When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo
Hi Arthur, The main PDB fetch is the contents of the crystallographic asymmetric unit, whereas the biological unit is the known or guessed biologically relevant assembly based on that structure. Sometimes they are the same, but often they’re not… this page at the RCSB PDB has a good explanation: <https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-ass...> I see that the link I had in the Chimera manual to explain “biounit” no longer works, so I’ll update it to use the link above instead. The current terminology is “biological assembly,” which makes more sense. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 14, 2017, at 12:52 PM, Arthur Szabo <agszabo@outlook.com> wrote:
When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo
Elaine Thank you A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb. Can this be handled, or is the size to large to download. I tried to fetch it by PDB index, but it just seemed to stall or was way too large. Regards arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, August 14, 2017 4:42 PM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] biounit Hi Arthur, The main PDB fetch is the contents of the crystallographic asymmetric unit, whereas the biological unit is the known or guessed biologically relevant assembly based on that structure. Sometimes they are the same, but often they’re not… this page at the RCSB PDB has a good explanation: <https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-ass...> I see that the link I had in the Chimera manual to explain “biounit” no longer works, so I’ll update it to use the link above instead. The current terminology is “biological assembly,” which makes more sense. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 14, 2017, at 12:52 PM, Arthur Szabo <agszabo@outlook.com> wrote:
When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo
Hi Arthur, It’s probably too big for your computer and/or for reasonable speed of interaction in Chimera (display changes, rotation etc.). The structure is so large that it’s being downloaded in mmCIF format and Chimera is rather slow to open mmCIF. It might load eventually if you waited a really long time (many minutes?), but then rotation etc. would still be slow. Our new software ChimeraX is developed to handle such large structures and mmCIF format much better and faster, but it also depends on having a reasonably up-to-date computer. Download could still be slow depending on the speed of your connection with the database. As for the computer, we recommend using one from the “last 3 years” although it is certainly possible it might work on older computers too. ChimeraX commands have a lot of similarities with Chimera commands, but there are differences, and most functions are command-only (not in the menu). Nevertheless, should be easy to try downloading the program and seeing if it runs on your computer, and if so, entering command “open 4v9d” to see how that goes. ChimeraX is still in pre-release but available to download, and it has a lot of display options and image-saving. The ChimeraX home page has links to download and User Guide on the left: <http://www.rbvi.ucsf.edu/chimerax/index.html> The bottom example in the ChimeraX image gallery is a ribosome: <http://www.rbvi.ucsf.edu/chimerax/gallery.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 14, 2017, at 3:19 PM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
Thank you
A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb.
Can this be handled, or is the size to large to download. I tried to fetch it by PDB index, but it just seemed to stall or was way too large.
Regards
arthur
Dear Chimera, Is it possible when using Matchmaker to move an associated density map with it? Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures. Thanks Hernando
Hi Hernando, In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> However, Chimera does not have this matchmaker option, and things may be more complicated. If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to: (1) superimpose the atomic structure (let’s call it model #2) onto another atomic structure (#1) (2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> However, if the map and its structure weren’t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don’t think that would work. The Chimera “match” (but not matchmaker) command does have an “active” option to bring other models that are activated for motion (movable with the mouse) along during the match. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2017, at 6:15 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera,
Is it possible when using Matchmaker to move an associated density map with it? Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures.
Thanks Hernando
Sorry, my mistake, this ChimeraX matchmaker command option only brings along atomic models currently. We’ll look into whether it can be expanded to other kinds of models (maps etc.) Elaine
On Aug 16, 2017, at 10:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
As of tomorrow, the ChimeraX matchmaker ‘bring’ option will be able to bring along any kind of models. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 16, 2017, at 11:10 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Sorry, my mistake, this ChimeraX matchmaker command option only brings along atomic models currently. We’ll look into whether it can be expanded to other kinds of models (maps etc.)
Elaine
On Aug 16, 2017, at 10:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
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Hi Hernando, The trick you want is to use “matrixcopy” with the “moving” option to move additional models using the same motion. First matchmaker an extra copy of the atomic model (#5) then move the original copy (#3) and associated density map (#4) to align with it matchmaker #1 #5 matrixcopy #5 #3 moving #4 https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> Tom
On Aug 16, 2017, at 10:54 AM, Elaine Meng wrote:
Hi Hernando, In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
However, Chimera does not have this matchmaker option, and things may be more complicated.
If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to:
(1) superimpose the atomic structure (let’s call it model #2) onto another atomic structure (#1)
(2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
However, if the map and its structure weren’t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don’t think that would work.
The Chimera “match” (but not matchmaker) command does have an “active” option to bring other models that are activated for motion (movable with the mouse) along during the match. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2017, at 6:15 AM, Hernando J Sosa wrote:
Dear Chimera,
Is it possible when using Matchmaker to move an associated density map with it? Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures.
Thanks Hernando
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine
(2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3
did the trick for me. Thanks! (much better than trying to fit manually map into map each time). I will try ChimeraX later. Best H. -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, August 16, 2017 1:54 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Matchmaker & fit map into map Hi Hernando, In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> However, Chimera does not have this matchmaker option, and things may be more complicated. If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to: (1) superimpose the atomic structure (let’s call it model #2) onto another atomic structure (#1) (2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> However, if the map and its structure weren’t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don’t think that would work. The Chimera “match” (but not matchmaker) command does have an “active” option to bring other models that are activated for motion (movable with the mouse) along during the match. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 16, 2017, at 6:15 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera,
Is it possible when using Matchmaker to move an associated density map with it? Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures.
Thanks Hernando
Elaine Presumably in order to run ChimeraX one needs to have Windows 10 as an operating system. When I bought this computer three years ago it had Windows 8 on it. I got rid of that and loaded Windows 7. Being in the middle of writing a text with lots of figures I wanted to stay with Windows 7 and not have to learn a new operating system. I could have loaded Windows 10 for free, but for the same reasons I declined. art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, August 14, 2017 6:52 PM To: Arthur Szabo <agszabo@outlook.com> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] biounit Hi Arthur, It’s probably too big for your computer and/or for reasonable speed of interaction in Chimera (display changes, rotation etc.). The structure is so large that it’s being downloaded in mmCIF format and Chimera is rather slow to open mmCIF. It might load eventually if you waited a really long time (many minutes?), but then rotation etc. would still be slow. Our new software ChimeraX is developed to handle such large structures and mmCIF format much better and faster, but it also depends on having a reasonably up-to-date computer. Download could still be slow depending on the speed of your connection with the database. As for the computer, we recommend using one from the “last 3 years” although it is certainly possible it might work on older computers too. ChimeraX commands have a lot of similarities with Chimera commands, but there are differences, and most functions are command-only (not in the menu). Nevertheless, should be easy to try downloading the program and seeing if it runs on your computer, and if so, entering command “open 4v9d” to see how that goes. ChimeraX is still in pre-release but available to download, and it has a lot of display options and image-saving. The ChimeraX home page has links to download and User Guide on the left: <http://www.rbvi.ucsf.edu/chimerax/index.html> The bottom example in the ChimeraX image gallery is a ribosome: <http://www.rbvi.ucsf.edu/chimerax/gallery.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 14, 2017, at 3:19 PM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
Thank you
A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb.
Can this be handled, or is the size to large to download. I tried to fetch it by PDB index, but it just seemed to stall or was way too large.
Regards
arthur
Hi Arthur, ChimeraX might work on your Windows 7 system, it’s just not “guaranteed” … you would have to try it to find out. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2017, at 6:55 PM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
Presumably in order to run ChimeraX one needs to have Windows 10 as an operating system.
When I bought this computer three years ago it had Windows 8 on it. I got rid of that and loaded Windows 7. Being in the middle of writing a text with lots of figures I wanted to stay with Windows 7 and not have to learn a new operating system. I could have loaded Windows 10 for free, but for the same reasons I declined.
art
participants (5)
-
Arthur Szabo -
Elaine Meng -
Eric Pettersen -
Hernando J Sosa -
Tom Goddard