[Chimera-users] Chimera-users Digest, Vol 204, Issue 20

[Oliver Clarke]

Hi Dieter,

Two things to try (alone or together):

1. Do a global search - first position your model in approximately the expected location, but without regard to orientation, and them something like:

fitmap #1 #2 search 100 radius 5

(assuming #1 and #2 are model and map respectively).

You should get a interactive table with candidate orientations, where hopefully there will be a clear separation between correct and incorrect solutions.

Second - low pass filter the map. Fitmap will have a higher radius of convergence and be less prone to getting bogged down in local minima if you lowpass filter the map aggressively (10-15 Å is often a good place to start).

Good luck!

Cheers
Oli

> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 22 Apr 2020 14:24:16 +0200
> From: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Fitting model into map
> Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00 at meduniwien.ac.at>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> Hi,
> 
> ??? I always spend many hours placing a pdb model into a density map of 
> a virus with Tools > Volume Data > Fit in Map. Usually I have to move 
> the model around to find a more or less good fit manually, otherwise 
> Chimera does not find anything. I also tried by first making a molmap 
> followed by something like 'fitmap #0 #1 resolution 4'. I am convinced 
> that there is a better way of doing this but so far I was unable to find 
> it. Can anybody please give me a quick hint!
> 
> Thanks, Dieter
> 
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: dieter.blaas at meduniwien.ac.at
> ------------------------------------------------------------------------
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 22 Apr 2020 09:31:29 -0400
> From: Greg Pintilie <gregdp at gmail.com>
> To: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> Cc: chimera-users <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Fitting model into map
> Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> You could try Segment Map followed by Fit to Segments (both in the Tools -> Volume Data menu). More details and a tutorial here if needed:
> https://cryoem.slac.stanford.edu/ncmi/resources/software/segger <https://cryoem.slac.stanford.edu/ncmi/resources/software/segger>
> 
> Greg
> 
>