Re: [ccp4bb] Chiral volume outliers SO4

ilto:a.purk...@mail.cryst.bbk.ac.uk] > Sent: Friday, July 13, 2012 14:09 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Chiral volume outliers SO4 > > Dear Robbie and ccp4bb, > > Is 1N1 not a different type of problem though, where a chirality restraint i

Re: [ccp4bb] large difference between r & rfree during refinement

Hi Faisal, It looks like your restraints are simply not tight enough. Try optimizing the restraint weight. You should also run more cycles of refinement to make sure it converges. The initial gap between R and R-free is pretty small. Did you do much refinement before this run? Cheers, Rob

Re: [ccp4bb] protein sequence database with conservation score annotation

maintainers because I’ m not sure this service is public yet. You can also cheat a bit and just get the HSSP for the closest homologue in the PDB. HTH, Robbie Joosten Netherlands Cancer Institute From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ?? Sent: Wednesday

Re: [ccp4bb] compatibility issue between coot and refmac

Dear Norman, Refmac version 5.0 sounds unlikely, the version with CCP4 6.3 is 5.7.0029. Anyway, your DNA seems to have asterisks in the atom names, which is 'so last decade' (they were removed in 2008). Refmac and Coot may not be equally forgiving for legacy formats. IMO neither should be. The

Re: [ccp4bb] B-iso vs. B-aniso

ng to PDB_REDO's strict criteria anisotropic B-factors are acceptable in two thirds of the cases. This was tested with Refmac on 285 PDB entries; ShelX's new restraints may well increase the success rate. HTH, Robbie Joosten Netherlands Cancer Institute www.cmbi.ru.nl/pdb_redo > ---

Re: [ccp4bb] ideal rms bond length

to do that. Shameless plug: PDB_REDO has such an automated procedure. HTH, Robbie Joosten Date: Wed, 3 Oct 2012 03:19:48 +0530 From: faisaltari...@gmail.com Subject: [ccp4bb] ideal rms bond length To: CCP4BB@JISCMAIL.AC.UK Dear all i request you to please answer my basic query about the

Re: [ccp4bb] anisotropic refinement

underestimate because the B-factor model used wasn't stored properly for the older entries. If more accurate numbers are needed, they can be mined from the PDB_REDO databank. HTH, Robbie Joosten Netherlands Cancer Institute www.cmbi.ru.nl/pdb_redo > Date: Thu, 11 Oct 2012 12:17:39 -070

Re: [ccp4bb] Convention on residue numbering of fusion proteins?

Hi Meindert, The PDB will let you do what you want and as a result there are a few PDB entries with crazy residue numbering. I would use insertion codes only for real insertions or engineered linkers. Like Nat said, they are a nightmare for many programmers which is why they are poorly supported b

Re: [ccp4bb] Ca or Zn

Dear Kumar, If you build the sites as Ca2+, you can use a few things for validation: - Ca2+ ions are exclusively coordinated by oxygens - The bond valance method (implemented in e.g. WASP and WHAT_CHECK) can be used to check whether a calcium ion makes sense. Do this before (reciprocal space) refi

Re: [ccp4bb] occupancy vs. Bfactors

Hi Grant, This is part of the recurring side chain discussion. There is no consensus in the community about what the optimal approach is. In your current approach you are adding a model parameter (occupancy) to improve the fit with the experimental data (remove negative difference density). You

Re: [ccp4bb] how many cycles to settle B-factor?

Hi Jim, The speed at which the B-factor converges depends on many factors. The B-factor restraint weight that Herman and I mentioned (the one you should optimise before changing occupancies!) is an important factor. Also the position of your atomic coordinates WRT where they should end up is im

Re: [ccp4bb] thanks god for pdbset

Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule f

Re: [ccp4bb] thanks god for pdbset

lem at all. In practice, as Ed pointed out, it is a big mess. Cheers, Robbie > -Original Message- > From: Ian Tickle [mailto:ianj...@gmail.com] > Sent: Wednesday, December 05, 2012 17:26 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] thanks god

Re: [ccp4bb] thanks god for pdbset

> Hi Robbie, > > On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: > > Hi Ian, > > > > It's easy to forget about LINK records and such when dealing with the > > coordinates (I recently had to fix a bug in my own code for that). > > The problem

Re: [ccp4bb] refining against weak data and Table I stats

Hi Douglas, Using two Table Is is a good way to show the difference between the two cut-offs, but I assume you will only discuss one of the models in your paper. IMO you only need to deposit the high res model, so there should be no problems with resolution conflicts in the PDB file. The annotator

Re: [ccp4bb] refining against weak data and Table I stats

Hear, Hear! [rant]This *biological difference* thinking may be the source of some of the poor 'protein + ligand' structures in the PDB that look like the ligand was fitted without any attention to the rest of the model (or the refinement thereof). Well, at least these models are good teaching m

Re: [ccp4bb] Hi clashscore

Hi Supratim, The clashscore gives the relative number of clashes, not their severity. This makes it difficult to see what your specific problem is. Sever clashes (with large overlaps) are usually the result of errors in your model and need individual attention. Light bumps can usually be solved by

Re: [ccp4bb] B-factors

Dear Urmi, The way you switched from Phenix to Refmac may not have resulted in the flat B-factor model in Ethan's paper. You should really do a thorough test in which you reset the B-factors before you start refinement. Shameless plug: PDB_REDO will do this automatically and has a few fallback

Re: [ccp4bb] refmac5 vs phenix refine mixed up

I noticed that Refmac has done the 1vs0 thing correct for ages, which is very useful because mix-ups between the work set and test set used to be quite common in the reflection files at the pdb (Refmac saved me a lot of extra work with this). Dealing with this problem is very simple as the small

[ccp4bb] FW: [ccp4bb] off topic: DSSP

running 10.5 to test this. If it doesn't work, please send me the output so I can try to infer the required extra changes. best regards, -maarten Van: Robbie Joosten [robbie_joos...@hotmail.com] Verzonden: zaterdag 26 januari 2013 10:16 Aan: Maarten Hekk

Re: [ccp4bb] freerflag bug

Hi Ed, I've had this problem as well. It's the result of the very small R-free set fraction. There is an error routine that catches really small R-free sets, but 0.5% gets through and triggers ar problem. My workaround is to just use a larger R-free set fraction (more than 1%). The version number

Re: [ccp4bb] edit chi angles of DNA in coot

Hi Lisa, I'm not sure it's the source of your problem, but your atom names are still in PDBv2 format. That's 'so last decade'. Start by fixing that. There must be a CCP4 tool that will do that. You can also use the MolProbity server to fix the format. For the developers: the problem with atom a

Re: [ccp4bb] off topic: DSSP

Hi Nat, DSSP recently went open source with a very liberal license. So you can consider using the real DSSP now. This may also be the moment to integrate DSSP in CCP4. Cheers, Robbie Sent from my Windows Phone From: Nat Echols Sent: 2013-01-28 17:32 To: CCP4BB@J

Re: [ccp4bb] RMSD Citation

Note that we discuss rmsZ values in the paper, not rmsd. This is done on purpose; rmsd values do not take the standard deviation of bond lengths into account. This makes it needlessly difficult to compare values. Consider reporting rmsZ instead of rmsd. Cheers, Robbie Sent from my Windows Phon

Re: [ccp4bb] generating electron density from PDB and structure factor file

Hi Bhat, You can run Refmac for 0-cycles to make the maps. If you use unrestrained refinement, you don't have to mess with restraint files. There is also an option in Coot to do this. But if you are in Coot anyway, you might as well get the maps from EDS directly or (after installing a plugin: ht

Re: [ccp4bb] generating electron density from PDB and structure factor file

Just to add some more possibilities: - You can download maps from EDS or models and maps from PDB_REDO straight into CCP4mg. - You can download PDB_REDO maps and models into PyMOL using this plugin (http://www.cmbi.ru.nl/pdb_redo/pymol.html) for which we should thank Ed Pozharski. Note that th

Re: [ccp4bb] refmac5 MMA bug

Hi Ed, This is a 'compatability' option in Refmac that internally renames atoms. If you comment out 'MMA .C7 CM' in your mon_lib_list.cif file, the problem will disappear. Cheers, Robbie > Date: Sun, 10 Feb 2013 23:35:25 -0500 > From: epozh...@umaryland.edu > Subject: [ccp4

Re: [ccp4bb] refmac5 MMA bug

b] refmac5 MMA bug > > On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote: > > This is a 'compatability' option in Refmac that internally renames > > atoms. If you comment out 'MMA .C7 CM' in your > > mon_lib_list.cif file,

Re: [ccp4bb] Link problem with Refmac.

Hi Ian, The warning refers to a MET 59 in chain A whereas you only have MET 72. That is very suspicious. Non-sequential residues further apart than x Angstrom automatically get a gap record. Have you tried a newer version of Refmac, because this feature was added quite a while ago? What is your se

Re: [ccp4bb] Link problem with Refmac.

s must be a common problem: how do others handle this? E.g. pdbset > blindly renumbers with a increment of 1 (and anyway it doesn't renumber > any LINK, SSBOND & CISPEP records as I do) so it would have the same > problem. > > > Cheers > > > -- Ian > >

Re: [ccp4bb] Improving Homology Models

Hi Jacob, I'm usually pretty happy with the automated modeling pipeline in YASARA. The various model building steps have different types of minimization and refinement to get rid of bumps as best as it can. Added bonus (and shameless plug): it uses PDB_REDO structures as input if those are better

Re: [ccp4bb] Building sugars

Hi Folmer, Just to add some tips: > Concerning the naming as one molecule: the sugar monomers get the same > chain ID as the protein they are connected to and arbitrary residue numbers. > I usually start numbering from 1000 to prevent overlap with the numbering > of the amino acids. 1) Just don't

Re: [ccp4bb] Building sugars

rpose there's no need to be > concerned about insertion codes ;-) > > > The glycosciences.de link is really useful. There does not seem to be a test to > verify correct PDB nomenclature though. Or perhaps RAF (for raffinose, a tri- > saccharide) is OK to use? > > > Be

Re: [ccp4bb] Rfree flag

Hi Tim, Our approach is a bit different. We first try to establish whether the R-free set is biased, by checking whether R-free is surprisingly low compared to R given the data parameter ratio. If this is the case (or if we chose a new R-free set for some reason, e.g. because it was too small) PDB

Re: [ccp4bb] validating ligand density

Dear Srinivasan, Although the Twilight program can only look at deposited PDB entries, the tips about ligand validation in the paper are very useful. I suggest you start from there. You can use EDSTATS in CCP4 to get real-space validation scores. Also look at the difference map metrics it gives (

Re: [ccp4bb] validating ligand density

Btw, the book is good reading. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Tuesday, March 12, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb]

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

Dear Sonali, There is no such thing as an ideal rmsd for bonds and angles given resolution. IMO you should use rmsZ which also doesn't have an ideal value. If its below 1 your good. As for the isotropic vs anisotropic, you can use a hamilton test if you do two refinements changing only the B-fa

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

Small addition to Ian's comment. The value you give with 'weight auto $value' is a starting value. Refmac will gradually change it if needed (it's autoweighting after all) and your starting value does matter somewhat. Based on Ian's advice PDB_REDO uses a starting value of 2.50 which seems to do

Re: [ccp4bb] Rfree reflections

Hi Tim, I don't think the 5-10% or 500-1000 reflections are real rules, but rather practical choices. The error margin in R-free is inverse proportional with the number of reflections in your test set and also proportional with R-free itself. So for R-free to be 'significant' you need some absolut

Re: [ccp4bb] Rfree reflections

h nowadays computers and a simple script. But > that's probably like reminding people of not using R_int anymore in favour of > R_meas... > > Cheers, > Tim > > On Tue, Mar 26, 2013 at 10:24:51AM +0100, Robbie Joosten wrote: > > Hi Tim, > > > > I don&

Re: [ccp4bb] Puzzling Structure

Waters are moved during annotation using the perceived space group's symmetry operation. So if the authors give the wrong space group, then the annotation pipeline understandably messes things up. If the originally uploaded PDB file was kept by PDBe, then the problem can be recovered quite easily b

Re: [ccp4bb] Puzzling Structure

this particular case attempting to calculate R-factor using data and model > files and making sure that the R you get is not twice as large as published one > would entirely suffice -:) > > Pavel > > > > From: Robbie Joosten > To:

Re: [ccp4bb] Puzzling Structure

Cheers, Robbie > > Cheers >Martyn > > > > ------ > On Sat, Apr 13, 2013 23:03 BST Robbie Joosten wrote: > > >Hi Martyn, > > > >> A shame then that these 'helpful' annotators did not make use of > >> Pavel's basic sanity on the space g

Re: [ccp4bb] Angle restraints

Hi Kavya, Which validation program did you use? How big is the deviation (in sigma values)? Is it the only outlier? What is your overall bond angle rmsZ? Using external restraints is a bit over the top here, especially if it is the only outlier. If your rmsZ is high (close to or over 1) then y

Re: [ccp4bb] Angle restraints

Dear Kavya, First try Herman's suggestions. You can try changing the restraint weight but it will probably not solve the problem; it may hide it. If you cannot solve the problem and you did the best you can do, you can deposit the model with the outlier. The PDB does not reject models with (min

Re: [ccp4bb] Alternate sugar conformations in refmac 5.5.0110

Hi Markus, You could try changing your Refmac version. The version you are using is ancient. You may have an old version in your PATH next to the new one because your CCP4 seems up to date. AFAICT there is nothing wrong with the LINKR or the HETATM records Sent from my Windows Phone __

Re: [ccp4bb] LINK or LINKR

Hi Eleanor, The recent versions of Refmac work well with the records in PDB format. According to the list of bug fixes on the website, Refmac should now take the distance from the PDB file (it used to complain about the distance record). Changing the 1.48 to 1.61 in the new LINK record should d

Re: [ccp4bb] refinement hanging--what am I missing?

Hi Patrick, Did you try using a different refinement program (e.g. Refmac)? Which type of NCS restraints did you use, global or local (torsion- or distance-based)? Have you tried optimizing your restraint weights? Have you tried running a huge number of refinement cycles? You can also try running

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB!

Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden: 24

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)

ge files. > > Regards, > Rachel > > > > > > Rachel Kramer Green, Ph.D. > > RCSB PDB > > kra...@rcsb.rutgers.edu > > > > > > Twitter: https://twitter.com/#!/buildmodels > > Facebook: http://www.facebook.com/RCSBPDB > &g

[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 t

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,

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 life

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] 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] 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 > -Original

[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 th

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 the

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 On

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: CCP4BB@JI

[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 funct

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

uently, > 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. &g

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, 2021

[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] 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 ex

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 <176a9d5ebad7-dmarc-requ...@jiscmail.a

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: CCP4BB@JISCMAIL.AC.U

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 the

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 Message

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 1

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, Ma

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 Tha

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 05

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 Mar

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 give

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 > -Origina

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 how

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 mod

[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, 3fvl

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 opti

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

[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] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

There is nothing wrong with discussing sex at work, either theorethical http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1sex or experimental http://www.rcsb.org/pdb/explore/explore.do?structureId=3sex ?? Sent from my Windows 10 phone Van: Reza Khayat

Re: [ccp4bb] programmatically get mtz files from PDB_REDO

Hi Rob, You are right that the two characters are the middle two of the PDBid. The server that generates the list of entries is being fixed. Cheers, Robbie Verzonden vanaf mijn Windows 10-telefoon Van: R.D. Oeffner Verzonden: vrijdag 25 november 2016 18:52 Aan: CCP4BB@J

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

Hi Gerard, EDS has made the life of many structural biologist easier (and some crystallographers harder) by providing maps at a time when reading reflection files from the PDB was still a total nightmare and real-space scores when it still was a such a hassle to calculate them. I don’t know h

Re: [ccp4bb] jligand help

Hi Nicholas, CCP4 6.5 is end-of-life and no longer supported. Please upgrade to version 7.0. Apart from the obvious benefit of having up-to-date softeare, JLigand should also work. Cheers, Robbie Sent from my Windows 10 phone Van: Nicholas Larsen Verz

Re: [ccp4bb] Calculation of generalised R-factor?

The value for the Hamilton test is written by Refmac as the weighted R-factor. There was a follow-up paper that showed that you shouldn’t use the normal R-factor for the Hamilton test. PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac logfiles to the bselect prog

Re: [ccp4bb] Calculation of generalised R-factor?

uesday, December 20, 2016 15:46 > To: Robbie Joosten ; CCP4BB > > Subject: Re: [ccp4bb] Calculation of generalised R-factor? > > Dear Robbie, > > > thanks for your reply. According to the REFMAC5 manual, the weighted R- > factor is just: > > > weighted R fact

Re: [ccp4bb] Unknown electron density blob

PEG likes to hang around where it is unwelcome: http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full Cheers, Robbie Sent from my Windows 10 phone Van: Bernhard Rupp Verzonden: dinsdag 24 januari 2017 23:20 Aan: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Unknown electron density blob, pdb convention for partially ordered ligands

Hi Tristan, There are PDB entries that have this, but this makes matters a bit more complicated in annotation. You have to define LINKs and leaving atoms. Consistency would be nice here, but that is lacking in these entries. Cheers, Robbie Sent from my Windows 10 phone Van: Tristan C

Re: [ccp4bb] variation in freerflag

Hi Tim, I was discussing that with a student today, because we observe the same thing when we make test sets for k-fold cross validation. It is an implementation choice. You can random sort and then bin, or you can assign a random number to each reflection and translate that to a bin. The lat

Re: [ccp4bb] variation in freerflag

:29 To: Robbie Joosten Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] variation in freerflag Hi Robbie, I had long wondered how to flag the fields in game minesweeper with a deterministic algorithm. When I read about 'random sort and bin' I though this was quite a beautiful way. I

Re: [ccp4bb] variation in freerflag

Adding to this: the current test set generation in freerflag has one brilliant feature and that is reproducibility. If you misplace your test set, you can reproduce the same one if you run freerflag on the same complete set of reflections. This was an excellent design choice. It has proved very

Re: [ccp4bb] Twinning and R-Free

Hi Alun and Kay, PDB_REDO does some more extended twinning testing with among others Phaser, so it would be worthwhile to have a look at that. On the server it refuses to do twinned refinement if there is no clear indication of twinning even if the user assumed twinning before. The fact the

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 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 (http://journals.iucr.o

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 fi

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, 20

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] 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 fract

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