[Chimera-users] scripting & density

Tom Goddard goddard at sonic.net
Fri May 12 13:40:17 PDT 2017


Hi Matt,

  The threshold and subtract operations each create a new copy of the data in memory and the original will be have all its data loaded.  So the operations I suggested would take 3 times 64 Gbytes or 192 Gbytes.  Unless your machine has at least 128 Gbytes (plus virtual memory which is usually ~3x physical memory), it won’t work the way I suggest.  If you have 128 Gbytes of memory or more I think what I suggest will be as fast as the disk speed will allow (probably take tens of minutes).  If you have less memory then Python could do it just using 64 Gbytes for the one copy of the data in memory, or if you used fancy Python it could be done one plane at a time, so any small amount of memory would suffice.

	Tom

> On May 12, 2017, at 10:23 AM, Dougherty, Matthew T wrote:
> 
> Considering the files are 64GB in size, what would be more efficient, chimera script or python?
> 10% difference, 10x, 100x, etc
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
> =================================================
> =================================================
> From: Tom Goddard
> Sent: Friday, May 12, 2017 12:07:47 PM
> To: Dougherty, Matthew T
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] scripting & density
>  
> ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
> Hi Matt,
> 
>   You would use vop threshold to make a map that has only the values 50-74 and then subtract it from the original map, and repeat with the range 90-110.
> 
> vop thresh #0 min 50 set 0 max 74 setmax 0
> vop subtract #0 #1
> 
>   Tom
> 
>> On May 12, 2017, at 8:42 AM, Dougherty, Matthew T  wrote:
>> 
>> Hi,
>> 
>> I have a dataset, its values are 1-255.  I would like to modify the density values using a script.
>> Specifically, I would like to set density values 50-74 & 90-110 to the value of zero.
>> Is there a way to do that using scripting, or do I need to do that using python?
>> 
>> Matthew Dougherty
>> National Center for Macromolecular Imaging
>> Baylor College of Medicine
>> =================================================
>> =================================================
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