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

[Oliver Clarke]

That would be a great option to have Tom for sure, I would use it a lot!

Oli

> On Apr 22, 2020, at 1:25 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> 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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>