Hi Mike,
We used them for all our ribosome structures (Amunts et al Science, Brown
et al Science, Fernandez et al Cell, Wong et al eLife). We've recently
also used it for gamma-secretase, but that hasn't been published yet.
HTH,
S
> Hi Sjors,
>
> can you point to some publications that used these scripts? I’d like to
> look at their results.
>
> Regards,
>
> mike
>
>> On May 20, 2015, at 4:49 AM, Sjors Scheres <[log in to unmask]>
>> wrote:
>>
>> Dear all,
>> Perhaps this is a good moment to highlight the link sent by Alan Brown
>> below. It encompasses almost 2 years of experience in building and
>> refining atomic models in high-resolution EM maps using COOT and REFMAC.
>> At LMB, these scripts and instructions have become an important part of
>> our structure determination pipeline. It may also be useful in your
>> work.
>> Best,
>> Sjors
>>
>>
>> On 05/20/2015 09:30 AM, Alan Brown wrote:
>>> Hi Chris,
>>>
>>> We have a script (locres.csh), available from
>>> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/em_fitting/em_fitting.html
>>> that will calculate the local FSC for each chain in a folder of PDBs
>>> using Relion for both the mask creation and the post-processing.
>>>
>>> Best wishes,
>>>
>>> Alan
>>>
>>>
>>>
>>> On 20 May 2015, at 08:36, Sjors Scheres <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> a. this is true: the 2 unfil.mrc will NOT be masked
>>>> b. you'll calculate a final FSC in the postprocessing program. You can
>>>> give any mask you like, and the randomized phase approach (see Chen et
>>>> al
>>>> Ultramicroscopy 2013) will correct for its effects on the FSC curve.
>>>> If
>>>> you let the mask cover only the best ordered bit of the map, it will
>>>> be
>>>> higher than when you include the more floppy bits. This gives an
>>>> indication of local resolution, much like ResMap would. In a recenty
>>>> accepted paper on the spliceosome tri-snRNP we did this for many small
>>>> regions, and got very similar results as resmap.
>>>> Make sure your masks are always with a soft-edge, so their effects on
>>>> the
>>>> FSC are not very large. It doesn't matter which program you use to
>>>> make
>>>> the masks.
>>>> HTH,
>>>> Sjors
>>>>
>>>>
>>>>> Sjors and users-
>>>>>
>>>>> I am using a mask during refinements in Relion, which eliminates the
>>>>> small
>>>>> ribosomal subunit, thus, keeping its multiple conformations from
>>>>> affecting
>>>>> alignments driven by the lsu.
>>>>> I created this mask from a volume "made" in Chimera and then used
>>>>> relion_mask_create.
>>>>>
>>>>> My question is two-fold:
>>>>>
>>>>> a. The 3d half volumes made at each itr are masked by this volume,
>>>>> but I
>>>>> presume that the final 3d volume
>>>>> that is made when Relion converges will not be masked by this volume,
>>>>> is
>>>>> this correct?
>>>>>
>>>>> b. Given that part a above is true, then I presume that the final fsc
>>>>> calculated automatically in Relion will reflect the
>>>>> properties of the entire 3D volume, including the region that had
>>>>> been
>>>>> masked out during
>>>>> refinement, which may lower the overall resolution.
>>>>>
>>>>> While I can think of a number of ways to make a mask, what is the
>>>>> appropriate or best way to make
>>>>> a mask and the use Relion to calculate an fsc for the good region of
>>>>> the
>>>>> map.
>>>>>
>>>>> Of course ResMap can be used as a guide, but getting an fsc for the
>>>>> good
>>>>> region would be useful and
>>>>> in my reading its not clear how this is done.
>>>>>
>>>>> cheers,
>>>>>
>>>>> C Akey
>>>>>
>>>>
>>>> --
>>>> Sjors Scheres
>>>> MRC Laboratory of Molecular Biology
>>>> Francis Crick Avenue, Cambridge Biomedical Campus
>>>> Cambridge CB2 0QH, U.K.
>>>> tel: +44 (0)1223 267061
>>>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>>
>>
>> --
>> Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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