Dear Almudena,
You can actually pass on both the phases and the poly-Ala trace from
SHELXE to BUCCANEER followed by REFMAC. The new CCP4 pipelines CCP4i2
and CCP4 Online do this (this is after all the CCP4bb!). The R-factors
from REFMAC will then give a good indication as to whether the structure
is solved.
If the resolution of your native data is good enough (better than about
2.5A) the CC against the native data that SHELXE outputs each
autotracing cycle will give you a rather reliable indication as to
whether the structure is solved. A value greater than 25% indicates that
the structure is 'solved'. This criterion has been very thoroughly
tested by AMPLE (in the current CCP4) and ARCIMBOLDO (included in the
next version of CCP4). See the papers about these programs.
Best wishes, George
On 30.07.2015 11:31, Almudena Ponce Salvatierra wrote:
> Dear all,
>
> I would like to ask your opinion on something (I was actually not
> expecting to work...but it did!!).
>
> I am now solving a protein of 135 kDa. I did SIRAS within SHELX and
> the poly ala trace I discarded, but I kept the density modified map.
>
> I gave the map and the sequence to buccaneer and it gave back 1532
> residues built in 133 fragments. This looked more like a spaghetti
> dish (excuse me, I'm used not NA rather than proteins), with lots of
> small fragments... but I wanted to give it a try and gave it to Phaser
> for molecular replacement (here is where I was having the most
> doubts). I gave it along with a native data set collected at 2.9
> Angstroms and phaser gives a TFZ score of 90.6 plus an LLG of
> 4512.88. So, it looks like it is a correct solution!!
>
> Now the question is, this is mostly a poly-ala thing, with lots of
> fragments... can I think that actually this is a solution? I want to,
> actually, I mean, at the end these short pieces are oriented respect
> to each other in a specific manner, even if they're not connected, and
> phaser could place it. But now my question is, how or from where do I
> start to make it continuous? Or to complete the structure...
>
> Any comments on this are more than welcome!!
>
> Best wishes,
>
> Almu
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
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