Re: [Chimera-users] Chimera-users Digest, Vol 204, Issue 20
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@meduniwien.ac.at> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Fitting model into map Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00@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@meduniwien.ac.at ------------------------------------------------------------------------
------------------------------
Message: 3 Date: Wed, 22 Apr 2020 09:31:29 -0400 From: Greg Pintilie <gregdp@gmail.com> To: Dieter Blaas <dieter.blaas@meduniwien.ac.at> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Fitting model into map Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047@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
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@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@meduniwien.ac.at> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Fitting model into map Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00@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@meduniwien.ac.at ------------------------------------------------------------------------
------------------------------
Message: 3 Date: Wed, 22 Apr 2020 09:31:29 -0400 From: Greg Pintilie <gregdp@gmail.com> To: Dieter Blaas <dieter.blaas@meduniwien.ac.at> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Fitting model into map Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@meduniwien.ac.at> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Fitting model into map Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00@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@meduniwien.ac.at ------------------------------------------------------------------------
------------------------------
Message: 3 Date: Wed, 22 Apr 2020 09:31:29 -0400 From: Greg Pintilie <gregdp@gmail.com> To: Dieter Blaas <dieter.blaas@meduniwien.ac.at> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Fitting model into map Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@meduniwien.ac.at> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Fitting model into map Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00@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@meduniwien.ac.at ------------------------------------------------------------------------
------------------------------
Message: 3 Date: Wed, 22 Apr 2020 09:31:29 -0400 From: Greg Pintilie <gregdp@gmail.com> To: Dieter Blaas <dieter.blaas@meduniwien.ac.at> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Fitting model into map Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@meduniwien.ac.at> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Fitting model into map Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00@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@meduniwien.ac.at ------------------------------------------------------------------------
------------------------------
Message: 3 Date: Wed, 22 Apr 2020 09:31:29 -0400 From: Greg Pintilie <gregdp@gmail.com> To: Dieter Blaas <dieter.blaas@meduniwien.ac.at> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Fitting model into map Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Dieter Blaas -
Oliver Clarke -
Tom Goddard