Re: [ccp4bb] Structures refined ad mentula canis (this is Latin)

anomalous scattering Zn in all three anom diff maps, and the allBiso was the highest ( 15 sigma v 12 Sigma for the others..) Is that significant? probably not! All models and maps overlapped very closely of course. Eleanor Dodson On Wed, 30 Oct 2024 at 10:45, Italo Carugo Oliviero

Re: [ccp4bb] a twinning question..

LESS)" in > https://www.globalphasing.com/autoproc/wiki/index.cgi?ComparisonProcessing202409 > . > > I. > > > On Tue, Oct 8, 2024 at 6:21 PM Eleanor Dodson > wrote: > >> Yes - I read that but didn't attach pseudo-twinning problems to it.. >> E >

Re: [ccp4bb] a twinning question..

t 2). > > Cheers > > -- Ian > > > On Tue, Oct 8, 2024 at 6:08 PM Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Maybe we need the two BBs to cross fertalise? >> E >> >> On Tue, 8 Oct 2024 at 17:52, Rafael Marques

Re: [ccp4bb] a twinning question..

Biomolecular > Universidade de São Paulo > > Bacharel em Ciências Biológicas > Universidade Federal de São Carlos > > phone: +55 16 99766-0021 > > * "A sorte acompanha uma mente bem treinada"* > *_________

Re: [ccp4bb] a twinning question..

sts! But I >> agree that the L test is one of the best, and the server uses a variant of >> it which gives more accurate estimates of the twin fraction. >> >> Cheers >> >> -- Ian >> >> >> On Tue, Oct 8, 2024 at 4:01 PM Eleanor Dodson < >

[ccp4bb] a twinning question..

I have always had great faith in the L test and other statistics to detect twinning.. But now I have a puzzling data set. Seems to be orthorhombic with a, b and c all different One molecule/asymm unit and no NC translation.. BUT clear indication of twinning given by second moments, etc.. I have s

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Eleanor > suggests but even modest limit to 1.9 Å and then structures at 1.9-2.5 and > 2.5-3.0 show the effect clearly. We looked at several other groups of atoms > (backbone/side chains at the protein core, at the protein surface, DNA > phosphates/bases, waters at the interfaces or boun

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

All interesting points.. (And good to see a reference to *" P.A. Machin, J.W. Campbell, M. Elder (Eds)Refinement of Protein Structures, SERC Daresbury Laboratory, Warrington, UK (1980)"* - for those who remember, a super exciting discussion over what was feasible for refinement, and how to do it! )

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level? As Edward suggests - if you omit a well ordered feature the resultant difference maps often show high positive density and a surrounding complementary "sag

Re: [ccp4bb] Comparing datasets with different resolution/quality

I Am thinking about this problem re a set of four carbohydrate binding proteins - all isomorphous but with different Ligands and weird solvent features.. first task was to get all sets with same indexing convention! (SoacegroupP65) That can be done at the data processing stage by giving one as the

Re: [ccp4bb] Tools for identifying possible contaminants

In fact I believe that is what the SIMBAD script does - searches the PDB archive first for cell dimensions, and only then checks possible MR matches.. On Thu, 4 Jul 2024 at 10:26, Clemens Vonrhein < daef624adb06-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear Kyle, > > I often like lookint at the

Re: [ccp4bb] mystery blob!

Thank you all for the ideas! On Wed, 26 Jun 2024 at 16:49, MARCHOT Pascale wrote: > > *One of these green little gosts?* > > *P * > > -- > *De :* CCP4 bulletin board de la part de Eleanor > Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.a

Re: [ccp4bb] merging of datasets

I second martin’s suggestion.. it is not essential but it is sensible to give the lively best as the first entry then the other sets are scaled and indexed to match it.. I use ccp4i2 for this . You will get quite a voluminous report which is very helpful Good luck Eleanor On Fri, 21 Jun 2024 at

Re: [ccp4bb] help with wwPDB validation warning

Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2 Eleanor On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação < d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > > I am currently validating a structure for deposition in the wwPDB and > encountered the following warnin

Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

Well, REFMAC output a (mislabelled) F SIGF which was detwinned so if you deposited the REFMAC output I guess that is detwinned.. Do you have the original REFMAC input still? Eleanor On Thu, 6 Jun 2024 at 15:18, Ben Bax wrote: > Hi, > I am just re-refining an old twinned dataset - which I will

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Hmm - rather tricky! I would do an MR search with the crystal model v the EM density, Steps would be: 1) convert EM density to "structure factors". - there are tools which do this .. 1a) You need to go back to ccp4i - program sfall to read map to generate SFs from map - then cad or sftools to add

Re: [ccp4bb] valine difference map interpretation

Your pictures 1 3 & 4 don't seem to show multiple occupancy? Maybe the difference map 2 is saying - too much complexity ?? Eleanor On Thu, 30 May 2024 at 23:29, Michael Colaneri wrote: > Dear All, > We have alternate conformations for a number of residues in a structure > and one is a Val that I

Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

With that translation (x,1/2,1/2) lots of your reflections with k and l Odd will be relatively weak and those zones usually have higher r factors. Look at the plots of reflection zones in hklview and you will probably notice weak and strong zones. The translation will make selecting the soacegrou

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

But are there two conformations of the disulphide? or one disulphide and one broken link? Eleaor On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude wrote: > I have done this in shelxl or phenix refinement, you can define occupancy > groups (or free variables in shelxl) so that 472A and 384A are one g

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Well - I turn off occupancy refinement once there is a sort of consensus.. Disulphides often break after long exposures and you see the positive and negative blobs clearly. I must admit I usually just set 0.5 as occ , fix the surviving disulphide link and let the B values suggest a better ratio tha

Re: [ccp4bb] refmac5 version 5.8.0425 corrupts B-factors..?

That result looks really bizarre but it is hard to make a sensible comment without more details..maybe you could attach the whole log file for the refmac run. What input reflection dAta are you using ? You couldn’t have picked up a Sharpened set by any chance? (It is always good practice to make

Re: [ccp4bb] Rescale merged data?

If you are using CCP4I2 and use the task "Import merged data" that sort of reprocesses that data through AIMLESS. You get all the usual graphsv resolution - completeness, I/SigI , Wilson plot, Second moments etc and from those can make a sensible decision on where the resolution limit should be set

Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

I like to use difference maps between Fa and Fb .. It is a bit tricky now to set them up..but they do highlight changes. Obviously 1) you need to have the same spacegroup and cell, and the same indexing convention. (Easy to check this in the data processing task when importing the second data set.

Re: [ccp4bb] request for applications

It. Will probably take me a. Full year to draft the. Application - is that too slow? On Mon, 1 Apr 2024 at 09:22, Frank Von Delft < bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> wrote: > Oh dear, your prime number oversupply crashed the crypto Ponzi scheme > market. Will you accept $10e2 propo

Re: [ccp4bb] mixture

This is best done by calculating the structure factors for the part you want to fix. (make sure the occupancies are set yo 0.8) The REFMAC hklout will contain F SIGF etc plus FCALC PHIcalc for that bit Define this file as your input hkl Then refine the 20% structure (occs=0.2) with input LABI FP=F

Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

That is extremely likely! - certainly REFMAC will do that.. If 5% missing using DFcalc is a good thing - if 35% is missing not wise.. Eleanor On Mon, 4 Mar 2024 at 07:53, Ben Bax wrote: > > Fcalc maps look fantastic. Are you sure they were not using an Fcalc for > the missing 35% of the data? >

Re: [ccp4bb] Rwork and Rfree the same?

Well REFMAC tells you how many reflections are used.. And if you do mtzdmp data.mtz that will tell you too.. With such low completeness R factors are pretty meaningless - you must have many more parameters than observations so that does often give low Rfactors.. On Wed, 28 Feb 2024 at 16:21, Jus

Re: [ccp4bb] Rwork and Rfree the same?

Well - it is extremely surprising! How many reflections are there in the "work" set (Rwork) and the "free" set (Rfree)? I suspect that somehow all the reflections are in both sets?? Eleanor On Wed, 28 Feb 2024 at 15:11, Justin Cruite wrote: > Hi everyone, > > > > What does it mean if your Rwork

Re: [ccp4bb] Difficult Molecular replacement

Hmm - that is pretty confident that the spacegroup for this cell is P2 21 21 (72.61 73.73 147.23 90 90 90 ..) There are some strong reflections along the "a" axis *From pointless log* Lattice unit cell after reindexing: deviation 0.88 degrees 72.61 73.73 147.23 90.00 90.00 90.00 $TABLE: Ax

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

Various (all depressing) possibilities.. You don’t say what the sequence ID to the models us Your protein is flexible with poor fit to the available models. How well do those overlap? The bioinformatics tools in i2 give you pictures showing this. Look at them and see if there are sensible places t

Re: [ccp4bb] Difficult Molecular replacement

think the easiest way to resolve this > unambiguously is to solve in P1, and let that uncover the true symmetry. > > Best wishes, > > Randy > > > On 21 Feb 2024, at 13:56, Pedro Matias wrote: > > > > But curiously, all the 4 best solutions correspond to a SG with

Re: [ccp4bb] Difficult Molecular replacement

Lots of comments, but it would be easier to actually look at your integrated data! Some of the stats look a bit ropey - 621 reflections labelled as outliers by PHASER? Very anisotropic Moments go mad at the highest resolution.. The good news - extremely strong signal from the rotation function mea

Re: [ccp4bb] i2run crank2 problem

Hmm - I can't help with the scripting question, but it solved easily from the I2 interface? This is run on a Mac. CRANK2 called SHELX - found SE with weak signal.. Some difference between hand It traced ALA - R factor 41% Then BUCCANEER or MODELFIR quickly built and sequenced the rest.. Eleanor

Re: [ccp4bb] Coot SSM Superpose Problem

Isnt this what you want? output of CCP4I2 fitting buccaneer to the other.. On Fri, 16 Feb 2024 at 09:46, zx2...@connect.hku.hk wrote: > Dear all, > > Following the advice provided by Paul and Yi Min, the "*Symm Shift > Reference Chain Here*" function has proven successful! > > I am deeply grate

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

That pxmaths document was put together by Maria Turkenburg, with a bit of input from me long long ago, but then the theory hasn't changed much in that time. My old reference was Srinvasen & Parthasarathy >From crystallography in India.. Influential books by him and his associates (R. Srinivasan, S

Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

If I remember for coefficients with FOM and a precise PHI calculated, A = FOM*cos(phi) B = FOM*sin(phi) C=D=0 If you have a probability curve for PHI. 0 to 360 such as you get from experimental phasing, A B C D mirror this bimodal curve better .. On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar < 000

Re: [ccp4bb] Data reprocessing

Did you make the original deposition ? If so the pdb accepts re-depositions... If it was done by someone else I guess the courteous thing is to notify them and maybe talk to the pdb- redo team? Cheers Eleanor On Sat, 27 Jan 2024 at 01:53, Lucas Souza wrote: > Dear all, > > After auditing and re

[ccp4bb] MOLREP bug..

I give MOLREP am input mtz with space group R32:H or R32 or H32 (entered as R32:H) But MOLREP claims the SG is default_PST_limit : 0.250 of origin peak PST will not be used. If you like to use PST, use keyword PST = Y * Space group : H 3* No: 146 Sett: 2 Cell: 185.73

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

THere must be some error in the calculation of the CC - or you are over optimistic about what constitutes a fit! What does the COOT density fit show? Eleanor On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI < 7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote: > You can also try the CCPEM

[ccp4bb] How do I restrain B values?

I thought it was possible to stop B values on bonded atoms from fluctuating wildly? But I am quite unable to follow the newly formatted documentation.. To unsubscribe from the CCP4BB list, click the following link: https://w

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hmmm - I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2.. The program BAVERAGE gives you a plot of mean B value residue by residue.. *baverage* - averages B over main and side chain atoms SYNOPSIS¶

Re: [ccp4bb] Query on density fitting to phosphate

Back to the value of an anomalous map - IF the anomalous data is good enough to give a significant peak at a sulphur position, you might expect to get a peak at a well ordered phosphate- if no sulphur peaks not much hope... On Mon, 25 Dec 2023 at 19:51, Tom Peat < b7e4a7a8af49-dmarc-requ...@j

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

Well - are any of our names worth pricing?! Very very suspect.. Eleanor On Fri, 15 Dec 2023 at 14:41, Robbie Joosten wrote: > Hotel booking scammers for instance. > > Cheers, > Robbie > > On 15 Dec 2023 15:34, Frank von Delft wrote: > > I mean, who'd actually want that list anyway?! > > On 15/1

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Very very interesting analysis - Thankyou! On Fri, 1 Dec 2023 at 18:01, Tom Terwilliger < b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Roberto, > Thanks for the link to the DeepMind site! I hadn't seen that and now I > read it and the paper that they link to. It looks to me as tho

Re: [ccp4bb] Occupany refinement protocol amd best practices

Pavel has listed the papers that describe the underlying maths but unless you have high resolution data (> 1.9A say?) unscrambling results from occupancy plus B factor refinement is problematic to say the least.. Think about residues such as ARG or LYS where the termini are often extremely wobbly

Re: [ccp4bb] low resolution data refinement

Q0. Echoing Randy - how accurate is your starting model - Xray structure at resolution 1.5A or high quality EM or NMR?? Q1. Are the solutions the same? There is a CCP4 tool in ccp4i2 - Match my model which will check this taking into account symmetry and origin shifts. On Tue, 21 Nov 2023 at 14

Re: [ccp4bb] low resolution data refinement

Sorry - the simplest answer - is get higher resolution data! But there are some improvements possible. How clear is your MR solution. What is the similarity between model and your sequence? Etc. On Tue, 21 Nov 2023 at 12:03, Yahui Liu wrote: > Dear all, > I got a protein crystal dataset of 4.3

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

You seem pretty near to having solved your structure! Ignoring the data problems.. Extra steps I might have used. 1) Self rotation function. (in CCP4I2 the task is under data analysis ..) Does it suggest a NCS operator? If so is this a two fold? which might mean you have a dimer.. 2) Now you hav

Re: [ccp4bb] Mean B value in refmac5

Are there some atoms with occupancies < 1.0 ? You would need to weight those Bs by occ On Sun, 5 Nov 2023 at 11:34, Ian Tickle wrote: > The arithmetic mean B value from the structure as quoted everywhere is > pretty meaningless anyway and 10 Ang.^2 either way is probably not > significant. Let's

Re: [ccp4bb] About model building

Hmmm - r 50% rather suspect.. do the MR solutions from phaser and molten agree? Eleanor On Mon, 6 Nov 2023 at 05:10, Sam Tang wrote: > Dear all > > Thanks for all the input. I will definitely try out in the coming couple > of days. To provide more information: > - the data was checked in Xtriage

Re: [ccp4bb] About model building

IF your MR solution is correct ( ie r factor falls on refinement to 40% say) and your protein A is roughly 50% of the complex, and IF your data is good to 1.9A (assumed SG correct etc) I would do my best to correct any obvious rebuilding needed for protein A, ( r factor should fall further if this

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

an Plot* > > > > *Favored (%)* > > 97.83 > > *Allowed (%)* > > 1.38 > > *Outliers (%)* > > 0.79 > > *Average B-factor (Å)* > > 28.0 > > *macromolecules (Å)* > > 28.65 > > *ligands (Å)* > > 48.98 > > *solvent (Å)*

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as pretty acceptable? E On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude wrote: > As suggested by the (conflicting) observations of Eleanor and Nicholas, > it’s not clear whether you are showing data collection statistics for the > f

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Well - you probably could use data to a higher resolution I/SigI and CC 1/2 are quite high. The better the resolution the better the model usually. On the other hand your Rmerge is high-ish. Hard to comment without seeing the data processing results. Look at the plots of 2nd moment, wilson plot,

Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

Hmm - I can give you scripts to use SHELX? Eleanor On Wed, 11 Oct 2023 at 11:02, fuxingke wrote: > Dear Colleagues, > Reacently, for SAD experiment, I find SOLVE and SHARP can refine the > variables > of heavy atoms, such as occupancies, coordinates and thermal parameters. > But how to use

Re: [ccp4bb] Intractable outliers in wwPDB validation report

Well - some outliers are infix able! There are various reasons - floppy residues like arg or lys In multiple positions; strain due to protein folding constraints, etc. I use the validation report to check for obvious modelling errors but if you can’t find any, you have to just submit the results o

Re: [ccp4bb] the structures of Nucleic acid

I am afraid most scientists will use the most straightforward technique! If SAD is available the PHOSPHATE backbone of DNA will provide sufficient signal to allow SAD to work, and you get an unambiguous answer to whether it is A-DNA or B or Z... MR will usually work of course as well Eleanor On M

Re: [ccp4bb] Occupancy Refinement limitation

-zero value and vice versa if it is the only conformation present > it will be less than unity. > > I will take a look at the references! Very much appreciated. > Matt > > On Wed, 6 Sept 2023 at 02:08, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> w

Re: [ccp4bb] Occupancy Refinement limitation

Well - occupancy refinement is particularly imprecise, and highly correlated with temperature factors. Also the population for a surface ARG or LYS may well have more than two conformations, whereas some internal residue is better defined. There is also the Q of solvent - dual occupancies will gene

Re: [ccp4bb] New density quiz

I dont know what it is - but thats a beautiful map! What was in the crystallisation pot, do you know? Eleanor On Tue, 29 Aug 2023 at 18:22, Bijelic, Aleksandar < abae22057430-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear CCP4 members, > > I found the attached density in some of my structures an

Re: [ccp4bb] An unknown but strong positive electron density in my crystal

THank you - it is on a two fold axis you said? That means it could be a sort of average of a molecule.. Eleanor PS Any anomalous peaks? On Mon, 14 Aug 2023 at 10:32, Yue Li wrote: > Hi everyone, > > Thank you for your replies. I have uploaded the figures to a website. The > link is here: > > y

Re: [ccp4bb] An unknown but strong positive electron density in my crystal

Hmm - I cant see a picture.. Your email has this.. img src="data:image/png;base64,iVBORw0KGgoNSUhEUgAAAq0AAAJPCAYAAABW0O0iAXNSR0IArs4c6QRnQU1BAACxjwv8YQUJcEhZcwAAFxEAABcRAcom8z8AAP+lSURBVHhe7P3nkzRJl92JVaXWWVlay0fL1lq+ql+t9Wg9mBmMBDEDDAEMFobdxYJL7tKMNO432n7hn+k8v+PhmZGRkVlZT/fb/XR3l

Re: [ccp4bb] High Temperature Factors with TLS

You need to tell us more details - is this a deposited structure? Eleanor On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M. wrote: > Hello All, > > A general questions though phenix.refine is being used for refinement. A > student I am working with has a structure that was solved and initially >

Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

Hmmm -are the two ano maps contoured at the same level? You can check this by setting the SCROLL option to the ano map. The 2mFo-DFc maps look pretty identical..which suggests the two input mtz files are similar. You can get more information by viewing the inputs to make sure the values are the sa

Re: [ccp4bb] How to calculate experimental residual electron density map

You would hope it would show some hydrogen positions.. Eleanor On Mon, 24 Jul 2023 at 13:47, Ankur Kumar Singh wrote: > Dear Prof. Eleanor Dodson, > Thank you for the response. I will try generating difference map as told > and will update. > > - > Regards, > Ankur K

Re: [ccp4bb] How to calculate experimental residual electron density map

hy not calculate structure factors without hydrogen atoms and look at the difference map? Eleanor On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh < a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear Members, > I am trying to generate an experimental residual electron density map for > a

Re: [ccp4bb] How to deal with tNCS?

No attachments Lande Fu? Your C2221 cell is pretty obviously related to the orthorhombic one. (a b c )-C2221 ~ (2b 2c a)P212121 The cell volume of C2221 cell is ~ 4 x P212121 cell. - 8 symmetry related copies for C2221 and 4 for P212121 so if there are 2 molecules in P212121 ASU you expect 4 in th

Re: [ccp4bb] How to deal with tNCS?

Well - it is hard to comment without more information, but many crystals do have tNCS and yield perfectly satisfactory solutions.. How many molecules do you expect in the asymmetric unit? Look at the Matthewscoefficient suggestions to guess that. What are the fractional coordinates of the Patterso

Re: [ccp4bb] Peculiar issue with C2 datasets

C2 Cell : Average unit cell: 119.05 84.31 107.99 90.00 91.50 90.00 Space group: C 1 2 1 C2 shift ( if I have read your image correctly..) 60.32 2.137. 0.088 In fractions 60.32/119.05 2.137/84.31 0.00. = 0.504 0.023 0.00 See this site C121 has alt origin 1/2, ?,0 so your solution

Re: [ccp4bb] Translational NCS (tNCS)

WELL - with such high LLG and translation NCSthe high R factors are a bit surprising.. The Patterson info does not give the relative height of the origin peak to the off origin one.. Questions which I would check. Look at the data processing carefully. Are there bad batches? Could the space group b

Re: [ccp4bb] Script to refine water molecules - help

waters Good luck Eleanor On Mon, 26 Jun 2023 at 21:44, De La Torre Marquez, Pedro Luis < pedro_delatorremarq...@meei.harvard.edu> wrote: > Thanks Eleanor. > > Yes, only refine waters. > > Best regards, > > Pedro > ---------- > *From:* Eleanor

Re: [ccp4bb] Script to refine water molecules - help

Do you mean only refine waters? In a general refinement run the waters will be refined along with protin/ligands etc.. Eleanor On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis < pedro_delatorremarq...@meei.harvard.edu> wrote: > Dear all, > > I hope everything is going well. > Back in

Re: [ccp4bb] British X-ray Crystallographers

Very interesting one from Katherine Lonsdale- thank you On Thu, 25 May 2023 at 21:21, CCP4BB < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > I found these audio clips on the BBC website - might be of interest - > > https://www.bbc.co.uk/archive/dame_kathleen_lonsdale/z6v8kmn > > https:/

[ccp4bb] Obituary for Alexei Vagin for those who are interested

>From Louise Jones - Acta cryst editor We put together an obituary for Alexei with contributions from his friends and colleagues in Moscow and the UK L*ouse says: I am hoping to put the obituary online this afternoon.* *The page numbers have not yet been assigned but it can be cited with the* *d

Re: [ccp4bb] NCS consideration during refinement vis-a-vis ligand occupancy and flexible loops

As Robbie says, in such a case I just blindly refine with local NCS restraints - this should improve the greater part of the model and thus provide you with clearer maps. It is quite common for different copies of the monomer to have differences - after all the crystal environment will be different

Re: [ccp4bb] new PDB file format

Ha ha! On Sat, 1 Apr 2023 at 05:34, James Holton wrote: > Anyone who has ever had to lecture a student for writing their unit cell > lengths to dozens of decimal places is going to love the new PDB > format. It is more compact, more realistic, and less misleading to the > poor, downstream consu

Re: [ccp4bb] Alexey Vagin

Alexei certainly contributed in MANY ways to Study Weekends! Fun memories.. Eleanor On Sun, 26 Mar 2023 at 20:00, Jurgen Bosch wrote: > Sorry to hear, he helped me a very long time ago during my PhD time when I > was running into troubles with some of his programs. > > The York CCzp4 weekends we

Re: [ccp4bb] [i2dev] Alexey Vagin

Thank you Eugene for letting us know. He contributed so much to crystallography, and was a good friend too. MOLREP is such a well designed program, and he kept up his innovative ideas - a true behind-the-scenes shaker and mover.. Eleanor On Sun, 26 Mar 2023 at 19:29, 'Eugene Krissinel - STFC UKRI'

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

all for your help ! > > GIA > > > > > Le 22/03/2023 à 07:10, Eleanor Dodson a écrit : > > You have tried all spacegroups within point groups? P2 p21 c222 c2221?. > > On Wed, 22 Mar 2023 at 03:01, Lijun Liu wrote: > >> If data processing to be ok and all

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

You have tried all spacegroups within point groups? P2 p21 c222 c2221?. On Wed, 22 Mar 2023 at 03:01, Lijun Liu wrote: > If data processing to be ok and all possible monoclinic and orthorombic SG > gave unreasonable high Rs, maybe good to give a try with p1 space group? > Since > the p-lattice

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

cell 66.3 66.3 83.9 90.2 90.1 98.7. P2 or P21 cell Cell volume:364551.812 Data line--- cell 86.4 100.6 83.9 90.0 90.2 90.0. Cell volume double - C2 or C222 or C2221 cell Cell volume:729240.938. ie How many residues in your model? It is hard to decide much without

Re: [ccp4bb] To Trim or Not to To Trim

Thank you for such a careful analysis of modelling a "true" structure. You should publish this James. It shows amongst other things, how R factors depend on our modelling of solvent which is not represented as individual atoms (And also I think on how the scales are derived between observation and

Re: [ccp4bb] anomalous data usage

ng independent of i2, you have to >>> dig around a bit to find which output file contains the columns you need. >>> > >>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com >>> > >>> > Sent from Proton Mail mobile >>>

Re: [ccp4bb] anomalous data usage

fIf you are using ccp4I2 for some forgotten reason the final output has one reflection with I+ and I-, another with Imean, another with Fmean - aagghh On Mon, 13 Mar 2023 at 19:40, Ian Tickle wrote: > > Hi Gottfried > > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default. > > Cheers > >

Re: [ccp4bb] Structural alignment and classification

Does Superpose or GESAMT align multiple structures? And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 etc? Eleanor On Mon, 6 Mar 2023 at 14:53, Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Or you could use Gesamt - also in CCP4. > > Harry > > >

Re: [ccp4bb] Structural alignment and classification

See the answer last week to my query about aligning nmr structures - use Theseus . I wonder if it could be used for this task too? Eleanor On Mon, 6 Mar 2023 at 07:35, Armando Albert wrote: > Dear all, > I want to align several structures we obtained from a fragment screening > campaign and clu

[ccp4bb] NMR structires

I have been looking at 1hiq - an NMR structure with 20 models. I had always assumed that an attempt had been made to overlap the first with the second, third etc, but this does not seem to be so for this structure.. Have I been labouring under a misapprehension? Eleanor Dodson

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC . It notes these atoms are too close but carries on refinement happily enough.. But when I read the structure into COOT and try to refine the A copy

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

I thought that REFMAC tolerated dual occupancies if the sum of the two conformers was <= 1.0? Eleanor Will test.. On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some > refine

Re: [ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

Usually you can bully coot into doing it but by bit. Say you need to renumber A 1-8. I often have to change the chain id to Z say then renumber Z. And so on . Then go back once you have finished and reset chain id fir Z1-8 to A. Tedious but possible! Or just run a few cycles of buccaneer with your

Re: [ccp4bb] Careless and negative Wilson B-factor

The tool must have sharpened your data - sometimes enhancing the outer data does improve the electron density.. So I wouldnt worry about that "negative" B factor - it is doubtless a result of the "careless" run, and not presumably the one you got at the data processing step.. Eleanor On Fri, 6 Ja

Re: [ccp4bb] A challenging MR problem

d. Is there a way to do MR to predict where the > missing domains will go in the rest of the chains, based on my > solved structure? > > > > Thanks for all the helpful suggestions!! > > > > M > > > > On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson < > 0

Re: [ccp4bb] A challenging MR problem

Well you could just try the buccaneer pipeline. It would use the phases from your solved domain and try to fit the missing sequence. What are your twin fractions? And what is the resolution? Eleanor On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote: > Dear Medhanjali DasGupta, > unless the resolutio

Re: [ccp4bb] Low resolution and high anisotropy

How to deal with poor data is a challenge. Look at the images - see at what resolution there is detectable diffraction. Then run a self rotation function.Do you expect a trimer? dimer? etc and does the self rotation give any clues? Are your models dimers? trimers? etc. Eleanor On Wed, 26 Oct 2022

Re: [ccp4bb] Two Questions About SHELX

- Those reflections are equivalent: - P6/mmm - reflections h,k,l k,-h-k,l -h-k,l. all due to 3 fold - hkl equiv to -h,-k,l because of 6 foldnes h,k,l equiv to k,h,-l. due to t extra 2 fold So -1,3,1. 3,-2,1 and -2,-1,1 equiv Also 1,-3,1 -3,2,1. 2,1,1 Etc.. etc OK? Eleanor

[ccp4bb] Anisotropy

There have been several discussions lately where anisotropy has been an issue. I have always believed weak unreliable data does little harm to refinement or maps because it is given a very low weight in any calculation. Weighting, in REFMAC anyway. is set partly using the Rfree for that resolution

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

Dear Matt, Your data past 2.5A is awfully weak, and wont contribute much to any map you calculate. Each term at the outer resolution will have a very low weight. I sometimes cling to the belief that the weak data may help the B factor refinement, but there isnt much evidence of that. There is a fee

Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

We probably need more detail to help you. Have you looked carefully at the data processing? Is the Rmerge or Rpim reasonable for all batches? Is there any suggestion of twinning? Does the wilson plot look linear? (These hexagonal SGs can be twinned) How many copies of your molecule do you expect

[ccp4bb]

Is that the right way round? Atomic no K 19, Na 11 Call something K when it should be NA - B factor will shoot to reduce the atom contribution. Call something Na when it should be K - B factor will become very small.. As you say - check which fits best with the surrounding atoms.. On Thu, 8 S

Re: [ccp4bb] Lower b-factors with increasing T

Hmmm - very puzzling.. One expects the for the atoms to more or less match the Wilson B for the data sets.. There are some mini bugs which can mislead you. Is your average a mean or an RMS value? RMS ones can be hugely inflated if you have a few crazily high Bs and the refinement programs can out

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