Arcimboldo Lite

ARCIMBOLDO_LITE runs in two macrocycles. In the first macrocycle, all copies of the search fragments are placed with Phaser and optimized with SHELXE. Similar solutions are clustered. A number of substructure solutions equal to the number of physical cores minus one is subject to density modification and autotracing with SHELXE, prioritizing according to top LLG and CC. Arcimboldo Lite runs on all cores of a single machine, without requiring a grid, supercomputer or database.

Input

  • The default value of the rmsd for model helices is 0.2 Å (this value can be increased).

  • It is mandatory to define the number of helices to search and their length (length needs to be specified according to secondary-structure prediction or previous knowledge about the target structure).

  • The molecular weight, number of components and estimated rmsd should be defined for the PHASER search.

Coil coiled mode

represent a search algorithm to probe and verify alternative helix directions

Coil coiled mode entails:

  • VRMS calculation in the refinement step to optimize the RMSD parameter in order to maximize the LLG.

  • Activation of PHASER’s packing filter at translation, so at least one translated solution will pass the packing check.

  • Generate and probe reverse helices. At resolution below 2 Å it was frequently observed that placement of the first helices occasionally took place in the correct position but in reversed direction and at low resolution are not distinguishable from the PHASER figures of merit.

  • Final verification step, an additional step that generates perturbations of the substructure leading to the best solution and compares their scores before and after extension. As the reverse helices this will be only activated at a resolution worse than 2 Å.

  • SHELXE with helical sliding, which improves the autotracing of the coiled-coil structures.

Output

Arcimboldo report window summarizes your job results. Search and expansion tables are updated in real-time and can help to judge parameterization.

A search and expansion tables show:

LLG (Log-likelihood-gain)

displays how well the given model explains data in comparison with random atoms. The LLG has to be positive (as high as possible), and it should increase as the solution progresses.

Note

The LLG allows to compare of different models against the same data set, but the LLG values for different data sets should not be compared with each other.

Guide to expected LLG values

Top solution correct?

<25 -no

25-36 -unlikely

36-49 -possibly

49-64 -probably

>64 -definitely

Zscore

The signal of placement is indicated by its translation-function Z-score (TFZ). It is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. signal-to-noise is judged

Guide to expected translation-function Z-score (TFZ-score)

TFZ-score

less than 5 not a solution

5 - 6 unlikely a solution

6 - 7 possibly a solution

7 - 8 probably a solution

more than 8* definitely a solution

  • 6 for 1st model in monoclinic space groups

CC correlation coefficient

CC more than 25% indicates the solution is found

CC calculated on all data is reliable when atomic resolution data are available but at a lower resolution, all random collections of a large enough number of unconstrained atoms show equally high CC values.

For online documentation and tutorials visit www.chango.ibmb.csic.es

ARCIMBOLDO_LITE tutorials can be found here

References

McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., Read R.J. (2007) Phaser Crystallographic Software. J. Appl. Cryst. 40: 658-674

Rodríguez DD, Grosse C, Himmel S, González C, Martínez de Ilarduya I, Becker S, Sheldrick GM & Usón I (2009) Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods 6, 651– 653.

Sammito, M., Millan, C.,Frieske, D., Rodriguez-Freire, E., Borges, R. J., & Uson, I.(2015) ARCIMBOLDO-LITE: single-workstation implementation and use Acta Cryst. D71, 1921-1939.

Millán C, Sammito M, Usón I (2015) Macromolecular ab initio phasing enforcing secondary and tertiary structure. IUCrJ 2, 95-105.

Millán C, Sammito M. D, McCoy A. J, Nascimento A. F. Z, Petrillo G, Oeffner R. D, Domínguez-Gil T, Hermoso J. A, Read R. J, Usón I (2018) Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination. Acta Cryst. D74: 290-304

Caballero I, Sammito M, Millán C, Lebedev A, Soler N, Usón I (2018) ARCIMBOLDO on coiled coils. Acta Cryst D74, 194-204,

Uson, I., Sheldrick, G.M. (2018) An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features. Acta Cryst. D74: 106-116