Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Harry,It might be better now, but there used to positively charged aspartates in the PDB. You have a better chance taking charges out of the CCD for your atoms of interest. I'm not saying all charges in the CCD are correct, but they are much more reliable. If you find errors, please report them

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Harry,Deducing the element from the atom name has always been unreliable so since PDB version 3 you have to get it from columns 77-78. There is no implied element in the atom name anymore.HTH,RobbieOn 15 May 2024 12:28, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:Hi folks

Re: [ccp4bb] Rescale merged data?

If I may add to that: Please deposit the full dataset, not just the set of reflections you end up using. This allows people to use all the data if they are interested.Cheers,RobbieOn 17 Apr 2024 22:35, "Hekstra, Doeke Romke" wrote: Hi Matt,   I appreciate disagreement and comments from

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

Make sure everything is built. Sometimes it is the crystallisation agents that sit at surprising places: https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2923 Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of > Murpholino Peligro > Sent: Tuesday, April

Re: [ccp4bb] isymop reference for ISYM column in MTZ files

If I understand the documentation correctly (https://www.ccp4.ac.uk/html/mtzformat.html), it refers to the symmetry operations as they are stored in the header of the MTZ file. So the source of the MTZ file might make a difference. The safest way of using this data is to follow the header and not

Re: [ccp4bb] what is isomorphous?

Hi Carlos, In a practical setting you don't have to be very purist. The memory with respect to the reflection data is lost if you refine to convergence. Now there was are recent discussion on refinement convergence and again you can be quite purist here. However, if you go through a few cycles

Re: [ccp4bb] Automated refinement convergence

Hi Robert, I see your point but extending the number of cycles to reach convergence has a big risk of going into infinite loops (which you point out). In the case of Refmac stopping early is not really needed as it is very fast anyway; a few unnecessary cycles won't take that long. Generally

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

suggest looking at various possibilities until one finds some compromise which works. Not as intellectually gratifying as having a cut and dry answer to these questions that come up rather frequently.  Thanks again for the stats and description.  cheers, tom  From: Robbie Joosten Sent: Sunday

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

eeded. I won't claim that this is the best protocol for each of the cases, but I guess they are decent starting points for most. Cheers, Robbie > -Original Message- > From: Tom Peat > Sent: Saturday, January 6, 2024 21:42 > To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten > > Su

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

One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques.Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are

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

Hotel booking scammers for instance. Cheers,RobbieOn 15 Dec 2023 15:34, Frank von Delft wrote:I mean, who'd actually want that list anyway?! On 15/12/2023 13:23, Gerard Bricogne wrote: > Dear all, > >   I just received this a moment ago, and it looks most suspicious. Can > any action

Re: [ccp4bb] Alternatives to X

Hi David, Thank you for the Mastodon links. I like the idea of Mastodon, but many servers do blanket bans against other servers, particularly if these are very libertarian (e.g. have too much "Freeze Peach"). Your Mastodon 'heritage' seems to matter a lot. Nevertheless, it's good to see that

[ccp4bb] Downtime for PDB-REDO, AlphaFill, DSSP and CCD.

Friday 3rd of November 22:00h until Saturday 4th of November 16:00h (Amsterdam time). We will try to minimise the downtime. We apologise for the inconvenience. Best wishes from our entire team, Robbie Joosten

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

I couldn't either. People should add pictures as attachements rather than pasting them inline. Cheers,RobbieOn 11 Aug 2023 19:08, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:Hmm - I cant see a picture..Your email has this..img src="">etc etc etc..But have you checked the

Re: [ccp4bb] High Temperature Factors with TLS

Although the effect should be quite small, is the wavelength in your reflection file consistent with the actual wavelength? Another option is that specific filters on atom types were used in the TLS refinement. I would refine the models with another program (REFMAC/Buster/PDB-REDO) to see if

Re: [ccp4bb] Binding affinity in AutoDock Vina

Are you doing self-docking or are you analysing the models as-is? Not all binding poses in the PDB are realistic and things like atomic clashes have a massive energy penalty.Have you looked at the model in the electron density? You can also try the pdb-redo version op the same pdb entry to see if

Re: [ccp4bb] PDB redo R free

ree would be small, and Rfree would be > meaningless, as R-free set is not "free". > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > > Robbie Joosten 于2023年4月28日周五 > 15:26写道： > > > Hi Qixu, > > >

Re: [ccp4bb] PDB redo R free

Hi Qixu,PDB-REDO tries to have a minimum number test set reflections to reduce the error margin in R-free. As Tim says this is not a problem but if you reach out privately we can change your calculation to use your current testset. That is not recommended though.Cheers,RobbieOn 28 Apr 2023 04:51,

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

The fact that your protomers have different density levels does not mean they are structurally different. The prior assumption should be that they are the same unless proven otherwise. So I would keep the (local!) NCS restraints in the initial stages and only remove them if it becomes apparent

Re: [ccp4bb] Issue about cif file of ligand

Dear Ning, There is a separate bulletin board for anything Phenix. You can try the CCP4 program AceDRG to generate restraint from a SMILES string. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Ning Li > Sent: Monday, April 3, 2023 18:17 > To:

Re: [ccp4bb] new PDB file format

WHAT_CHECK has a check for suspiciously rounded coordinates. I have never seen it triggered.Cheers,RobbieOn 3 Apr 2023 10:11, James Holton wrote: Thanks to everyone for being such good sports! It is good to know that there is still room for good-natured funny in what can be

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

Hi Markus, Just to make sure that things are clear: PDB-REDO adds missing side chains (that is a design choice) and it also adds missing loops if, and only if, there is a homologous template, there is sufficient density (although the criteria are rather forgiving), and the geometry of the loop

Re: [ccp4bb] Unidentified density

This is always hard to see this way, but it looks like glycerol at first glance. Try to fit that. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of zeyaul > islam > Sent: Tuesday, February 21, 2023 12:13 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb]

[ccp4bb] Fill-your-own-model with AlphaFill and other updates

Dear bulletin boarders, The previous version of this post did not come through. Apologies if this turns out to be a double post. To celebrate the publication of our AlphaFill paper (https://www.nature.com/articles/s41592-022-01685-y), we have released a new version of our https://alphafill.eu

[ccp4bb] Fill-your-own-model with AlphaFill and other updates

Dear bulletin boarders, To celebrate the publication of our AlphaFill paper (https://www.nature.com/articles/s41592-022-01685-y), we have released a new version of our https://alphafill.eu website. It has some (we hope) useful new features: - AlphaFold V3 and V4 entries (all Uniprot entries)

[ccp4bb] AlphaFill and PDB-REDO downtime this Friday and Saturday

Dear CCP4bb-ers,Due to construction and electrical maintenance work, AlphaFill, PDB-REDO and all related services will be down or poorly reachable between 18:00h CET November 4th and 12:00h November 5th.My apologies for the inconvenience.Best wishes,Robbie To unsubscribe from the CCP4BB list,

Re: [ccp4bb] bond angle deviation listing in refmac log

Hi Garib, > Are these related to the side chain of ARG? In the monomer library sigmas are > capped from below - 1.5degree. > In the PDB these sigmas might be very small and tiny differences could be > given > as outliers. > Another reason might be that in the monomer library these two angles are

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

The combination of paired refinement and anisotropy should not be a problem, but I think there are a few catches depending on the implementation. I'll reason from the PDB-REDO implementation of paired refinement which was made assuming a "you get what you get" set of reflections without the

[ccp4bb] Problem downloading models maps in from PDBe in Coot

Not sure if this is a PDBe bug or a Coot bug (or a combination thereof)... I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB using Accession Code', I do not get any models so I guess the target URL is wrong. When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs,

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

Hi Pavel, There are a number of DNA structures that are complete made up out of alternate atoms. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Pavel > Afonine > Sent: Wednesday, August 24, 2022 00:02 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] ISO

Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

Hi Jan, I would advise against playing with occupancies because it adds a complication that has side effects on the density and is easily overlooked by the users of your model. There are many Jeffamines on the market, so figuring out which is the one you have is the first step. Depending on

Re: [ccp4bb] PDB to AlphaFold via Uniprot

Hi Paul, From the PDB file get the Uniprot primary accession code (see DBREF) and use this to get the Alphafold model using 3D-beacons (https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/). You can also use 3D-beacons to get the related AlphaFill model (just saying...). Cheers, Robbie >

Re: [ccp4bb] Checking X-ray sequence (no more protein).

Hi Jon, There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX respectively. You can just use those. AFAICT there no such thing for VAL/THR ambiguities. You could look for the most likely canadidata based on multiple sequence alignments. Refinement of both alternatives can

Re: [ccp4bb] Missing double bonds in the ligand

Dear Anil,Bond orders are not captured in PDB files explicitly. The way bonds are shown depends on the program and possibly additional information sources (i.e. molecular restraint or topology files). So this is just a "problem" with Schrödinger.Cheers,RobbieOn 7 Jul 2022 21:00, "Dr. Anil Kumar

Re: [ccp4bb] Easy/Silly question

BMA is mannose, not maltose > -Original Message- > From: CCP4 bulletin board On Behalf Of Krieger, > James M > Sent: Friday, July 1, 2022 09:59 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Easy/Silly question > > How about BMA for beta-D-maltose? > > > On 1 Jul 2022, at

Re: [ccp4bb] Regarding R factor value

Depending on how you process the model, the reported R-value becomes invalid. So you need to get it from the PDB entry before processing or recalculate it with respect to the experimental data. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of > Abhilasha

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

mtzdump is a command line tool, so you have run it from a terminal. There is also a shorthand version for lazy people like me (notice the missing 'u'): mtzdmp something.mtz Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of > Rituparna Saha > Sent: Tuesday,

Re: [ccp4bb] Regarding File conversion

cif2pdb will do the trick if conversion is all you need. I use mmCQL to first rename 'chains' before converting. For both see: https://github.com/PDB-REDO/cif-tools Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Frederic > Vellieux > Sent: Tuesday, April

Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

Dear Ines, The latest version of DSSP (https://github.com/PDB-REDO/dssp) also annotates the coordinate file in pdb or mmCIF. Note that mmCIF is preferred as you can do a more complete annotation. The latest version of mkdssp will be in CCP4 version 8. Cheers, Robie > -Original

Re: [ccp4bb] sftools

Hi Eleanor, I actually add the wavelength to an mtz file with CAD: cad \ HKLIN1 $WORKDIR/raw_nowavel.mtz \ HKLOUT $WORKDIR/raw.mtz \ <> $WORKDIR/mtz_creation.log LABIN FILE 1 ALLIN DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH END eof I have no experience adding dataset names as

Re: [ccp4bb] off topic -- pymol error message

This means that you have an O-umlaut in your PDB file. That should never happen! PDB files should only have basic ASCII characters, not UTF-8. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of 陈成 > Sent: Tuesday, April 5, 2022 13:12 > To:

Re: [ccp4bb] Phenix/refmac incompatibility?

Hi Eleanor,This seems to be a caused by a bug in an older version of Phenix. We used to see quite a few examples of this on the PDB-REDO server, but not recently. Renumbering is the only solution I'm afraid.Cheers,RobbieOn 30 Dec 2021 20:05, Eleanor Dodson

Re: [ccp4bb] Search for a particular motif [off-topic]

You can analyse your hits with DSSP to see the secondary structure afterwards.Cheers,RobbieOn 19 Oct 2021 21:58, Guillaume Gaullier wrote: Hello, ScanProsite almost does what you want, but since it only searches sequence databases, it has no notion of secondary structures and therefore cannot

[ccp4bb] PDB-REDO downtime

Dear BB-ers, Due to electrical maintenance at our host institute pdb-redo.eu will be unavailable from 20:00h (Amsterdam) on October 15th to roughly 12:30h on October 16th. Apologies for the inconvenience. Best wishes, Robbie Joosten

Re: [ccp4bb] PDB file secondary structure annotations

Yes, you can use DSSP 4.0 (https://github.com/PDB-REDO/dssp) to directly annotate your structure model in PDB or mmCIF format. The latter is recommended. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Neno > Vuksanovic > Sent: Thursday, September 16,

Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

requently, > because it allows a lot of mathematical operations on data in mtz files. > I also use sftools to produce lists of average data values against > resolution (that I plot then with gnuplot). I can't recall having used > coordconv at all. > > Best regards, > > Dirk. > &

[ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

For model validation, this paper used machine learning (Random Forest) to detect peptide problems: https://doi.org/10.1107/S1399004715008263 Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Bernhard > Rupp > Sent: Tuesday, August 3, 2021 22:00 > To:

Re: [ccp4bb] pictures in emails

Hear hear! On top of that, I look at my emails as plain text (so I can see where links go, much more secure). This means that I don't see that there is supposed to be a picture unless I convert the message back to HTML. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board

Re: [ccp4bb] PDB-REDO question

Hi Joern, Yes, these values are all stored in a file called data.json that each entry has. The keys that are most relevant are: BLTBEST (geometric restraint weight) BBEST (B-factor restraint weight) BREFTYPE (B-factor model) DOTLS (Whether or not TLS refinement is used) ISTWIN (Whether or not

[ccp4bb] PDB-REDO downtime

Dear CCP4bb-ers, The server room that hosts the PDB-REDO infrastructure will be getting a new air conditioner soon. This means that PDB-REDO will be unavailable from 20:00h (CET) on April 18th until the same time on the 19th (give or take). After that PDB-REDO will be available again, cooler

Re: [ccp4bb] coot & other graphics programs draw too many bonds

Hi Fred, I think this is a problem of not having the right description of the compound. Have you tried using a restraint file for the compound in Coot so the bonds are properly defined? Note sure if Coot uses them, but perhaps also remove all the CONECT records. Cheers, Robbie >

Re: [ccp4bb] poly-dN model

Hi Reza, The equivalent for UNK (not ALA!) is residue N for RNA and DN for DNA. HTH, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Reza > Khayat > Sent: Saturday, March 13, 2021 14:53 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] poly-dN model > > Hi, > > >

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

Big fan of Ubuntu here. The Long Term Support versions work very well and everything you need is on them. At the same time Debian tends to be less conservative that the Red Had universe which typically makes it easier to get modern things running. Also the Ubuntu on WSL (Windows) is a lifesaver

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

Hi Tim, Very good points. The big picture is hard to grasp and we end up taking political choices rather than anything else. I'm very glad that we can outsource these choices to others every four year here. Lockdowns may save lives in the here and now, but the global economic damage makes

Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

All the (library) code is open source with a BSD license, so yes this is possible. Cheers, Robbie > -Original Message- > From: Boaz Shaanan > Sent: Monday, January 18, 2021 22:57 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rama-Z,

[ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

Dear all, During the last CCP4 meeting, Oleg presented our collaboration with the Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, some asked for a convenient way to get this score. You are now welcome to use: https://pdb-redo.eu/tortoize This is a quick and easy way

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Dear Jasmine, I have a few questions about this bit: // As some users pointed out, single NAG could be just a part of the glycan that the author chose to build, as most natural N-glycans must have stem of a common core of 5 monosaccharides or its fucosylated version, such as those modeled in

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

new carbohydrate chain assignment > convention that has been recently adopted by PDB introduces confusion, > not just for PDB-REDO but also - and especially - for end users. > >>> > >>> Could we kindly ask PDB to improve consistency by either assigning a > >&g

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

covalently > linked to a protein chain)? This inconsistency is independent of the file > format… > > Best, Luca > > > On 4 Dec 2020, at 18:30, Robbie Joosten > mailto:robbie_joos...@hotmail.com> > > wrote: > > Dear Dale, > > Yes, go

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

here N-/O-glycans inherited the same chain ID of the protein to which they are attached)? The current hybrid solution hardly seems optimal... >> >> Best regards, >> >> Luca >> >>> On 3 Dec 2020, at 20:17, Robbie Joosten wrote: >>> >>>

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Dear Zhijie, In generally I like the treatment of carbohydrates now as branched polymers. I didn't realise there was an exception. It makes sense for unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as these might change during model building or, in my case, carbohydrate

Re: [ccp4bb] Refmac not handling microheterogeneity?

Hi Ian, AFAIK there is no clean solution for this and I imagine this problem goes very deep into the internal representation of the model in REFMAC. That said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a solution would be very welcome. Cheers, Robbie > -Original

Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)

Hi Julia, For a table 1 you should make a sensible split of the atoms over which you calculate the mean. You might need to pool certain chains. There is not really convenient tool for that because the choice depends on the biology/biochemistry of your system. In practice, the easiest way is

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

I’m with Dale on this, the scientifically prudent thing is to set the rules and then play by them. Not to change the rules as you go. Of course, in a teaching environment where you know the correct answer, it is good to be educational and learn how to dig a bit more. However, in a scientific

Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

Working on your bills with the entire bulletin board. Is that crowdsourcing or what?  > -Original Message- > From: CCP4 bulletin board On Behalf Of Kevin > Denkmann > Sent: Tuesday, October 20, 2020 15:27 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Kevin Denkmann lädt Sie zur

Re: [ccp4bb] over-fitting? over-refinement?

A related way of looking at things is saying that you model is over-fitted when you increase your model's precision without (noticeably) gaining accuracy. Ethan describes the cases in which you add a lot of parameters in you model. The test he describes in his paper works great, I use it all

[ccp4bb] PDB-REDO downtime on October 17th

Dear BB'ers, Due to electrical maintenance and testing at the Netherlands Cancer Institute, the PDB-REDO server and databank will be unavailable on Saturday October 17th from approximately 6:00h to 16:00h CEST (Amsterdam local time). Sorry for the inconvenience, Robbie

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

Indeed, and that is why testing new developments in courses is so important because there you get naïve users. Obviously, this has been very difficult this year. It is also exactly the reason why you do need to have developers at courses, not just power users. For those struggling to get used

Re: [ccp4bb] taking information from a deposited structure

Dear Kahkashan,That is totally fine as long as you make it clear that you used this PDB entry. That's what the PDB is for.Just make sure you check the model with the electron density from EDS or pdb-redo. Cheers,RobbieOn 9 Sep 2020 07:41, Firdous Tarique wrote:Dear CCP4 community members.I have

Re: [ccp4bb] metal coordination at low resolution - restraints

Yes, and the Zn is tetrahedral with a vacancy which makes then angles a bit more open. It's a good thing insulin makes nice crystals  Cheers, Robbie > -Original Message- > From: Eleanor Dodson > Sent: Tuesday, September 8, 2020 12:59 > To: Robbie Joosten > Cc: CCP4BB

Re: [ccp4bb] metal coordination at low resolution - restraints

On 8 Sep 2020, at 10:40, Robbie > Joosten <mailto:robbie_joos...@hotmail.com> > wrote: > > Hi Elanor, > > The distances are in the dictionaries > but the angles i

Re: [ccp4bb] metal coordination at low resolution - restraints

> Sent: Tuesday, September 8, 2020 11:38 > To: Robbie Joosten ; Garib N Murshudov > > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls lmb.cam.ac.uk> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > Robbie - could that be added to the distributed dictio

Re: [ccp4bb] metal coordination at low resolution - restraints

Hi Anna, Yes you can do this in Refmac by adding external restraints. If you have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) you can also use PDB-REDO to generate the restraints automatically. The restraints are written to the output so you can continue using them in

Re: [ccp4bb] Omega angles with molprobity

Hi Joana, By default it only lists non-trans peptides. Theis command worked for me: molprobity.omegalyze tempdir/3bwh/pdb3bwh.pdb nontrans_only=False Cheers, Robbie > -Original Message- > From: Joana Pereira > Sent: Friday, September 4, 2020 12:04 > To: Robbie Jooste

Re: [ccp4bb] Omega angles with molprobity

Hi Joana, molprobity.omegalyze seems to do what you want. Just run it on the command prompt. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Joana > Pereira > Sent: Friday, September 4, 2020 11:29 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Omega

[ccp4bb] PDB-REDO downtime

Hi everyone,Due to major electrical work at our institute, PDB-REDO will be down from Sunday August 16th 20:00h CET to Tuesday August 18th 11:00h CET.Any calculations still running at the start of the downtime will be restarted once we are back online, but feel free to email me to remind me on

Re: [ccp4bb] Quote source inquiry

e corrected > > model which still only put it at the ~50th percentile) > > > > - another good indicator was the clashscore (went from 44 to 7) > > > > - the original model did not include an Rfree, but the R-value (>0.3 > > at 1.6Å > > resolution) ought to have

Re: [ccp4bb] Quote source inquiry

the 1990s? We > analysed these effects, or at least Victor Lamsin did, and we applauded him. > Cheers Eleanor > > On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein > mailto:vonrh...@globalphasing.com> > > wrote: > > > Hi Robbie, > >

Re: [ccp4bb] Quote source inquiry

Hi Ian, Errors in cell dimensions can have a large effect in MX with certain refinement doctrines. The school of "bond length rmsd must be $NUMBER" (which is still going strong unfortunately) will suffer from poor R-factors because the target cannot be satisfied without harming the fit to the

[ccp4bb] B-factor distributions

Posted on behalf of Gert Vriend: This article didn't make it to Nature Methods (...), but might be of interest to theoreticians interested in B-factor distributions: https://journals.calstate.edu/pump/article/view/2409/2168 Gert Vriend

Re: [ccp4bb] Completeness question

020 14:18 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Completeness question > > Dear Robbie, > > On Sat, May 30, 2020 at 08:36:06AM +, Robbie Joosten wrote: > > I've been looking at some recent PDB entries that have much lower >

Re: [ccp4bb] Completeness question

data if you deposit the whole sphere..eleanorOn Sat, 30 May 2020 at 09:36, Robbie Joosten <robbie_joos...@hotmail.com> wrote:Hi Everyone, I've been looking at some recent PDB entries that have much lower spherical) completeness than reported in the coordinate file. One

Re: [ccp4bb] Completeness question

largely contiguous, not alternating as here. > > > I think the only solution here is to get the authors to deposit the data > correctly: is there any commonality of the authors for the structures where > you have noted this problem? > > > Cheers > > > -- Ian &g

[ccp4bb] Completeness question

Hi Everyone, I've been looking at some recent PDB entries that have much lower spherical) completeness than reported in the coordinate file. One reason for this is that the data were anisotropicly truncated, another reason is some mess-up with the deposition of the reflection data. There is a

Re: [ccp4bb] PDB file header lines...

Hi Harry, You need this: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL Essentially you have to make sure a MODEL has a number and a closing tag. It is read as a real PDB record so you have to make sure it is correct BIDEN is not PDB compliant and will be

Re: [ccp4bb] Fwd: Refmac error

Hi Eugene, We recently had this with a student as well and at least in PDB format the files are salvageable by doing a simple search and replace from , to . Rather than going completely American, you can also just change the number format. In Windows 10 this is Settings > Time & Language >

Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

> On 26/04/2020 16:21, Abhishek Anan wrote: > > Dear all, > > > > I have a peptide crystal structure at 0.97 Å that contains two surface > > exposed Methionine. The CE atoms of both MET have a suspiciously high > > b-factor >40 and a positive density. In addition, the sulfur atom SD > > has a

Re: [ccp4bb] Ligand discrimination

Hi Nicolas, VHELIBS does a good job at that. Keep in mind though that the distinction between additives and functional molecules is done based on a list of compounds. There are compounds that can serve both as crystallisation agent and ligand in different contexts. Cheers, Robbie >

Re: [ccp4bb] Hydrogens in PDB File

Hi Dale, You make very valid points and there are good reasons to keep the refined hydrogen positions (methyl twists an protonation of HIS are good examples). There is a way of distinguishing refined a modelled hydrogens in mmCIF and we should start using that. About protonation of hustidines:

Re: [ccp4bb] What resolution - X-ray diffraction round this time

Hi Dusan, I don't know what the correct answer is but I think it is safe to see that your referee has outdated views (trying to stay polite here). I/sigI > 2.0 with decent completeness would be not be seen as to agressive by most (but as too conservative by others!). From that cut-off you

Re: [ccp4bb] disulfides in coot

Hi Sam, Once a disulfide bridge is made Coot will restrain the sulfur atoms to bind. The way out is deleting one of the side chains and adding it back while making sure the sulfurs do not get too close. HTH, Robbie On 18 Feb 2020 11:24, Sam Tang wrote: Dear all A very technical question

Re: [ccp4bb] Refmac5 question

Hi Joern, The logic behind it this is that those are hydrogen position that are uncertain due to possible flips and free rotation (tyr, thr, ser). You should probably only set these occupancies to 1.00 after you have studies the local hydrogen bonding network. Cheers, Robbie > -Original

Re: [ccp4bb] Remember the turkey?

If there is a better term because the current one is incorrect or unsuitable, I'm all for changing it. We changed GRID to AIDS (the name was factually wrong) and the names of quarks were also changed in the history of particle physics (because we found better terms). At the same time we still

Re: [ccp4bb] technical question

Or use the residue name MHO if SME has the wrong hand around the sulfur. Cheers, Robbie On 29 Nov 2019 21:47, Paul Emsley wrote: On 29/11/2019 18:06, amit gaur wrote: > I want to replace a particular methionine in a pdbwith methionine sulfoxide( > an oxidized form of > methionine). Can body

Re: [ccp4bb] TLS parameters

Hi Eleanor, The blocks are reliably recorded in PDB entries but in some cases the renumbering of residues was not pushed through to TLS groups. Certain selections cannot be captured in the PDB format, for instance the split in main chain and side chain that Refmac allows. Fortunately that

Re: [ccp4bb] why does Coot ignore CONECT?

Hi Paul, I think this is a very good call as CONECT records are notoriously unreliable. Many PDB files don't have them and many programs don't update them when you change atom numbers. Even in annotated PDB entries there are many problems with those. It's better to forget about them altogether

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Hi Chris, You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you want to make a map in this case. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Chris Fage > Sent: Monday, September 30, 2019 14:00 > To:

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Are you sure you used the right columns in FFT? AFAIK Coot uses FWT and PHWT. I thought the more recent PyMOL versions finally had MTZ support, or is this just for the incentive version? Also if it is for looking at the structure and making figures, perhaps try CCP4mg. It has proper MTZ

Re: [ccp4bb] What OS do you use?

Since the answers are open, the analysis will involve a lot of curation. I'm interested in the final results. Cheers, Robbie On 22 Sep 2019 04:45, Murpholino Peligro wrote: I want to know what operating system you use. For that I made a poll, it is anonymous, quite simple and plus you get to

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