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Topics - clarebonk

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SCHNAaP/SCHNArP / GLH_build() Memory Leak
« on: May 15, 2009, 09:11:20 pm »
I took out the printf()s from GLH_build() and hard coded the user-response values that I want, so that I do not have to enter them in every time I run the function.  When I call GLH_build() in a loop, my memory usage increases with each iteration.  I assume this behavior is not wanted.  There seems to be a memory leak somewhere.  I tried looking through the code to make sure the mallocs are all freed, but I have not found any red flags.  Any idea why/where this is happening?


SCHNAaP/SCHNArP / SCHNArP: Global Parameters
« on: March 19, 2009, 10:13:43 pm »
I am trying to build an RNA using only global parameters (not CEHS parameters).

So, I run schnarp and first enter #2 for "Use GLOBAL helical parameters."  Then I enter #2 again for "Use a full set of GLOBAL parameters."  The next thing schnarp wants is a Sequence-GLH parameter file name.  The default is "GLH_seq.dat".  I've read both READMEs, looked in the Example directory, and googled, but I am not sure how a Sequence-GLH parameter should be formatted.  Of course, I can look through the function step_GLH in rebuild.c to see how it reads in the file and emulate that, but I was wondering if there was a better source of information.

Also, step_GLH calls function comp_base in cmn_fncs.c to ensure no illegal bases exist.  However, only ATCG are hard coded as valid bases.  Since I'm trying to build RNA, I have Uracils.  Is this function going to cause me problems once I do get a GLH_seq.dat file?  Or, does functionality not exist for building RNA from purely global parameters?

Thanks ahead of time!

« on: March 11, 2009, 07:59:11 pm »
I am working on an RMSD minimization procedure.  I create (with my own c code) an initial RNA helix from a reduced pdb file, then I use 3DNA's analyze and rebuild to make a new helix.  I find the RMSD between the original helix and the one created with rebuild.  I use Powell's minimizatoin method to find bp_step parameters that give the minimum RMSD between the original helix and the one created with 3DNA's rebuild.

My problem is that the minimization procedure calls 3DNA's rebuild many, many times and I have no way of integrating the executables into my c code.  Since I do many other calculations, I need the code to be fast and efficient.

I've read both SCHNAaP and SCHNArP papers, and both conclusions state the source code is available upon request from the authors.

May I access the c code?  I, of course, will be happy to cite the authors' work and take no credit for that particular portion of the methodology.  It would save me a lot of time if I didn't have to rewrite the code myself.

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.