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

[Marcin Wojdyr]

> It sounds as though you need the power of the script. You can (from memory) 
> run pdbcur to drop the aniso lines and hydrogen atoms, which helps.

Or from command-line:
gemmi convert --anisou=no --remove-h in.pdb out.pdb

> You could probably get it to delete everything except CA's too.

this would be:
gemmi convert --select='CA[C]' --anisou=no --minimal in.pdb out.pdb

(--minimal drops REMARKs and other metadata)



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

[Marcin Wojdyr]

>
> >  • Alignment of one-letter atom name such as C starts at column 14, while 
> > two-letter atom name such as FE starts at column 13.
>
> indicating a rule does exist.

There are programs that don't read/write the element from columns
77-78, so this rule still matters, but using it is less reliable, as
Robbie wrote. After I wrote a function that reads pdb files for gemmi,
over the next few years I received feedback about cases in which the
element columns are absent and the element determined from the atom
name is incorrect. The problem is primarily with 4-character atom
names that can't be aligned, because they use all the four columns
anyway. I added such comments to the code [1] when trying to get it
right:

  // Atom names HXXX are ambiguous, but Hg, He, Hf, Ho and Hs (almost)
  // never have 4-character names, so H is assumed.

  // Similarly Deuterium (DXXX), but here alternatives are Dy, Db and Ds.
  // Only Dysprosium is present in the PDB - in a single entry as of 2022.

  // Old versions of the PDB format had hydrogen names such as "1HB ".
  // Some MD files use similar names for other elements ("1C4A" -> C).

  // ... or it can be "C210"

[1] 
https://github.com/project-gemmi/gemmi/blob/148f37b7c6561c3a255a6a4dd75d6bae888e/include/gemmi/pdb.hpp#L302



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

[Marcin Wojdyr]

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 using gemmi:
> https://gemmi.readthedocs.io/en/latest/mol.html#reading
> https://gemmi.readthedocs.io/en/latest/mol.html#id3
>
> Best wishes,
> Martin



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Re: [ccp4bb] mtz/cif file for depostion

[Marcin Wojdyr]

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 <
b793af054fc6-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>   thanks to all who answered. Gemmi and uniqueify did not help, "Export
> MTZ" from the toolbar did. "Merge experimental data objects to MTZ" from
> "Export and Deposition" did not help me.
>
> I think, it's not the programs, though. The problem now seems to me the
> missing Fs. "Export MTZ" seems to convert to Fs without asking. Trying to
> upload Iplus and Iminus only for validation (or deposition) did not work. I
> thought it would be better (closer to the experimental data) to use I
> instead of F, and therefor intentionally tried to deposit Is only. Is it
> really obligatory to deposit F? Wouldn't it be better to deposit I instead
> of F?
>
> Greetings
>   Gottfried
>
>
>
> Am Freitag, den 09-02-2024 um 23:39 schrieb Jon Cooper:
>
> From your refmac refinement job in i2, this should give you the combined
> mtz?
>
> [image: test.jpg]
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with Proton Mail  secure email.
>
> On Friday, 9 February 2024 at 17:54, Palm, Gottfried <
> b793af054fc6-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear all,
>   I have problems preparing my experimental data (XRD) for deposition. I
> have two mtz files, which work well for refmac5, with an FREER column in
> one file and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file.
> I merged them into one mtz file with cad (in ccp4i).
> The validation server doesn't take two separate mtz files, but complains
> about missing data in the merged file. I guess because FREER ended up in
> "Columns common to all datasets" and the other columns in "Dataset #1:
> 356211/DEFAULT/NATIVE".
> Can I somehow move the FREER column to Dataset #1?
> With "Merge experimental data objects to MTZ Export 'old' style MTZ file"
> in ccp4i2, the problem is the same.
> I also tried converting to cif many ways, but failed.
> I have used OneDep at EBI.
>
> Best Regards
>   Gottfried
>
> --
>
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Re: [ccp4bb] Deprecation of MMTF-format files for the PDB archive

[Marcin Wojdyr]

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
parsing CIF).
Since none of them are well-suited for molecular graphics web apps,
several years ago three new formats were introduced: MMTF from RCSB,
mmJSON from PDBj and BinaryCIF from PDBe.

The MMTF project was focused on compression of files, but it wasn't
just transcribing mmCIF, it was also rethinking what is needed and how
to simplify things. It included outreach to the community and as a
result the format is now supported by PyMOL, JMol, etc. But it's
deprecated.

mmJSON is a 1:1 transcription of mmCIF in JSON. As such, it's more
useful than PDBML, except that it's only available from PDBj and
doesn't even have a spec.

BinaryCIF combines the 1:1 approach with the compression schemes from
MMTF (i.e. it uses different compression schemes for different fields
in a coordinate file).

To make a quick comparison, I took the largest file in the PDB: 8glv.

Here are the sizes (MB, gzipped ->uncompressed):
  mmCIF (cif.gz): 84 -> 432
  PDBML (xml.gz): 114 -> 4076
  MMTF (mmtf.gz): 24 -> 37
  mmJSON (json.gz): 51 -> 484
  BinaryCIF (bcif.gz): 24 -> 45

In Python, I got:
json.gz parsed in 9.5s using built-in gz and json modules
bcif.gz parsed in 24s using py-mmcif module from RCSB,
xml.gz didn't parse with built-in ElementTree or lxml on my box – 16GB
of memory is not enough.
For comparison, cif.gz is parsed using gemmi in about 10s.

mmJSON is larger than BinaryCIF, but it's parsed 2.5x faster. I guess
in C++ it would be 10x faster than in Python (using zlib-ng instead of
zlib reduces decompression time from 2s to 0.5s; libraries such as
simdjson and glaze can parse a few GBs of JSON per second). Possibly,
it's also true about BinaryCIF, which currently doesn't have a C++
library (although the python module is a C++ extension).

So, given that MMTF is now deprecated, we have three CIF-avoiding
formats: PDBML, mmJSON and BinaryCIF. If this number were to be
further reduced, IMO it'd be best to leave one simple, well-documented
JSON-based format. It'd check all the boxes, except perhaps when the
network bandwidth is truly the bottleneck and it's worth compressing
the coordinates as much as possible.

Marcin

On Fri, Jan 19, 2024 at 8:57 PM Jose Duarte
 wrote:
>
> From July 2024 the PDB file archive will not be offered in the compressed 
> MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF 
> format, which has been available since 2020. Details on how to access 
> BinaryCIF (BCIF) data files for the entire PDB archive are available here.
>
> RCSB PDB support is ready to assist with any issues or questions at 
> i...@rcsb.org.
>
> Best wishes
>
> Jose
>
> ---
> Jose Duarte
> RCSB Protein Data Bank
> San Diego Supercomputer Center
> UC San Diego
> La Jolla CA, USA
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

[Marcin Wojdyr]

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~ ABCDE


On Wed, Sep 20, 2023 at 4:53 PM Putnam, Christopher
 wrote:
>
> Would it be reasonable to reserve one of the remaining three-character CCD ID 
> for use in PDB files that means “this component cannot be represented using a 
> three character ID code”?
>
>
>
> A translation for each ambiguous residue in the PDB file to the correct code 
> could be provided in the REMARKs.
>
>
>
> This way you can still provide files in the legacy PDB format, even if the 
> file can’t be directly used for refinement.
>
>
>
> Thanks.
>
>
>
> Chris Putnam



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

[Marcin Wojdyr]

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 of atom names (and both sets of residue names) are
always identical, so they can't carry additional information.

Best wishes
Marcin



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

[Marcin Wojdyr]

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 announcement, the mapping is provided at
many levels:

> Sequence mappings are provided in _pdbx_sifts_unp_segments and
_pdbx_sifts_xref_db_segments categories for each segment,
_pdbx_sifts_xref_db at residue level, and _atom_site at atom level.

I wonder, wouldn't it be sufficient to provide the mapping at the residue
level? Repeating it for every atom actually makes working with the files
harder.

For two reasons.

One is that additional identifiers will be confusing. IMO it's the main
problem with mmCIF from the beginning -- too many identifiers. Every atom
has two chain names, two sequence IDs, two residue names and two atom
names. My guess is the IUCr committee tried to make both depositors and PDB
happy. The depositor could name the chain or atom as they like, and if the
PDB doesn't like the names, they can use the second set of names. (please
correct me if you were there). Currently the PDB changes both sets of ids
during deposition, so the "author" IDs are not really author's, but we
still have these two sets. In some older entries author's chain B is PDB's
chain A, and author's chain A is PDB's chain B. I think it's not
controversial that having two alternative names for one thing is not
particularly helpful here and, in this respect, the PDB format was designed
better.
These are old problems and I don't have hope that the double naming will be
dropped. But the new file looks like this:

[image: new-cif.png]

It has four different sequence IDs.
2 – "author" ID, the same as in the PDB
1 – "label" ID
3 – new one, apparently the same as 2 for polymers and the same as 1 for
non-polymers  Am I missing something?
4 – UniProt-compatible
Could we avoid it?

The second reason is bloat. I maintain code for working with CIF files
(it's even used in PDBe) and just yesterday a user commented that reading
5j7v-assembly1.cif (4.7GB) requires a lot of memory. If we store each word
from such a file in the simplest way in C++ (as a string), we use, say, 32
bytes per word. 5GB file with short words easily takes up 40GB of memory
just for storing the words. I could work on optimizing it, but it'd help if
the files were not bloated even more. The NextGen Archive has 24% more
words in the atom table. All redundant.

Thanks for reading,
Marcin



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Re: [ccp4bb] issues running PANDDA with anisotropic data

[Marcin Wojdyr]

>
> 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 2FOFCWT_fill and 
> PH2FOFCWT_fill so PANDDA can ‘see’ the correct data columns
>
> NB: output .mtz name must still be ‘refine.mtz’ as PANDDA only checks the 
> top-level directory for each refinement and ‘pipedream.mtz’ symlinks pointing 
> to ‘pipedream/pipedreamDir/refine/refine.mtz’ are already in place.
>
> Full path:
>
> model_building/target_x/pipedream/pipedreamDir/refine/refine.mtz

Not tested (it can be better to have a copy of the files before testing it):

for f in model_building/target_x*/pipedream/pipedreamDir/refine/refine.mtz; do
  sed -i 's/2FOFCWT-iso-fill/2FOFCWT_fill/g' $f
done

The spaces after "_fill" are to preserve the length - the header
records in mtz must have 80 characters.



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

[Marcin Wojdyr]

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
for smoothly changing values, but for noisy data it will amplify the
noise. Did anyone test if the choice of interpolation method
(tri-cubic vs tri-linear) makes a practical difference in any
crystallographic application?



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Re: [ccp4bb] help request (synchrotron schedules)

[Marcin Wojdyr]

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:
https://project-gemmi.github.io/pdb-stats/calendar.html


On Mon, May 2, 2022 at 7:38 PM Artem Evdokimov
 wrote:
>
> Dear CCP4-ers :)
>
> I used to have a handy chart where major synchrotron schedules were all drawn 
> out as lines (across an entire year) with shutdowns and other blackout dates 
> marked such that it was pretty easy to find what synchrotron is open for 
> business at what week/month. This schedule took me a while to assemble since 
> not every synchrotron handily posts their shutdown schedule and one has to 
> call friends and ask around.
>
> Needless to say, being a putz that I am, I eventually lost this lovely 
> document. So, I wonder - does anyone here have something similar that they 
> won't mind sharing? If enough people share (even individual schedules) I am 
> happy to post the resulting schedule back here for everyone to enjoy...
>
> Many thanks!
>
> Artem
>
> - Cosmic Cats approve of this message
>
> 
>
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Re: [ccp4bb] Regarding File conversion

[Marcin Wojdyr]

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 conversion from mcif file format to PDB format 
> of proteins.
> Is there any program or software that can be used to change one format to 
> another format. KIndly guide me about programs used for file conversion or 
> any other medium like python script or R script to convert the file format 
> without changing the coordinates  of the file.
> Thankyou
>
> 
>
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Re: [ccp4bb] Maps on mobile phones.

[Marcin Wojdyr]

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 edges in common, nearly all of 
> the contour lines (except the ones at the edges of the map box) get drawn 
> twice, or at least are sent to three.js twice for drawing, which doesn't seem 
> terribly efficient?! Is there a nicer way of doing this?

I was also concerned about it when writing UglyMol. It was ~6 years
ago. Drawing maps as lines was definitely affecting speed, because fps
was lower when the number of lines was huge. So to reduce duplicated
lines I calculated new tables for the marching cubes algorithms - with
lines instead of triangles in the tables. This allowed me to reduce
some (most of?) duplicates. I don't remember the details, but the
script that I used for calculating tables is here:
https://github.com/uglymol/uglymol/blob/master/tools/isolut.py

Then I was disappointed, because it didn't change the fps. I don't
know why. And I don't know how to check where the bottleneck in the
graphics pipeline is (vertex shader, fragment shader or something
else?). I guess optimizing map rendering would require someone with
expertise in 3D graphics rendering.

> Finally, its been asked before, but is there a nice way in CCP4i2 to output 
> maps that cover the coordinates of the structure, rather than the asymmetric 
> unit?

The maps that cover asu are, on average, smaller. They contain the
list of symmetry operators that expand the map to the whole unit cell.
So such maps may actually be better. Or, even better, use MTZ files. I
think UglyMol is still the only web viewer that can show maps from
MTZ, but it works on mobile web browsers (it's not designed for
mobile, but rendering works) and you can re-use parts of it.
https://uglymol.github.io/view/

Best wishes,
Marcin



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

[Marcin Wojdyr]

Then I'm afraid you'd need to first use CAD to combine both mtz files
(merged intensities and map coefficients) into one merged mtz file.
Or perhaps there is a better way - I don't know. Perhaps ccp4i2 and
Ccp4 Cloud can combine MTZ files.

I'll think about supporting multiple merged MTZs in mxdepo.html in the future.

Best,
Marcin

On Fri, 14 Jan 2022 at 17:42, Dom Bellini - MRC LMB
 wrote:
>
> Hi Marcin,
>
> This is very helpful, thanks a lot. Ezra and Jasmine from wwPDB have
> also replied just to me that they will send me a work around asap; if it
> will differ from your method I will post it.
>
> Can I please also ask you would be the best way to proceed if I would
> like to combine, as well as the merged data used for refinement and the
> unmerged mtz file, also the mtz output from the refinement software
> containing the map coefficients?
>
> 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 extensions include image
> > numbers and rotation angles) and if the software that you use doesn't
> > output such ready-to-use files, you need to first input two files:
> > - merged data that was used for refinement (MTZ or mmCIF)
> > - scaled unmerged data (MTZ or XDS_ASCII)
> > to this converter:
> > https://project-gemmi.github.io/wasm/mxdepo.html
> > and then you can upload the resulting cif file to the wwPDB deposition 
> > system.
> >
> > Best wishes
> > Marcin
> >
> > On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
> >  wrote:
> >> Dear Jasmine,
> >>
> >> But can we now upload two mtz/mmcif files now for the structure factors? 
> >> as in, the one from the processing software containing the raw data, as 
> >> well as the one with the weighted amplitudes and the phases from 
> >> Refinement software? Or do we still have to use CAD to create a single mtz 
> >> file and then convert it to mmcif for depostion? Or is there another 
> >> better way to do it?
> >>
> >> Many thanks for your help,
> >>
> >> Dom
> >>
> >>
> >>
> >>
> >> On 13/01/2022 19:19, Jasmine Young wrote:
> >>
> >> Dear all,
> >>
> >> Extensions to the PDBx/mmCIF dictionary for reflection data with 
> >> anisotropic diffraction limits, for unmerged reflection data, and for 
> >> quality metrics of anomalous diffraction data are now supported in OneDep.
> >>
> >> In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was 
> >> convened to develop a richer description of experimental data and 
> >> associated data quality metrics. Members of this Data Collection and 
> >> Processing Subgroup are all actively engaged in development and support of 
> >> diffraction data processing software. The Subgroup met virtually for 
> >> several months discussing, reviewing, and finalizing a new set dictionary 
> >> content extension that were incorporated into the PDBx/mmCIF dictionary on 
> >> February 16, 2021. A reference implementation of the new content 
> >> extensions has been developed by Global Phasing Ltd.
> >>
> >> These extensions facilitate the deposition and archiving of a broader 
> >> range of diffraction data, as well as new quality metrics pertaining to 
> >> these data. These extensions cover three main areas:
> >>
> >> scaled and merged reflection data that have been processed to take account 
> >> of diffraction anisotropy, by providing descriptors for that anisotropy, 
> >> in terms of (1) a parameter-free definition of a cut-off surface by means 
> >> of a per-reflection “signal” and a threshold value for that signal, and 
> >> (2) the ellipsoid providing the best fit to the resulting cut-off surface;
> >> scaled and unmerged reflection data, by providing extra item definitions 
> >> aimed at ensuring that such data can be meaningfully re-analysed, and 
> >> their quality assessed independently from the associated model, after 
> >> retrieval from the archive;
> >> anomalous diffraction data, by adding descriptors for numerous relevant, 
> >> but previously missing, statistics.
> >>
> >> The new mmCIF data extensions describing anisotropic diffraction now 
> >> enable archiving of the results of Global Phasing’s STARANISO program. 
> >> Developers of other software can make use of them or

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

[Marcin Wojdyr]

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 need to first input two files:
- merged data that was used for refinement (MTZ or mmCIF)
- scaled unmerged data (MTZ or XDS_ASCII)
to this converter:
https://project-gemmi.github.io/wasm/mxdepo.html
and then you can upload the resulting cif file to the wwPDB deposition system.

Best wishes
Marcin

On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
 wrote:
>
> Dear Jasmine,
>
> But can we now upload two mtz/mmcif files now for the structure factors? as 
> in, the one from the processing software containing the raw data, as well as 
> the one with the weighted amplitudes and the phases from Refinement software? 
> Or do we still have to use CAD to create a single mtz file and then convert 
> it to mmcif for depostion? Or is there another better way to do it?
>
> Many thanks for your help,
>
> Dom
>
>
>
>
> On 13/01/2022 19:19, Jasmine Young wrote:
>
> Dear all,
>
> Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic 
> diffraction limits, for unmerged reflection data, and for quality metrics of 
> anomalous diffraction data are now supported in OneDep.
>
> In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was 
> convened to develop a richer description of experimental data and associated 
> data quality metrics. Members of this Data Collection and Processing Subgroup 
> are all actively engaged in development and support of diffraction data 
> processing software. The Subgroup met virtually for several months 
> discussing, reviewing, and finalizing a new set dictionary content extension 
> that were incorporated into the PDBx/mmCIF dictionary on February 16, 2021. A 
> reference implementation of the new content extensions has been developed by 
> Global Phasing Ltd.
>
> These extensions facilitate the deposition and archiving of a broader range 
> of diffraction data, as well as new quality metrics pertaining to these data. 
> These extensions cover three main areas:
>
> scaled and merged reflection data that have been processed to take account of 
> diffraction anisotropy, by providing descriptors for that anisotropy, in 
> terms of (1) a parameter-free definition of a cut-off surface by means of a 
> per-reflection “signal” and a threshold value for that signal, and (2) the 
> ellipsoid providing the best fit to the resulting cut-off surface;
> scaled and unmerged reflection data, by providing extra item definitions 
> aimed at ensuring that such data can be meaningfully re-analysed, and their 
> quality assessed independently from the associated model, after retrieval 
> from the archive;
> anomalous diffraction data, by adding descriptors for numerous relevant, but 
> previously missing, statistics.
>
> The new mmCIF data extensions describing anisotropic diffraction now enable 
> archiving of the results of Global Phasing’s STARANISO program. Developers of 
> other software can make use of them or extend the present definitions to suit 
> their applications. Example files created by autoPROC, BUSTER (version 
> 20210224) and Gemmi that are compliant with the new dictionary extensions are 
> provided in a GitHub repository.
>
> These example files, and similarly compliant files produced by other data 
> processing and/or refinement programs, are suitable for direct uploading to 
> the wwPDB OneDep system. Automatic recognition of that compliance, 
> implemented by means of explicit dictionary versioning using the new 
> pdbx_audit_conform record, will avoid unnecessary pre-processing at the time 
> of deposition. This improved OneDep support will ensure a lossless round trip 
> between data processing/refinement in the lab and deposition at the PDB.
>
> wwPDB strongly encourages structural biologists to always use the latest 
> versions of structure determination software packages to produce data files 
> for PDB deposition. wwPDB also encourages crystallographers wishing to 
> deposit new structures together with their associated diffraction data to use 
> the software which guarantees consistency between data and final model. This 
> consistency is difficult to achieve when separate diffraction data files and 
> model coordinate files are pieced together a posteriori by ad hoc means.
>
> wwPDB also encourages depositors to make their raw diffraction images 
> available from one of the public repositories to allow direct access to the 
> original diffraction image data.
>
>
> --
> Regards,
>
> Jasmine
>
> ===
> Jasmine Young, Ph.D.
> Biocuration Team Lead
> RCSB Protein Data Bank
> Research Professor
> Institute for Quantitative Biomedicine
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Rd
> 

Re: [ccp4bb] Add hydrogens

[Marcin Wojdyr]

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 most popular one for adding hydrogens. I
don't know if there are any newer and better programs than reduce as of
today.

Best,
Marcin


On Wed, 29 Sept 2021 at 13:04, Sam Tang  wrote:

> Dear community
>
> This may appear to be a silly question -- I am trying to add hydrogens to
> the structure in PDB 1CDW. My initial thought is to run a single run of
> refinement with a refinement program. It happens that I cannot locate the
> map coefficients under the entry (am I missing something?) So... is there
> an easy way to do what I want in this case?
>
> Warm regards
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] using chooch

[Marcin Wojdyr]

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:
https://github.com/xraypy/XrayDB/tree/master/data_sources/chantler/fine
and also here:
https://www.nist.gov/pml/x-ray-form-factor-attenuation-and-scattering-tables
And from this web server:
https://xraydb.xrayabsorption.org/scattering/Br/1000/5/50

On Tue, 20 Jul 2021 at 17:02, Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Thank you all - excellent solutions and choice can stay unhappy..
>
> On Tue, 20 Jul 2021 at 13:27, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Or Bernard's:
>>
>> http://www.ruppweb.org/new_comp/anomalous_scattering.htm
>>
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>>  Original Message 
>> On 20 Jul 2021, 12:45, Tim Gruene < tim.gru...@univie.ac.at> wrote:
>>
>>
>> Dear Eleanor, not sure how to make Chooch happy, but maybe Ethan Merrit can 
>> make you happy: there is his excellent server for the anomalous signal for 
>> X-ray scattering at http://skuld.bmsc.washington.edu/scatter/ When you 
>> choose Br instead of Grr, you find 
>> http://skuld.bmsc.washington.edu/scatter/data/Br.dat, or you read your 
>> values from the interactive plot 
>> http://skuld.bmsc.washington.edu/scatter/AS_form.html Best, Tim On Tue, 20 
>> Jul 2021 12:28:16 +0100 Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Grr - stuck at home 
>> - what is f' and f' for Br??? > > All nicely tabulated on my desktop but not 
>> here.. > > So use chooch.. > but it grumbles about file name null  > > 
>> How can I make it happy? > Any help gratefully received > > Eleanor > > > 
>> eleanor@wombat cysbfull % chooch -e Br -e 0.92 > 
>> == > chooch-5.0.9 > by 
>> Gwyndaf Evans Copyright (C) 1994--2013 > gwyn...@gwyndafevans.co.uk > > G. 
>> Evans & R. F. Pettifer (2001) > J. Appl. Cryst. 34, 82-86. > 
>> == > > License information > 
>> --- > Chooch comes with ABSOLUTELY NO WARRANTY; for details 
>> > type `chooch -w'. This is free software, and you are > welcome to 
>> redistribute it under certain conditions; > type `chooch -c' for details. > 
>> > You should have received a copy of the GNU General Public License > along 
>> with this program; if not, write to the Free Software > Foundation, Inc., 59 
>> Temple Place - Suite 330, Boston, MA > 02111-1307, USA. > > -e: Atomic 
>> element = Br > -e: Atomic element = 0.92 > Fluorescence scan filename: 
>> (null) > Chooch output > > 
>>  > > 
>> To unsubscribe from the CCP4BB list, click the following link: > 
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This 
>> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list 
>> hosted by www.jiscmail.ac.uk, terms & conditions are > available at 
>> https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the 
>> Centre for X-ray Structure Analysis Faculty of Chemistry University of 
>> Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A 
>>  To 
>> unsubscribe from the CCP4BB list, click the following link: 
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>>
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>
>
> 
>
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Re: [ccp4bb] Meaning of a pdb entry

[Marcin Wojdyr]

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 may require an extended 
> description to make such depositions fully functional. I will ask the PDB, 
> but this made me optimistic. It would be easy to implement Tim's method if it 
> works for deposition.

I think it won't work.

(1) One entry can contain an ensemble of many models. 4PTH has 250
models and each atom has occupancy 0.004. It's similar to alternative
locations, but taken to extremes.

(2) One entry can contain a single model and multiple datasets. 5RKZ
has 1500+ datasets from crystals soaked with different compounds. You
can concatenate reflection mmCIF files, but only the first block is
used for validation. I suppose all the models were similar, so one can
obtain them by refining the single deposited model to each dataset.

I don't think you can meaningfully deposit multiple datasets with
corresponding models in a single entry. (2) is probably the closest to
what you want.

Best wishes,
Marcin



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Re: [ccp4bb] Meaning of a pdb entry

[Marcin Wojdyr]

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 refinement" of a crystal structure. So it's one refinement
of one dataset, but with multiple models.

> I assume it is already possible to store multiple structure factor files (for 
> refinement, for phasing, different crystals etc) under the same entry.

yes

> In my mind, it would be a small step to associate different data sets 
> distinguished by crystal ID or data block with a particular model number, but 
> maybe it is not that simple.
>

It'd be a substantial change, but indeed, the changes in the file
format would not be that big. As you wrote, model IDs would need to be
associated with crystal IDs. And probably other associations would be
needed, such as unit cell with crystal.

> I do not want to create multiple pdb entries just to provide evidence for the 
> robustness/reproducibility of crystals and crystallographic models. I would 
> rather use different pdb entries for different sampling intentions: for 
> example entry 1 contains all the control crystals, entry 2 contains all the 
> crystals subjected to treatment A, etc.

I think it's similar to PanDDA depositions, but I don't know what's
the current best practice.
Initially, one Deposition Group would have hundreds of PDB entries
(each with a single dataset). But later on I've seen entries with a
single model and hundreds of datasets. I haven't looked into it
closely, so perhaps someone else can advise.

Concatenating multiple mmCIF files (with coordinates) would produce a
syntactically valid file, but I don't think that such file would get
through the deposition process.

Marcin



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

[Marcin Wojdyr]

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: http://watcut.uwaterloo.ca/tools/makemultimer/docs
> 
> 3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat
> 
> 4. BiologicalUnit in pymol:
> https://pymolwiki.org/index.php/BiologicalUnit
> 
>
> (CCP4bb is amazing)
>
> Frank
>
> On 25/05/2021 20:44, Frank von Delft wrote:
> > Hello all - this presumably has a really simple solution:
> >
> > For a PDB file with a (correct) biomolecular assembly record (REMARK
> > 350), what program do I use to generate and write out the coordinates
> > of the biomolecular assembly (or one of them).
> >
> > Thanks
> > Frank
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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[ccp4bb] deposition of unmerged data

[Marcin Wojdyr]

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 deposit (mmCIF or MTZ), in
this web app:

https://project-gemmi.github.io/wasm/mxdepo.html

If you use GPhL software - it already has tools that prepare mmCIF
files with unmerged data, use them instead of this web app.

Having unmerged data will help method developers, so even if you
already uploaded the experimental data file, but your deposition is
not locked yet (or if it can be unlocked), and if you can find scaled
unmerged data, please add it!

In case of any problems with the web page - let me know.

Regards,
Marcin



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

[Marcin Wojdyr]

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 et al.  : f'=-0.665752, f''=1.332521
  Sasaki et al. : f'=-0.75942 , f''=1.306888
  diff f''=-0.97 %

As you see, all these commands give slightly different values. I was
told that nowadays XrayDB (not in CCP4) provides the most accurate
values:

$ python3 -c "import xraydb; print(xraydb.f1_chantler('Sr', 9699.91))"
-0.657390314908364

Crossec is the original code from Don Cromer. Gemmi, one of the cctbx
tables, and I think Ethan's server also use code that stems from it,
but with corrections added later when this code was circulating, such
as Kissel & Pratt, Acta Cryst. A46, 170 (1990).

Marcin

On Fri, 22 Jan 2021 at 21:40, Mitchell D. Miller
 wrote:
>
> You can also use the ccp4 legacy program crossec ---
> http://legacy.ccp4.ac.uk/html/crossec.html
>
> for your case --
>
> echo -e "NWAV 1 1.2782\nATOM Sr\nEND\n" | crossec | grep SR
>
>Atom symbol and number SR   38
>   $TABLE:Wave length v F' and F"-  SR   :
>   $GRAPHS:Lambda v F' and F" SR   :A:2,3,4: $$
> SR  1.2782-0.7663 1.3068
>
>
> I often ran it from a script to lookup the f'/f" for various elements via
> a script crossec.sh which takes arguments of wavelength followed by a
> list of elements
>
> #!/bin/bash
> #egrep '^ATOM|^HETATM' | cut -c77-78 file.pdb | sort -u`
>
> for atom in "$@"
>do
> if [ "$atom" != "$1" ]
>   then
> echo -e "NWAV 1 $1\nATOM $atom\nEND\n" | crossec | awk '/^
> Lambda  F/ {getline ; getline ; print $0}'
>   else
>echo "Atom_type   Lambda F"\'" F"\"
> fi
> done
>
>
>
> Quoting Bernhard Rupp :
>
> > ...or you can use the old anoweb app
> >
> > http://www.ruppweb.org/new_comp/anomalous_scattering.htm
> >
> >
> >
> > http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr
> > 
> > =1=100=K=Cu=1000=2=1=700=Submit
> >
> >
> >
> > HTH, BR
> >
> > From: CCP4 bulletin board  On Behalf Of rohit kumar
> > Sent: Friday, January 22, 2021 11:36
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom
> >
> >
> >
> > Hello All,
> >
> >
> >
> > I have data collected at Wavelength: 1.2782 (For Sr Heavy atom) with
> > a resolution of 1.6 A. I was trying to run Crank in ccp4 for SAD
> > phasing and It  asks me to fill the values of (scattering factors) f
> > and f" for the heavy atom.
> >
> > Can anyone please help with this, how to calculate or where to find
> > these f and f" values for Sr heavy atoms?
> >
> >
> >
> > Please let me If you need any information from my side.
> >
> >
> >
> > Thank you in advance
> >
> >
> >
> >
> >
> >
> > --
> >
> > Regards
> > Dr. Rohit Kumar Singh
> >
> > Postdoctoral fellow
> >
> >
> >
> >
> >
> >
> >
> >   _
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB
> > 
> > =1
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
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> 
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Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Marcin Wojdyr]

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 of non-standard 
> settings of space group 18 (which should be discouraged, to phrase it mildly)
>
> on the mmcif from the PDB
>
> _symmetry.space_group_name_H-M   "P 21 2 21" ß
>
> _symmetry.Int_Tables_number  18
>
> #
>
>
>
> leads to a problem because the resulting mtz file has the standard 18 symbol
>
>
>
> Type  Merged MTZ
>
> Space group   P 21 21 2 ß
>
> Space group confidenceX  (confidence flag is not set)
>
> Cell 88.578  44.416  71.56490  90  90
>
>
>
> Not sure if this is a loss of information when generating the mmcif upon 
> submission,
>
> or the SG is retrieved solely by SG number not symbol (the latter can give 
> rise to a few more such situations).
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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

[Marcin Wojdyr]

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 same was recommended in the mmCIF documentation.
Currently, these IDs are described as non-mandatory, alternative IDs,
which suggests (to those few software developers that read the
documentation) that they shouldn't be relied upon.

It'd also be good if the IDs that are recommended for use in
publications weren't changed afterwards as it happened in this
remediation.
Carbohydrate remediation was indeed consulted with the community over
a long time, but perhaps this particular change wasn't made clear. I
always assumed that only the primary (wwPDB internal) IDs are to be
changed, not the ones that were used in publications.

Best regards,
Marcin



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

[Marcin Wojdyr]

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 sequence numbers, and three residue names).

In your example:
J 4 NAG 1 I NAG 1 A NAG 1310 n

J - asym_id = _atom_site.label_asym_id
I - pdb_asym_id = _atom_site.auth_asym_id (?!)
A - auth_asym_id = n/a

(correct me if I got it wrong, but I see that _atom_site.auth_asym_id
corresponds to _pdbx_branch_scheme.pdb_asym_id and not to auth_asym_id
as one could expect).

How to call these chain IDs? When I write software documentation, I
need to refer to chain IDs (and sequence numbers), but I can't find
proper words to clearly tell which ID I'm referring to. I was using
hard to read names such as auth_asym_id, but now I see that even this
is ambiguous.

BTW, when you write that wwPDB encourages depositors to use the
wwPDB-assigned chain ID in publications, which of the two
wwPDB-assigned chain IDs do you mean?

Thank you,
Marcin



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

[Marcin Wojdyr]

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
>
> as a pointer into the _entity_poly_seq table.

I think you inferred the relation between tables from textual
description. This should be avoided.
The relations are defined formally in the category
_pdbx_item_linked_group_list. In this case the relation between
atom_site and entity_poly_seq has three items that are to be matched
together:

_atom_site.label_comp_id = _entity_poly_seq.mon_id
_atom_site.label_entity_id = _entity_poly_seq.entity_id
_atom_site.label_seq_id = _entity_poly_seq.num

>  It has to be an signed
> integer (although I'm not clear on what a negative value for a pointer
> means).

Do you interpret "pointer" as a row index? That's not how it's used. I
don't think that you can point to a position in the mmCIF table. In
general a "pointer" could be negative or not even numeric if the value
it points to is negative or not numeric. Although in this case
label_seq_id must be >=1, because that's the allowed range
(_item_range).

> In that table there is a data item _entity_poly_seq.num,
>
> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity_poly_seq.num.html
>
> which is not a pointer, not an ID, but a name for that particular

(it's not a pointer because there is no such a thing as a pointer in
the mmCIF technology. Or is there?)

> _entity_poly_seq row.  It must be a number that is unique and
> sequential, and presumably indicates a "sequence number".  Note that the
> rows in _entity_poly_seq can be listed in the loop_ in any order.

For the record, here is the description:
"The value of _entity_poly_seq.num must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number and that the sequence
numbers must progress in increasing numerical order."

> This means that the _atom_site.label_seq_id could be "3", pointing
> to the third entry in _entity_poly_seq which happens to have its .num
> equal to "1".

No. If _atom_site.label_seq_id is 3 it points to _entity_poly_seq.num that is 3.

> You may not think that someone would choose to do this,
> but if the first .num is -15 you can't avoid a mismatch.  In either case
> the mmCIF is perfectly acceptable and the meaning is absolutely clear.

It's formally guaranteed to be >= 1. Although it's not guaranteed that
the sequence starts with 1, because mmCIF has no way to do this. And
it's not explicitly stated in the description. So you could argue that
the sequence numbers can start with 15.
Now, the intention of _atom_site.label_seq_id has always been that
it's the position wrt the full sequence (PDB people: correct me if I'm
wrong). This is how it's interpreted by the PDB people and software.
But no one thought to explicitly write that in addition to "increasing
numerical order" the numbers must start with 1. What to do in such a
case?

There are much better examples of lacking description.
For example, if you'd interpret anisotropic ADPs according to the
mmCIF description you'd get wrong values (for non-orthogonal systems).
Because the description was copied from the small-molecule spec which
uses different axes than PDB.
Or take auth_seq_id: originally it was used for sequence ID, then it
was changed to sequence number and the definition has not been
updated.
You could find many more examples. ( has been extensively
debated during PDBx/mmCIF WG meetings this year).

My take in all such cases is that it's better to interpret things how
they are used and how they were intended to be interpreted rather than
hold to the wording used in the specification. In an ideal world the
specification would be always correct and would cover all corner
cases. But in the meantime it's better to focus on getting things done
with what is available.

> You also can't assume that the row with
> _entity_poly_seq.num equal to "3" is chemically linked to the one with
> .num equal to "2", much less the chemical nature of such a link.
> _entity_poly_seq is not a data table that defines chemistry, only
> "sequence".

OK, so how do you propose to find links between polymer residues?
The table with connections doesn't list peptide bonds in a protein
chain - they are implicit.

Marcin



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

[Marcin Wojdyr]

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 terminology correctly) are simply database "indexes".

No, entity is a somewhat different thing (multiple chains can point to
the same entity). entity_id is specified in addition to label_asym_id
and auth_asym_id.
asym = "structural element in the asymmetric unit" (so-called chain).

> The values of indices are meaningless in themselves, they are just
> unique values that can be used to unambiguously identify a record. In
> principle, you could just assign random ISO characters (I don't think
> mmCIF allows unicode) and the mmCIF would be considered identical.

And then you'd use this random string also in a publication when
referring to the chain, and in the user interface?

> You are trying to force meaning to the characters with an index, and
> that puts multiple types of information in a single field. As Robbie
> said already exists, if you want to encode connectivity into the data
> base you have to add records that define that connectivity.  That places
> the connectivity information explicitly in the data models and allows
> standard data base tools to track and validate.

No one was proposing to replace connectivity with names.
It was about naming that will be easier to work with for people.

> learn the sequence you have to go to the mmCIF records that define the
> connectivity between residues.  It is entirely possible that "3" comes
> before "1" because these indexes don't contain any information, other
> than being unique within the chain.

In mmCIF you have label_seq_id that must be both unique and
sequential. So 3 is always the third residue wrt to the full sequence.



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

[Marcin Wojdyr]

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 identifiers, including two separate
chain names (and both are present in all files from the wwPDB). The
one discussed here is auth_asym_id (author's chain ID - used in pdb
files), the other one is label_asym_id (let's call it label chain ID).
Having two sets of identifiers is obviously confusing (as can be seen
by just looking at any mmCIF file) and it'd help a lot if the two IDs
were consistent: the label chain ID could start with the corresponding
author's chain ID. For example, similarly to what Tristan proposed,
author's chain A could be split into label chains Amain, Ag1, Ag2,
etc.

Marcin



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

[Marcin Wojdyr]

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,
>
>
>
> from ccp4i classic, the DIMPLE User Guide link (box top right) to
>
> http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_difference_map_generation_with_DIMPLE
>
> returns an error message
>
> “Fatal error: Uncaught TypeError: Argument 1 passed to wfReportException() 
> must be an instance of Exception, instance of Error given, called in 
> /home/ccp4wiki/public_html/wiki/includes/Exception.php on line 205 and 
> defined in /home/ccp4wiki/public_html/wiki/includes/Exception.php:168 Stack 
> trace: #0 /home/ccp4wiki/public_html/wiki/includes/Exception.php(205): 
> wfReportException(Object(Error)) #1 [internal function]: 
> wfExceptionHandler(Object(Error)) #2 {main} thrown in 
> /home/ccp4wiki/public_html/wiki/includes/Exception.php on line 168”
>
>
>
> Can you reproduce that behavior?
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] dimple, skip pointless?

[Marcin Wojdyr]

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 regards,
Marcin



Marcin

On Sat, 29 Feb 2020 at 12:16, Guenter Fritz
 wrote:
>
> Dear all,
>
> I was going through the options in dimple. Is it possible to skip the
> checking of the space group by pointless?
>
> Thanks in advance and best regards,
>
> Guenter
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Generating symmetry mates using python

[Marcin Wojdyr]

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 the SCALE1 record
doesn't give the sufficient accuracy. In the example in your script
you have 6 significant digits in the unit cell lengths in CRYST1, but
only 4 significant digits in SCALE1. (The accuracy of SCALE1 is
problematic in general; sometimes it needs to be manually removed when
a program reads it in preference to CRYST1.)

Then one may find out that the 3x3x3 supercell is not sufficient. If
the molecule is far from the origin, symmetry operations send it far
away. For example, 5M3H annotates (in the mmCIF format) hydrogen bond
between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit cells
in the z direction. Since you already use fractional coordinates in
your script you could tell directly from the center-of-mass
coordinates how many unit cells it should be shifted. Say, you have
x=3.1, so to shift it near the origin you shift it by 3 unit cells
along x.

But even if all the molecules are shifted near the origin, the 3x3x3
cell is still not sufficient to find contacts.
See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here it in
its unit cell, colored by the chain id:
https://gemmi.readthedocs.io/en/latest/_images/3nwh.png
Or 5XG2 – a monomer in P21. Two copies of the chain are rainbow-colored here:
https://gemmi.readthedocs.io/en/latest/_images/5xg2.png
These chains span over more than 4 unit cells in one direction. One
could use big enough supercell, but it'd be slow. I suppose that even
using a 3x3x3 supercell is slow. The alternative is to do the distance
calculation in fractional coordinates modulo 1.

Then you needs to consider atoms on special positions. If you apply
symmetry operations to an atom on a 4-fold symmetry axis you get 4
atoms in the same place. So this needs to be handled. The atom may not
be exactly on the axis, because the refinement program may not
constrain its position. So the symmetry operations should produce, I
think, 4 alternative locations of the same atom. But you could also
have an atom near the symmetry axis bonded to its symmetry mate - then
the symmetry operations should produce different atoms. So the
procedure requires a cut-off distance or a heuristics to distinguish
the two cases.

Then, if you'd like to expand non-crystallographic symmetry from the
MTRIX records - this is another complication. And so on...

So I'd recommend using one of many available programs for finding
contacts or interactions. If none of them is suitable - then try
crystallographic libraries.
I didn't document yet how to find the contacts using gemmi, but I'll
do it in the coming weeks (or months). Cctbx and clipper are other
(more mature) libraries worth checking.

Best wishes,
Marcin


On Sat, 11 Jan 2020 at 02:11, Zhijie Li  wrote:
>
> Hi Orly,
>
> REMARK 290 should be the easiest way for generating symmetry mates. Other 
> routes are just going to give you the same results. As Jonathan already 
> pointed out, the symm ops do not garantee that the symm copies are close to 
> each other.  The most simple-minded solution to this problem would be simply 
> generating 3x3x3 unit cells so that the unit cell in center will be complete. 
> An upgrade to this is to compute the center of mass of the symmetry copies in 
> each of the 3x3c3 cells and find which one is closest to the orignal 1555 
> copy.  Just for fun, I wrote a little python script that does this 
> (attached). In this script for unit cell translation and calculating 
> center-center distances, I converted the Cartesian coordinates to fractional 
> coords first. Then after the translation,I used the inverse of the SCALE1 
> matrix to get the shifted Cartesian coords. This way I don't need to read 
> wikipedia on geometry . But as noted in the script the distances should 
> better be calculated in Cartesian.
>
> Zhijie
>
> 
> From: CCP4 bulletin board  on behalf of orly avraham 
> 
> Sent: Friday, January 10, 2020 3:30 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Generating symmetry mates using python
>
> Hi all,
>
> I am a crystallographer currently employing computational methods as well as 
> experimental crystallography.
> I am trying to generate symmetry mates in python (working with pandas 
> dataframes), in order to analyze inter-sub-unit interactions. To do so I am 
> trying to use the info in "REMARK 290 CRYSTALLOGRAPHIC SYMMETRY" and manually 
> (using numpy) perform a matrix multiplication with the relevant translation 
> (xyz*rotation + translation).
> For some reason this doesn't work consistently and I feel I need to use the 
> info in CRYST1 to obtain the unit cell and multiplication matrix. Here I ran 
> into trouble with extracting the correct symmetry 

Re: [ccp4bb] Dimple anomalous peaks

[Marcin Wojdyr]

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 Tue, 3 Dec 2019 at 13:36, Eugene Osipov  wrote:
>
> Dear Richard,
> yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've 
> specified - final mtz still contains only "normal" maps but now I see 
> anomalous phases in anode.pha
> In order to get difference anomalous maps I still have to run refmac5 with
> LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-) FREE=FreeR_flag
> Is it possible to specify in dimple which columns I want it to use during 
> restrained refinement, either F/SIGF or anomalous pairs F+/SIGF+ and F-/SIGF-?
> May be it is possible to modify source code to tell dimple to run refmac5 
> with specified LABINs?
> Kind regards,
> Evgenii
>
>
> вт, 3 дек. 2019 г. в 12:31, Gildea, Richard (DLSLtd,RAL,LSCI) 
> :
>>
>> Dear Evgenii,
>>
>> Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? 
>> Dimple runs shelxc to obtain the input reflection file for anode, which 
>> requires anomalous intensities as input.
>>
>> I.e. it essentially runs the following commands:
>>
>> $ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca
>>
>> $ shelxc anode << EOF
>> SAD anode.sca
>> CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0
>> SPAG P 41 21 2
>> EOF
>>
>> $ cp dimple/final.pdb anode.pdb
>>
>> $ anode anode
>>
>> At Diamond we run dimple --anode on the free.mtz file generated by xia2, 
>> which contains the following columns:
>>
>> label#valid  %valid min max type
>> F 32162  99.75%0.01 3130.76 F: amplitude
>> SIGF  32162  99.75%0.01  102.51 Q: standard deviation
>> DANO  31745  98.46% -271.19  227.37 D: anomalous difference
>> SIGDANO   31745  98.46%0.00  124.40 Q: standard deviation
>> F(+)  31777  98.55%0.01 3130.76 G: F(+) or F(-)
>> SIGF(+)   31777  98.55%0.01  102.51 L: standard deviation
>> F(-)  27431  85.08%0.02 2758.00 G: F(+) or F(-)
>> SIGF(-)   27431  85.08%0.01   91.95 L: standard deviation
>> ISYM  32243 100.00%   -1.002.00 Y: M/ISYM, packed partial/reject 
>> flag and symmetry number
>> IMEAN 32162  99.75%   -0.31  780.55 J: intensity
>> SIGIMEAN  32162  99.75%0.00   24.65 Q: standard deviation
>> I(+)  31777  98.55%   -0.48  780.55 K: I(+) or I(-)
>> SIGI(+)   31777  98.55%0.00   24.65 M: standard deviation
>> I(-)  27431  85.08%   -0.44  609.14 K: I(+) or I(-)
>> SIGI(-)   27431  85.08%0.00   16.78 M: standard deviation
>>
>> E.g.:
>>
>> $ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng
>>
>> Cheers,
>>
>> Richard
>>
>> Dr Richard Gildea
>> Data Analysis Scientist
>> Tel: +441235 77 8078
>>
>> Diamond Light Source Ltd.
>> Diamond House
>> Harwell Science & Innovation Campus
>> Didcot
>> Oxfordshire
>> OX11 0DE
>> 
>> From: CCP4 bulletin board  on behalf of Eugene Osipov 
>> 
>> Sent: 03 December 2019 10:22
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: [ccp4bb] Dimple anomalous peaks
>>
>> Dear CCP4 community,
>> I can't figure out how to tell Dimple to use F(+)/F(-) columns and search 
>> for anomalous peaks.
>> I was trying to run dimple in the next form:
>> dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
>> In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to use 
>> --fcolumn F(+) I gen an error.
>> My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and 
>> their differences in DANO.
>> Can someone tell how to calculate anomalous difference maps from dimple run?
>> Thanks in advance,
>> --
>> Evgenii Osipov
>> Laboratory for Biocrystallography,
>> Department of Pharmaceutical Sciences,
>> KU Leuven O
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>>
>> --
>>
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>> attachments are free from viruses and we cannot accept liability for any 
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Re: [ccp4bb] Live stream of CCP4 Study Weekend?

[Marcin Wojdyr]

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 
> https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:-1

I also use it on Firefox on Linux and it works for me. I got
redirected to almost the same address, except that the last digit is
4:
https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:4
(I had to enable Flash)



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Re: [ccp4bb] Python3 and MTZ

[Marcin Wojdyr]

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 and using the
subset of the language that works with both interpreters.
It's an extra burden and if one is learning Python choosing any of the
two versions will make it easier.



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Re: [ccp4bb] new ContaMiner features

[Marcin Wojdyr]

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 use ContaMiner or similar service). This feature is implemented
> in HKL3000, but it can also be done quickly on the PDB webpage.

Even better, one can use SAUC which finds also matches in different
space groups by comparing dimensions of the Niggli (reduced) cell.
http://iterate.sourceforge.net/sauc/

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

[Marcin Wojdyr]

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,
>
> Apologies for the slightly off-topic, but I was wondering if anybody knew of
> a paper/textbook where a protein model was built by multiple people (ranging
> from novice to experienced builders) and compared. I believe the conclusion
> was that while the overall trace was broadly correct, experienced builders
> maintained better geometry compared to beginners.
>
> I distinctly remember reading it a couple of years ago but cannot seem to
> find the figure. If anybody knows of this figure/paper/textbook it would be
> much appreciated if you could point me in the direction.
>
> Yours faithfully,
> Shintaro

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

[Marcin Wojdyr]

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 (HETATM for all non-standard residues).
Example: https://files.rcsb.org/view/5ABS.pdb

Marcin

Re: [ccp4bb] Problem with ViewHKL 1.08

[Marcin Wojdyr]

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, Marta Sanz Gaitero wrote:
 Dear all;
 
 I have reinstalled ccp4i recently and everything seems to work fine but
 ViewHKL. Every time I try to visualize a .mtz file the program gets opened
 but without loading the .mtz. Then it gets frozen and I have to kill it.
 In the command line the messages I get are:
 
 **SYMMETRY OPERATOR ERROR**
 
  Error in interpreting symop  -X+1/2,  -Y, Z+1/2
 
 
  CCP4 library signal ccp4_parser:Failed to interpret symop string
 (Success)
  raised in symop_to_mat4 
 
  **SYMMETRY OPERATOR ERROR**
 
  Error in interpreting symop  X+1/2,  -Y+1/2, -Z
 
 
  CCP4 library signal ccp4_parser:Failed to interpret symop string
 (Success)
  raised in symop_to_mat4 
 
  **SYMMETRY OPERATOR ERROR**
 
  Error in interpreting symop  -X,  Y+1/2, -Z+1/2
 
 
  CCP4 library signal ccp4_parser:Failed to interpret symop string
 (Success)
  raised in symop_to_mat4 
 Spacegroup_registry: ASU warning, LGhash=0x33b45b40
 Spacegroup_registry: ASU fail
 File 
 /media/marta/TOSHIBA/Ciencia/17_koji/20150626Xaloc/ch186/x4/b2x4/ccp4irepro/b2x4_3_0001_scaled1_refmac1.mtz
 is not an MTZ file
 
 My operative system is Linux Mint 17 (Qiana). Does some of you have any idea
 of what may be happening and how I can solve it?
 
 Thank you very much,
 Best regards
 
 Marta Sanz
 
 

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

[Marcin Wojdyr]

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

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

[Marcin Wojdyr]

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 fix (patch attached) and it seems to work,
It requires compilation from source, so for now use the workaround
above.

Marcin


On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote:
 Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check
 graphic driver problems (or update them from the vendor, by the way,
 controller model Intel HD 4000). Taking some time with this today, I still
 feel I will have to study further before making changes.
 This poses me yet other question, though maybe it escapes the discussion
 list scope, that I must search further: how (and where) different are the
 resources used by the virtual machine compared to the host machine, such
 that this graphical behavior is different.
 Yours,
 
 Jorge
 
 On 05/16/2015 08:39 PM, Jorge Iulek wrote:
 Dear all,
 
 My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are
 virutal) and 8 GB memory.
 For a number of  coot versions in it (including the newest one), coot
 answers slowly to rotating, but specially the space bar translate is even
 more slow (from residue x to x+1 etc.).
 Curiously, in either CentOS or even openSuSE in oracle virtualboxes
 (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB
 memory, it goes much faster, at a very reasonable speed. How could be
 that? In principle I thought that the multicore configuration of the host
 machine might be the culprit.
 So, for coot tasks, I have been using the virtual machine, but that is
 impractical.
 The closest to this problem I found was
 https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I
 could not devise any trial to solve the problem. Even trying the
 http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
   
 http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
 
  configuration did not solve the problem satisfactorily.
  I tried to search wider, but could not find other suggestions. Should 
  you have one, I would be glad to try.
  Sincerely yours,
 
 Jorge
 
 
 

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--- src/graphics-info.cc2014-12-02 16:00:08.0 +
+++ src/graphics-info.cc2015-05-18 18:29:45.420807088 +0100
@@ -1920,7 +1920,8 @@
} else { 

   glRasterPos3f(x,y,z);
-  glPushAttrib (GL_LIST_BIT);
+  glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+  glDisable(GL_FOG);
   for (unsigned int i = 0; i  s.length(); i++)
 glutBitmapCharacter (graphics_info_t::atom_label_font, s[i]);
   glPopAttrib();
@@ -4649,7 +4650,8 @@
   // GLfloat pink[3] =  { 1.0, 0.8, 0.8 };
   GLfloat pink[3] =  { font_colour.red, font_colour.green, 
font_colour.blue };
   glColor3fv(pink);
-  glPushAttrib (GL_LIST_BIT);
+  glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+  glDisable(GL_FOG);
   void *font = graphics_info_t::atom_label_font;
   font = GLUT_BITMAP_TIMES_ROMAN_24;
   for (unsigned int i=0; igeneric_texts_p-size(); i++) {
--- src/graphics-ligand-view.cc 2014-09-08 20:54:39.0 +0100
+++ src/graphics-ligand-view.cc 2015-05-18 18:27:23.714796284 +0100
@@ -307,7 +307,8 @@
 
 void
 graphics_ligand_atom::bitmap_text(const std::string s) const {
-   glPushAttrib (GL_LIST_BIT);
+   glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+   glDisable(GL_FOG);
for (unsigned int i = 0; i  s.length(); i++)
   glutBitmapCharacter (GLUT_BITMAP_HELVETICA_10, s[i]);
glPopAttrib();

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

[Marcin Wojdyr]

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 that needs to be done.

Marcin

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Re: [ccp4bb] CCP4 PATH variable

[Marcin Wojdyr]

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 low-priority issue.
We'll try to do something with it for the next release.

Marcin

On Thu, Mar 12, 2015 at 07:49:15PM +, Petr Leiman wrote:
 Dear Community,
 
 What is the reason of placing the CCP4 PATH and other path-related variables 
 in front of existing variables? This forces a linux system to use 
 CCP4-distributed wish in all applications by default. Note that the ccp4i 
 script calls CCP4 distributed wish explicitly with its full path. 
 
 This might be trivial, and the fix is also trivial, but trivial things like 
 that cause a lot of lost time and head scratching when tcl/tk programs 
 compile without errors and perform some operations correctly but segfault on 
 others - all due to a mixup of libraries and wish executables caused by CCP4 
 wish.
 
 Would it be possible to append CCP4 path variables by default instead of 
 rather rudely jumping in front of the queue?
 
 Thank you,
 
 Petr
 
 --
 Petr Leiman
 EPFL
 BSP 415
 CH-1015 Lausanne
 Switzerland
 Office: +41 21 69 30 441
 Mobile: +41 79 538 7647
 Fax: +41 21 69 30 422
 http://lbbs.epfl.ch

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Re: [ccp4bb] Building static libs.

[Marcin Wojdyr]

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 you
tried to build it again you got message:
*** Skipping [module] (package and dependencies not updated) ***
In such case either remove the install directory or do:

./build --force libccp4

Cheers
Marcin

On Sat, Mar 14, 2015 at 12:17:16PM +, Ian Tickle wrote:
 Hello All
 
 I want to build static libs (libccp4.a etc.), basically to avoid hassle
 when deploying executables of my own programs to other machines that are
 not on my LAN and don't have up-to-date compilers or system libraries.
 
 I downloaded the CCP4 sources  followed instructions in the README,
 basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4
 etc.' which claimed to be successful.  But I can't find libccp4*.a
 anywhere.  In fact 'find' says that the only .a files are in the
 cmake-3.0.2 directory and are called 'libtest*.a'.  I found
 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be
 building the dynamic libs.  I also tried 'setenv STATIC 1' but got the same
 result.
 
 What am I doing wrong?
 
 Cheers
 
 -- Ian

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Re: [ccp4bb] Coot and PISA

[Marcin Wojdyr]

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, pisa_interfaces)
and press Enter.

Or pisa_assemblies instead of pisa_interfaces, depending what you want.

BTW you can only issue one command in that little window,
the second one gives error:
  File 
/home/wojdyr/ccp4/ccp4-6.5/lib/python2.7/site-packages/coot/coot_gui.py, line 
125, in warning_event
tag1 = textbuffer.create_tag(foreground=red,weight=pango.WEIGHT_BOLD)
NameError: free variable 'textbuffer' referenced before assignment in enclosing 
scope

Marcin

On Mon, Feb 09, 2015 at 05:20:41PM +0100, Maria Jose Sanchez Barrena wrote:
 Dear all, 
 I am using Coot 0.8.1, that is part of the CCP4 version 6.1. When trying to 
 run PISA from Coot, after choosing the pdf file, I get the following message: 
 “your pisa version is too old. Need at least v1.06”. However, when running 
 CCP4mg (part of the same CCP4 package), I am able to run PISA and get these 
 wonderful interaction surfaces and so on…
 I find all this quite difficult to understand…. Any suggestion about what´s 
 going on?
 
 Many thanks in advance,
 
 Maria José 

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Re: [ccp4bb] serial MR / refinement

[Marcin Wojdyr]

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 results to be put.
The results include pictures of blobs of el. density not accounted for
by the model -- places where a ligand is suspected.

Best,
Marcin


On Tue, Feb 03, 2015 at 12:00:20PM +0100, Eike Schulz wrote:
 Dear all,
 
 I am looking for a way to automate molecular replacement and refinement 
 runs.
 
 From ligand / fragment screening trials we have many datasets of the same 
 protein with various resolutions (2.8 – 1.2Å). The apo-structure is known 
 and well refined. The cell constants are fairly similar but not in all 
 cases identical, hence I would prefer a MR run prior to the refinement. 
 
 I am sure this can somehow be realised with some shell-script but maybe 
 there is some more sophisticated way of realising this? 
 
 I would also be happy for partial solutions or general advise to the 
 problem.
 
 Best regards
 
 Eike

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Re: [ccp4bb] Privateer fails to run

[Marcin Wojdyr]

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 at 04:28:07PM +, Jon Agirre wrote:
 Hi Jan,
 
 Privateer relies on Clipper-minimol, which in turn uses MMDB. According to
 MMDB's error code description list (
 https://www.ebi.ac.uk/pdbe/docs/cldoc/object/cl_obj_irets.html) :
 
 Error_WrongEntryID 3 A PDB or mmCIF record that ought to display
 this entry's ID, shows an ID contradicting to that in header.
 
 I've been able to replicate the error by opening a PDB file downloaded from
 PDBe and changing the HEADER line to show a different PDB ID. Is that your
 case?
 
 Thanks for your interest,
 
 Jon
 
 On 12 January 2015 at 15:59, Jan Stransky jan.stransky.c...@gmail.com
 wrote:
 
  Dear all,
  I am experiencing some troubles with running Privateer. It seems to fail
  to read a PDB file. The Error message:
 
  Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
  terminate called after throwing an instance of 'clipper::Message_fatal'
  Aborted
 
  Any ideas?
  Best regards,
  Jan
 
 
 
 
 -- 
 Dr Jon Agirre
 York Structural Biology Laboratory / Department of Chemistry
 University of York, Heslington, YO10 5DD, York, England
 http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
 +44 (0) 1904 32 8253

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Re: [ccp4bb] CCP4 Release 6.5

[Marcin Wojdyr]

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 reproduce it.
The icon was apparently updated (C:\CCP4\6.5\...) by the installer.
The command is the same as in the previous versions, except for
the path (6.5 instead of 6.4).

Hard to tell what didn't work without more details. Sometimes
changing environment variables in the registry has no effect until
rebooting or logging out and in. Maybe this was the case.

Marcin

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Re: [ccp4bb] Fedora Core 20 issues

[Marcin Wojdyr]

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 Roberts wrote:
 Hi all,
 
 So, I know this probably isn’t the right place, but I’m certain most of you 
 here have battled/fixed this issue.  I just did a clean install of FC20 on an 
 AMD dual core system.  I opted for the 32 bit version, as these workstations 
 are used for multiple things (and I find that it’s just easier most of the 
 time, though 64 bit may be where I need to go eventually).
 
 Anyway - when running chimera - my computer constantly freezes.  Obviously 
 I’m missing something.  I’m not doing anything fancy - I use Zalman monitors 
 connected to generic video cards.
 
 I can run coot fine - I don’t know about ccp4i (it seems to run, but I 
 haven’t challenged it in any way).
 
 Any thoughts on where I should start here?
 
 Thanks
 
 Dave

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Re: [ccp4bb] 6.4.0.1 update questions

[Marcin Wojdyr]

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 the v6.4.0 binaries and we replaced it
with v6.4.0.1, but I don't remember what it was.

 - If using the JHBuild approach to do this,  how does one specify no
 updates should be pulled beyond the sources  used to build the last binary
 distribution?

If you mean instructions at http://devtools.fg.oisin.rc-harwell.ac.uk
replace
bzr+http://oisin.rc-harwell.ac.uk/bzr/devtools/trunk
with
bzr+http://oisin.rc-harwell.ac.uk/bzr/series-64/devtools
and you will get v6.4.0 + all updates.

If you don't want updates, download source packages v6.4.0
and do, for example:
BUILD_STATIC=1 ./build clipper

The source tarball includes so-called lightweight checkouts of all
repositories and thin wrappers for building and updating.
For example, ./build clipper does the same as:
./checkout/devtools/cj build --no-network clipper

Best,
Marcin

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Re: [ccp4bb] 6.4.0.1 update questions

[Marcin Wojdyr]

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 had complaints from 2 or 3 people regarding this.
Static libraries are not included because:
- they are not used to build CCP4
- Fortran and C++ libraries have compiler-specific ABI
  (in particular, Intel Fortran and GFortran binaries are not compatible)
- during the last 2 years we've added dozens libraries (mostly 3rd-party
  ones), some of them are used by python extensions and must be
  compiled as DSOs. So we'd need to decide for which ones we provide
  static versions.

If more people need it, we could include header files and maybe
static libraries built with the most popular compiler (GCC) for libccp4,
mmdb, clipper (what else?).

 Is  a source distribution
 available that matches the file versions used to build  a given binary
 install ?

source tarball is available from the CCP4 download page

 I've  built libraries via  JHBuild but this seems oriented towards
 building the current development sources rather than those from the last
 release.

It's for both. If you use static libraries you can use the latest
version as well. But if you prefer version 6.4.0 the easiest way
is to download the source tarball.

Marcin

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Re: [ccp4bb] Acorn, CRANK

[Marcin Wojdyr]

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 when I ran Acorn it
 gives me the error message Segmentation fault.

Acorn sometimes segfaults on Linux. The same happens when using previous
CCP4 versions (6.3 and 6.2).
We don't have time to investigate the cause, but since the program seems
to work fine (and faster) when compiled with Intel Fortran compiler,
in the next release we'll use Intel compiler to build Acorn
and maybe a few other programs. (now it's GFortran)

Marcin


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

[Marcin Wojdyr]

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 includes mmdb, libccp4,
clipper) you may change --disable-static to --enable-static in conf.py.
Or even better, in user's configuration file (cj.rc) add a line:
autogenargs = autogenargs.replace('--disable-static','--enable-static')

Libraries with different build systems usually can build only one version
(static or shared) at time.

(I haven't noticed this post at first, it's nested in a thread
with different subject)

Marcin

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

[Marcin Wojdyr]

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:
http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/cprodrg/trunk/download/head:/prodrg.param-20121005112644-zpoo2favxepvzj8p-80/prodrg.param

Marcin

On Thu, Jun 12, 2014 at 04:19:46PM -0700, Ethan A Merritt wrote:
 Earlier this year for the first time I got back a validation report from the
 PDB for a deposited structure that included wwPDB validation of a ligand.
 This is great stuff. I approve. I am happy.
 
 Unfortunately the validation check reported problems with my ligand.
 This is bad. I am unhappy.  What went wrong?
 
 A long story follows.  Skip to the end for the TL;DNR summary.
 
 Basically I am advocating to treat errors, omissions, or inadequacies
 in the CCP4 ligand dictionaries as bugs in exactly the same sense
 as program bugs.   Report them when you find them, get them fixed
 in CCP4 updates, and down the road we will all have better structures.
 
  Long version 
 
 Since last year I have been happily using the integrated tools Coot,
 Jligand, cprodrg, and refmac5 to sketch a ligand, generate a dictionary,
 fit to initial difference density, and refine.  In the absence of an 
 independent
 validation check, I thought everything was working acceptably.
 The bad grade on my wwPDB validation report [pun intended] made 
 me look into the guts of this tool chain more carefully trying to see
 what went wrong.
 
 In short here is what happens:
 
 - coot fires up jligand
 
 - I sketch the compound and click accept
 
 - jligand creates a file prodrg-in.mdl that contains only
   atom type, connectivity, single/double bond flag
 
 - cprodrg takes this and assigns each atom a more complete
   chemical label, for example
   O  15.9994  CARBONYL OXYGEN (C=O)
   CH2  12.011   ALIPHATIC CH2-GROUP
   NR  14.0067  AROMATIC NITROGEN
 
 - cprodrg then categorizes each bond by the assigned types of
   the two bonded atoms, and similarly categorizes each bond angle
   by the assigned types of its three constituent atoms.
 
 So far so good.  Now comes the problematic part.
 
 - cprodrg tries to find a target geometry (ideal bond length or angle)
   for each category by matching against the contents of the file
   .../Prodrg/param/ff/default
  If an exact match is not found, it falls through to ... well I'm not
  sure exactly what the rule is for falling through.  This is the part
  that goes wrong.
 
 The content of this default parameter file is rather impoverished.
 My ligand contained a pyrazole  (5-membered ring with 2 adjacent
 nitrogens).  The nitrogens were assigned a category 
   NR5  14.0067  NITROGEN (5-RING)
 But the default file contains no bond or angle entries for this
 atom type, so it falls through to the only N-N bond it does contain
   NSP - NSP  target length 1.12Å
 That's miles off, or at any rate more than 1/3 Å  off, the expected
 length of 1.396Å tabulated in the Mogul database for a pyrazole.
 (The wwPDB report listed a target of 1.37Å).
 
 I don't expect perfection, but target errors of more than 0.3Å in
 bond length are large compared to the expected accuracy of even
 a modest resolution protein structure.  No wonder the wwPDB 
 validation report flagged it as a 13 sigma outlier in the refined
 structure.  
 
  TL;DNR version 
 
 The $CCP4/share/prodrg/prodrg.param file does not contain
 target values for many bond types that are correctly identified
 by prodrg itself.
 
 Adding a single line handling NR5-NR5 bonds to the source file 
 ccp4-6.4.0/src/Prodrg/param/ff/default
 yields a significant improvement in my refined protein structure.
 Even the R/Rfree are improved, which surprised me.
 These were identical runs except for the regenerated ligand dictionary.
 
 Would it be appropriate to report this as a bug?I think so.
 
 Where should I report it?

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Re: [ccp4bb] error in starting imosflm

[Marcin Wojdyr]

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 it does more harm than good.
Marcin

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

[Marcin Wojdyr]

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)

That's Apple compiler. It supports C and C++ but not Fortran,
so you also need a Fortran compiler such as gfortran.

 checking for gcc... gcc-4.2.1
 checking whether the C compiler works... no

Did you set CC=gcc-4.2.1?

Marcin

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

[Marcin Wojdyr]

BTW, we got one report from a sysadmin who has built ccp4
using Clang (Apple compiler 5.0)  + gfortran 4.8 from:
http://gcc.gnu.org/wiki/GFortranBinaries#MacOS
So it's likely that at least one lab is using CCP4 built with Clang.
I'm not aware of any benchmarks, though.

Marcin

On Mon, Mar 03, 2014 at 12:04:20PM +, Harry Powell wrote:
 Hi
 
 If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing 
 either the High Performance Computing gcc/gfortran or investing in the Intel 
 Compilers. 
 
   http://hpc.sourceforge.net/ 
 
   http://software.intel.com/en-us/intel-compilers (if you have )
 
 Performance-wise, there's not much to choose between them these days.
 
 Clang just doesn't cut the mustard, and rolling your own compilers from the 
 gcc archive can be fraught with difficulty and lead to incorrectly 
 functioning compilers.
 
 On 3 Mar 2014, 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 Marcin,
  
  Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. 
  
  As is shown, it can identify gcc for gcc-4.2.1
  
   checking for gcc... gcc-4.2.1
   checking whether the C compiler works… no
  
  But indicating that the C compiler does not work.
  
  I will try Fortran compiler shortly and let you know.
  
  Best,
  
  Donghui
  
  
  
  On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk 
  wrote:
  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)
  
  That's Apple compiler. It supports C and C++ but not Fortran,
  so you also need a Fortran compiler such as gfortran.
  
   checking for gcc... gcc-4.2.1
   checking whether the C compiler works... no
  
  Did you set CC=gcc-4.2.1?
  
  Marcin
  
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  addressee please notify us of receipt by returning the e-mail and do not 
  use, copy, retain, distribute or disclose the information in or attached to 
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 --
 ** note change of address **
 Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
 Cambridge Biomedical Campus, Cambridge CB2 0QH
 Chairman of European Crystallographic Association SIG9 (Crystallographic 
 Computing) 
 
 
 
 
 
 
 
 
 

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

[Marcin Wojdyr]

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
(it's more like ~2x faster for Phaser).

 need to compile the code from source rather than taking the binary 
 versions

These programs are already compiled with openMP in CCP4

 Even if the CCP4 apps are not parallel themselves, they can access
 a parallel version of libraries e.g. FFTW, LAPACK. Again you will 
 probably need to compile CCP4 from source and link with the correct 
 libraries. 

It's possible, but I doubt it it will make noticeable difference.
Refmac runs don't spend much time in LAPACK. Probably the same with
FFTW which is used by programs that use Kevin's clipper.

One thing that can make a big difference is env. variable
GFORTRAN_UNBUFFERED_ALL. It shouldn't be set. If it is set, some
programs run a few times slower.

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

[Marcin Wojdyr]

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 email CCP4 helpdesk (c...@ccp4.ac.uk).

Marcin

On Mon, Dec 16, 2013 at 12:53:58PM -0500, Parthasarathy Sampathkumar wrote:
 Yes Uli. I have the same issue, but not solve it yet :-(
 
 Partha
 
 
 On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de 
 ulrich.goh...@mdc-berlin.de wrote:
 
   Dear colleagues,
 
  Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the
  following error when I fill in the file box for the data file:
 
  CCP4i encountered an error when trying to extract the data from data.mtz.
  You can view the output from the mtzdump program etc. + crash of the GUI.
 
  Now, running mtzdump gives me this:
 
   http://www.hkl-xray.com/data-upload-form-and-bug-report./mtzdump:
  /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.1' not found (required by
  /xprogs/CCP4/CCP4-6.4.0/destination/ccp4-6.4.0/bin/../lib/libccp4f.so.0)
 
  In /usr/lib64 I have softlinked libgfortran.so.3 - libgfortran.so.3.0.0
  (did so in 2011).
 
  I am not sure what I need to update here and how. I am running Novell's
  SLES 11 on a 64 bit system with the libgfortran43 runtime library
  installed. I have also checked file permissions (incl. tmp directories),
  and I cannot find anything obvious. I cannot remember having had similar
  problems with v6.3.0 in the beginning.
 
  Has anyone encountered the same problem and solved it yet?
 
  My apologies if this has been discussed already; I searched the archive
  and I couldn't find a similar thread.
 
  Cheers,
 
   Uli
 
 
  ---
 
  dr ulrich gohlke
 
  *staff scientist - m**acromolecular structure and interaction*
 
  max-delbrück-center for molecular medicine (mdc)
 
 
  +49 30 9406 - 2725 (w)
 
  +49 30 9406 - 2548 (fax)
 
  ulrich.goh...@mdc-berlin.de
 
 
 
 
  http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
 
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Re: [ccp4bb] lib32gfortran3 needed for 64-bit ccp4?

[Marcin Wojdyr]

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 this still be necessary for the
 64-bit CCP4? I'll keep this package on my client workstation install
 list for now.

Is it Linux? Could you copy the error message?
No 32-bit libraries should be needed.
Could you also copy the output of:

which sortmtz
ldd /path/to/ccp4-6.4.0/bin/sortmtz
md5sum /path/to/ccp4-6.4.0/bin/sortmtz

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

[Marcin Wojdyr]

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 clearly there are differences between STAR and CIF grammars.
I'm not interested enough in these format to continue this thread
much longer. When I was writing CIF parser 5 years ago I also had
impression that there are mistakes in the CIF spec. If that's true,
IMO listing (and then fixing) these mistakes can prevent different
CIF dialects. Recommending STAR spec as extra reading can't.

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

[Marcin Wojdyr]

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 to translate it into input for any kind of parser generator. I
 suggest that you use International Tables vol. G instead (chapter 2.1 or
 section 2.2.7). It is unfortunate that the later, correct, grammar is

I don't have these tables, but could you be more specific what's incorrect
in the version from the IUCR website?

I just googled cif lexers and the two ones I looked into also refer
to the same URL that I used:
cctbx: http://cci.lbl.gov/cctbx_sources/ucif/cif.g
JMol: 
http://caagt.ugent.be/CaGe/jmol/org/jmol/adapter/smarter/CifReader.RidiculousFileFormatTokenizer.html

If there are discrepancies between IUCR website and IT vol.G and it would
be worth to list them.

Marcin
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Scanned by iCritical.

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

[Marcin Wojdyr]

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 IT ones as well.

I'm not active, but after finding and opening IT vol. G on page 28
I see exactly the same lines that you gave as examples.
So I'm not convinced.

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

[Marcin Wojdyr]

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 sure that you would not want to be the
 creator of yet another one :-) Correct tokenising is a necessary
 (but not sufficient) condition for preventing the problem getting
 worse.

This reminded me that I was looking into CIF grammar several years
ago. I took Appendix A: A formal grammar for CIF:
http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf
and I used it (after necessary syntax modification) in Boost.Spirit,
which is one of many parser generators.

Then I noted two things that may be errors in the specification:

- no whitespace between LoopHeader and LoopBody

 see DataItems: LoopHeader ends with Tag, LoopBody starts with
 Value, but there is no WhiteSpace between.

- extra | in TokenizedComments (...eol |}...)

Am I right?

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

[Marcin Wojdyr]

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 that anyone tested it.

We have daily binary bundles (Windows and Linux) for testing here:
http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/
(the location is not permanent)
Here are instructions:
-
These builds are only for testing. If anything does not work as expected,
email CCP4 helpdesk c...@ccp4.ac.uk and we will fix it ASAP.

On Windows

Download and unpack to a path with no spaces.
No installation (nor uninstallation of previous version) is needed.
Just click a batch file in the top directory: ccp4i.bat starts ccp4i,
ccp4-cmd.bat starts command line with CCP4 environment set.

On Linux

Download either 32- or 64-bit version. Unpack. Run script BINARY.setup.
Then source one of the bin/ccp4.setup-* files.
-

Note that edstat doesn't seem to have ccp4i interface (on any platform),
you'd need to use it from command line.

Regards
Marcin
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Re: [ccp4bb] Dimple on windows?

[Marcin Wojdyr]

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:
http://devtools.fg.oisin.rc-harwell.ac.uk/files/dimple-1.3.zip
(that's a version for windows prepared today).
Requires installed CCP4 6.3 and WinCoot (coot is only for making images).
It also uses Raster3d which is included in the zip.

Basic usage:
dimple.bat input.mtz input.pdb output_dir

But first try running tests/test.bat to check if it works.
It's not much tested yet.

Regards
Marcin
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Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

[Marcin Wojdyr]

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, 35.1s and 18.7s.
I'd speculate that most of the difference was caused by different
compiler version (GCC 4.7 vs 4.4). Times are avg of two runs, on i7
(sandy bridge), Fedora 18.


It's good for us if some users test new versions before they are in
ccp4 release, so we try to make compilation of individual programs easy.
If you like to try what's in bazaar repository, here is instruction
http://devtools.fg.oisin.rc-harwell.ac.uk/
I'm also putting repository snapshot here:
http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/ccp4-latest-source.tar.bz2
with all programs/modules in a separate top-level directory.
Have a look at the build-all.sh script there to see how it can be built.
For example, in case of refmac, with $HOME local as installation dir,
in mmdb and libccp4 subdirectories do:
./configure --prefix=$HOME/local  make install
and in lapack and refmac directories:
cmake -DCMAKE_INSTALL_PREFIX=$HOME/local .  make install

compiler options can be passed through env vars, e.g.
export CFLAGS=-O2
export CXXFLAGS=-O2
export FFLAGS=-O2

Marcin


On Fri, Mar 01, 2013 at 10:39:30PM +0100, Tim Gruene wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Hello Ed,
 
 did you try creating a ccp4 tree from source and replacing the refmac
 source? Maybe that ccp4 environment will help you compile refmac - at
 least with refmac I had the least trouble compiling when I got the
 ccp4 source.
 
 Why are you trying to do this anyhow? Do Garib's binaries not work
 under this Ubuntu installation?
 
 Best,
 Tim
 
 On 02/27/2013 06:27 PM, 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 ccp4_parser:Failed to open
  external command
  file (Success) raised in ccp4_parser 
  
  (hardly a success).  Potentially relevant details are that I had to
  compile libccp4 and libmmdb to get to this point.  If I don't 
  configure the CCP4, I get this when trying to run refmac
  
  CCP4 library signal ccp4_general:Cannot open 
  environ.def (Error)
  raised in ccp4fyp  refmacgfortran:  Cannot open environ.def 
  refmacgfortran:  Cannot open environ.def
  
  So perhaps it's some incompatibility between libccp4/libmmdb that I
  compiled and those that came with CCP4 installation (by the way, 
  the new update feature rocks indeed).  But I tried lifting these 
  libraries from CCP4 installation when compiling refmac and I get 
  the same segmentation fault.
  
  Any suggestions for troubleshooting/advice on how to compile
  refmac from source are appreciated.
  
  Refmac version is 5.7.0032.
  
  Cheers,
  
  Ed.
  
 
 - -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
 
 iD8DBQFRMSASUxlJ7aRr7hoRAndOAKCSJo2xNOPnFQtXZVwVmtlozDnx2ACgjfoz
 EcnwFhUyH5ueOoI5LW5IVxg=
 =Gby6
 -END PGP SIGNATURE-
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Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

[Marcin Wojdyr]

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 did you get after compiling refmac?

If anyone wants to try it without compilation, daily built $CCP4/bin
directory for Linux x64 is at:
http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/
file linux-x64-cbin-*.tar.bz2 with the latest date.
It should work if you temporarily replace $CCP4/bin with the bin
directory from there.
But then move the original directory back, this new build is untested,
some programs may be missing or not working.

Regards
Marcin

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

[Marcin Wojdyr]

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 ccp4_parser:Failed to open external command
 file (Success)
  raised in ccp4_parser 
 
 (hardly a success).  Potentially relevant details are that I had to
 compile libccp4 and libmmdb to get to this point.

as shared libraries?

 So perhaps it's some incompatibility between libccp4/libmmdb that I
 compiled and those that came with CCP4 installation (by the way, the new

to see which libraries are used do:
ldd /path/to/newly/compiled/refmac5

and to use new refmac with new libraries do:
LD_LIBRARY_PATH=/path/to/newly/compiled/libs /path/to/new/refmac

Best
Marcin
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Scanned by iCritical.

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

[Marcin Wojdyr]

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 6.3.0 setup files are in bin/, these in include/ don't work
(unless you edit them). Sorry for confusion.

Marcin

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Re: [ccp4bb] CCP4 6.3.0 release

[Marcin Wojdyr]

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 from ccp4 website and ftp:
ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/CCP4-6.3.0.1.msi

Additionally ctruncate has been updated, some non-critical issues have
been fixed.

Marcin
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Scanned by iCritical.

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

[Marcin Wojdyr]

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 you'd like to test refmac 5.7 that will be included in CCP4 6.3
I can make pre-release binaries later this week and put it on ftp.
(I suppose it won't be slower than Linux version, but we'll see.)

One thing that slows down *both* Linux and Windows version is
the GFORTRAN_UNBUFFERED_ALL env. variable.
It was set as a temporary workaround in ver. 6.2, but has been already
removed from the coming release.
If you unset it for refmac from 6.2 you can get a few lines in the output
(in terminal) in wrong order, but the program should run notably faster.

 Most peculiaralthough I think but I do not know whether the linux
 binaries are 64 bit

If it's from CCP4 it's 32-bit.

You can check it by typing file /path/to/binary.
You'll get in the output either
ELF 32-bit LSB executable
or
ELF 64-bit LSB executable

Marcin

Re: [ccp4bb] cif_mmdic.lib

[Marcin Wojdyr]

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


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp 
(Hofkristallrat a.D.) 
Sent: Thursday, December 29, 2011 6:49 AM
To: ccp4bb
Subject: [ccp4bb] cif_mmdic.lib

Dear Developers,

A few observations during data import/export

ccp4i win 64 installed from ccp4-6.2.2.msi

a) cif2mtz 6.2 says:

 CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) 
(Raised in zzs_undump)
Cannot open file C:\CCP4\6.2\lib\data\cif_mmdic.lib for reading!

This file is in  C:\CCP4\6.2\lib
and not in
C:\CCP4\6.2\lib\data

- copying it there fixes the problem.

b) in 'Convert from MTZ', selecting SHELX as format, the HKL extension shows
up twice, plus a  comma, in the HKLOUT gui line

r3k78sf.hkl,.HKL

c) Question: any particular reason why the cell parameters and SG are not
read from the mmcif and need to be entered by hand?

d) is it normal that the header in the GUI window says
'CCP4 Program Suite 6.2.0 CCP4Interface 2.1.0 runing on .'
when I install 6.2.2 ? Or did something go wrong?

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the
production of this email.
-

Re: [ccp4bb] installation CCP4 on Win 7

[Marcin Wojdyr]

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:
https://help.ubuntu.com/community/HowToMD5SUM#MD5SUM_on_Windows
http://www.openoffice.org/dev_docs/using_md5sums.html

Let me know if the sums match.
Marcin



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of SUBSCRIBE CCP4BB 
Huo tong [heroho...@163.com]
Sent: Tuesday, December 06, 2011 3:26 AM
To: ccp4bb
Subject: Re: [ccp4bb] installation CCP4 on Win 7

Thank you for all your advices!
This time the window keeps staying on the screen. It says Program too big to 
fit in memory.
My PC has 2G memory, and I wonder if this memory cannot satifiy the CCP4.
If so, I think I'd rather install it on other work station.

Re: [ccp4bb] installation CCP4 on Win 7

[Marcin Wojdyr]

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

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of SUBSCRIBE CCP4BB 
Huo tong [heroho...@163.com]
Sent: Sunday, December 04, 2011 2:51 AM
To: ccp4bb
Subject: [ccp4bb] installation CCP4 on Win 7

Hi all:

I do not  know if any installation problem on Win7 was discussed ever on the 
bbs, but this problem really makes me confusing.
I download the CCP4 suit for windows on the CCP4 
website(http://www.ccp4.ac.uk/download/os.php), and there is something wrong 
when I try to install it. After I click the installer, a DOS window jumps out 
but quickly closes by itself and then nothing happens.
I suspect that the installation program is stucked by something and therefore 
it cannot run.
Is there any advices？
I will appreciate for that!

Re: [ccp4bb] Installation of CCP4 under Windows 7

[Marcin Wojdyr]

Two weeks ago we announced new experimental windows installer (only the 
installer itself was new, but the content -- files that are installed -- has 
not changes). The next revision of this installer fixes a few problems with 
environmental variables and includes updates that are available from our ftp 
site.
There is no real reason to download it if you have ver. 6.2.0 already 
installed, but for new installations it may work better.
You are welcome to try it.

ftp://ftp.ccp4.ac.uk/mww/CCP4-6.2.2.msi

Marcin

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@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, 
there is no point in upgrading if someone has version 6.2.0 already
installed.

When upgrading from older version, please uninstall old version 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
Sent: 08 November 2011 14:45
To: ccp4bb
Subject: 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 September 
we updated our build of Tcl and friends and it seems to work well with ccp4i 
and imosflm. We'll remove the recommendation of ActiveTcl from the website soon.

Cheers
Marcin


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert 
Oeffner
Sent: 08 November 2011 12:27
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7

Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few 
years. Whenever I run the CCP4 installer for all users on my Windows Vista PC 
as administrator it only creates desktop icons and startup menu item for the 
administrator account, not for other users. 

It appears that the CCP4 desktop icon shortcut is put in 
C:\Users\Administrator\Desktop and the start menu CCP4 folder is put in 
C:\Users\Administrator\AppData\Roaming\Microsoft\Windows\Start 
Menu\Programs\CCP4-Packages-6.2.0. Both of these paths are incorrect as they 
are invisible when logging in as another user.

I'm not sure where the CCP4 desktop icon shortcut should go but placing the 
startup folder in C:\ProgramData\Microsoft\Windows\Start Menu\Programs makes it 
accessible to other users.

On a separate note, it also appears that there is a bug in the ActiveTCL 
installer which is recommended to be installed on Vista platforms. It only 
makes file associations with tcl files for the user who installed this program. 
Consequently when double clicking the CCP4 icon as a different user than 
administrator windows prompts the user asking what program the  file should be 
opened with. Again this can be overcome by making the wish.exe program from the 
ActiveTcl folder the default program to use.


Regards,

Robert Oeffner, Ph.D.
Research Associate, Read group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234

Re: [ccp4bb] Installation of CCP4 under Windows 7

[Marcin Wojdyr]

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, 
there is no point in upgrading if someone has version 6.2.0 already
installed.

When upgrading from older version, please uninstall old version 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
Sent: 08 November 2011 14:45
To: ccp4bb
Subject: 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 September 
we updated our build of Tcl and friends and it seems to work well with ccp4i 
and imosflm. We'll remove the recommendation of ActiveTcl from the website soon.

Cheers
Marcin


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert 
Oeffner
Sent: 08 November 2011 12:27
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7

Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few 
years. Whenever I run the CCP4 installer for all users on my Windows Vista PC 
as administrator it only creates desktop icons and startup menu item for the 
administrator account, not for other users. 

It appears that the CCP4 desktop icon shortcut is put in 
C:\Users\Administrator\Desktop and the start menu CCP4 folder is put in 
C:\Users\Administrator\AppData\Roaming\Microsoft\Windows\Start 
Menu\Programs\CCP4-Packages-6.2.0. Both of these paths are incorrect as they 
are invisible when logging in as another user.

I'm not sure where the CCP4 desktop icon shortcut should go but placing the 
startup folder in C:\ProgramData\Microsoft\Windows\Start Menu\Programs makes it 
accessible to other users.

On a separate note, it also appears that there is a bug in the ActiveTCL 
installer which is recommended to be installed on Vista platforms. It only 
makes file associations with tcl files for the user who installed this program. 
Consequently when double clicking the CCP4 icon as a different user than 
administrator windows prompts the user asking what program the  file should be 
opened with. Again this can be overcome by making the wish.exe program from the 
ActiveTcl folder the default program to use.


Regards,

Robert Oeffner, Ph.D.
Research Associate, Read group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234

Re: [ccp4bb] Installation of CCP4 under Windows 7

[Marcin Wojdyr]

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 September 
we updated our build of Tcl and friends and it seems to work well with ccp4i 
and imosflm. We'll remove the recommendation of ActiveTcl from the website soon.

Cheers
Marcin


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert 
Oeffner
Sent: 08 November 2011 12:27
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7

Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few 
years. Whenever I run the CCP4 installer for all users on my Windows Vista PC 
as administrator it only creates desktop icons and startup menu item for the 
administrator account, not for other users. 

It appears that the CCP4 desktop icon shortcut is put in 
C:\Users\Administrator\Desktop and the start menu CCP4 folder is put in 
C:\Users\Administrator\AppData\Roaming\Microsoft\Windows\Start 
Menu\Programs\CCP4-Packages-6.2.0. Both of these paths are incorrect as they 
are invisible when logging in as another user.

I'm not sure where the CCP4 desktop icon shortcut should go but placing the 
startup folder in C:\ProgramData\Microsoft\Windows\Start Menu\Programs makes it 
accessible to other users.

On a separate note, it also appears that there is a bug in the ActiveTCL 
installer which is recommended to be installed on Vista platforms. It only 
makes file associations with tcl files for the user who installed this program. 
Consequently when double clicking the CCP4 icon as a different user than 
administrator windows prompts the user asking what program the  file should be 
opened with. Again this can be overcome by making the wish.exe program from the 
ActiveTcl folder the default program to use.


Regards,

Robert Oeffner, Ph.D.
Research Associate, Read group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234