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

[Tom Goddard]

Ok, I made a ChimeraX feature request for a fitmap option to do the low pass filtering for you.

	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3098

  Tom



> On Apr 22, 2020, at 10:27 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> 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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>>> 
>> 
> 
>