Re: [ccp4bb] Dimple on windows?

On Tue, May 28, 2013 at 11:44:55AM +, Björn Kauppi wrote: Is there any way to install the dimple script on my windows CCP4i installation? It will be included in the next version of the ccp4 suite. For now you can try command-line version from:

Re: [ccp4bb] I can not find edstat in ccp4i

On Sun, Sep 08, 2013 at 10:33:31PM -0700, Ezequiel Noguera wrote: I'm trying to run edstat, but I can not find it in the list of programs of CCP4-6.2 or -6.3. How I can run it under Windows? Thanks It's been added at some point to Windows build (after 6.3). It should work, but I don't think

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

On Wed, Sep 18, 2013 at 03:41:34PM +0100, Peter Keller wrote: I hope that this isn't quite what you meant There are already mutually-incompatible CIF dialects out there that have been created by developers coding to their own understanding and interpretations of the CIF/STAR format. I am

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

Hi Peter, On Thu, Sep 19, 2013 at 10:28:22AM +0100, Peter Keller wrote: http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf ... This grammar seems to be based on the 1994 J. Chem. Inf. Comp. Sci one, which has some serious errors. I would strongly discourage anyone from trying

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

On Thu, Sep 19, 2013 at 04:38:12PM +0100, Peter Keller wrote: If there are discrepancies between IUCR website and IT vol.G and it would be worth to list them. It is not a matter of discrepancies: they are rather different, and if you are active in this area, you really need to see the

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

On Fri, Sep 20, 2013 at 11:51:57AM +0100, Peter Keller wrote: The STAR grammar in chapter 2.1 is the accurate one. If you look at page 18, you will see that the productions for quoted text strings are completely different from the ones in chapter 2.2. Different, but look equivalent to me. But

Re: [ccp4bb] lib32gfortran3 needed for 64-bit ccp4?

On Mon, Nov 11, 2013 at 03:15:46PM -0500, Roger Rowlett wrote: Just ran into an error running SORTMTZ in CCP4-6.4.0. Looks like SORTMTZ requires libgfortran.so.3 32-bit version. I get an error message of the missing library if I do not install lib32gfortran3 (32-bit fortran libraries). Should

Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz

Dear Partha and Uli, We haven't tested it on SLES11 and we overlooked this problem. It will be fixed in updates. For now as a workaround do: ln -s libgfortran.so.3.0.0 $CCP4/lib/libgfortran.so.3 (hopefully works, I cannot test it now) Usually the quickest way to have such problems solved is to

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

On Tue, Dec 17, 2013 at 03:32:52PM +, Adam Ralph wrote: Dear Chang, Some CCP4 progs can be used with a multi-core machine, using OpenMP threads (including refmac it would appear). You will I think only phaser and aimless. Of course using 4 cores doesn't mean running 4 times faster

Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

, at 11:08, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear

Re: [ccp4bb] error in starting imosflm

On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote: Harry, I've run into this problem before with other programs when I switch between v6.3 v6.4. I think the problem is this code in ccp4.setup-sh: if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then We can remove this condition if

Re: [ccp4bb] ccp4 ligand tools + wwPDB validation = bug reports?

Dear Ethan, Alexander Schuettelkopf has sent us modified PRODRG parameter file to fix this issue. We'll distribute it in CCP4 updates soon. If you'd like to test it now, the prodrg.param file is here:

Re: [ccp4bb] CCP4-JHBuild: how to build both static and shared libs?

On Tue, Jul 08, 2014 at 07:50:42AM +0100, Alastair Fyfe wrote: Is there a JHBuild setting for requesting both static and shared libs? The default seems to only build *.so(s) and setting _build_static=True in conf.py only yields *.a(s). For libraries that use autotools for building (that

Re: [ccp4bb] Acorn, CRANK

On Mon, Jun 30, 2014 at 09:42:43PM -0500, Maher Alayyoubi wrote: Hi everyone, I have two questions: 1- I was trying to run the program Acorn, on a SAD dataset (Se derivative) that was scaled in scalepack/HKL2000. converted to .mtz using scalepack2mtz, then edited in REVISE and Ecalc. But

Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

On Sat, Apr 07, 2012 at 08:42:47AM -0700, Bernhard Rupp (Hofkristallrat a.D.) wrote: Something the developers might be interested in: The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x slower than those from the linux distribution run Thanks for benchmarking. If

Re: [ccp4bb] CCP4 6.3.0 release

Two Windows-specific problems have been reported and fixed yesterday: - cif_mmdic.lib is in %CCP4%\share\ccif, should be in %CCP4%\lib - rapper doesn't work (missing DLL) cif_mmdic.lib can be moved manually, so if you don't use rapper there is no need to update. Installer with fixes is available

Re: [ccp4bb] Only su (root) can get ccp4i to run

On Tue, Oct 09, 2012 at 11:18:29AM +0200, vellieux wrote: Ta very much Tim, what I did was to edit the ccp4.setup-csh file in order to change the line: setenv CCP4I_TCLTK /usr/local/bin into: setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin You may source bin/ccp4.setup-csh instead. In ccp4

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On Wed, Feb 27, 2013 at 12:27:46PM -0500, Ed Pozharski wrote: I am trying to compile refmac from source on a machine running Ubuntu 12.04. In a nutshell, after some troubleshooting I end up with executable that generates a segmentation fault. Log-file states that CCP4 library signal

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

One reason to compile refmac on Linux is that it can be faster. I've just run $CEXAM/unix/runnable/refmac5-simple.exam example with refmac from CCP4 6.3.0, from Garib's website and compiled with GCC 4.7.2 only with -O3 option (all are 64-bit versions). Running times were, correspondingly, 32.2s,

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On 4 March 2013 13:55, epozh...@umaryland.edu wrote: On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote: Running times were, correspondingly, 32.2s, 35.1s and 18.7s. Numbers are almost too impressive to believe :) It also puzzled me, but I haven't done more careful benchmarking yet. What

Re: [ccp4bb] Installation of CCP4 under Windows 7

Hi, Thanks for listing all the problems. We are testing a new installer for Windows now. It's written from scratch (we switched from InstallShield to WiX) and if we don't find any issues with it we'll put it on ftp tomorrow. ActiveTcl should not be necessary with this and future versions. In

Re: [ccp4bb] Installation of CCP4 under Windows 7

first and if there are any CCP4 environmental variables left, please delete them manually. The next release will handle upgrades automatically, but we need to do more tests. Marcin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marcin Wojdyr

Re: [ccp4bb] Installation of CCP4 under Windows 7

@JISCMAIL.AC.UK] On Behalf Of Marcin Wojdyr Sent: 11 November 2011 18:42 To: ccp4bb Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7 I've uploaded a new installer here: ftp://ftp.ccp4.ac.uk/mww/CCP4-6.2.1.msi The content is the same, the version was changed only for technical reason

Re: [ccp4bb] installation CCP4 on Win 7

Hi, It's hard to tell what's the problem, perhaps the installer is corrupted and you can re-download it and try again. You may try this one: ftp://ftp.ccp4.ac.uk/mww/CCP4-6.2.2.msi (it's 6.2.0 regardless the filename, the same content in new package) Best, Marcin

Re: [ccp4bb] installation CCP4 on Win 7

2GB of memory should be enough. I'd start from checking that the downloaded file is not corrupted. I've added md5 and sha1 sums to the directory with .msi installers: ftp://ftp.ccp4.ac.uk/mww/ You can read how to check md5 sums for example here:

Re: [ccp4bb] cif_mmdic.lib

Dear Bernhard, a) will be fixed in the next release by changing %MMCIFDIC%; for now the workaround is what you wrote. Thanks for reporting it. d) it's ok, ccp4-6.2.2.msi is a new packages for version 6.2.0. Someone else may address b) and c) Regards, Marcin

Re: [ccp4bb] 6.4.0.1 update questions

On Thu, Jul 31, 2014 at 08:08:32PM -0700, Alastair Fyfe wrote: 2)6.4.0 binary bundles no longer include header files or static libraries. Thus to build local utilities the binary installation must be supplemented with a source build (at least of the libraries). [I think it's about Linux] We

Re: [ccp4bb] 6.4.0.1 update questions

On Mon, Aug 04, 2014 at 12:31:30PM -0700, Alastair Fyfe wrote: - the CCP4 source downloads page references v6.4.0 whereas the binary downloads page references v6.4.0.1. However, from your reply it sounds as if the two correspond to same sources snapshot. Something must have been wrong with

Re: [ccp4bb] Fedora Core 20 issues

FWIW for CCP4 we'd recommend 64-bit Linux. Our 64-bit Linux version is downloaded now 6x more often than 32-bit one. So it's more tested, and for some datasets pointless and aimless require more than 4GB of memory (which is 32-bit limit). Marcin On Mon, Sep 29, 2014 at 02:05:32PM -0400, David

Re: [ccp4bb] serial MR / refinement

Dear Eike, we have a simple automation exactly for this problem: a pipeline called DIMPLE. In Diamond it's run automatically after data collection, if the user provided pdb file. If you have CCP4 installed try: dimple file.mtz file.pdb output_dir The last arg is a directory where you want

Re: [ccp4bb] Privateer fails to run

While most (all?) CCP4 programs use the MMDB library for reading PDB files, handling of incorrect PDBs is not consistent. Default settings in MMDB (and in clipper) are strict, but most of the programs use a combination of options that make it more liberal (SetFlag()). Marcin On Mon, Jan 12, 2015

Re: [ccp4bb] Coot and PISA

Coot thinks that PISA version is 1.06, although it's 2.0.2. That coot extension (and many others) have two versions, one in Scheme and one in Python. The latter works, but it's not in the menu. As a workaround: Calculate Scripting Python and type: molecule_chooser_gui(Choose molecule,

Re: [ccp4bb] CCP4 Release 6.5

On Mon, Dec 22, 2014 at 10:43:27AM +0100, Bernhard Rupp wrote: Upon windows upgrade with default settings, the previous desktop icon 6.4 command line C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl will not work anymore. I forgot to reply to this in December. I couldn't

Re: [ccp4bb] CCP4 PATH variable

Dear Petr Moving CCP4 to the end of the PATH could cause some problems, for example on Linux CCP4 truncate would be shadowed by relatively new truncate from GNU coreutils. We've been aware that having tclsh, wish, etc in $CCP4/bin could cause conflicts, but since no one complained it was a

Re: [ccp4bb] Building static libs.

Dear Ian, Hard to tell without more details. What options are passed to the configure scripts in mmdb2 and libccp4? (you can find it in the output) The options include either --disable-shared --enable-static or the other way around. Maybe you built it before setting BUILD_STATIC, and then when

Re: [ccp4bb] how to properly remove balbes from ccp4i installation?

Hi Murpholino On Wed, May 13, 2015 at 07:30:06PM -0500, Murpholino Peligro wrote: and ubuntu/windows7 dual setup). So B and I were trying to make some space...by deleting the 3GB Balbes folder (sudo rm -rf /usr/local/bin/BALBES). Is that the best way of removing BALBES? Yes, that's all

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate Scripting Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better

[ccp4bb] ANN: CCP4 6.5 for 32-bit Windows

The Win32 version has been added in the download area: http://www.ccp4.ac.uk/download/#os=windows Apologies for the long delay. On behalf of the CCP4 group Marcin Wojdyr -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use

Re: [ccp4bb] Problem with ViewHKL 1.08

Dear Marta, as a workaround, before starting ViewHKL change locale settings to have '.' as a decimal point. For example, from command line: LC_ALL=C viewhkl or LC_NUMERIC=C viewhkl It's a bug in ViewHKL and/or in symop_to_mat4() in libccp4. Marcin On Thu, Jul 02, 2015 at 11:43:08AM +0200,

Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people

It sounds a bit like this paper from a year ago: https://www.nature.com/articles/ncomms12549 apart from the conclusion: here the point is that amateurs build higher quality models than crystallographers. On 20 November 2017 at 20:25, Shintaro Aibara wrote: > Dear All,

Re: [ccp4bb] Removing a ter line present in the middle of the chain

On 7 November 2017 at 12:28, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE residues > as HETATM and that was a BAD THING.. I don't dispute this, but that's what the pdb spec from the PDB requires

Re: [ccp4bb] new ContaMiner features

On 2 December 2017 at 00:31, Ivan Shabalin wrote: > Instead, we just used the search of the > unit cell parameters in the PDB, which is much faster (but works only if the > structure of this particular artifact in the same SpGr is in PDB! otherwise, > one should

Re: [ccp4bb] Python3 and MTZ

On 7 June 2018 at 05:29, graeme.win...@diamond.ac.uk wrote: > Dear Kay, > > Yes, it’s writing code to be compatible with Python2 and Python3 - in real > life they are largely idiomatically similar, with well documented differences > e.g. In other words, it's learning both Python2 and Python3

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

On Wed, 9 Jan 2019 at 10:28, Kay Diederichs wrote: > > Sorry, I need some additional help with this. > > If I use my browser (Firefox or Chrome on Linux) to go to > http://sas.stfc.ac.uk/p.jsp?i=2 it gets redirected to >

Re: [ccp4bb] Dimple anomalous peaks

Dear Evgenii, it indeed makes sense to (optionally) use F+/- for refinement, but it just hasn't been requested before and I didn't think about it myself. I'm opening a ticket to not forget about it: https://github.com/ccp4/dimple/issues/13 and I'll get back to it later. Best wishes, Marcin On

Re: [ccp4bb] dimple, skip pointless?

Dear Guenter, No, unless you intend to start with MR (option -M0) -- in such case pointless is not run. I could add such option, although it may take a while before it's done and before it goes as an update to CCP4 7.1. Do you want to skip pointless to save time, or you get wrong result? Best

Re: [ccp4bb] Generating symmetry mates using python

Hi Zhijie, it's good and instructive to implement such things from the ground up, but there are many special cases that one would be discovering while testing this procedure, so if the time is limited it may be better to use an existing solution. For instance, here one may find out that using

Re: [ccp4bb] [ccp4dev] Broken wiki link to dimple from ccp4i

Dear Bernhard, I can reproduce it also when opening the main page of https://ccp4wiki.org/ Thanks for reporting it. In case of DIMPLE more up to date documentation is at: https://ccp4.github.io/dimple/ Regards, Marcin On Fri, 20 Mar 2020 at 17:02, Bernhard Rupp wrote: > > Dear Developers, > >

Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

Dear Bernhard, CCP4 has an alternative command-line tool for this; less tested but happens to preserve P 21 2 21: gemmi cif2mtz input.cif output.mtz Marcin On Wed, 6 Jan 2021 at 20:39, Bernhard Rupp wrote: > > Dear Developers, > > > > running cif2mtz in ccp4i (or from the console) in the case

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

On Fri, 4 Dec 2020 at 22:36, Dale Tronrud wrote: > > It is very important not to read more meaning into a data tag than > is actually defined in the mmCIF spec. _atom_site.label_seq_id is defined > > http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.label_seq_id.html >

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

On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote: > > Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is > exactly the problem. It's not about "creating meaning" but about consistent naming. For humans. > "chain names" ( or "entity identifiers" if I > recall the mmCIF

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

Dear Jasmine, thank you for this explanation. It's the best explanation of this remediation I've read. The use of IDs may confuse people, so I'd like to reiterate it and ask for clarification. Every residue in the mmCIF format has three (3) independent chain IDs assigned to it (and three

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

On Fri, 4 Dec 2020 at 09:21, Luca Jovine wrote: > > Yes Tristan, that would be even better - also because such an Ag1, Ag2,… > system could conveniently fall back on a single-character chain A, when > generating legacy PDB format files from the mmCIF ones. mmCIF already has two sets of

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 fully agree with this recommendation: > To use the wwPDB-assigned chain ID in publications, > _atom_site.auth_seq_id _atom_site.auth_comp_id, and > _atom_site.auth_asym_id can be used for the residue number, residue ID, > and chain ID, respectively. It would help a lot if the

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

another one: gemmi convert --assembly=N input.pdb output.pdb On Wed, 26 May 2021 at 07:30, Frank von Delft wrote: > > Thanks for the quick responses! I was looking for a command-line tool > (should have said). Here's the list: > > 1. phenix.pdb.biomt_reconstruction > 2. Makemultimer.py:

Re: [ccp4bb] Meaning of a pdb entry

Dear Gergely, For authoritative advice you'd need to ask the PDB. Below is my take. > I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif > format for storing multiple crystallographic models. It's possible, there are a few examples such as 2VTU. They represent "ensemble

Re: [ccp4bb] Meaning of a pdb entry

Dear Gergely, > > Thank you for these examples! It is reassuring to see that multiple > crystallographic models do not break validation for example. I assume only > the validation of the first model and first reflection file is shown. I can > imagine that it is still a substantial change and

[ccp4bb] deposition of unmerged data

Dear All, as was announced by the PDB a month ago, it's now possible to include scaled unmerged data in a deposition to the PDB (before that it was possible only in a limited way). You can do it by simply adding unmerged data (from MTZ or XDS_ASCII file) to the data file that you'd normally

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

One can also use: $ gemmi fprime Sr --wavelength=1.2782 Element E[eV]Wavelength[A] f' f" Sr9699.91 1.2782 -0.637561.3067 or $ $CCP4/lib/py2/cctbx/bin/cctbx.eltbx.show_fp_fdp --wavelength=1.2782 --elements=Sr Wavelength: 1.2782 Angstrom Element: Sr Henke

Re: [ccp4bb] Add hydrogens

Dear Sam, if you want to add hydrogens on "riding" positions in the same way that Refmac adds them, here is a command that aims to do exactly the same thing: gemmi h 1cdw.pdb output.pdb Otherwise, a program called reduce from MolProbity (distributed with both Phenix and CCP4) is probably the

Re: [ccp4bb] using chooch

When I was looking into the calculation of f'/f'' last year I was told that data assembled by Chantler is more accurate than calculations based on Cromer-Liberman (used by most of MX programs). Chantler's data is available here:

Re: [ccp4bb] Maps on mobile phones.

Hi Jon, > Another thing is that the results of the contouring are sent out in groups of > 3 points which are the vertices of triangles forming the surface. Hence, I > orthogonalize them and get three.js to draw them as just that - triangles. My > worry is that, since the triangles all have

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

t; Many thanks, > > D > > On 14/01/2022 16:32, Marcin Wojdyr wrote: > > Dear Dom, > > > > you can upload only a single data file to OneDep. > > Currently, if you want to deposit unmerged data with extensions > > introduced in 2021 (importantly, these exten

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

Dear Dom, you can upload only a single data file to OneDep. Currently, if you want to deposit unmerged data with extensions introduced in 2021 (importantly, these extensions include image numbers and rotation angles) and if the software that you use doesn't output such ready-to-use files, you

Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

I'm using a similar scheme for converting mmCIF to PDB with 'gemmi convert'. 1. Long CCD codes are replaced with 3-character codes that end with a tilde (ABCDE -> AB~) 2. The HETNAM record is used to store the original CCD codes (in columns 72-79). HETNAM AB~

Re: [ccp4bb] Regarding File conversion

Plenty of options. I'll add one maintained by me. Type: gemmi convert file.cif file.pdb or use it here: https://project-gemmi.github.io/wasm/convert/cif2pdb.html Marcin On Tue, Apr 19, 2022 at 2:01 PM Abhilasha Thakur wrote: > > Hello!! > Greeting of the day, > > I want to know regarding file

Re: [ccp4bb] Help with One dimensional electron density calculation

On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine wrote: > Map values are calculated using tricubic interpolation. Optionally you can > choose a less accurate eight-point interpolation (use interpolation keyword > for this). > I've been wondering which one is better. Tri-cubic is more accurate

Re: [ccp4bb] help request (synchrotron schedules)

If you'd be interested in historical synchrotron schedules, they can be approximately guessed from pdb data, from data collection dates. Unfortunately, in many entries the dates are random, so there is significant noise there. Here is how it looks:

Re: [ccp4bb] issues running PANDDA with anisotropic data

> > My scripting is not great so I wondered if anyone could hep me with a short > script to recursively look for ‘refine.mtz’ within subdirectories from the > top-level ‘model-building’ directory and then run CAD to change the column > names from 2FOFCWT-iso-fill and PH2FOFCWT_iso-fill to

Re: [ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available

Hi Rasmus, > The two parallel sets of chain, residue, and atom names are actually > necessary for NMR structures - it is not just to keep the depositors > happy. Is there a PDB entry that exemplifies this? I admit I don't know how the chemical-shift based naming works, but I see that both sets

Re: [ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available

Dear all, I looked at the atom table (atom_site) in the NextGen archive. It has 5 new columns: pdbx_label_index (another sequence ID) and four columns for SIFTS mapping at atom level. I used SIFTS in the past and having it in the coordinate file can simplify things. But as was stated in the

Re: [ccp4bb] mtz/cif file for depostion

Dear Gottfried, is there any error message when uploading I+/I- fails? Many entries in the PDB have only intensities (for example, 7bb9 has only I+/I-), so it must be possible unless something has changed recently. Best, Marcin On Mon, Feb 12, 2024 at 11:54 AM Palm, Gottfried <

Re: [ccp4bb] Deprecation of MMTF-format files for the PDB archive

Thanks for the update. I've been keeping track of what formats are supported by the PDB for a while. Just in case anyone finds it useful, here are my notes. wwPDB distributes files in three formats: mmCIF (primary, full name: PDBx/mmCIF), PDB (legacy), and PDBML (mmCIF in XML, probably to avoid

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Thanks Martin for writing about gemmi. It also has a command-line program: gemmi convert input.pdb input.cif https://gemmi.readthedocs.io/en/latest/utils.html#convert On Fri, Feb 23, 2024 at 12:44 PM Martin Malý wrote: > > Dear Harry, > > You can try to read your PDB file and save it as mmCIF