loading atomic coordinates without drawing or calculating bonds
Hello, I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms. Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations? Thanks in advance, Bests, Veysel Berk
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
On Aug 5, 2009, at 2:52 AM, Veysel Berk wrote:
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Hi Veysel, I don't know if there's a particular reason you want these points to be atoms, but one alternative is the use the ".sphere" directive of Chimera's BILD format (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html ) to depict your points. If you do need them to be atoms, there is no way to suppress the connectivity search for XYZ files without editing the Python code for reading that file format. If you are willing to do that then the change is pretty trivial. In the __init__.py file of the ReadXYZ module there is a line that looks like this: connectMolecule(m) either delete that line or insert a '#' symbol just in front of the 'c' to comment it out. You will find ReadXYZ in the 'share' subdirectory of your Chimera installation. On a mac it will actually be in the 'Contents/Resources/share' subdirectory and you will have to right click on the Chimera icon and choose "Show Package Contents" to see the application subdirectories in the Finder. I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab
Hi Veysel, You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it. You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command. Tom -------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@cgl.ucsf.edu Date: 8/5/09 2:52 AM
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
Hi Veysel, Ok, I put a script xyzsdmap.py on the Chimera scripts web page that reads x,y,z and sigma x, sigma y, sigma z values (6 column text file) and makes the volume data set from Gaussians using those parameters. If you also have different amplitudes for the points that could be handled by reading another column and modifying the "weights" array in the script. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom -------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: Tom Goddard Date: 8/5/09 1:31 PM
Dear Tom,
It looks like a great idea. I will try both options today and let's see of it works for me.
Thanks very much for your advise.
would it be possible to implement to define three more column on the xyz file for standard deviations of Gaussians in each dimensions to calculate the volume data in future releases of the script? Is it technically doable? My localization data have x, y, z and sigx, sigy, sigz.
Bests,
Veysel Berk Department of Molecular & Cell Biology University of California, Berkeley
On Aug 5, 2009, at 10:34 AM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Veysel,
You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it.
You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this.
http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command.
Tom
-------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@cgl.ucsf.edu Date: 8/5/09 2:52 AM
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
-------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Tom Goddard To: Veysel Berk Date: 8/5/09 10:34 AM
Hi Veysel,
You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it.
You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this.
http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command.
Tom
-------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@cgl.ucsf.edu Date: 8/5/09 2:52 AM
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
Thanks Tom, It works very well for converting fluorescent localization data into volume data. Now, single molecule field may benefit on the great features of Chimera! Bests, Veysel Berk Department of Molecular & Cell Biology University of California, Berkeley Stanley Hall #431 Berkeley, CA 94720 510-666 2740 On Wed, Aug 5, 2009 at 3:00 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Veysel,
Ok, I put a script xyzsdmap.py on the Chimera scripts web page that reads x,y,z and sigma x, sigma y, sigma z values (6 column text file) and makes the volume data set from Gaussians using those parameters. If you also have different amplitudes for the points that could be handled by reading another column and modifying the "weights" array in the script.
http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: Tom Goddard Date: 8/5/09 1:31 PM
Dear Tom,
It looks like a great idea. I will try both options today and let's see of it works for me.
Thanks very much for your advise.
would it be possible to implement to define three more column on the xyz file for standard deviations of Gaussians in each dimensions to calculate the volume data in future releases of the script? Is it technically doable? My localization data have x, y, z and sigx, sigy, sigz.
Bests,
Veysel Berk Department of Molecular & Cell Biology University of California, Berkeley
On Aug 5, 2009, at 10:34 AM, Tom Goddard <goddard@cgl.ucsf.edu><goddard@cgl.ucsf.edu>wrote:
Hi Veysel,
You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it.
You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this.
http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command.
Tom
-------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@cgl.ucsf.edu Date: 8/5/09 2:52 AM
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
-------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Tom Goddard To: Veysel Berk Date: 8/5/09 10:34 AM
Hi Veysel,
You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it.
You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this.
http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command.
Tom
-------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users@cgl.ucsf.edu Date: 8/5/09 2:52 AM
Hello,
I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
participants (3)
-
Eric Pettersen -
Tom Goddard -
Veysel Berk