[Chimera-users] loading atomic coordinates without drawing or calculating bonds

[Tom Goddard]

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 at 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 at 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 at 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
>>
>>
>>     

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