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

[Tom Goddard]

I second Oliver's second recommendation, low pass filter the map to 10-15 A, fit into that, it often converges nicely in one try with no fiddling since the radius of convergence is high -- you could start 10 Angstoms off and 45 degrees rotated.  Then start at that position and fit into the full resolution map.  I've used this recipe so many times I often thought I should build it in as an option to fitmap where it automatically makes the low res map.

	Tom


> On Apr 22, 2020, at 10:18 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> 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
>> 
>> 
> 
> 
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