Re: [phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Pavel, this is an interesting concept. It seems related to the SQUEEZE command in platon - even the name appears to suggest a relationship. I did not understand the maths entirely: Are they similar concept, or do I misinterprete? Best, Tim On Wednesday, April 20, 2016 07:28:16 AM Pavel Afonine wrote:

Hello,

it's good to know it was useful for you, thanks for feedback! I afraid it's too new so that we don't have a publication to cite yet. We are working on a manuscript but it may take a little while before it appears somewhere. For now I guess you can use this link (unless Dorothee has a better idea)

http://www.phenix-online.org/presentations/phenix_polder.pdf

and use official Phenix citation:

Acta Cryst. D66, 213-221 (2010).

That's all we have at the moment anyway.

All the best, Pavel

On 4/20/16 04:18, Lund Bjarte Aarmo wrote:

...

DearDorothee and phenixbb,

I found this software very useful for protein-fragment complexes with weak electron density. I was wondering how the software should be cited?

Kind regards,

Bjarte Aarmo Lund

PhD candidate

UiT – The arctic university of Norway

*From:*[email protected] [mailto:[email protected]] *On Behalf Of *Dorothee Liebschner *Sent:* 22. mars 2016 21:46 *To:* PHENIX user mailing list *Subject:* [phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent

Dear phenix users,

Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix.

Usage:

phenix.polder model.pdb data.mtz selection='chain A and resseq 123’

Phenix.polder calculates omit maps for atom selections by preventing the bulk solvent mask to flood into the atom selection area and its vicinity. The tool can be useful in cases where the density of the selected atoms is weak and possibly obscured by bulk solvent.

Polder produces less biased maps compared to procedures where the atom selection occupancy is set to zero, and the atoms are included in the solvent mask calculation (in that case, the resulting difference density can have similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent and therefore prevents misinterpreting bulk solvent density as omit density.

If you want to know more about how the tool is working and to see some examples, have a look at the presentation file: https://www.phenix-online.org/presentations/phenix_polder.pdf.

The documentation page can be found here:

www.phenix-online.org/version_docs/dev-2356/reference/polder.html

Best wishes,

Dorothee

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

- -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFXF9NpUxlJ7aRr7hoRApIFAKCZ6gKgFMeeU4DSZfr5i/5Z3inC/ACeOmIh sjQCpCYG2CkH/N/RoIfhApQ= =t+dS -----END PGP SIGNATURE-----