Script for positioning particles according the coordinates.
Dear colleagues, I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on? Thank you in advance, Alexander
Hi Alexander, By "particle" do you mean an atomic molecular model (e.g. PDB file)? Do you already know the desired rotation and translation for each particle? Or do you want to calculate those fits? What you want is probably possible but I need more details to give specific advice. Chimera is not memory efficient with its molecular models, so if your particles are proteins with several thousand atoms and you want to load 300 of them, you will need a lot of memory (~2 Kbytes / atom). Tom
Dear colleagues,
I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on?
Thank you in advance,
Alexander
Hi Alexander, If you just want spheres for your particles, if you reformat your file into "XYZ" format then Chimera can read that: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/xyz.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 7, 2011, at 10:26 AM, Tom Goddard wrote:
Hi Alexander,
By "particle" do you mean an atomic molecular model (e.g. PDB file)? Do you already know the desired rotation and translation for each particle? Or do you want to calculate those fits? What you want is probably possible but I need more details to give specific advice. Chimera is not memory efficient with its molecular models, so if your particles are proteins with several thousand atoms and you want to load 300 of them, you will need a lot of memory (~2 Kbytes / atom).
Tom
Dear colleagues,
I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on?
Thank you in advance,
Alexander
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Hi Alex, There are two scripts (placem.py and place.py) on the Chimera Python scripts web page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts that will place models at specified positions. With the placem.py script you specify the models/maps to open and the x,y,z translations and optionally the rotation as a quaternion, one model on each line. You can repeat the same model. The place.py script places multiple copies of a single model specifying translation and rotation using a 3 by 4 matrix. Tom
Hi Tom,
When I told about particles I meant electron-density maps (mrc, spider, imagic or ccp4 formats). I know all orientation of the particles and even more all of them a turned already -- what I need is only to place all of them in exact positions. Of cause I can do it manually, but it is bit boring.
Thank you for the help in advance,
Alex
Dear colleagues,
I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on?
Thank you in advance,
Alexander
participants (3)
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Alexander MYASNIKOV -
Eric Pettersen -
Tom Goddard