[Chimera-users] Memory allocation

Jonathan LS Esguerra jonathan.esguerra at gmm.gu.se
Tue Sep 12 16:08:29 PDT 2006

I also encounter memory problems (quite often) because I'm working with 
large structures such as the ribosome.
When I try to restore .py sessions as large as 40 Mb, Chimera terminates 
after around 5-10 minutes and throws a memory error.
It doesn't help that my machine runs on dual pentium 4 processors (2.8 GHz 
each) and 2.0 Gb RAM.
I just gave up saving too large sessions in my PC when working with whole 
ribosome structures.

I have had some correspondence a long time ago with Eric Pettersen regarding 
He suggested me the following:

"....if you have access to another Windows machine with more that 1 GB of 
memory, you might try restoring the .py session file there and see if it 
works and produces a .pyc file.  If it does, you could copy the .pyc file 
back to your machine and be able to restore the session while bypassing the 
compilation step.

Another alternative if you are a little Python-savvy is to open Chimera's 
Python shell (Tools->Programming->IDLE) and compile the .pyc file yourself 

    import py_compile
    py_compile.compile('full path to .py file', 'same path except with 
    [remembering that backslashes in quoted strings need to be doubled]
then stop Chimera and start a new one in which you try to restore the 

The important difference between .py and .pyc files is that .py files are 
portable between different computer architectures and therefore can safely 
be distributed to other people and/or used on other machine types whereas 
.pyc files are not guaranteed to be portable."

I have not really tried the trick above since at the moment, I'm the only 
one here at the lab with a PC with 2 GB RAM...and still I couldn't restore 
my large sessions. I have been trying to install Chimera in our linux 
cluster here but have had some setbacks with missing libraries,,,and some 
other things to do... :(


Jonathan LS Esguerra, MSc Bioinformatics
PhD student, Microbiology/Functional Genomics
Cell and Molecular Biology-Microbiology
Göteborgs University

Box 462, Medicinaregatan 9C
40530 Gothenburg City

Tel:+46 (0)31-7733738
Fax:+46 (0)31-7732599

----- Original Message ----- 
From: "Thomas Goddard" <goddard at cgl.ucsf.edu>
To: <brmorgan at clarku.edu>
Cc: <chimera-users at cgl.ucsf.edu>
Sent: Tuesday, September 12, 2006 10:39 PM
Subject: Re: [Chimera-users] Memory allocation

>  Chimera does not have any fixed amount of memory allocated.  It will
> use whatever is available.  If you load large molecular systems
> (100,000 atoms) or large volume data sets (> 100 Mbytes) your computer
> may start swapping (transfering data back and forth to disk because it
> does not fit in memory).  That can dramatically slow down any
> computation by factors of 10 or 100.  The only real solution is to use
> a machine with more memory, or load smaller systems in Chimera.
>  Are you working with molecules or volume data?  There are tricks to
> reducing the data size depending on the type of data.
> Tom

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