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

[Dieter Blaas]

Thanks to all for the great suggestions! Saves me a lot of time....

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
------------------------------------------------------------------------

On 22.04.2020 19:34, Tom Goddard wrote:
> 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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>>>>
>>
>
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