From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Fri Sep 16 2011 - 14:52:47 CDT

Hi Kirby,

I am writing the code in numpy for QR factorization. Since I dont have any
gaps in my alignment the problem reduces to simple QR factorization.

But to answer your question :
I get this error message : "couldn't read directory "/usr/tmp/": too many
open files" after 1092 files. And this makes me use only 1092 files.

I am loading using GUI, select all the files from import data. I do have the
latest version.

Thanks,
Santhosh

On Fri, Sep 16, 2011 at 2:22 PM, Kirby Vandivort <kvandivo_at_gmail.com> wrote:

> Santhosh,
>
> We have successfully loaded about 100,000 sequences into the version of
> MultiSeq that is being distributed with VMD 1.9 (are you using the latest
> version?), so I want to make sure that everything is working as it should.
>
> How are you attempting to load the 16,000 frames?
>
> Thanks,
>
> Kirby
>
>
>
> On Fri, Sep 16, 2011 at 8:13 AM, Vijay Vammi <vsvammi_at_iastate.edu> wrote:
>
>> Hello,
>>
>> I have a 8ns simulation with about 16000 frames. I want to cluster these
>> frames to get representative structures.
>>
>> I want to use the QR factorization method as described in "Evolutionary
>> Profiles Derived from the QR Factorization of Multiple Structural Alignments
>> Gives an Economy of Information" by Patrick O’Donoghue and Zaida
>> Luthey-Schulten. I see that this has been part of multiseq plugin in VMD. I
>> have couple of questions regarding its use :
>>
>> 1). Since we are dealing with rather large number of PDB's, is it
>> advisable that I run this via command line instead of GUI. I tried using the
>> GUI but I see that multiseq did not load all the frames but only 2000 of
>> them.
>>
>> 2). In the actual implementation the problem becomes multi-dimmensional
>> because of gaps, since I dont have gaps in the structure alignment the
>> problem should be reducible to traditional QR factorization. (noofCAAtoms*3
>> X numframes would be the size of matrix I am trying to decompose.). Would be
>> it be much faster and better if I use numpy or Matlab instead of VMD to get
>> this done? Please correct me if I am wrong here.
>>
>> Any help or advice on this is appreciated.
>>
>> Thanks
>> Santhosh
>>
>
>
>
> --
>
> Kirby Vandivort
>
>