When fitting a pdb to a map, go to options > use map simulated from atoms.
It will create a simulated map at the desired resolution and use it for the fitting.
Then we follow the same protocol as you do.
Best,
Amedee
> On Jan 26, 2016, at 2:59 PM, Sjors Scheres <[log in to unmask]> wrote:
>
> Hi Amedee,
> Definitely worth a try. How does one do it there? And have you ever
> compared FSC_model-vs-map of pdb-derived maps made in Chimera with another
> method?
> Thanks,
> Sjors
>
>> Dear Sjors,
>>
>> Since you fit the result in Chimera, why don’t you directly simulate the
>> map in chimera?
>> Any issues doing that, since it is quite straightforward?
>>
>> Best,
>>
>> Amedee
>>
>>
>>> On Jan 26, 2016, at 2:22 PM, Sjors Scheres <[log in to unmask]>
>>> wrote:
>>>
>>> Dear Pierre-Damien,
>>>
>>> We usually use EMAN2 (e2pdb2mrc.py) to make mrc files from PDBs. But as
>>> far as I understand it (Steve may hopefully point out that I'm wrong!)
>>> the
>>> origin gets displaced with the generated mrc maps. We then usually use a
>>> quick fit-in-map from UCSF Chimera (and then 'vop resample onGrid) to
>>> replace the pdb-derived on top of the original reconstruction. Then, you
>>> should indeed expand this mask and put a soft edge on it (we use
>>> relion_mask_create for that). Finally, just run the postprocessing step
>>> from the GUI with the mask to get a resolution-estimate for that
>>> region-only. You can do all these steps for all different proteins in
>>> your
>>> complex. Actually, it is often very useful to have differently-filtered
>>> maps when you're building and refining the atomic models anyway.
>>>
>>> I think ResMap is a sound alternative to the local-resolution estimation
>>> problem. Note you can conveniently run it from the GUI using the same
>>> half-maps you would use for the postprocessing. It usually doesn't take
>>> very long to run and you don't need a cluster for it. In this case,
>>> always
>>> provide a mask around the entire complex (as for example obtained in the
>>> postprocessing step).
>>>
>>> As a reviewer casted doubts on the actual resolution numbers generated
>>> by
>>> Resmap, we compared both approaches last year for different regions of
>>> the
>>> tri-snRNP spliceosomal complex, see the supplementary material of Nguyen
>>> et al, Nature 2015. You'll see that the results are fairly consistent,
>>> so
>>> either approach would be OK.
>>>
>>> HTH,
>>> Sjors
>>>
>>>
>>>> Hello everyone,
>>>> I would like to know what is the procedure to compute the resolution
>>>> (from the fsc curve) for each factor within a complex.
>>>>
>>>> If I understood correctly, I made a plan but I have some unanswered
>>>> questions :
>>>> -you generate a mask from your pdb protein model (cp from pdb in spider
>>>> or fit in map using chimera with the generation of a map filtered to X
>>>> resolution)
>>>> -you will have to pad your mask, expand it, threshold it and align it
>>>> with your initial volume
>>>> -multiply your mask to your two "half" maps (generated by relion refine
>>>> command)
>>>> -compute the fsc curve with the masked "half" maps
>>>>
>>>> Is there an easy way to do all this without using several programs ?
>>>> What is the exact command in relion to compute only the fsc without
>>>> running a refinement ?
>>>>
>>>> Another alternative would be to use resmap. But how do you EASILY
>>>> generate a map from the pdb model which can have the same dimensions as
>>>> your EM map ? And it seems to me that resmap is much more time
>>>> consuming
>>>> than the first solution...
>>>>
>>>> Thank you in advance for your help
>>>>
>>>> Pierre-Damien
>>>>
>>>
>>>
>>> --
>>> 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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