you feed the partial solution to ACORN and se if that gives a good map. I would expect it would if the numbers

Re: [ccp4bb] help needed to interpret a SRF

Well - you dont give details o f resolution but the sovent content and the peak of 0.51 would suggest a possible dimer in crystal 1 Crystal 2 is so different it might well have a dimer in a different orientation. I would try to see if there was a relationship between Xtal 1 and Xtal 2 - can

Re: [ccp4bb] AW: [ccp4bb] Molecular replacement with template having low sequence identity

Please tell us what worked. Eleanor On 6 June 2017 at 04:52, Shankar Prasad Kanaujia wrote: > Dear All, > > I am very happy to inform you that I have finally solved the structure. > Thanks to all for your kind suggestions. > > With best regards, > Shankar > > On Wed, Aug

Re: [ccp4bb] PAK=0 problem

James is absolutely right = the wonder of crystallography is that the difference map can theoretically pinpoint errors and suggest what is missing in your model.. But also check your data - modern synchrotrons often measure some reflections to a high resolution limit, but the noise can get

Re: [ccp4bb] PAK=0 problem

PAK=0 is GOOD - i.e. there are no clashes between symmetry equivalent molecules. So I think you have solved your structure. Eleanor On 15 September 2017 at 07:20, rohit kumar wrote: > Dear all, > > During MR using PHASER with a 1.8 A data, I found that the PAK=0 but all >

Re: [ccp4bb] doubt regarding MR search model

You need to provide a bit more information. First of all about the data processing.. Is the space group correct? ways of being misled are: Non-crystallographic translations with a shift of ~0.5 along an axis - say a. This will generate absences in the odd h 0 0 reflections and can make the

Re: [ccp4bb] How to rotate subunits

Hmm - that is a bit vague.. There is a CCP4 program pdbset pdbset xyzin monomer.pdb rotate polar theta phi kappa shift x y z But you need to know what to rotate and shift.. Easier is to find a model and fit your monomers over the model. Once you have the rotation done - pISA will tell you the

Re: [ccp4bb] AW: [ccp4bb] doubt regarding MR search model

round of > automated model building has brought down the R values. The Rwork,Rfree > stand at 0.29,0.35 (monomer search model) and 0.30, 0.35 (dimer search > model). There is good scope for building residues in both cases. But which > one do I go ahead with is my question. > > &g

Re: [ccp4bb] Aperiodic protein crystals

There are several examples in the literature. I would ask Andre Lebedev andrey.lebe...@stfc.ac.uk. He discussed this to some extent in his hD thesis. Eleanor On 17 September 2017 at 05:18, Stewart, Charles E [BIOTC] < cstew...@iastate.edu> wrote: > Dear all, > > > I am looking for suggestions

Re: [ccp4bb] doubt regarding MR search model

hough the probability is high? > > If my space group is indeed correct, how do I decide whether to go ahead > with the results generated by the monomer search model or the dimer? > > Please share your thoughts. > > > Thanks, > Satvik > > On Mon, Sep 18, 2017 at 7:36

Re: [ccp4bb] TYC not linked to previoys amino-acid

n? Is it something like > C-terminus amilation? If it is the case then better approach is to use TYR > and C-terminus amilation modification. I do not remember how it works, but > if it is the case then i can find out. > > > Regards > Garib > > > On 16 Oct 2017, at 07:06, E

Re: [ccp4bb] HKL to mtz

Is your HKL file unmarked scaled data from XDS? If so read it directly into the Data Reduction task (pointless / aimless truncate) to produce a merged mtg file. If the data is already merged, then f2mtz can convert it to an mtg Eleanor On 6 October 2017 at 07:05, Ruud Hovius

Re: [ccp4bb] High R/Rfree after MR

I would be worried by a structure with these R values, whether or not there is anisotropy to consider. Several times when this has happened to me the spacegroup turns out to be wrong. You do not give any details of the solution but especially if there is some non-crystallographic translation you

Re: [ccp4bb] areaimol missing symmetry mates

Eugene is away but I think the PISA symmetry checking only looks at 2 unit cells in all directions from the origin, so if the origin chain is far away you may lose contacts. .. As someone says - always try to place the molecule reasonably close to the origin. There is an old program pdbset

Re: [ccp4bb] AW: [ccp4bb] C-terminal amide

You have labelled the TYC as an L-peptide in the dictionary have you? ( Look at any peptide for the position and format for the label ) I thought REFMAC would then automatically creat a peptide link between residue n and n+1 Eleanor PS and remove the TER record! On 13 October 2017 at 08:08,

Re: [ccp4bb] How to search 2 models (ensembles) in Molrep

Hmm - I will think tomorrow. MOLREP certainly can read NMR ensembles but there you have several models in one file each heading MODEL 1 ... MODEL 2 ... etc. Eleanor On 6 September 2017 at 19:32, Xiao Lei wrote: > Dear Crystallographers, > > How to search 2 models

Re: [ccp4bb] Short peptide outliers

That seems strange! You couldn't have built it in the wrong direction could you? Or have bound a L-handed peptide? There are outliers which can be explained by interactions with other features but it would be very very unlikely that all the residues were outliers Eleanor On 1 October 2017

Re: [ccp4bb] Short peptide outliers

s issues! > Thanks again! > Meytal > > 2017-10-01 23:12 GMT+03:00 Eleanor Dodson <eleanor.dod...@york.ac.uk>: > >> That seems strange! You couldn't have built it in the wrong direction >> could you? >> >> Or have bound a L-handed peptide? >> &g

Re: [ccp4bb] query of B chain model of protein

Not much idea. I tend to build small amounts at the termini of your current model using the better model as a guide then re-refine and hope you can keep going.. Eleanor On 2 October 2017 at 15:42, Vikram Dalal wrote: > Hi all, > > > I am solving a protein data of 2.6

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