Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812
Hi Hannah, I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera. ChimeraX reads the same bild format and is generally much better with large data. <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah
Thanks Elaine, I tried that but unfortunately it didn't help . What is odd to me is that both chimera and chimerax can open mrc/ccp4 files that are substantially larger without too much trouble. Best wishes Hannah On 05/01/2021 19:37, Elaine Meng wrote:
Hi Hannah, I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera. ChimeraX reads the same bild format and is generally much better with large data.
<https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah
-- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812
Hi Hannah, We could look at why Chimera and ChimeraX can't open a 10 Mbyte BILD file if you report a bug using Chimera(X) menu entry Help / Report a Bug... and attach an example file. Usually BILD files are much smaller than this so it may be nobody ever tried a file that large. I'm guessing it is not a memory limitation. More likely it is some O(n**2) behavior of the reader, in other words if you have N points or line or arrows in the file it is coded poorly and taking N*N operations to read it. A clue to that could be deduced if you have BILD files of different sizes that do open, how long in seconds do files of different sizes take to open? Tom
On Jan 12, 2021, at 9:52 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Thanks Elaine,
I tried that but unfortunately it didn't help . What is odd to me is that both chimera and chimerax can open mrc/ccp4 files that are substantially larger without too much trouble.
Best wishes
Hannah
On 05/01/2021 19:37, Elaine Meng wrote:
Hi Hannah, I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera. ChimeraX reads the same bild format and is generally much better with large data.
<https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah
-- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom
Telephone : 01223 252812
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
HI Hannah, You didn't say which version of ChimeraX you used. There was a change just after the 1.0 release that dramatically sped up opening large bild files. That fix is in the 1.1 release. But I'm sure there's still room for improvement. So yes, please report it as a bug and supply the bild file so we can figure what's going wrong in your case. -- Greg On 1/12/2021 10:21 AM, Tom Goddard wrote:
Hi Hannah,
We could look at why Chimera and ChimeraX can't open a 10 Mbyte BILD file if you report a bug using Chimera(X) menu entry Help / Report a Bug... and attach an example file. Usually BILD files are much smaller than this so it may be nobody ever tried a file that large. I'm guessing it is not a memory limitation. More likely it is some O(n**2) behavior of the reader, in other words if you have N points or line or arrows in the file it is coded poorly and taking N*N operations to read it. A clue to that could be deduced if you have BILD files of different sizes that do open, how long in seconds do files of different sizes take to open?
Tom
On Jan 12, 2021, at 9:52 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Thanks Elaine,
I tried that but unfortunately it didn't help . What is odd to me is that both chimera and chimerax can open mrc/ccp4 files that are substantially larger without too much trouble.
Best wishes
Hannah
On 05/01/2021 19:37, Elaine Meng wrote:
Hi Hannah, I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera. ChimeraX reads the same bild format and is generally much better with large data.
<https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom
Telephone : 01223 252812
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Greg and Tom, You make fine points! I was using Chimera-X 0.93 and now I downloaded 1.1 it can (after a few mins of thinking) open the 70Mb bild files that I require :) If I run into problems again though now I know that I can submit bug reports. I can submit one of these massive files if you wanted to optimise the file opening. Thank you for your help. Hannah On 12/01/2021 23:43, Greg Couch wrote:
HI Hannah,
You didn't say which version of ChimeraX you used. There was a change just after the 1.0 release that dramatically sped up opening large bild files. That fix is in the 1.1 release. But I'm sure there's still room for improvement. So yes, please report it as a bug and supply the bild file so we can figure what's going wrong in your case.
-- Greg
On 1/12/2021 10:21 AM, Tom Goddard wrote:
Hi Hannah,
We could look at why Chimera and ChimeraX can't open a 10 Mbyte BILD file if you report a bug using Chimera(X) menu entry Help / Report a Bug... and attach an example file. Usually BILD files are much smaller than this so it may be nobody ever tried a file that large. I'm guessing it is not a memory limitation. More likely it is some O(n**2) behavior of the reader, in other words if you have N points or line or arrows in the file it is coded poorly and taking N*N operations to read it. A clue to that could be deduced if you have BILD files of different sizes that do open, how long in seconds do files of different sizes take to open?
Tom
On Jan 12, 2021, at 9:52 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Thanks Elaine,
I tried that but unfortunately it didn't help . What is odd to me is that both chimera and chimerax can open mrc/ccp4 files that are substantially larger without too much trouble.
Best wishes
Hannah
On 05/01/2021 19:37, Elaine Meng wrote:
Hi Hannah, I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera. ChimeraX reads the same bild format and is generally much better with large data.
<https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/download.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.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 Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb@mrc-mbu.cam.ac.uk> wrote:
Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom
Telephone : 01223 252812
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812
participants (4)
-
Elaine Meng -
Greg Couch -
Hannah Bridges -
Tom Goddard