Re: [ccp4bb] Rfree from another mtz file

I totally agree. And because the new dataset is of higher resolution, there will be new reflections in the test set anyway. Now if you want to use the same testset always for series of isomorphous datasets (even though you do not need to), you can do this: - Use unique to make a full set of

Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

Well, it's not exactly normal. We could use some extra information... Exactly the same, or just very similar? Are the values high or low? Is it a viral capsid? Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Tung Thanh Dinh >

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

Refmac fills in the reflections that are given in the input MTZ file without observed amplitudes/intensities. So if you only want to fill in low resolution reflections you have to shape your MTZ file accordingly. This is non default behaviour because typically all missing reflections up to the

Re: [ccp4bb] Improve your previously released coordinates with OneDep

Hi Jonathan, It would be great if you deposit missing reflection data. It is very commendable. I don't know what the policy is, but I have seen quite a few legacy entries for which the data were deposited (or corrected) much later than the model. Sometimes more than 20 years. These kept the

Re: [ccp4bb] Questionable Ligand Density - Part 2

@4) Ligand density is a social construct in which the privileged blue en green density suppress the red density. The analogy of the nobility and the bourgeoisie suppressing the worker is completely obvious ;) Cheees, Robbie On 24 Jul 2019 20:13, Bernhard Rupp wrote: Dear Ligand Hunters,

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Even though PDB-REDO cannot salvage this model without extensive rebuilding which is what Tristan showed, it is fun to look at the maps and B-factors near the ligand. The B-factors go way up and the negative difference density disappears, as does most of the 2mFo-DFc density. It’s obviously not

Re: [ccp4bb] challenges in structural biology

Hi James, Related to Joel's post, how does on interpret the wealth of structural data we already have comprehensively. If you have 30 structures of the same protein in slightly different states, how do you inspect the differences? Cheers, Roobie On 17 Jul 2019 13:44, Joel Sussman wrote: Dear

Re: [ccp4bb] Bidentate GLU vs two monodentate GLU in metalloproteins

Hi Chandra, That is an intriguing question. The problem is that even if you would data mine this, the data in the PDB would be incredibly skewed to whatever we managed to crystalise. And then there is the problem of poorly modeled metal sites. So the true answer will be elusive. Purely

Re: [ccp4bb] Fo-Fc density close to cysteine residue

I think this is very wise. It can be better to say that you don't know then to guess if people will take your answer for granted. Cheers, Robbie On 11 Jul 2019 11:09, Raz Zarivach <33371661b7b1-dmarc-requ...@jiscmail.ac.uk> wrote: Hi All With so many alternative suggestions, wouldn't be

Re: [ccp4bb] resolution

You cannot directly compare R-factors because they are calculated over different sets of data. It's apples and oranges. Your R-factor gap is a bit large too, perhaps your model can be improved a bit for instance by using tighter geometric restraints. Cheers, Robbie > -Original

Re: [ccp4bb] resolution

Another reason to cut the data (temporarily!) is to avoid discussion later when you try to publish your model. You need to be able to defend your high resolution cut-off against the R-merge zealots. The paired refinement test to find a good resolution cut-off works well for that. It is based on

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

of REFMAC - at least then you know what the scaling algorithm might be Eleanor On Mon, 1 Jul 2019 at 14:22, Robbie Joosten mailto:robbie_joos...@hotmail.com>> wrote: If you are using SFTOOLS you might as well use the CORREL function to calculate things. Datamining is easier though. Eve

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

If you are using SFTOOLS you might as well use the CORREL function to calculate things. Datamining is easier though. Every PDB-REDO entry has a data.json file that has all the numbers you need. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board

Re: [ccp4bb] RAMACHANDRAN outlier of Thr

Hi Shijun, Yes there are differences in Ramachandran validation implementations. Just look at where your supposed outlier lies on the Ramachandran plot. If it is close to the edge of the distribution, I wouldn't worry about it. Cheers, Robbie > -Original Message- > From: CCP4 bulletin

Re: [ccp4bb] Has anybody put CCP4 into a singularity container?

a of what Frank > meant, which is probably what you intended!? > Do I have to read also the Supplement to find out more, or could you explain > to CCP4BB readers what a singularity container's (???) advantages are? > > thanks, > > Kay > > > On Wed, 29 May

Re: [ccp4bb] Has anybody put CCP4 into a singularity container?

Hi Frank, Yes we have, see https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3353 Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Frank > von Delft > Sent: Wednesday, May 29, 2019 14:38 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Has anybody put CCP4

Re: [ccp4bb] weight term and geometry

Hi Luca, You should not settle for poor results here. With the most recent CCP4 and PDB-REDO versions refining with an N-terminal CXM works fine. I guess there is something wrong with the restraint generation. Make sure your residues are sequentially numbered and in your PDB file the CXM

Re: [ccp4bb] PyMOL now packaged as a snap on Linux

Hi Pedro, FC 23 has been end-of-life for 2.5 years now. You rally cannot expect it to be supported. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Where is M.Harding's website for metal coordination geometry

Hi Xiaoshan, MetalPDB is not quite the same, but I like it a lot http://metalweb.cerm.unifi.it Cheers, Robbie n 7 May 2019 01:27, "Min, Xiaoshan" wrote: Hi I am trying to find out if the website metal coordination groups in proteins is still accessible.

Re: [ccp4bb] Difference in the TLS origin calculation

It seems that the selections and the origins got moved around. Reported value from group 1 matches the calculated value from group 6. Perhaps you had a problem with a PDB to mmCIF converter. Or just with non-sequential numbering of your TLS groups. Cheers, Robbie On 27 Apr 2019 06:25, "Ethan

Re: [ccp4bb] Big density blobs near Arg and His residues or Thr residues

I would try chloride and potassium in those sites and see whether that refines well. Cheers, Robbie On 17 Apr 2019 07:49, WENHE ZHONG wrote: Dear all, We found a huge density blob close to residues Arg and His (see attached) and another big density blob near three Thr residues (see attached)

Re: [ccp4bb] ORCID being mandatory for PDB depositions

Than it is easy enough. You mustn't create an ORCid for others, this could indeed get you into GDPR trouble as you are sharing personal data without consent. So that leaves the practical bit. If deposition requires an ORCid and a collaborator does not have an ORCid despite your requests, then

Re: [ccp4bb] Backup of whole synchrotrons

> -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Peter Keller > Sent: Monday, April 01, 2019 12:04 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Backup of whole synchrotrons > > Hi Robbie, > > On 01/04/2019 07:2

Re: [ccp4bb] Backup of whole synchrotrons

I don't think making this GDOR complient is that hard. It's all pretty well defined what you store (everything), where you store it, and why. There are some philosophical problems with allowing users to have their data deleted. Assuming the copy is good enough to reproducing the experiment.

Re: [ccp4bb] Deposition requirement of anomalous pairs?

Hi Eleanor, That would be a great idea. We would use these data a lot for validation. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Eleanor > Dodson > Sent: Wednesday, March 20, 2019 13:21 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Deposition

Re: [ccp4bb] Configuration of inositol hexaphosphate

Hi Karthik, There are currently three epimers of inositol hexaphosphate in the PDB: I6P (one axial), IHP (the same, which shouldn't be allowed), KGN (two axial, next to each other). I could not find other configurations. Which restraint file for COOT/CCP4 are you referring to? It might need

Re: [ccp4bb] Java based structural database websites

Hi Nick, A bit of a hack I suppose, but you could use a (single use) VM with some old windows version that still works. E-mailing the developers directly is the way to go to figure out whether you can expect an update. We had a similar problem with our own webserver (the Crystallographic

Re: [ccp4bb] Refmac5 refinement question

Hi Ray, Not necessarily close to 1.00 but rather 1.00 or lower. Cheers, Robbie -Original Message- From: Raymond Brown [mailto:ray-br...@att.net] Sent: Tuesday, March 12, 2019 15:56 To: Robbie Joosten Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac5 refinement question Hi Robbie

Re: [ccp4bb] Refmac5 refinement question

Hi Ray, This is how I see it: Because different bond length and angle target tolerances/sigmas you cannot compare them on an absolute scale. What is less likely? A two 0.020A deviation in the CD1-CG in PHE or a the same deviation in the CD1-CG bond in LEU. If you think they are equally likely,

Re: [ccp4bb] Ramachandran outliers

Hi Tereza, Rather than opting for a technological fix in a reciprocal space refinement program you should look at all the outliers in Coot and see if they are fixable. If they are severe outliers, you need to rebuild by peptide flipping and possibly by more invasive actions. If you have small

[ccp4bb]

Hi Sanaz, That is not a very well-defined question. To just get some info on an mtz file you can use mtzdmp from the command line (mtzdmp foo.mtz). Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Sanaz Asadollahpour > Sent:

Re: [ccp4bb] clashscore question

Hi Xiaodi, Please read the PDB validation report for the individual clashes and see if these are symmetry or alternate related. If you have been playing around with atomic occupancies, this also affects which atoms are taken into account for the clashscore. Also, which hydrogen model did you

Re: [ccp4bb] Survey for the CCP4 community study

Hi Marie-Hélène, Thanks for having such a wide 5-20 years category. Keeps me from feeling really old ;) I can honestly say that I've learned a lot on the BB and that some of the discussions have really broadened my knowledge beyond the standard books. I try to pay it forward whenever I can. It

Re: [ccp4bb] Selecting best chain for NCS

Hi Chetan, Unless the model is horrendously far away from the final result, I would do the following instead of the chain copying: - Start from chain A with NCS ghosts in COOT and go through the model residue by residue. Refine 3-residue windows. If you see NCS deviation. Cycle through the

[ccp4bb] Paired refinement in PDB-REDO

Dear CCP4BB-ers, A recent discussion on the CPP4BB made it clear that people want an easy way to run paired refinement on their data. This option has always been available in the PDB-REDO webserver (https://pdb-redo.eu), but it was (un)cleverly hidden in automation (see

Re: [ccp4bb] Refmac5 crashes with coordinates last refined in 2009

Hi Derek, Try removing any MODRES records in your PDB file. This might solve the carbohydrate related issues. Cheers, Robbie On 28 Nov 2018 17:24, Derek Logan wrote: Hi, I'm trying to finish off refinement of a structure I last refined in 2009, but Refmac5 is crashing with very odd

Re: [ccp4bb] VERY old mtz file..

We'll, you never know when someone wants the data. I do know that I was incredibly impressed when you managed to conjure up the experimental data for 2ins (from 1982!) a few years ago. Cheers, Robbie P.S. this was a really fun thread to read :D On 14 Nov 2018 16:04, Eleanor Dodson

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

Hi Tristan, Erroneous LINK records happen quite a lot and used to be the combination of aggressive annotation software and depositors not paying attention to the comments from the annotators. They make up a large fraction of the bug reports I have sent to the PDB over the years. They are

Re: [ccp4bb] CC work / free

Hi Clement, Refmac actually does write out CCwork and CCfree out in its log files, so you can already check to see whether this you can use these metrics as you propose. We use these values in PDB-REDO to do paired refinement. IMO this is a better way of finding a high-resolution cut-off than

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

Hi Hugo, Perhaps you should play with your refinement strategy. Use a decent number of cycles and a sensible restraint weight (something that gives you rmsZ < 1.0 and good R-factors). Anisotropic B-factors are probably needed and make your model as complete as your maps allow. You could try

Re: [ccp4bb] Search by name on the PDB fails

-- Forwarded message -- From: Robbie Joosten Date: 2 Oct 2018 07:45 Subject: Re: [ccp4bb] Search by name on the PDB fails To: Murpholino Peligro Cc: Ligand-Expo is the place to be. It has search by name, identifier, SMILES and (my favourite, chemical formula). You can get

Re: [ccp4bb] planar restraints definition in .cif file for refmac

Hi George, In your CCP4 installation there is a file called mon_lib_list.cif which has a few examples of the correct syntax. You can for instance use the description of a peptide bond. HTH, Robbie On 17 Sep 2018 19:05, George Lountos wrote: Hi all: I want to adjust a .cif file for a ligand

Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

Hi Tobias, I don't know of any specific claims made about this but you'd better check the data yourself if you find an example. A nice paper by Bill Hunter and his team (http://scripts.iucr.org/cgi-bin/paper?S1744309111005835) showed a case where Co2+ was an essential ion for crystallisation ,

Re: [ccp4bb] unexpected errors in LSQKAB

Hi Eleanor, You point out two major problems with PDB files. The TER record nightmare is pretty bad. Although it seems that at least now they are written by programs, they end op at the weirdest places due to aggressive addition of the TERs. At the same time, they are sometimes missing when

Re: [ccp4bb] How to fix residual B value problem in pdbredo

Hi Kahkashan, Thanks for your faith in pdb-redo. I'm glad you are happy with the results. If you download the zip file with all output, there is a file called _final_tot.pdb this one has the total B-factors as ANISOU records. Cheers, Robbie On 16 Aug 2018 18:11, Firdous Tarique wrote:

Re: [ccp4bb] Sulphate or phosphate?

If the site is not really selective, I would model the one with the highest concentration. If your data are really good an anomalous. Map would help. Cheers, Robbie Sent from my Windows 10 device From: CCP4 bulletin board on behalf of David Schuller

Re: [ccp4bb] identifying bound ions

Hi Herman, Whatcheck does his as well for the metals. Chloride is not highly coordinated, likes nitrogens, and has long coordination lengths (over 3A). Sulfate gives huge blobs and sticks out in difference density or ridiculously low B-factors. HTH, Robbie Sent from my Windows 10 device

Re: [ccp4bb] unidentified electron density

Hi Harsh, Just try a slightly longer PEG molecule: PGE (in PDB nomenclature). That's the version with 3 glycol units. Others are (in order of increasing size) PG4, 1PE, P6G, P33, PE8, 2PE, XPE, 12P, 33O, and P3E. This list comes from a paper that shows that PEG can go to all sorts of nasty

Re: [ccp4bb] Wavelength mismatch during PDB deposition

Hi Santhosh, The seems to be the result of a rounded value in the SF file and a truncated value in the PDB. I suppose that the PDB file you are depositing actually does have the wavelength (it lives in REMARK 200, but depending on which refinement program you used it may also be in REMARK 3,

Re: [ccp4bb] R-flag choose

Dear Shijun, For refinement you want to use as much good data as possible to get a good model. At the same time you want to make sure that your model is predictive for related data that was not used for making that model. This wat they call holdout validation and that is exactly the idea

Re: [ccp4bb] Unidentified electron density blob

I'd like to add the more current CCP4 solution: AceDRG. It works really well and you only need to feed it the SMILES string of your compound. Also keep in mind that many compounds are actually already in the CCP4 dictionary. Finding out whether a compound is, is a two-step procedure: 1) Go to

Re: [ccp4bb] disulfate bond ?

That’s because the ones om the left seem to be dragged into the wrong density. Sphere refine in Coot should clear that right up. After that it may very well look like a disulfide. Cheers, Robbie Sent from my Windows 10 phone From: CCP4 bulletin board on

Re: [ccp4bb] [ccp4bb] Oxford University Press

pitalists need to add a few lines to their balance sheets best, jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie Joosten Gesendet: Freitag, 29. Juni 2018 13:42 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betre

Re: [ccp4bb] Oxford University Press

papers and cannot get them from ResearchGate, I'm sure they can find them on another online collection, a hub of some sort ;) Cheers, Robbie > -Original Message- > From: Bernhard Rupp [mailto:hofkristall...@gmail.com] > Sent: Friday, June 29, 2018 13:23 > To: 'Robbie Joos

Re: [ccp4bb] Oxford University Press

Were they open access papers? If they were, than OUP is being too aggressive (IMO), but otherwise it makes sense. I also find the ResearchGate is rather aggressive in bugging you to upload papers that are readily available from the publisher. The whole business bit in scientific publishing is a

Re: [ccp4bb] Python3 and MTZ

Right you are Kay. It would be very weird to start developing things on Python 2.7 right now. Its days are numbered: https://pythonclock.org/ Cheers, Robbie Sent from my Windows 10 phone From: CCP4 bulletin board on behalf of Kay Diederichs Sent:

Re: [ccp4bb] Problems with HEC in CCP4

edu> Sent: Tuesday, May 15, 2018 8:07:38 PM To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problems with HEC in CCP4 Does this mean- if the pdb file has standard PDB link records involving HEC, like LINK SG CYS A 32 CAB HEM A 93 1555 1555 1.8

Re: [ccp4bb] Problems with HEC in CCP4

Vonrhein <vonrh...@globalphasing.com> Sent: Tuesday, May 15, 2018 6:21:35 PM To: Robbie Joosten Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problems with HEC in CCP4 Hi, On Tue, May 15, 2018 at 02:21:59PM +, Robbie Joosten wrote: > A link describes a chemical bond between two

Re: [ccp4bb] Problems with HEC in CCP4

Note: I took 4qo5 just as example of cytochrome c to show issues with HEC and do not intend to insult authors of original paper. 2018-05-15 12:00 GMT+03:00 Robbie Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>>: Addendum: 4qo5 actually lacks the right LINK rec

Re: [ccp4bb] Problems with HEC in CCP4

AIL.AC.UK> On Behalf Of Robbie > Joosten > Sent: Tuesday, May 15, 2018 10:51 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Problems with HEC in CCP4 > > Hi Eugene, > > The problem is not in the HEC.cif file but with the LINKs which modify the > chemistry. These we

Re: [ccp4bb] 2014 GRC Photos

Hi Paul, Thanks for sharing this blast from the past. Happy Easter, Robbie Sent from my Windows 10 phone From: CCP4 bulletin board on behalf of Paul Emsley Sent: Sunday, April 1, 2018 1:46:51 PM To:

Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot

Dear Laurant, Perhaps not a complete answer to your question, but more of a strategy. You can let the Ramachandran plot in COOT only show the outliers which would make everything a bit more tangible. Then only go for the massive outliers, these are the problems that need rebuilding (e.g.

Re: [ccp4bb] Resolution cut off

Dear Vandna, Paired refinement is indeed the most reliable way to see whether the higher resolution data help your refinement. It is done automatically on the pdb-redo.eu server if the resolution of the data used in refinement so far is lower than the resolution of your dataset (by at least

Re: [ccp4bb] PDB redo and biased/unbiased R-free

b site, my > understanding is that rather than calculating Rfree from the re-refinement, > various other quality measures are used to calculate an expected Rfree/R > ratio consistent with other structures of similar quality. > This ratio is then multipled by R to yield an esti

Re: [ccp4bb] "Atomic resolution"

Hi Ivan, I agree that the Hamilton test is quite useful in this context. We added it in PDB-REDO quite a while ago (http://www.cmbi.ru.nl/pdb_redo/reprints/CCP42011.pdf). Since that paper we have learned that at 18 reflections/atom is not enough to consistently pass the Hamilton test. We

Re: [ccp4bb] Add OXT quits COOT ..

Hi Ruud, Shameless plug: if you run PDB-REDO with the correct sequence, OXT atoms are added automatically. Cheers, Robbie Sent from my Windows 10 phone From: CCP4 bulletin board on behalf of Ruud Hovius Sent:

Re: [ccp4bb] LINK vs LINKR

Actually, PDB_EXTRACT works great to convert your PDB file to mmCIF and you can feed it your other relevant log files ((E.g. From XDS, Aimless, Phaser and you refinement program). This saves you a lot of time in the deposition. Cheers, Robbie Sent from my Windows 10 phone

Re: [ccp4bb] LINK vs LINKR

Hi John and Eleanor, The absence of a LINKR equivalent in the mmCIF dictionary is a shame. The mapping to a full description of the bond (bond order, residue modifications, geometric targets) rather than just a statement that two atoms are connected (with a limited set of types), is something

Re: [ccp4bb] Electrostatic Potential: Poisson-Boltzmann

If you cannot trust the surface of your protein, perhaps you should not look at the the potential on the surface. Instead you can look at the field around your protein. This is less precise, but also less sensitive to local errors. If you want to know how your peptide finds your protein, this

[ccp4bb] Dubious slide aggregator slideplayer.com

Dear CCP4BBers, Yesterday I ran into one of my talks at Slideplayer.com, a slide aggregator that makes money from advertising. You can watch presentations for free (surrounded by ads), but to download them you have advertise for Slideplayer by posting on social media. The presentations are

Re: [ccp4bb] PDB-REDO

Hi Florian, Have a look at the outlier rejection Phenix uses for reflections. You may have a few dodgy reflections that mess up the maps. That can give weird ‘layered’ maps. Cheers, Robbie Sent from my Windows 10 phone From: Florian Schubot Sent: vrijdag 20

Re: [ccp4bb] exclude water from anisotropic refinement in PDB_REDO

Hi Abhishek, At the moment, there isn't. However, the decision to use anisotropic B-factors is based on comparing the refinement a fully isotropic model with that of a fully anisotropic model using the Hamilton test. So it should be safe to use anisotropic B-factors for all atoms. Cheers,

Re: [ccp4bb] Creating a covalent bond

Dear Jiyong Su, The go-to program for this is currently jligand from CCP4. To define a link you load both compounds (ASP and your thing), delete the leaving atoms (don't forget the hydrogens), define the bond (right click to change the bond order if needed). Then you can save the definition

Re: [ccp4bb] restraints for pseudo-amino acids within a peptide chain

Hi David, You can copy the TRANS definition from the CCP4 dictionary and hack it to match your atom names. It’s in a file called mon_lib_list.cif Cheers, Robbie Sent from my Windows 10 phone From: david lawson (JIC) Sent: woensdag 27 september 2017 17:44 To:

Re: [ccp4bb] R free flag

Hi Rashi, Rather than use the mtz file from EDS you should use he mmCIF reflection file from the PDB directly and convert it. If the authors deposited the test set, you can keep it this way. Otherwise you need to select a new test set. Note that if you want to optimize an existing PDB entry,

Re: [ccp4bb] PAK=0 problem

Hi Rohit, There are many refinement settings you can tweak and some local rebuilding in COOT based on difference density and validation reports can also help. PDB-REDO can help you a bit with this and it should be able to optimize your settings for Refmac. To avoid too much of a black box,

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

...I would not recommend trying that. Sorry for the fat finger, Robbie Sent from my Windows 10 phone From: Robbie Joosten<mailto:r.joos...@nki.nl> Sent: 12 September 2017 21:46 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Risk assessment for heavy

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

Liquid mercury cannot be absorbed very well through the skin. Also ingestion seems to be much less risky than breathing in mercury vapours. My thermodynamics lecturer at uni was convinced that you can drink liquid mercury with no health risk, but I would not rec Sent from my Windows 10 phone

Re: [ccp4bb] Issue with disulphide bond

Hi Ameya, If you do sphere refinement in coot on the disulfide bridges and repeat the final refinement, it should be solved. Cheers, Robbie Sent from my Windows 10 phone From: ameya benz Sent: 10 September 2017 09:19 To:

Re: [ccp4bb] "reset" a structure before re-refinement

In most cases resetting the B-factors would be enough to perturb the model. Cheers, Robbie Sent from my Windows 10 phone From: Andrew Leslie Sent: 17 August 2017 17:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] "reset" a

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

In addition: pdb-redo automatically makes (homology-based) hydrogen bond restraints for Refmac at this resolution. You could gibe those a try. Cheers, Robbie Sent from my Windows 10 phone From: Sudipta Bhattacharyya Sent: 13 July 2017 06:25 To:

Re: [ccp4bb] to fix angle between ligand and residue atoms

Hi Markus, You can add plenarity restraint to your LINK. You can model it after one of the peptide LINKs in the mon_lib_list.cif file from CCP4. Cheers, Robbie Sent from my Windows 10 phone Van: Markus Heckmann Verzonden: maandag 3 juli 2017 16:46

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear Meytal, Perhaps the problem can be solved by increasing the restraint weight in Refmac, perhaps your model needs more substantial rebuilding. Look at hydrogen bonding, you may need to flip a few peptides. Also a wrongly fitted side-chain may distort the backbone enough to cause a

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

Hi Pavel, Similar results in PDB-REDO https://pdb-redo.eu/db/5xql, nothing wrong but clear room for improvement. That said, I would hope that the epositors set the record straight on the data completeness or conjur up the missing reflection data. Cheers, Robbie Sent from my Windows 10 phone

Re: [ccp4bb] Error in assignment of symmetry operators

Hi Radu, This may be caused by the coordinates being too many unit cells away from the origin. In COOT you can easily ‘symmetry move coordinates here’ to a place closer to the origin. Hope this helps, Robbie Sent from my Windows 10 phone Van:

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

Hi Eleanor, From PDB format 3.3: * Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record. * The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which

Re: [ccp4bb] N-linked glycosylation check

Hi Jan, I do the same thing, but it would be nice if there was a consistent target. I noticed that the targets (and their sigmas) used by the PDB validation software don't fully coincide with the 'ideal' values from their own Chemical Component Dictionary. How are supposed to correct the

Re: [ccp4bb] N-linked glycosylation check

Hi Chris, Not a direct answer to your question, but I notice that there are two TER records for the same residue. We've been noticing a lot of problems with leftover TER records. Any idea where they came from? It probably won't help, but try deleting those. Cheers, Robbie > -Original

Re: [ccp4bb] Problem with Mg2+ binding site refinement

Hi Clemens, > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Clemens Vonrhein > Sent: Friday, June 16, 2017 12:42 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Problem with Mg2+ binding site refinement > > Hi, > > On Fri, Jun 16, 2017

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

Hi Wolfram, We recently moved pdb-redo to a new domain, so the entry you are interested in is at https://pdb-redo.eu/db/2h58 This entry at 1.85A resolution was indeed refined with anisotropic B-factors based on the Hamilton R ratio test. There was no paired refinement for this entry. We only

Re: [ccp4bb] BMA NAG FUC

Hi Bernhard, We had the same problem recently and it looks like a bug. The workaround is to give it an alternative name the same as the name it should have. So FUC your FUC etc ?? Cheers, Robbie Sent from my Windows 10 phone Van: Bernhard Rupp Verzonden:

Re: [ccp4bb] very high B-factor

Hi Vipul and Qiaoling, Setting occupancies to 0 will give somewhat misleading results. It is good to test whether density will disappear or not, but not for the final model. Users of the model might misinterpret it. Especially if you start leaving out 'random' poorly fitting atoms. High

Re: [ccp4bb] Refmac library

Hi Brian, It's called MED. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > brian walker > Sent: Monday, May 01, 2017 14:52 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac library > > Is there a 3 letter code for

Re: [ccp4bb] CH-bond length discrepancies

Hi Bernhard, You touch a valid point. You get different clash scores in MP depending on how you add hydrogens when you run it (unless this was solved recently). So you can essentially cheat the program by choosing a different H addition function. I don't get why this option exists at all. If

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

Hi Alex, You are not giving the number after refinement without the twin refinement. Nevertheless, R-free drops like this are not unheard of. You should check your Refmac log file, it would warn you of potential space group errors. Refmac will also give you a refined estimate of the twin

Re: [ccp4bb] waters with positive FoFc peaks?

How are the peaks coordinated? Regular coordination with 5 or more ligands has ion written all over it. Different difference density peak heights can be caused by differences in effective B-factor restraint weight but also by differences in relative scattering factors of oxygen and whatever you

Re: [ccp4bb] prodrg in coot

Dear Jiri, You don't need to buy anything, but you should update your COOT (stand-alone or with CCP4). The current version is 0.8.8. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > chemocev marker > Sent: Monday, April 3,

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

I agree that you should try to use all the data. There is nothing wrong with solving your structure with the data you trust and then extending the resolution when your model is in an advanced state of refinement. If you worry whether your data has added value, you can use paired refinement to

Re: [ccp4bb] one metalloid making multiple covalent bonds - generating library

Hi Thiyaga, Rather than compounds, you should define LINKs. You can do this in the CCP4 program jligand. You may also want to define angle restraints depending on your resolution. In Refmac you can do that as external restraints. A similar situation is described in this

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

Hi Eleanor, This is covered in PDB_REDO: we figure out whether the B-factors are totals or residuals. Wouter Touw has made the BDB (http://www.cmbi.ru.nl/bdb/) a databank in which all B-factors are represented as the isotropic component of the total B-factor. This is quite useful if you want

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