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

[Harry Powell]

Hi Nick

doesn’t look encouraging - 

> ~/maxit/maxit-v8.120-prod-bin-linux/bin/maxit-v8.01-O -i 1A9W_A.pdb -o 1
> Initial filter libaray failed

No need to worry - since the pdb2cif from the pdb-redo team works, and they’re 
the ones who produce AlphaFill, they can always help out if (when) things go 
wrong!

best wishes and thanks again 

Harry

> On 23 Feb 2024, at 14:00, Nicholas Clark 
>  wrote:
> 
> Hi Harry,
> 
> Unfortunately, I did not see that the latest binary update was from 2008. I 
> do not have access to any newer binaries for Linux, as I'm on MacOS. 
> 
> Maybe you can use the MineProt software from the quote I mentioned previously 
> to (in a roundabout way) accomplish the CIF file generation?
> 
> "“Huiwenke:
> 
> MineProt (https://github.com/huiwenke/MineProt) can be used to curate 
> AlphaFold predictions, where PDBs are converted into CIFs using MAXIT 
> (https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files 
> support Mol* visualization and downstream analysis such as AlphaFill 
> (https://github.com/PDB-REDO/alphafill).
> Another possible option is to use MAXIT directly, while it needs several 
> additional steps to make generated CIF files support older versions of Mol*. 
> Please refer to 
> https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php.”;
> 
> Best,
> 
> Nick
> 
> 
> 
> -- Forwarded message -
> From: Nicholas Clark 
> Date: Fri, Feb 23, 2024 at 8:03 AM
> Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
> To: Harry Powell 
> Cc: Harry Powell 
> 
> 
> Hi Harry,
> 
> MAXIT binaries are located here:
> 
> https://sw-tools.rcsb.org/apps/MAXIT/binary.html
> 
> Best,
> 
> Nick
> 
> 
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
> 
> Cell: 716-830-1908
> 
> 
> On Fri, Feb 23, 2024 at 7:58 AM Harry Powell  
> wrote:
> Hi Nick
> 
> Thanks for responding, but see my earlier reply to Avinash - the build 
> doesn’t like my brand-new, hot off the production line Linux and the location 
> of pre-built exes is not obvious.
> 
> best wishes
> 
> Harry
> 
> > On 23 Feb 2024, at 12:43, Nicholas Clark 
> >  wrote:
> > 
> > Hi Harry,
> > 
> > Have you tried MAXIT from the PDB? It can be installed locally:
> > 
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D=0
> > 
> > Best,
> > 
> > Nick Clark
> > 
> > Nicholas D. Clark (He/Him)
> > PhD Candidate
> > Malkowski Lab
> > University at Buffalo
> > Department of Structural Biology
> > Jacob's School of Medicine & Biomedical Sciences
> > 955 Main Street, RM 5130
> > Buffalo, NY 14203
> > 
> > Cell: 716-830-1908
> > 
> > 
> > On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
> > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Martin, Marcin, Arturo, Avinash
> > 
> > First off, I’m **NOT** saying that there’s anything wrong with the CIF 
> > files produced by these routes - just that AlphaFill doesn’t like them (it 
> > *does* like CIFs from AlphaFold - 
> > 
> > > alphafill process alphafold.cif filled.cif
> > > 1DKE =--- 
> > >  14%
> > 
> > But (while Alphafold models are wonderful, have put us all out of jobs, 
> > etc, etc) they are just a starting point for my project and, for this 
> > purpose, no good in themselves.
> > 
> > Martin, Marcin - gemmi would be a good way to go, but - 
> > 
> > > >>> import gemmi
> > > >>> structure = gemmi.read_structure('old.pdb')
> > > >>> structure.make_mmcif_document().write_file('new.cif')
> > > 
> > > alphafill process new.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > > gemmi convert old.pdb gemmi.cif
> > > alphafill process gemmi.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > :-(
> > 
> > Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
> > interface - 
> > 
> > > alphafill process pymol.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > 
> > Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
> > help page says 
> > 
> > > Note: It is highly recommended to utilize binary distribution,
> > 
> > it’s not obvious where to get this. So I download and try to 

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Randy John Read]

Hi Huw,

When I was at the workshop, I have to admit that after ccp4i2 refused to do it 
I switched to Phenix and used phenix.reflection_file_converter! It would be 
better if i2’s reindex or change spacegroup task didn’t refuse, and I guess 
this might improve after the overly-zealous consistency checking is relaxed, or 
cad could be used following your suggestion.

As for how to report this in a publication, we actually ran into this when 
working on a Hyp-1 complex structure with Mariusz Jaskolski and Zbyszek Dauter, 
where the crystals were apparently perfectly tetartohedrally twinned. The 
apparent space group was some variant of P422 (which is how the data were 
processed and merged) but the true space group was identified as one choice of 
C2. Merging in the correct space group gave only 73% completeness, but the 
statistics for the data processed in higher symmetry were very similar so the 
expanded data set was used and deposited 
(https://doi.org/10.1107/s1399004713030319). Statistics for processing in both 
space groups were presented in Table 1.

Best wishes,

Randy

> On 23 Feb 2024, at 13:45, Huw Jenkins  wrote:
> 
> Hi Randy,
> 
>> On 23 Feb 2024, at 11:49, Randy John Read  wrote:
>> 
>> Why would we want to impose an arbitrary restriction on users for this 
>> relatively common scenario.
> 
> If the user has the unmerged data this can be imported into CCP4i2 via the 
> data reduction task and merged in P1. How would you expand the merged data to 
> P1 - using cad from a script? Perhaps this should be made possible in CCP4i2 
> after the merged data were imported. i2 already has a "Reindex or change 
> spacegroup" task (using POINTLESS)  but it won't do this:
> 
> "FATAL ERROR:
> Specified SPACEGROUP P1 must belong to same crystal system and point group
> as the input space group P 41 21 2"
> 
>> 
>> Note that this kind of confusion between twinning and true symmetry will 
>> mostly arise when the twin fractions are close to equal. Then: a) the 
>> twin-related intensities should really be measurements of the same thing, 
>> and you get more precise data by making them equal; b) the superimposed 
>> diffraction patterns will obey the higher symmetry, although the spots might 
>> start to split at higher resolution.
>> 
>> I would also argue that, if the twin fractions are experimentally 
>> indistinguishable from being equal, processing in higher symmetry and 
>> expanding the data to the correct lower symmetry is the correct approach to 
>> take for your final data set. 
> 
> That's a fair comment. In that case would you then report the merging 
> statistics for the higher symmetry data in "Table 1" and note that the merged 
> data were subsequently expanded to the correct lower symmetry?
> 
> 
> Huw


-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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

[Nicholas Clark]

Hi Harry,

Unfortunately, I did not see that the latest binary update was from 2008. I
do not have access to any newer binaries for Linux, as I'm on MacOS.

Maybe you can use the MineProt software from the quote I mentioned
previously to (in a roundabout way) accomplish the CIF file generation?

"“Huiwenke:

MineProt (https://github.com/huiwenke/MineProt) can be used to curate
AlphaFold predictions, where PDBs are converted into CIFs using MAXIT (
https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files
support Mol* visualization and downstream analysis such as AlphaFill (
https://github.com/PDB-REDO/alphafill).
Another possible option is to use MAXIT directly, while it needs several
additional steps to make generated CIF files support older versions of
Mol*. Please refer to
https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php
.”"

Best,

Nick



-- Forwarded message -
From: Nicholas Clark 
Date: Fri, Feb 23, 2024 at 8:03 AM
Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
To: Harry Powell 
Cc: Harry Powell 


Hi Harry,

MAXIT binaries are located here:

https://sw-tools.rcsb.org/apps/MAXIT/binary.html

Best,

Nick


Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Fri, Feb 23, 2024 at 7:58 AM Harry Powell 
wrote:

> Hi Nick
>
> Thanks for responding, but see my earlier reply to Avinash - the build
> doesn’t like my brand-new, hot off the production line Linux and the
> location of pre-built exes is not obvious.
>
> best wishes
>
> Harry
>
> > On 23 Feb 2024, at 12:43, Nicholas Clark <
> b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hi Harry,
> >
> > Have you tried MAXIT from the PDB? It can be installed locally:
> >
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D=0
> >
> > Best,
> >
> > Nick Clark
> >
> > Nicholas D. Clark (He/Him)
> > PhD Candidate
> > Malkowski Lab
> > University at Buffalo
> > Department of Structural Biology
> > Jacob's School of Medicine & Biomedical Sciences
> > 955 Main Street, RM 5130
> > Buffalo, NY 14203
> >
> > Cell: 716-830-1908
> >
> >
> > On Fri, Feb 23, 2024 at 7:36 AM Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Martin, Marcin, Arturo, Avinash
> >
> > First off, I’m **NOT** saying that there’s anything wrong with the CIF
> files produced by these routes - just that AlphaFill doesn’t like them (it
> *does* like CIFs from AlphaFold -
> >
> > > alphafill process alphafold.cif filled.cif
> > > 1DKE
>  =---  14%
> >
> > But (while Alphafold models are wonderful, have put us all out of jobs,
> etc, etc) they are just a starting point for my project and, for this
> purpose, no good in themselves.
> >
> > Martin, Marcin - gemmi would be a good way to go, but -
> >
> > > >>> import gemmi
> > > >>> structure = gemmi.read_structure('old.pdb')
> > > >>> structure.make_mmcif_document().write_file('new.cif')
> > >
> > > alphafill process new.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> > > gemmi convert old.pdb gemmi.cif
> > > alphafill process gemmi.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> > :-(
> >
> > Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics
> interface -
> >
> > > alphafill process pymol.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> >
> > Avinash - Maxit *might* work, but I fell at the first hurdle - although
> the help page says
> >
> > > Note: It is highly recommended to utilize binary distribution,
> >
> > it’s not obvious where to get this. So I download and try to build from
> source, and get (after unpacking and setting ENVs) -
> >
> > > make
> > > Warning: this seems to be an unsupported operating system.
> > >
> > > Supported systems are:
> > >   SunOS .. version 4.1.x and 5.2 or higher
> > >   Linux .. any version
> > >   SGI IRIX ... version 5.3-6.4
> > > make: *** [Makefile:32: compile] Error 1
> >
> > which is odd, because this is a new Linux system installed this week
> >
> > > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> > > Rocky Linux release 9.3 (Blue Onyx)
> >
> > best wishes all
> >
> > Harry
> >
> >
> >
> > >
> > > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
> > >
> > 

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Huw Jenkins]

Hi Randy,

> On 23 Feb 2024, at 11:49, Randy John Read  wrote:
> 
> Why would we want to impose an arbitrary restriction on users for this 
> relatively common scenario.

If the user has the unmerged data this can be imported into CCP4i2 via the data 
reduction task and merged in P1. How would you expand the merged data to P1 - 
using cad from a script? Perhaps this should be made possible in CCP4i2 after 
the merged data were imported. i2 already has a "Reindex or change spacegroup" 
task (using POINTLESS)  but it won't do this:

"FATAL ERROR:
Specified SPACEGROUP P1 must belong to same crystal system and point group
as the input space group P 41 21 2"

> 
> Note that this kind of confusion between twinning and true symmetry will 
> mostly arise when the twin fractions are close to equal. Then: a) the 
> twin-related intensities should really be measurements of the same thing, and 
> you get more precise data by making them equal; b) the superimposed 
> diffraction patterns will obey the higher symmetry, although the spots might 
> start to split at higher resolution.
> 
> I would also argue that, if the twin fractions are experimentally 
> indistinguishable from being equal, processing in higher symmetry and 
> expanding the data to the correct lower symmetry is the correct approach to 
> take for your final data set. 

That's a fair comment. In that case would you then report the merging 
statistics for the higher symmetry data in "Table 1" and note that the merged 
data were subsequently expanded to the correct lower symmetry?


Huw


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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Ian Tickle]

On Fri, Feb 23, 2024 at 9:58 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:

> While I get where you are coming from, it is still from a mathematical
> standpoint correct to consider e.g. a tetragonal crystal as monoclinic -
> P21 is a subgroup of P43212 (say) so strictly it is possible and correct -
> if experimentally unlikely - to have the situation we are discussing here
> occur.
>

Actually all values of beta are equally likely (up to a certain point,
larger angles, say > 120, obviously become much less likely because it's
likely that the cell can be transformed into one with a smaller angle).
90. is just as likely as 90.0001, and 90.0002, and 90.0003 ... .  If I
ask what's the chance that the next structure determination in monoclinic
will have beta = 91.2345 it's exactly the same chance as it will have beta
= 90. .  Logically if we exclude 90. on the grounds that it's very
unlikely we should exclude all values!  Obviously if I ask what's the
chance beta will be _anything_ other than 90, that's a false comparison.
10 heads in a row has a chance of 2^-10 and so does any random sequence I
name before the toss (say HHHTTHHTHT): the point is I'm doing the choosing.

Cheers

-- Ian



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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[David Waterman]

Hi Harry,

I remember the C222/P622 confusion from some of Phil's old slides, and I
thought that was an impressive case! It probably appears in a few places on
the internet, but one I found just now is slide 15 of this presentation:
https://www.ccp4.ac.uk/schools/DLS-2015/course_material/Datareduction2015.pdf

Cheers
-- David


On Fri, 23 Feb 2024 at 10:17, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Graeme (I may well have mentioned this when we shared an office) et al
>
> I’ll add something from my small-molecule crystallography days, when we
> used point detectors - so this would be pre-1996 which was the last time I
> used one of these machines.
>
> I don’t remember which structure it was (feel free to go through the CSD
> to check on my behalf, but many structures were not deposited in those days
> and languish in a PhD thesis!); I had a dataset with three 90º angles, but
> the processing statistics (and overall cell volume) indicated quite plainly
> that it was monoclinic (probably P21). I re-refined the unit cell as if it
> were triclinic and the “best” 90 degree angle with the smallest ESD was the
> one that corresponded to the monoclinic beta; the two 90º angles refined
> away from their true value more.
>
> A result of that experiment was that (since then) I never assumed that the
> values of the angles from the data processing showed unambiguously that I
> had a high symmetry solution. I believe that Pointless arose after a
> hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be
> faulty here).
>
> Best wishes
>
> Harry
>
> > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hi Huw
> >
> > (first: thank to Phil for picking this up; it caused much confusion)
> >
> > While I get where you are coming from, it is still from a mathematical
> standpoint correct to consider e.g. a tetragonal crystal as monoclinic -
> P21 is a subgroup of P43212 (say) so strictly it is possible and correct -
> if experimentally unlikely - to have the situation we are discussing here
> occur.
> >
> > Also, under merging data to investigate twinning is a current bb topic.
> >
> > Telling users to “fiddle the parameters” so that the strict test is
> satisfied feels like a non-ideal answer: a warning when importing such data
> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this
> is unusual, I hope you know what you are doing” rather than a flat out
> error.
> >
> > Literally I got involved as I had a dials user ask me how to do this
> parameter fiddling in a more niche case and I thought that was a suboptimal
> solution to an artificial problem :-)
> >
> > On a personal note, I think it is important that the tools we develop
> still allow people to explore problems rather than railroading them down
> one true route which is the only allowed way to look at a problem: we learn
> a lot by exploring odd corners as here.
> >
> > Best wishes Graeme
> >
> >> On 23 Feb 2024, at 09:49, Huw Jenkins  wrote:
> >>
> >> [You don't often get email from h.t.jenk...@me.com. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification ]
> >>
> >> Hi Graeme,
> >>
> >>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>>
> >>> Processing a data set in lower than necessary symmetry e.g. tetragonal
> as monoclinic you _cannot_ import the merged MTZ file into i2 because it is
> impossible to have 90 degree angles for P21
> >>
> >> I had a look at the code in CCP4i2 that generates the errors in the
> screenshots you posted. The first one is only generated if two cell
> parameters are *exactly* equal and the second is generated when beta is
> between 89. and 90.0001 degrees.
> >>
> >> I think these tests should only fail if the data were processed
> assuming higher symmetry so that unit cell parameters were restrained and
> then the space group changed to a lower symmetry one. Isn't the correct
> approach when the true symmetry is lower than originally assumed to repeat
> the data processing without applying constraints imposed by the higher
> symmetry - because, for example, cell parameters refined assuming cell
> length/angle constraints may not predict the reflection positions as well
> as if these restraints were not applied, reflections assumed to be symmetry
> equivalent when they weren't may lead to suboptimal scaling etc etc?
> >>
> >>
> >> Huw
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright and
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> > Any opinions expressed within this e-mail are those 

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[David Waterman]

Hi Huw,

This is tricky because in certain situations the cell parameter esds can
get lost. For example if best_unit_cell= has been passed during scaling or
merging with DIALS. Or, if cell parameter refinement was done using the
LFBGS engine, in which case the esds are not calculated.

Cheers
David


On Fri, 23 Feb 2024, 10:40 Huw Jenkins, <
288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:

> > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> >  so strictly it is possible and correct - if experimentally unlikely -
> to have the situation we are discussing here occur.
>
> I believe this is only technically possible because the MTZ format does
> not store esds on the unit cell parameters? In the thaumatin example
> processing the dataset here  - https://zenodo.org/records/4916649 -
> assuming monoclinic symmetry results in unit cell:
>
> 58.176(2), 150.543(4), 58.2050(18), 90.0, 90.1058(9), 90.0
>
> The situation you describe would result in for example:
>
> 58.1087(18), 150.543(4), 58.1087(15), 90.0, 90.(1), 90.0
>
> and the test should really only fail for:
>
> 58.1087(18), 58.1087(18), 150.400(5), 90.0, 90.0, 90.0
>
> i.e. where a=b have same value and esd (as they were constrained to be
> identical and esd on beta is 0 as it was constrained to be 90.
>
>
>
> > Telling users to “fiddle the parameters” so that the strict test is
> satisfied feels like a non-ideal answer: a warning when importing such data
> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this
> is unusual, I hope you know what you are doing” rather than a flat out error
>
> I think you have misunderstood here. I was suggesting telling users to
> integrate/scale the data without imposing higher symmetry was the correct
> thing to do? I don't see how "fiddling of parameters" is required.
>
> But I agree i2 should allow an override of this test.
>
>
> Huw
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Many thanks to all that replied.

Ida’s suggestion of pdb2cif from the PDB-REDO people is the only one that’s 
worked to date (“worked” in this context means produces a CIF that AlphaFill 
accepts without complaining - can’t imagine why).

Now off to play with my voids…

As they say, standards are wonderful - that’s why there are so many of them.

Have a great weekend

Harry

> On 23 Feb 2024, at 12:46, Ida de Vries  wrote:
> 
> Dear Harry, 
> 
> You could also try to use pdb2cif from the cif-tools: 
> https://github.com/PDB-REDO/cif-tools. The only strict requirement for a PDB 
> formatted file is that it has a HEADER at the first line. After installation, 
> running from the command line is as simple as: pdb2cif file.pdb . 
> 
> Best regards, 
> 
> Ida
> 
> On 23-02-2024 13:43, Nicholas Clark wrote:
>> Hi Harry,
>> 
>> Have you tried MAXIT from the PDB? It can be installed locally:
>> 
>> https://sw-tools.rcsb.org/apps/MAXIT/index.html
>> 
>> Best,
>> 
>> Nick Clark
>> 
>> Nicholas D. Clark (He/Him)
>> PhD Candidate
>> Malkowski Lab
>> University at Buffalo
>> Department of Structural Biology
>> Jacob's School of Medicine & Biomedical Sciences
>> 955 Main Street, RM 5130
>> Buffalo, NY 14203
>> 
>> Cell: 716-830-1908
>> 
>> 
>> On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Hi Martin, Marcin, Arturo, Avinash
>> 
>> First off, I’m **NOT** saying that there’s anything wrong with the CIF files 
>> produced by these routes - just that AlphaFill doesn’t like them (it *does* 
>> like CIFs from AlphaFold - 
>> 
>> > alphafill process alphafold.cif filled.cif
>> > 1DKE =---  
>> > 14%
>> 
>> But (while Alphafold models are wonderful, have put us all out of jobs, etc, 
>> etc) they are just a starting point for my project and, for this purpose, no 
>> good in themselves.
>> 
>> Martin, Marcin - gemmi would be a good way to go, but - 
>> 
>> > >>> import gemmi
>> > >>> structure = gemmi.read_structure('old.pdb')
>> > >>> structure.make_mmcif_document().write_file('new.cif')
>> > 
>> > alphafill process new.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> > gemmi convert old.pdb gemmi.cif
>> > alphafill process gemmi.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> :-(
>> 
>> Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
>> interface - 
>> 
>> > alphafill process pymol.cif filled.cif
>> > Structure file does not seem to contain polymers, perhaps 
>> > pdbx_poly_seq_scheme is missing?
>> 
>> 
>> Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
>> help page says 
>> 
>> > Note: It is highly recommended to utilize binary distribution,
>> 
>> it’s not obvious where to get this. So I download and try to build from 
>> source, and get (after unpacking and setting ENVs) - 
>> 
>> > make
>> > Warning: this seems to be an unsupported operating system.
>> >  
>> > Supported systems are:
>> >   SunOS .. version 4.1.x and 5.2 or higher
>> >   Linux .. any version 
>> >   SGI IRIX ... version 5.3-6.4
>> > make: *** [Makefile:32: compile] Error 1
>> 
>> which is odd, because this is a new Linux system installed this week
>> 
>> > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
>> > Rocky Linux release 9.3 (Blue Onyx)
>> 
>> best wishes all
>> 
>> Harry
>> 
>> 
>> 
>> > 
>> > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
>> > 
>> > Dear Harry,
>> > 
>> > You can try to read your PDB file and save it as mmCIF using gemmi:
>> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D=0
>> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23id3=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=hWTaO6gd4gJkDaPGMB5e5cx5mCPaqpVKnrrNKcngeN4%3D=0
>> > 
>> > Best wishes,
>> > Martin
>> > 
>> > 
>> >> Hi folks
>> >> 
>> >> I am in the situation of having coordinates of apoproteins (i.e. 
>> >> polypeptide chains without prosthetic groups) in PDB format - but I need 
>> >> them in mmCIF format so I can run them through a locally built copy of 
>> >> AlphaFill.
>> >> 
>> >> I need something I can install locally, so web services are a no-no.
>> >> 
>> >> I’ve tried obabel and Coot to 

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

[Ida de Vries]

Dear Harry,

You could also try to use pdb2cif from the cif-tools: 
https://github.com/PDB-REDO/cif-tools. The only strict requirement for a 
PDB formatted file is that it has a HEADER at the first line. After 
installation, running from the command line is as simple as: pdb2cif 
file.pdb .


Best regards,

Ida

On 23-02-2024 13:43, Nicholas Clark wrote:

Hi Harry,

Have you tried MAXIT from the PDB? It can be installed locally:

https://sw-tools.rcsb.org/apps/MAXIT/index.html

Best,

Nick Clark

Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:


Hi Martin, Marcin, Arturo, Avinash

First off, I’m **NOT** saying that there’s anything wrong with the
CIF files produced by these routes - just that AlphaFill doesn’t
like them (it *does* like CIFs from AlphaFold -

> alphafill process alphafold.cif filled.cif
> 1DKE  =--- 14%

But (while Alphafold models are wonderful, have put us all out of
jobs, etc, etc) they are just a starting point for my project and,
for this purpose, no good in themselves.

Martin, Marcin - gemmi would be a good way to go, but -

> >>> import gemmi
> >>> structure = gemmi.read_structure('old.pdb')
> >>> structure.make_mmcif_document().write_file('new.cif')
>
> alphafill process new.cif filled.cif
> Structure file does not seem to contain polymers, perhaps
pdbx_poly_seq_scheme is missing?

> gemmi convert old.pdb gemmi.cif
> alphafill process gemmi.cif filled.cif
> Structure file does not seem to contain polymers, perhaps
pdbx_poly_seq_scheme is missing?

:-(

Arturo - I’ve never scripted PyMol, but saving as CIF from the
graphics interface -

> alphafill process pymol.cif filled.cif
> Structure file does not seem to contain polymers, perhaps
pdbx_poly_seq_scheme is missing?


Avinash - Maxit *might* work, but I fell at the first hurdle -
although the help page says

> Note: It is highly recommended to utilize binary distribution,

it’s not obvious where to get this. So I download and try to build
from source, and get (after unpacking and setting ENVs) -

> make
> Warning: this seems to be an unsupported operating system.
>
> Supported systems are:
>   SunOS .. version 4.1.x and 5.2 or higher
>   Linux .. any version
>   SGI IRIX ... version 5.3-6.4
> make: *** [Makefile:32: compile] Error 1

which is odd, because this is a new Linux system installed this week

> [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more
/etc/redhat-release
> Rocky Linux release 9.3 (Blue Onyx)

best wishes all

Harry



>
> On 23 Feb 2024, at 11:55, Martin Malý 
wrote:
>
> Dear Harry,
>
> You can try to read your PDB file and save it as mmCIF using gemmi:
>

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D=0


>

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23id3=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=hWTaO6gd4gJkDaPGMB5e5cx5mCPaqpVKnrrNKcngeN4%3D=0


>
> Best wishes,
> Martin
>
>
>> Hi folks
>>
>> I am in the situation of having coordinates of apoproteins
(i.e. polypeptide 

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

[Nicholas Clark]

Harry,

After a little digging, it seems this was previously reported as an issue
to AlphaFold… see:
https://github.com/google-deepmind/alphafold/issues/252

There are a few options others recommended or got to work in the comments.
Notably, MAXIT was used:

“Huiwenke:

MineProt (https://github.com/huiwenke/MineProt) can be used to curate
AlphaFold predictions, where PDBs are converted into CIFs using MAXIT (
https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files
support Mol* visualization and downstream analysis such as AlphaFill (
https://github.com/PDB-REDO/alphafill).
Another possible option is to use MAXIT directly, while it needs several
additional steps to make generated CIF files support older versions of
Mol*. Please refer to
https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php
.”


Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Fri, Feb 23, 2024 at 7:36 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Martin, Marcin, Arturo, Avinash
>
> First off, I’m **NOT** saying that there’s anything wrong with the CIF
> files produced by these routes - just that AlphaFill doesn’t like them (it
> *does* like CIFs from AlphaFold -
>
> > alphafill process alphafold.cif filled.cif
> > 1DKE
>  =---  14%
>
> But (while Alphafold models are wonderful, have put us all out of jobs,
> etc, etc) they are just a starting point for my project and, for this
> purpose, no good in themselves.
>
> Martin, Marcin - gemmi would be a good way to go, but -
>
> > >>> import gemmi
> > >>> structure = gemmi.read_structure('old.pdb')
> > >>> structure.make_mmcif_document().write_file('new.cif')
> >
> > alphafill process new.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
> > gemmi convert old.pdb gemmi.cif
> > alphafill process gemmi.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
> :-(
>
> Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics
> interface -
>
> > alphafill process pymol.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
>
> Avinash - Maxit *might* work, but I fell at the first hurdle - although
> the help page says
>
> > Note: It is highly recommended to utilize binary distribution,
>
> it’s not obvious where to get this. So I download and try to build from
> source, and get (after unpacking and setting ENVs) -
>
> > make
> > Warning: this seems to be an unsupported operating system.
> >
> > Supported systems are:
> >   SunOS .. version 4.1.x and 5.2 or higher
> >   Linux .. any version
> >   SGI IRIX ... version 5.3-6.4
> > make: *** [Makefile:32: compile] Error 1
>
> which is odd, because this is a new Linux system installed this week
>
> > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> > Rocky Linux release 9.3 (Blue Onyx)
>
> best wishes all
>
> Harry
>
>
>
> >
> > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
> >
> > Dear Harry,
> >
> > You can try to read your PDB file and save it as mmCIF using gemmi:
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D=0
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23id3=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=hWTaO6gd4gJkDaPGMB5e5cx5mCPaqpVKnrrNKcngeN4%3D=0
> >
> > Best wishes,
> > Martin
> >
> >
> >> Hi folks
> >>
> >> I am in the situation of having coordinates of apoproteins (i.e.
> polypeptide chains without prosthetic groups) in PDB format - but I need
> them in mmCIF format so I can run them through a locally built copy of
> AlphaFill.
> >>
> >> I need something I can install locally, so web services are a no-no.
> >>
> >> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill
> doesn’t like the files produced. Before I spend time searching through
> available options on the interweb, does anyone know of a utility that can
> provide me with suitable mmCIFs? Note that I *only* have the coordinates
> because they come from modelling.
> >>
> >> I’m assuming that I’ve run obabel 

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

[Nicholas Clark]

Hi Harry,

Have you tried MAXIT from the PDB? It can be installed locally:

https://sw-tools.rcsb.org/apps/MAXIT/index.html

Best,

Nick Clark

Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Fri, Feb 23, 2024 at 7:36 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Martin, Marcin, Arturo, Avinash
>
> First off, I’m **NOT** saying that there’s anything wrong with the CIF
> files produced by these routes - just that AlphaFill doesn’t like them (it
> *does* like CIFs from AlphaFold -
>
> > alphafill process alphafold.cif filled.cif
> > 1DKE
>  =---  14%
>
> But (while Alphafold models are wonderful, have put us all out of jobs,
> etc, etc) they are just a starting point for my project and, for this
> purpose, no good in themselves.
>
> Martin, Marcin - gemmi would be a good way to go, but -
>
> > >>> import gemmi
> > >>> structure = gemmi.read_structure('old.pdb')
> > >>> structure.make_mmcif_document().write_file('new.cif')
> >
> > alphafill process new.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
> > gemmi convert old.pdb gemmi.cif
> > alphafill process gemmi.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
> :-(
>
> Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics
> interface -
>
> > alphafill process pymol.cif filled.cif
> > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
>
>
> Avinash - Maxit *might* work, but I fell at the first hurdle - although
> the help page says
>
> > Note: It is highly recommended to utilize binary distribution,
>
> it’s not obvious where to get this. So I download and try to build from
> source, and get (after unpacking and setting ENVs) -
>
> > make
> > Warning: this seems to be an unsupported operating system.
> >
> > Supported systems are:
> >   SunOS .. version 4.1.x and 5.2 or higher
> >   Linux .. any version
> >   SGI IRIX ... version 5.3-6.4
> > make: *** [Makefile:32: compile] Error 1
>
> which is odd, because this is a new Linux system installed this week
>
> > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> > Rocky Linux release 9.3 (Blue Onyx)
>
> best wishes all
>
> Harry
>
>
>
> >
> > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
> >
> > Dear Harry,
> >
> > You can try to read your PDB file and save it as mmCIF using gemmi:
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23reading=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885643631876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=kPhUsO0dv9gty%2F08hhxQw5IlXdJGu%2BkXlxyLUKYNLm4%3D=0
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgemmi.readthedocs.io%2Fen%2Flatest%2Fmol.html%23id3=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C211237fcc56e48de6bda08dc346bc149%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442885648007195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=hWTaO6gd4gJkDaPGMB5e5cx5mCPaqpVKnrrNKcngeN4%3D=0
> >
> > Best wishes,
> > Martin
> >
> >
> >> Hi folks
> >>
> >> I am in the situation of having coordinates of apoproteins (i.e.
> polypeptide chains without prosthetic groups) in PDB format - but I need
> them in mmCIF format so I can run them through a locally built copy of
> AlphaFill.
> >>
> >> I need something I can install locally, so web services are a no-no.
> >>
> >> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill
> doesn’t like the files produced. Before I spend time searching through
> available options on the interweb, does anyone know of a utility that can
> provide me with suitable mmCIFs? Note that I *only* have the coordinates
> because they come from modelling.
> >>
> >> I’m assuming that I’ve run obabel and Coot correctly!
> >>
> >> obabel:
> >>
> >>> alphafill process protein_obabel.cif  filled.cif
> >>> Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >>
> >> Coot:
> >>
> >>> alphafill process protein_A-coot-0.cif filled.cif
> >>> Error reading file ‘protein_A-coot-0.cif'
> >>>  >> parse error at line 2: This file does not seem to be an mmCIF file
> >>
> >> Harry
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >>
> 

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

[Harry Powell]

Hi Martin, Marcin, Arturo, Avinash

First off, I’m **NOT** saying that there’s anything wrong with the CIF files 
produced by these routes - just that AlphaFill doesn’t like them (it *does* 
like CIFs from AlphaFold - 
 
> alphafill process alphafold.cif filled.cif
> 1DKE =---  14%

But (while Alphafold models are wonderful, have put us all out of jobs, etc, 
etc) they are just a starting point for my project and, for this purpose, no 
good in themselves.

Martin, Marcin - gemmi would be a good way to go, but - 

> >>> import gemmi
> >>> structure = gemmi.read_structure('old.pdb')
> >>> structure.make_mmcif_document().write_file('new.cif')
> 
> alphafill process new.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

> gemmi convert old.pdb gemmi.cif
> alphafill process gemmi.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

:-(

Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
interface - 

> alphafill process pymol.cif filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?


Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
help page says 

> Note: It is highly recommended to utilize binary distribution,

it’s not obvious where to get this. So I download and try to build from source, 
and get (after unpacking and setting ENVs) - 

> make
> Warning: this seems to be an unsupported operating system.
>  
> Supported systems are:
>   SunOS .. version 4.1.x and 5.2 or higher
>   Linux .. any version 
>   SGI IRIX ... version 5.3-6.4
> make: *** [Makefile:32: compile] Error 1

which is odd, because this is a new Linux system installed this week

> [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> Rocky Linux release 9.3 (Blue Onyx)

best wishes all

Harry



> 
> On 23 Feb 2024, at 11:55, 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
> 
> 
>> Hi folks
>> 
>> I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
>> chains without prosthetic groups) in PDB format - but I need them in mmCIF 
>> format so I can run them through a locally built copy of AlphaFill.
>> 
>> I need something I can install locally, so web services are a no-no.
>> 
>> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
>> doesn’t like the files produced. Before I spend time searching through 
>> available options on the interweb, does anyone know of a utility that can 
>> provide me with suitable mmCIFs? Note that I *only* have the coordinates 
>> because they come from modelling.
>> 
>> I’m assuming that I’ve run obabel and Coot correctly!
>> 
>> obabel:
>> 
>>> alphafill process protein_obabel.cif  filled.cif
>>> Structure file does not seem to contain polymers, perhaps 
>>> pdbx_poly_seq_scheme is missing?
>> 
>> Coot:
>> 
>>> alphafill process protein_A-coot-0.cif filled.cif 
>>> Error reading file ‘protein_A-coot-0.cif'
>>>  >> parse error at line 2: This file does not seem to be an mmCIF file
>> 
>> Harry
>> 
>> 
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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] mmCIF files from PDB format for AlphaFill

[Avinash Punekar]

Hi Harry,

You can do this using the MAXIT tool 
[https://sw-tools.rcsb.org/apps/MAXIT/index.html] which can be installed 
locally.

Best wishes,
Avinash



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

[Marta Martínez]

Hi Harry

Thank you for the information on how hard it is to work locally.  I wish 
you all the best!


Marta

El 2024-02-23 12:48, Harry Powell escribió:


Hi Marta

Thanks for this.

Unfortunately, I can't use a web resource for this - I have to do it 
locally (partly because I'm providing a web service, and it's better 
not to blame other providers when my service fails).


I'd be likely to be doing this > 1000 times a day (every day from now 
until I retire ;-)); I've found with other web resources that this can 
trigger DDOS protection systems (e.g. being temporarily banned…).


best wishes

Harry

On 23 Feb 2024, at 11:41, Marta Martínez  wrote:

Hi Harry

I use this link: 
https://urldefense.com/v3/__https://mmcif.pdbj.org/converter/__;!!D9dNQwwGXtA!XMcmybqK0HPR5lesHR0z2fmHCeayJ5FcnnIgg3d4jkoyOg2CkpZuOjcUUeOrMfxOKrT1yK5tcht0OqR8DJeJA06PTJioAK6PzQ$


to convert pdb to mmCIF .  Hope, it was usuful for your modelled 
coodinates.


Regards

Marta

El 2024-02-23 12:32, Harry Powell escribió:

Hi folks

I am in the situation of having coordinates of apoproteins (i.e. 
polypeptide chains without prosthetic groups) in PDB format - but I 
need them in mmCIF format so I can run them through a locally built 
copy of AlphaFill.


I need something I can install locally, so web services are a no-no.

I've tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
doesn't like the files produced. Before I spend time searching through 
available options on the interweb, does anyone know of a utility that 
can provide me with suitable mmCIFs? Note that I *only* have the 
coordinates because they come from modelling.


I'm assuming that I've run obabel and Coot correctly!

obabel:

alphafill process protein_obabel.cif  filled.cif
Structure file does not seem to contain polymers, perhaps 
pdbx_poly_seq_scheme is missing?

Coot:

alphafill process protein_A-coot-0.cif filled.cif
Error reading file 'protein_A-coot-0.cif'

parse error at line 2: This file does not seem to be an mmCIF file

Harry


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--
Marta Mª Martínez Júlvez
Profesora Titular de Universidad
Departamento de Bioquímica y Biología Molecular y Celular, Facultad de 
Ciencias

Instituto de Biocomputación y Física Sistemas Complejos (BIFI)
Universidad de Zaragoza
Pedro Cerbuna 12, 50009-Zaragoza Spain
Phone: 34 976 762841 Fax: 34 976 762123
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Flavoenzymes: action mechanisms and biotechnology
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Profesora Titular de Universidad
Departamento de Bioquímica y Biología Molecular y Celular, Facultad de 
Ciencias

Instituto de Biocomputación y Física Sistemas Complejos (BIFI)
Universidad de Zaragoza
Pedro Cerbuna 12, 50009-Zaragoza Spain
Phone: 34 976 762841 Fax: 34 976 762123
e-mail:mmart...@unizar.es
Flavoenzymes: action 

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Randy John Read]

In the recent crystallography workshop in Thailand, we had at least 3 cases 
brought by participants where we had reason to suspect that the data had been 
over-merged because of undetected twinning. Often there is more than one 
possible twinning operator and (as potentially in one of the cases brought up 
recently on this BB) the easiest way to sort out the true symmetry is just to 
expand the data to P1 and solve the structure by looking for the appropriate 
expanded number of copies. If the data are of reasonable quality 
(case-dependent) and the model is good (true more often than not, in these 
post-AlphaFold days), the multicopy MR solution can be pretty straightforward. 
Once you have a better idea of the true symmetry, then would be a good time to 
try reprocessing the data without assuming too high symmetry. Why would we want 
to impose an arbitrary restriction on users for this relatively common scenario.

Note that this kind of confusion between twinning and true symmetry will mostly 
arise when the twin fractions are close to equal. Then: a) the twin-related 
intensities should really be measurements of the same thing, and you get more 
precise data by making them equal; b) the superimposed diffraction patterns 
will obey the higher symmetry, although the spots might start to split at 
higher resolution.

I would also argue that, if the twin fractions are experimentally 
indistinguishable from being equal, processing in higher symmetry and expanding 
the data to the correct lower symmetry is the correct approach to take for your 
final data set. Obviously you still want to try to process the data in the 
correct space group to make this decision, looking at things like whether the 
observations related by true symmetry are more highly correlated than 
observations related by the twin operator(s).

Best wishes,

Randy

> On 23 Feb 2024, at 10:39, Huw Jenkins 
> <288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) 
>> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> so strictly it is possible and correct - if experimentally unlikely - to 
>> have the situation we are discussing here occur.
>
> I believe this is only technically possible because the MTZ format does not 
> store esds on the unit cell parameters? In the thaumatin example processing 
> the dataset here  - https://zenodo.org/records/4916649 - assuming monoclinic 
> symmetry results in unit cell:
>
> 58.176(2), 150.543(4), 58.2050(18), 90.0, 90.1058(9), 90.0
>
> The situation you describe would result in for example:
>
> 58.1087(18), 150.543(4), 58.1087(15), 90.0, 90.(1), 90.0
>
> and the test should really only fail for:
>
> 58.1087(18), 58.1087(18), 150.400(5), 90.0, 90.0, 90.0
>
> i.e. where a=b have same value and esd (as they were constrained to be 
> identical and esd on beta is 0 as it was constrained to be 90.
>
>
>
>> Telling users to “fiddle the parameters” so that the strict test is 
>> satisfied feels like a non-ideal answer: a warning when importing such data 
>> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is 
>> unusual, I hope you know what you are doing” rather than a flat out error
>
> I think you have misunderstood here. I was suggesting telling users to 
> integrate/scale the data without imposing higher symmetry was the correct 
> thing to do? I don't see how "fiddling of parameters" is required.
>
> But I agree i2 should allow an override of this test.
>
>
> Huw
> 
>
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-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
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Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi Marta

Thanks for this.

Unfortunately, I can’t use a web resource for this - I have to do it locally 
(partly because I’m providing a web service, and it’s better not to blame other 
providers when my service fails).

I’d be likely to be doing this > 1000 times a day (every day from now until I 
retire ;-)); I’ve found with other web resources that this can trigger DDOS 
protection systems (e.g. being temporarily banned…).

best wishes

Harry

> On 23 Feb 2024, at 11:41, Marta Martínez  wrote:
> 
> Hi Harry
> 
> I use this link: https://mmcif.pdbj.org/converter/
> 
> to convert pdb to mmCIF .  Hope, it was usuful for your modelled coodinates.
> 
> Regards
> 
> Marta
> 
> 
> 
> El 2024-02-23 12:32, Harry Powell escribió:
> 
>> Hi folks
>> 
>> I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
>> chains without prosthetic groups) in PDB format - but I need them in mmCIF 
>> format so I can run them through a locally built copy of AlphaFill.
>> 
>> I need something I can install locally, so web services are a no-no.
>> 
>> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
>> doesn’t like the files produced. Before I spend time searching through 
>> available options on the interweb, does anyone know of a utility that can 
>> provide me with suitable mmCIFs? Note that I *only* have the coordinates 
>> because they come from modelling.
>> 
>> I’m assuming that I’ve run obabel and Coot correctly!
>> 
>> obabel:
>> 
>>> alphafill process protein_obabel.cif  filled.cif
>>> Structure file does not seem to contain polymers, perhaps 
>>> pdbx_poly_seq_scheme is missing?
>> 
>> Coot:
>> 
>>> alphafill process protein_A-coot-0.cif filled.cif 
>>> Error reading file ‘protein_A-coot-0.cif'
>>>  >> parse error at line 2: This file does not seem to be an mmCIF file
>> 
>> Harry
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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>>  
>> 
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> 
> 
> -- 
> Marta Mª Martínez Júlvez
> Profesora Titular de Universidad
> Departamento de Bioquímica y Biología Molecular y Celular, Facultad de 
> Ciencias
> Instituto de Biocomputación y Física Sistemas Complejos (BIFI)
> Universidad de Zaragoza
> Pedro Cerbuna 12, 50009-Zaragoza Spain
> Phone: 34 976 762841 Fax: 34 976 762123
> e-mail:mmart...@unizar.es
> Flavoenzymes: action mechanisms and biotechnology
> https://bioquimica.unizar.es/biologia-estructural
> http://www.bifi.es/es/biofisica/



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

[Martin Malý]

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

On Fri, 2024-02-23 at 11:32 +, Harry Powell wrote:
> Hi folks
> 
> I am in the situation of having coordinates of apoproteins (i.e.
> polypeptide chains without prosthetic groups) in PDB format - but I
> need them in mmCIF format so I can run them through a locally built
> copy of AlphaFill.
> 
> I need something I can install locally, so web services are a no-no.
> 
> I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill
> doesn’t like the files produced. Before I spend time searching
> through available options on the interweb, does anyone know of a
> utility that can provide me with suitable mmCIFs? Note that I *only*
> have the coordinates because they come from modelling.
> 
> I’m assuming that I’ve run obabel and Coot correctly!
> 
> obabel:
> 
> > alphafill process protein_obabel.cif  filled.cif
> > Structure file does not seem to contain polymers, perhaps
> > pdbx_poly_seq_scheme is missing?
> 
> Coot:
> 
> > alphafill process protein_A-coot-0.cif filled.cif 
> > Error reading file ‘protein_A-coot-0.cif'
> >  >> parse error at line 2: This file does not seem to be an mmCIF
> > file
> 
> Harry
> #
> ###
> 
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Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Marta Martínez]

Hi Harry

I use this link: https://mmcif.pdbj.org/converter/

to convert pdb to mmCIF .  Hope, it was usuful for your modelled 
coodinates.


Regards

Marta

El 2024-02-23 12:32, Harry Powell escribió:


Hi folks

I am in the situation of having coordinates of apoproteins (i.e. 
polypeptide chains without prosthetic groups) in PDB format - but I 
need them in mmCIF format so I can run them through a locally built 
copy of AlphaFill.


I need something I can install locally, so web services are a no-no.

I've tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill 
doesn't like the files produced. Before I spend time searching through 
available options on the interweb, does anyone know of a utility that 
can provide me with suitable mmCIFs? Note that I *only* have the 
coordinates because they come from modelling.


I'm assuming that I've run obabel and Coot correctly!

obabel:


alphafill process protein_obabel.cif  filled.cif
Structure file does not seem to contain polymers, perhaps 
pdbx_poly_seq_scheme is missing?


Coot:


alphafill process protein_A-coot-0.cif filled.cif
Error reading file 'protein_A-coot-0.cif'

parse error at line 2: This file does not seem to be an mmCIF file


Harry


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--
Marta Mª Martínez Júlvez
Profesora Titular de Universidad
Departamento de Bioquímica y Biología Molecular y Celular, Facultad de 
Ciencias

Instituto de Biocomputación y Física Sistemas Complejos (BIFI)
Universidad de Zaragoza
Pedro Cerbuna 12, 50009-Zaragoza Spain
Phone: 34 976 762841 Fax: 34 976 762123
e-mail:mmart...@unizar.es
Flavoenzymes: action mechanisms and biotechnology
https://bioquimica.unizar.es/biologia-estructural
http://www.bifi.es/es/biofisica/



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[ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi folks

I am in the situation of having coordinates of apoproteins (i.e. polypeptide 
chains without prosthetic groups) in PDB format - but I need them in mmCIF 
format so I can run them through a locally built copy of AlphaFill.

I need something I can install locally, so web services are a no-no.

I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill doesn’t 
like the files produced. Before I spend time searching through available 
options on the interweb, does anyone know of a utility that can provide me with 
suitable mmCIFs? Note that I *only* have the coordinates because they come from 
modelling.

I’m assuming that I’ve run obabel and Coot correctly!

obabel:

> alphafill process protein_obabel.cif  filled.cif
> Structure file does not seem to contain polymers, perhaps 
> pdbx_poly_seq_scheme is missing?

Coot:

> alphafill process protein_A-coot-0.cif filled.cif 
> Error reading file ‘protein_A-coot-0.cif'
>  >> parse error at line 2: This file does not seem to be an mmCIF file

Harry


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[ccp4bb] Postdoc in Chromatin Biology

[Arimura, Yasuhiro]

Dear All,



I am excited to let you know that the Arimura Lab (launched in February 2024 in 
Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, USA) is looking 
for a Postdoctoral Fellow to help establish an inclusive, diverse, innovative, 
and collaborative research team.



The successful candidate must have a keen interest in chromatin biology and the 
courage to develop novel approaches. We are particularly interested in 
combining structural biology and genomics approaches.



The mission of the Arimura Lab is to elucidate the regulation mechanisms of 
biological events occurring in eukaryotic chromosomes. Our Lab will accomplish 
this elucidation by developing novel approaches. The lab currently possesses 
unique technology to determine the high-resolution cryo-EM structures of 
chromatin-related complexes isolated from interphase and M phase chromosomes 
formed in Xenopus (frog) egg extract (PMID: 34478647) and Magnetic Isolation 
and Concentration (MagIC)-cryo-EM, a technique enabling direct structural 
analysis of targets captured on nanomagnetic beads, which allows for the 
structural determination of scarce macromolecules (< 0.0005 mg/mL) in 
heterogeneous samples (PMID: 38328033 [preprint]).


The fellow will either work on implementing our unique technologies or further 
advancing them (e.g. combining them with genomics, applying these technologies 
to tissue culture cells) to elucidate the structural basis of the biological 
events occurring in eukaryotic chromosomes, such as the transcription 
regulation in euchromatin and heterochromatin, the mitosis-specific mechanisms 
that compact chromosomes and assemble kinetochores, and the accessible 
chromatin formation around transcription start site.


The Arimura Lab provides a supportive environment that strongly emphasizes 
individualized mentoring. Upon joining, we will prioritize your continued 
development as an independent scientist. We will collaborate with you to 
identify and develop plans to achieve your research and professional 
development goals. In addition, Fred Hutch and the Basic Sciences Division 
offer numerous career development opportunities, benefits, and competitive 
salaries (starting at approximately $68k, with scheduled raises to ~$91k by 
2027) for postdoctoral fellows.

Please visit the following link to learn more and apply.
https://careers-fhcrc.icims.com/jobs/27135/post-doctoral-research-fellow---arimura-lab/job

Best Regards,
Yasu Arimura

yarim...@fredhutch.org
Assistant Professor, Basic Sciences Division
Fred Hutchinson Cancer Center
1100 Fairview Ave N,
Seattle, WA 98109




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[ccp4bb] Post doc position at the Astbury Centre, University of Leeds, UK

[Joseph Cockburn]

Dear all,

We have a 3-year postdoc position to work on a highly interdisciplinary project 
to study the structure and dynamics of ciliary proteins, in collaboration with 
Dr George Heath, Prof. Colin Johnson and Prof. Michelle Peckham. Please don't 
hesitate to contact any of us for more details!

To apply for this role please go to:
https://jobs.leeds.ac.uk/Vacancy.aspx?ref=FBSMB1274

Deadline for applications: 05th March 2024.

Kind regards,

Joe


--
Dr Joseph J B Cockburn DPhil
Program Leader, Biochemistry and Medical Biochemistry
Group Leader and Lecturer in X-ray Crystallography
The Astbury Centre for Structural and Molecular Biology
School of Molecular and Cellular Biology
Faculty of Biological Sciences
University of Leeds
Leeds LS2 9JT
UK
+44 (0)113 3430758

Sometimes I need to send emails in the evenings or at weekends, but I don’t 
expect a reply outside of your normal working hours.




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[ccp4bb] Position is available (University of Liverpool, UK)

[Antonyuk, Svetlana]

UNIVERSITY OF LIVERPOOL
DEPARTMENT OF BIOCHEMISTRY AND SYSTEMS BIOLOGY

Cryo-EM STRUCTURAL BIOLOGY POSTDOCTORAL RESEARCH ASSOCIATE

Grade 7 (Salary range £38,250 - £40,521 pa)


An exciting opportunity has emerged to join the Molecular Biophysics 
Group to work on a BBSRC-supported 
collaborative project between the teams from University of Leeds and Liverpool 
aimed at answering fundamental questions on enzyme mechanism of 
quinol-dependent integral membrane nitric oxide reductases, a member of 
respiratory heme-copper oxidase superfamily. The project builds on our recent 
2.2Å cryoEM structure of this enzyme and aims to address a number of ambitious 
questions through well-informed point mutations and high resolution cryoEM 
structures. In addition to the isolated enzyme, we also aim to obtain the first 
structures of CuNiR-qNOR protein-protein complexes in catalytic turnover.

We require an experienced PDRA with fluency in several elements of a structural 
biology project including cryoEM data collection and processing, model building 
and structure refinement at high resolutions. Experience with protein 
expression and purification of membrane proteins is desirable. The PDRA will be 
assisted by a full-time research associate/research technician for producing 
wild-type and mutant qNOR membrane bound proteins in sufficient quantities for 
functional and cryoEM studies. The RA would also support in producing CuNIRs 
and its mutants following the established protocols in our laboratories.
You should also be able to work in a team and previous experience of working at 
multiple sites would be an advantage. The PDRA is expected to spend significant 
time (typically one week per month) at Leeds where you would be fully 
integrated into Muench’s group. Excellent verbal and written communication 
skills are essential. The post is available for immediate start for nearly 3 
years.

Please send your CV and cover letter to Professor Samar Hasnain 
(s.s.hasn...@liverpool.ac.uk), Dr Stephen 
Muench (s.p.mue...@leeds.ac.uk) and Dr Svetlana 
Antonyuk (s.anton...@liverpool.ac.uk)



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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Huw Jenkins]

> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) 
> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
>  so strictly it is possible and correct - if experimentally unlikely - to 
> have the situation we are discussing here occur. 

I believe this is only technically possible because the MTZ format does not 
store esds on the unit cell parameters? In the thaumatin example processing the 
dataset here  - https://zenodo.org/records/4916649 - assuming monoclinic 
symmetry results in unit cell:

58.176(2), 150.543(4), 58.2050(18), 90.0, 90.1058(9), 90.0

The situation you describe would result in for example:

58.1087(18), 150.543(4), 58.1087(15), 90.0, 90.(1), 90.0

and the test should really only fail for:

58.1087(18), 58.1087(18), 150.400(5), 90.0, 90.0, 90.0

i.e. where a=b have same value and esd (as they were constrained to be 
identical and esd on beta is 0 as it was constrained to be 90. 



> Telling users to “fiddle the parameters” so that the strict test is satisfied 
> feels like a non-ideal answer: a warning when importing such data could be 
> legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is unusual, 
> I hope you know what you are doing” rather than a flat out error

I think you have misunderstood here. I was suggesting telling users to 
integrate/scale the data without imposing higher symmetry was the correct thing 
to do? I don't see how "fiddling of parameters" is required.  

But I agree i2 should allow an override of this test. 


Huw 


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Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

[Stefano Trapani]

Dear Stuart

Thank you for your reply
Yes, you are right. 
The reports are not displayed for any project (not just the imported ones).
What should I look at to solve the problem ?

Stefano


- Mail original -
> De: "Stuart McNicholas" 
> À: "Stefano Trapani" 
> Cc: CCP4BB@jiscmail.ac.uk
> Envoyé: Vendredi 23 Février 2024 11:08:09
> Objet: Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to 
> another

> Dear Stefano,
>  I wonder if the problem is simply displaying any ccp4i2 reports on
> the new computer, rather than just the imported ones. Have you tried
> creating a completely new project and seeing if anything works in
> that? There are some potential things to think about in the log file.
> 
> Best wishes,
> Stuart
> 
> 
> On Fri, 23 Feb 2024 at 10:00, Stefano Trapani
>  wrote:
>>
>> Hi
>>
>> I am having troubles in transferring my ccp4i2 projects from one computer
>> (MacOS) to another (Linux).
>> First, I export my projects on the first computer by using the "Manage 
>> Projects
>> / Export" tool.
>> Then, I copy the .ccp4_project.zip files to the second computer.
>> Finally, I import the .ccp4_project.zip files on the second computer by using
>> the "Manage Projects / Import" tool (see screenshot 1.png)
>> Import runs OK (see screenshot 2.png), but all job reports seem to disappear
>> (see screenshot 3.png). After a while, the message "ERR_CONNECTION_TIMED_OUT"
>> appears in the report frame (see 3.png).
>>
>> What could be the reason of that ?
>>
>> I am attaching a log file.
>>
>> Best
>>
>> Stefano Trapani
>>
>> Maître de Conférences
>> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
>> -
>> Centre de Biologie Structurale (CBS)
>> 29 rue de Navacelles
>> 34090 MONTPELLIER Cedex, France
>>
>> Tel : +33 (0)4 67 41 77 29
>> Fax : +33 (0)4 67 41 79 13
>> -
>> Université de Montpellier
>> CNRS UMR 5048
>> INSERM UMR 1054
>> -
>>
>> 
>>
>> 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] i2 won't accept 90 degree angles in moniclinic

[Harry Powell]

Hi Graeme (I may well have mentioned this when we shared an office) et al

I’ll add something from my small-molecule crystallography days, when we used 
point detectors - so this would be pre-1996 which was the last time I used one 
of these machines.

I don’t remember which structure it was (feel free to go through the CSD to 
check on my behalf, but many structures were not deposited in those days and 
languish in a PhD thesis!); I had a dataset with three 90º angles, but the 
processing statistics (and overall cell volume) indicated quite plainly that it 
was monoclinic (probably P21). I re-refined the unit cell as if it were 
triclinic and the “best” 90 degree angle with the smallest ESD was the one that 
corresponded to the monoclinic beta; the two 90º angles refined away from their 
true value more.

A result of that experiment was that (since then) I never assumed that the 
values of the angles from the data processing showed unambiguously that I had a 
high symmetry solution. I believe that Pointless arose after a 
hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be faulty 
here).

Best wishes

Harry

> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) 
> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Huw
> 
> (first: thank to Phil for picking this up; it caused much confusion)
> 
> While I get where you are coming from, it is still from a mathematical 
> standpoint correct to consider e.g. a tetragonal crystal as monoclinic - P21 
> is a subgroup of P43212 (say) so strictly it is possible and correct - if 
> experimentally unlikely - to have the situation we are discussing here occur. 
> 
> Also, under merging data to investigate twinning is a current bb topic.
> 
> Telling users to “fiddle the parameters” so that the strict test is satisfied 
> feels like a non-ideal answer: a warning when importing such data could be 
> legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is unusual, 
> I hope you know what you are doing” rather than a flat out error.
> 
> Literally I got involved as I had a dials user ask me how to do this 
> parameter fiddling in a more niche case and I thought that was a suboptimal 
> solution to an artificial problem :-) 
> 
> On a personal note, I think it is important that the tools we develop still 
> allow people to explore problems rather than railroading them down one true 
> route which is the only allowed way to look at a problem: we learn a lot by 
> exploring odd corners as here. 
> 
> Best wishes Graeme
> 
>> On 23 Feb 2024, at 09:49, Huw Jenkins  wrote:
>> 
>> [You don't often get email from h.t.jenk...@me.com. Learn why this is 
>> important at https://aka.ms/LearnAboutSenderIdentification ]
>> 
>> Hi Graeme,
>> 
>>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) 
>>> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Processing a data set in lower than necessary symmetry e.g. tetragonal as 
>>> monoclinic you _cannot_ import the merged MTZ file into i2 because it is 
>>> impossible to have 90 degree angles for P21
>> 
>> I had a look at the code in CCP4i2 that generates the errors in the 
>> screenshots you posted. The first one is only generated if two cell 
>> parameters are *exactly* equal and the second is generated when beta is 
>> between 89. and 90.0001 degrees.
>> 
>> I think these tests should only fail if the data were processed assuming 
>> higher symmetry so that unit cell parameters were restrained and then the 
>> space group changed to a lower symmetry one. Isn't the correct approach when 
>> the true symmetry is lower than originally assumed to repeat the data 
>> processing without applying constraints imposed by the higher symmetry - 
>> because, for example, cell parameters refined assuming cell length/angle 
>> constraints may not predict the reflection positions as well as if these 
>> restraints were not applied, reflections assumed to be symmetry equivalent 
>> when they weren't may lead to suboptimal scaling etc etc?
>> 
>> 
>> Huw
> 
> 
> -- 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> 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 the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and 
> Wales with its registered office at Diamond House, Harwell 

Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

[Stuart McNicholas]

Dear Stefano,
  I wonder if the problem is simply displaying any ccp4i2 reports on
the new computer, rather than just the imported ones. Have you tried
creating a completely new project and seeing if anything works in
that? There are some potential things to think about in the log file.

Best wishes,
Stuart


On Fri, 23 Feb 2024 at 10:00, Stefano Trapani
 wrote:
>
> Hi
>
> I am having troubles in transferring my ccp4i2 projects from one computer 
> (MacOS) to another (Linux).
> First, I export my projects on the first computer by using the "Manage 
> Projects / Export" tool.
> Then, I copy the .ccp4_project.zip files to the second computer.
> Finally, I import the .ccp4_project.zip files on the second computer by using 
> the "Manage Projects / Import" tool (see screenshot 1.png)
> Import runs OK (see screenshot 2.png), but all job reports seem to disappear 
> (see screenshot 3.png). After a while, the message "ERR_CONNECTION_TIMED_OUT" 
> appears in the report frame (see 3.png).
>
> What could be the reason of that ?
>
> I am attaching a log file.
>
> Best
>
> Stefano Trapani
>
> Maître de Conférences
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
> -
> Centre de Biologie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
>
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
>
> 
>
> 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] i2 won't accept 90 degree angles in moniclinic

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Huw

(first: thank to Phil for picking this up; it caused much confusion)

While I get where you are coming from, it is still from a mathematical 
standpoint correct to consider e.g. a tetragonal crystal as monoclinic - P21 is 
a subgroup of P43212 (say) so strictly it is possible and correct - if 
experimentally unlikely - to have the situation we are discussing here occur. 

Also, under merging data to investigate twinning is a current bb topic.

Telling users to “fiddle the parameters” so that the strict test is satisfied 
feels like a non-ideal answer: a warning when importing such data could be 
legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is unusual, I 
hope you know what you are doing” rather than a flat out error.

Literally I got involved as I had a dials user ask me how to do this parameter 
fiddling in a more niche case and I thought that was a suboptimal solution to 
an artificial problem :-) 

On a personal note, I think it is important that the tools we develop still 
allow people to explore problems rather than railroading them down one true 
route which is the only allowed way to look at a problem: we learn a lot by 
exploring odd corners as here. 

Best wishes Graeme

> On 23 Feb 2024, at 09:49, Huw Jenkins  wrote:
> 
> [You don't often get email from h.t.jenk...@me.com. Learn why this is 
> important at https://aka.ms/LearnAboutSenderIdentification ]
> 
> Hi Graeme,
> 
>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) 
>> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Processing a data set in lower than necessary symmetry e.g. tetragonal as 
>> monoclinic you _cannot_ import the merged MTZ file into i2 because it is 
>> impossible to have 90 degree angles for P21
> 
> I had a look at the code in CCP4i2 that generates the errors in the 
> screenshots you posted. The first one is only generated if two cell 
> parameters are *exactly* equal and the second is generated when beta is 
> between 89. and 90.0001 degrees.
> 
> I think these tests should only fail if the data were processed assuming 
> higher symmetry so that unit cell parameters were restrained and then the 
> space group changed to a lower symmetry one. Isn't the correct approach when 
> the true symmetry is lower than originally assumed to repeat the data 
> processing without applying constraints imposed by the higher symmetry - 
> because, for example, cell parameters refined assuming cell length/angle 
> constraints may not predict the reflection positions as well as if these 
> restraints were not applied, reflections assumed to be symmetry equivalent 
> when they weren't may lead to suboptimal scaling etc etc?
> 
> 
> Huw


-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the 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 the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
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Wales with its registered office at Diamond House, Harwell Science and 
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Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

[Huw Jenkins]

Hi Graeme,

> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) 
> <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Processing a data set in lower than necessary symmetry e.g. tetragonal as 
> monoclinic you _cannot_ import the merged MTZ file into i2 because it is 
> impossible to have 90 degree angles for P21

I had a look at the code in CCP4i2 that generates the errors in the screenshots 
you posted. The first one is only generated if two cell parameters are 
*exactly* equal and the second is generated when beta is between 89. and 
90.0001 degrees.

I think these tests should only fail if the data were processed assuming higher 
symmetry so that unit cell parameters were restrained and then the space group 
changed to a lower symmetry one. Isn't the correct approach when the true 
symmetry is lower than originally assumed to repeat the data processing without 
applying constraints imposed by the higher symmetry - because, for example, 
cell parameters refined assuming cell length/angle constraints may not predict 
the reflection positions as well as if these restraints were not applied, 
reflections assumed to be symmetry equivalent when they weren't may lead to 
suboptimal scaling etc etc?


Huw  


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