Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template

You are quite right - 90+120 residues will not fit in a cell of 38.221 38.221 196.300 90.00 90.00 120.00 or 38.221 38.221 149.000 90.00 90.00 120.00 with symmetry P 6 2 2 . So either the cell is wrong, the symmetry is wrong, or the protein is not as you thought.. There is no point try

Re: [ccp4bb] Fixing Geometry Validation Issues (Plane/Bond Angle Outliers) in Coot and OneDep

Do remember that not all outliers are "errors". Some are "interesting" - the dictionary values predict ideal geometry in isolation but the protein fold can force bond angles for example into distorted conformations. How ready one is to believe these outliers are real depends on the quality of your

Re: [ccp4bb] free R in shells

That happens automatically - default resolution limit split in 20 shells.. But do you want to actually specify individual shells? E On Mon, 23 Jun 2025 at 12:35, Ben Bax wrote: > Hi, > How do you select R-free in shells with CCP4? >Thanks, Ben Bax > > ##

Re: [ccp4bb] Refmac occupancy refinement

Quality of your results depend very much on the resolution of your data I find… On Wed, 11 Jun 2025 at 01:40, Robert Oeffner wrote: > Thanks Pavel. I'll look into that method. I suppose having anomalous data > for the potassium ions yields an extra signal for those atoms and > significantly help

Re: [ccp4bb] How to address deposited structures poorly modeled?

Don’t be too judgmental- Phil Evans once said - well, I have spent 95% of my refinement time tweeking the 5% of the water molecules which no one will ever ever look at! Gross errors - bad; deliberate errors indefensible , but I don’t think I have ever deposited a structure which couldn’t be “impro

Re: [ccp4bb] How to address deposited structures poorly modeled?

Hmmm - of course you are free to contact the authors and explain what you have found. There are many sub-optimal structures deposited and the pdb tries to validate them ; more strictly now than in the past . In this case I would refer to the pdb-redo site and check if that has corrected some erro

Re: [ccp4bb] Requesting help with Twin Refinement

After inspecting the log files it is obvious the problem is in the data integration. (Wilson B negative! highest resolution shell stronger than low res, etc..) I think you used XDS for that? Do you have an alternative set of integrated unmerged data, eg done with DIALS? If so I would use that, or d

Re: [ccp4bb] Requesting help with twin refinement

oceeded with scaling and merging using AIMLESS. > > I have attached the AIMLESS log file for your review. > > I sincerely appreciate your continued support and valuable insights. > > Regards, > Janani Ganesh > > > On Wed, 28 May 2025 10:47:56 +0100, Eleanor Dods

Re: [ccp4bb] Requesting help with twin refinement

WEll - I think this explains your crazy B values - you have somehow *normalised* the data at processing stagr. >From the pointless log.. You usually dont need a reference data set and certainly not a set of calculated structure factors. Do you have CCP4I2 installed? If so just feed the integrated d

Re: [ccp4bb] Requesting help with Twin Refinement

Such crazy b values can’t be due to space group problem's. Could you have used TLS and not applied the results to the output coordinates? On Tue, 27 May 2025 at 09:01, Martin Malý wrote: > Dear Janani, > > There has been recently a significant development in twin refinement > algorithms in Serv

Re: [ccp4bb] Requesting help with Twin Refinement

Could you attach the pointless and aimless logs? On Tue, 27 May 2025 at 07:14, Janani Ganesh wrote: > Hello, > > I recently collected diffraction data and I was able to do the data > processing upto 1.88 Å. I observed the R-merge remained the same throughout > the resolution bins. I could solve

Re: [ccp4bb] problematic data

You say *:I ran Phaser in Phenix, it placed 18 molecules, but finds 3 MR solutions (top LLG 7962, TFZ 40). When I open the map in Coot it fits the model well, but there is a fair amount of residual density in between the different molecules (due to tNCS?). However, I can see positive density where

Re: [ccp4bb] Poor Statistics for 2.1 Angstrom X-ray Dataset

Hmmm - something is wrong here. The two sets of cell dimensions are closely relatable a1=a2. C2=2b1. C1=b2 but The beta angle 98 for the I2 space group is inconsistent.. can you see the predicted spots on an image? Re the translation peak (0.5,0,0) dies your model have any pseudo symmetry? Eleano

Re: [ccp4bb] Assembling a structure given phi, psi angles

Bob diamond wrote the first? Model building/ refinement program using this approach. The trouble was that small deviations in angles resulted in large positional errors farther down the chain and methods correcting the local Map features replaced it.. But the algorithms to go from angles to coordi

Re: [ccp4bb] symmetry of symmetry (equivalent of "Cheshire group" for point groups)

Not sure this has much meaning to "Cheshire cell for point groups". The definition implies there are various possible origins - not relevant for point groups.. *"“The Cheshire cell is the minimum volume which will allow a unique solution. For the first molecule it will be the cell which covers a vo

Re: [ccp4bb] viewing postscrippt files?

Thank you! I will try that.. Eleanor On Fri, 14 Mar 2025 at 10:37, Henry Man wrote: > Mac user here (15.3.1), have to jump through a few hoops, but I found this > a while back when I also wanted to open .ps files: > > https://superuser.com/questions/1769824/is-there-a-macos-command-line-tool-for

Re: [ccp4bb] viewing postscrippt files?

Hmm - I am using a Mac. It would be good if the programs could learn to write pdf! I can do a screenshot of course of the figure and use that. E On Fri, 14 Mar 2025 at 10:47, Wim Burmeister wrote: > Under linux, > > evince opens .ps files. > > All the best > > Wim > On 1

[ccp4bb] viewing postscrippt files?

Did anyone come up with a modern method to do this? MOLREP self rotation still writes postscript hklview ditto - it PRETENDS to offer a pdf from ccp4i2 but that only shows the axes! Help! Eleanor To unsubscribe from the CCP

Re: [ccp4bb] Refinement of partially occupied ligand when apo-protein contains chloride ions

Well - I only understand REFMAC but call the the Cl something different to the ligand - set both to have occupancy 0.5 , then the program will not check for clashes. You will need a dictionary to describe the ligand, and LINK records to define any contacts from protein to the CL. Is that clear eno

Re: [ccp4bb] Refinement of partially occupied ligand when apo-protein contains chloride ions

On Wed, 5 Mar 2025 at 15:43, stephen.c...@rc-harwell.ac.uk < 8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear CCP4 bb, > > I am trying to refine a ligand in the active site of my protein where the > ligand occupancy is ~50%. The empty active site contains two chloride ions > and the r

Re: [ccp4bb] Alternative ion occupancy refinement (anomalous)

Cant you more or less get a good idea of the occupancy from an anomalous difference map? You dont say what your wavelength is, but Tb and ca will probably have very different anomalous signals. With 1.3A data you should get a very clear map -I use the Ss to give a measure of expected signal then lo

Re: [ccp4bb] unable to fit the 11-amino-acid peptide

The lazy mans way - submit it to Modelcraft with the 11 peptide sequence and the rest of the structure as the "fixed model". Eleanor On Fri, 28 Feb 2025 at 08:53, Rigden, Dan wrote: > Dear Manjula > > You can use AlphaFold 3 (https://alphafoldserver.com/) to predict > structures of the phosphope

Re: [ccp4bb] Unit Cell Volume Confusion

We need a few more details. What is the spacegroup? Maybe the hexamer is generated by the spacegroup symmetry. Molecular replacement finds the contents of the asymmetric unit and leaves it up to you to decide on the oligermetric structure. the program PISA will analyse that for you.. \Eleanor On F

Re: [ccp4bb] George Sheldrick (1942-2025)

Thank you for this wonderful tribute. A great person… sadly mussed. Eleanor On Fri, 21 Feb 2025 at 22:21, Isabel Uson < cb655fae2581-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear Colleagues, > > > > it is with a heavy heart, that we must announce the passing of George > Michael Sheldrick. > > E

Re: [ccp4bb] Bonds Breaking After Refinement

ad, and any refinement steps from this point seem to be working > fine. > > Molecular replacement removed all the TER lines and corrected any > numbering in the file, as well as changed all the peptide atoms to "ATOM" > from "HETATM". > > All the best, > J

Re: [ccp4bb] Bonds Breaking After Refinement

ctly because these > residues were treated as "ligand" (outside the polymer; otherwise, > only "H" atom should be generated). > > Best regards, > Keitaro > > On Mon, 3 Feb 2025 at 21:39, Eleanor Dodson > wrote: > > > > Hmmm = Keitaro is rig

Re: [ccp4bb] Bonds Breaking After Refinement

bly due to an incorrect TER card. H2/H3 atoms (attached to N > atoms in the main chain) were also generated incorrectly because these > residues were treated as "ligand" (outside the polymer; otherwise, > only "H" atom should be generated). > > Best regards,

Re: [ccp4bb] Bonds Breaking After Refinement

he log file. As far as I > am aware we are not requesting unrestrained refinement. > > > > Best wishes, > > Joanna > > > > From: Eleanor Dodson > > Sent: 03 February 2025 10:47 > > To: Joanna Zukowska > > Cc: CCP4BB@jiscma

[ccp4bb] Fwd: ECA Crystallographic Computing

-- Forwarded message - From: Lutz, M.H. (Martin) Date: Mon, 3 Feb 2025 at 08:59 Subject: ECA Crystallographic Computing To: Lutz, M.H. (Martin) Dear colleagues, this e-mail contains information about the activities of the special interest group SIG-9 (Crystallographic Computing

Re: [ccp4bb] Bonds Breaking After Refinement

That is VERY odd - can you send a log file? And are you sure you arent accidentally requesting "unrestrained refinement"? In REFMAC that would be triggered by a keyword REFI UNRE Eleanor On Mon, 3 Feb 2025 at 09:37, Joanna Zukowska < 000100b050ebf83d-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi al

Re: [ccp4bb] Reduces the RSRZ outliers in the wwPDB validation report

I have been forced to think about deposition issues lately, because a) depositing a structure, and b) refereeing a paper which discusses PDB problems.. The GUIs in use in both CCP4 and Phenix offer tools to help the depositor but it is perhaps too easy to now deposit without due care and attention

Re: [ccp4bb] Question about Phaser rotation and translation search parameters

Look at this presentation by Airlie McCoy - it answers some of your questions. https://www.ccp4.ac.uk/schools/DLS-2014/course_material/day07/Airlie_McCoy_Phaser_MR.pdf The crystal symmetry is taken into account when choosing the range of angles to search. If you run MOLREP - another more limited

Re: [ccp4bb] data processing statistics

They cannot be deduced at Data Processing - your refinement summary will tell you how your model fits planarity, expected chirality etc.. Eleanor On Tue, 14 Jan 2025 at 10:53, Vitali James wrote: > Dear CCP4 community, > > If someone can share his knowledge about "How to calculate or find the th

Re: [ccp4bb] Analysing water molecules at protein interfaces

A very old fashioned hands on way to do it.. Run distang Find those H2O which contact two protein molecules.. 5od5.pdb has 3 chains.. distang xyzin CCP4_DOWNLOADED_FILES/5od5.pdb > d You get a list like this Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) av_bi+bj M 23 SD A

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

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