All of the suggestions of principal axes or PDB searches are very good If you would like to have something a little more “random” for whatever purpose you have, you could:
- decide on the symmetry you would like (e.g. P212121)
- compute an ASU volume knowing the Matthews coefficient (or selecting a valid
value, discussed earlier) and the molecular mass of your protein
- work out a total volume by multiplying the ASU volume by the number of
symmetry operations
- use CCTBX to give you a compatible unit cell
As follows
from cctbx import sgtbx
sg_p212121 = sgtbx.space_group_info("P212121”)
volume = 250_000 * len(list(sg_p212121.group().smx()))
cs = sg_p212121.any_compatible_crystal_symmetry(volume=volume)
print(cs.unit_cell())
uctbx.unit_cell((76.77195064595125, 99.80353583973663, 130.5123160981171, 90.0,
90.0, 90.0))
This I appreciate is “more work” but would meet the requirements you specified
Have fun & best wishes Graeme
> On 10 Nov 2025, at 16:06, Nichols, Charlie
> <[email protected]> wrote:
>
> Thinking outside the box (groan),
>
> You could also use the PDB advanced search function and search by molecular
> weight using a range around the calculated mass with spacegroup either fixed
> as P1 or unfixed.
>
> That will give you a list of similarly sized proteins with real packing
> environments and unit cells..
>
> Cheers, Charlie.
>
> From: CCP4 bulletin board <[email protected]
> <mailto:[email protected]>> On Behalf Of Oganesyan, Vaheh
> Sent: 10 November 2025 13:49
> To: [email protected] <mailto:[email protected]>
> Subject: Re: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model
>
> WARNING: This message was sent by an external party. Report suspicious
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>
> Hi,
>
> I’m not sure why would you want to know that or how useful that information
> may be, but you can enter the AF model to DALI server and see if you get a
> set of scores that are considerably higher than others.
>
> Vaheh
>
> Get Outlook for iOS
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> From: CCP4 bulletin board <[email protected]
> <mailto:[email protected]>> on behalf of Joseph Cockburn
> <[email protected]
> <mailto:[email protected]>>
> Sent: Monday, November 10, 2025 7:19:32 AM
> To: [email protected] <mailto:[email protected]>
> <[email protected] <mailto:[email protected]>>
> Subject: Re: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model
>
> Dear Xin,
> I don’t know of a dedicated tool that will do this for you. However, protein
> crystals have a well characterised range of density values, described by the
> Matthew’s coefficient (Vm). Vm values typically range from 1.6 to 3.5 Å3 of
> crystal volume per Da of protein. So given the molecular weight of your
> protein in Da, you can estimate the volume of crystal that each copy of the
> protein molecule will occupy. The crudest estimate of the unit cell
> parameters would be to take the cube root of that volume. A more
> sophisticated way of doing this would be to calculate the principal
> components of the radius of gyration tensor to give you a box around the
> molecule (as the previous poster suggested), then scale this volume up or
> down to give you a realistic Matthew’s coefficient.
> Kind regards,
> Joe
>
>
> ------------------------------------------------------
> Dr Joseph J B Cockburn
> Group Leader and Lecturer in X-ray Crystallography
> The Astbury Centre for Structural Molecular Biology
> Faculty of Biological Sciences
> University of Leeds
> Leeds LS2 9JT
> UK
> +44 (0)113 3430758 <tel:+441133430758>
>
> From: CCP4 bulletin board <[email protected]
> <mailto:[email protected]>> on behalf of Zhang Xin
> <[email protected]
> <mailto:[email protected]>>
> Date: Monday, 10 November 2025 at 06:29
> To: [email protected] <mailto:[email protected]>
> <[email protected] <mailto:[email protected]>>
> Subject: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model
>
> CAUTION: External Message. Use caution opening links and attachments.
> Dear all,
>
> I would like to ask a brief question.
> When only an AlphaFold-predicted PDB model is available and no diffraction
> data yet, is there any existing tool to estimate a reasonable unit cell
> (assuming space group P1)?
>
> If there are recommended tools or common practices for this, I would
> appreciate any suggestions.
>
> Best regards,
> Xin
>
>
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