[BiO BB] Are there servers or programs

[Mike Marchywka]

I  can verify that this link 
http://biotool.uni-koeln.de:8080/3dalign_neu/cgi-bin/3daligner.py

( liinked from http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html)

did function. I was able to compare two pdb files ( my current thing is 
oxidized cysteines
so I compared:

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=23527
to
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=23526

)

I downloaded the result and it even displayed in the rasmol I built under 
cygwin.
The resulting composite file was reasonably easy to manipulate- I can find 
the modified
sulfur and see how much it moved.

I'm not sure what original poster meant about returning coordinants  but 
they should be
pretty easy to extract. I think most of the stuff that came up displayed in 
rasmol or jmol.

FWIW, I got this to build but it doesn't seem to generate any output:
ftp://ftp.sdsc.edu/pub/sdsc/biology/CE/src/

( note new address as of 10-06)
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165r
( NOTE MORE NEWER  NUMBER )
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>From: "Shameer Khadar" <skhadar at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Are there servers or programs
>Date: Fri, 5 Jan 2007 11:09:47 +0530
>
>You can also try
>HOMSTRAD : http://www-cryst.bioc.cam.ac.uk/homstrad/
>DALI : http://www.ebi.ac.uk/dali/
>
>On 1/5/07, Shameer Khadar <skhadar at gmail.com> wrote:
>>
>>Hi,
>>There are plenty of programs/webservers available for structure
>>alignment.  First of all try this Wiki :
>>http://en.wikipedia.org/wiki/Structural_alignment_software . It is a good
>>starting point.
>>
>>Your second requirement is not clear to me
>>May be PASS2 Database @ NCBS : http://caps.ncbs.res.in/pass2 or 
>>DALI at EBIwill be useful to you.
>>
>>Thanks,
>>Shameer
>>
>>On 1/4/07, soorya kiran <kiran.soorya at gmail.com> wrote:
>> >
>> > Are there servers or programs (which are downloadable) which can used
>> > for structure alignment of proteins and where we can get the atomic
>> > co-ordinates of the protein after alignment?
>> >
>> >
>> > Srijith,
>> > SooryaKiran Bioinformatics (P) LTD,
>> > Industry Incubation Centre,
>> > University of Kerala,
>> > Karyavattom Campus,
>> > Thiruvananthapuram,
>> > Keralam,
>> > India. 695 581
>> > Ph : +91 (471) 2414593
>> > www.sooryakiran.com
>> > Email : kiran.soorya at gmail.com
>> >
>> >
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