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

#AHMED TOFAYEL# TOFAYEL001 at e.ntu.edu.sg
Sat Apr 29 04:40:13 PDT 2017

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,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Saturday, April 29, 2017 5:59:22 AM
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):

There is also a “localFSC” plugin to Chimera that you could get separately, see:
… 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.
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170429/caa908a0/attachment.html>

More information about the Chimera-users mailing list