Hi, I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint? Thanks a lot, 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 ------------------------------------------------------------------------
Hi Dieter, The global option is in the "fitmap" command only (not the dialog). See "fitmap" with global search options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global> There is also a video tutorial linked to that section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. ChimeraX has the same fitting as Chimera, if you ever want to switch. The command syntax is (slightly) different but methodology the same: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
On Oct 11, 2022, at 1:55 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint?
Thanks a lot, Dieter
Hi Elaine, thank you! Can you please give me an example for the command. To simulate a map from the pdb model at 10 A I tried "fitmap #1 #0 r 10" or "fitmap r 10 #1 #0" or "fitmap r=10 #0 #1" and many other combinations but I always get an error message! How are the parameters to be set? Thanks again, best 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 11.10.2022 18:23, Elaine Meng wrote:
Hi Dieter, The global option is in the "fitmap" command only (not the dialog). See "fitmap" with global search options:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
There is also a video tutorial linked to that section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. ChimeraX has the same fitting as Chimera, if you ever want to switch. The command syntax is (slightly) different but methodology the same: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
On Oct 11, 2022, at 1:55 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint?
Thanks a lot, Dieter
sorry for the previous truncated message: I simply could not find out how to specify the parameters like r or N. How would a command line look like to simulate a map e.g. at 10 A and run 2000 trials? ------------------------------------------------------------------------ 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 11.10.2022 18:23, Elaine Meng wrote:
Hi Dieter, The global option is in the "fitmap" command only (not the dialog). See "fitmap" with global search options:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
There is also a video tutorial linked to that section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. ChimeraX has the same fitting as Chimera, if you ever want to switch. The command syntax is (slightly) different but methodology the same: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
On Oct 11, 2022, at 1:55 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint?
Thanks a lot, Dieter
Hi Dieter, The option is "resolution r" where the keyword is "resolution" and the italicized "r" is the value. You have to give the keyword, or else there is no way for the program to know what the value is for: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#options> Example: fitmap #1 #0 resolution 10 ...if #1 is your atomic structure and #0 is your map. Also as mentioned in the documentation, if you want to do a global search you have to use the "search" keyword option with value "N" being the number of placements: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global> Example: fitmap #1 #0 resolution 10 search 2000 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2022, at 8:44 PM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
sorry for the previous truncated message: I simply could not find out how to specify the parameters like r or N. How would a command line look like to simulate a map e.g. at 10 A and run 2000 trials?
------------------------------------------------------------------------ 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 11.10.2022 18:23, Elaine Meng wrote:
Hi Dieter, The global option is in the "fitmap" command only (not the dialog). See "fitmap" with global search options:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
There is also a video tutorial linked to that section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. ChimeraX has the same fitting as Chimera, if you ever want to switch. The command syntax is (slightly) different but methodology the same: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
On Oct 11, 2022, at 1:55 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint?
Thanks a lot, Dieter
Hi Elaine, definitely that helps a lot :-). I find that examples are much more instructive than descriptions.... many thanks, best, 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 12.10.2022 17:31, Elaine Meng wrote:
Hi Dieter, The option is "resolution r" where the keyword is "resolution" and the italicized "r" is the value. You have to give the keyword, or else there is no way for the program to know what the value is for: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#options>
Example: fitmap #1 #0 resolution 10
...if #1 is your atomic structure and #0 is your map.
Also as mentioned in the documentation, if you want to do a global search you have to use the "search" keyword option with value "N" being the number of placements: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
Example: fitmap #1 #0 resolution 10 search 2000
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2022, at 8:44 PM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
sorry for the previous truncated message: I simply could not find out how to specify the parameters like r or N. How would a command line look like to simulate a map e.g. at 10 A and run 2000 trials?
------------------------------------------------------------------------ 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 11.10.2022 18:23, Elaine Meng wrote:
Hi Dieter, The global option is in the "fitmap" command only (not the dialog). See "fitmap" with global search options:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
There is also a video tutorial linked to that section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. ChimeraX has the same fitting as Chimera, if you ever want to switch. The command syntax is (slightly) different but methodology the same: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
On Oct 11, 2022, at 1:55 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint?
Thanks a lot, Dieter
participants (2)
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Dieter Blaas -
Elaine Meng