[Chimera-users] calculate FSC curve between experimental cryo EM map and model

[#AHMED TOFAYEL#]

Hi Elaine,


Thanks for your reply. Yes, I have ardently gone through http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012366.html  but ended up being confused as it seems no conclusion had been reached there, or I failed altogether to get the take home message from the discussion.


Also, the "LocalFSC" thingy is not what I am looking for...


But nevermind, lets wait for our "map expert" to be back in action and meanwhile I am waiting for others to bring in some appropriate answers.


Thanks a lot for taking time.


Best regards,

Tofayel




________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Saturday, April 29, 2017 5:59:22 AM
To: #AHMED TOFAYEL#
Cc: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] calculate FSC curve between experimental cryo EM map and model

Dear Tofayel,
Our map expert is away this week and next week.  All I can suggest is to take a look at this previous post (which you may have seen already):
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012366.html>

There is also a “localFSC” plugin to Chimera that you could get separately, see:
<http://www.rbvi.ucsf.edu/chimera/plugins/plugins.html>
… however, I don’t know if it is relevant to your question.

Sorry I couldn’t provide a more confident answer,  Maybe other EM folks on this list will have some thoughts.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 28, 2017, at 6:09 AM, #AHMED TOFAYEL# <TOFAYEL001 at e.ntu.edu.sg> wrote:
>
> Dear all,
> If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so?
>
> I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve.
>
> I am not sure if I am on the right track. My pixel size is 1.28.
> Best regards,
> Tofayel

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