[gmx-developers] do_dssp bugfix

[Carsten Kutzner]

Hi,

the do_dssp fixes are in CVS-HEAD now.

Carsten


On Apr 29, 2009, at 12:04 PM, Carsten Kutzner wrote:

> Hi,
>
> I have not commited yet since there were also other inconsistencies  
> in do_dssp:
>
> If one inputs a file with more than one chain
>
> - the area.xpm file would miss one y value per chain, since the  
> empty lines for
>  the chain separators were not taken into account
> - the averea.xvg output was incorrect for all chains other than the  
> first one,
>  again due to the chain separators. For the same reason the  
> totarea.xvg
>  contents were completely wrong
> - the scount.xvg file output was wrong for the "Coils" column, since  
> the chain
>  separators were counted as coils (they were assigned the same  
> symbol "~")
>
> I have corrected all these things and also a few minor ones:
>
> - there was an extra axis entry in the ss.xpm file leading to an  
> extra "0" at
>  the end of the x-axis
> - Now there is a special symbol "=" for chain separators such that  
> they can
>  be distinguished from Coil structures.
>
> The only question that I have before commiting is whether the ss.map  
> file
> is also used by other programs than do_dssp. In that file I added an  
> extra
> Chain_Separator entry, which I suppose is ignored by possible other  
> tools.
>
> Carsten
>
>
>
> On Apr 27, 2009, at 7:51 PM, David van der Spoel wrote:
>
>> Carsten Kutzner wrote:
>>> Hi,
>>> we have recently detected a memory problem in do_dssp.
>>> When do_dssp is given an input pdb containing more than 10 chains,
>>> memory corruption is likely to appear. This happens because the
>>> strip_dssp function assumes that the number of lines in the file  
>>> written
>>> by the dssp program is equal to the number of residues. However,
>>> the dssp output file also contains chain separators in separate  
>>> lines,
>>> resulting in an extra line per chain.
>>> For some reason, the affected arrays are currently snewed with  
>>> (nres+10)
>>> elements, allowing for 10 separate chains at most. I would suggest  
>>> to
>>> snew them with 2*nres-1 elements, allowing each residue to be a
>>> separate chain at most.
>>> The allocations that have to be extended are for the variables bb,
>>> average_area, av_area, norm_av_area, and accri[i].
>>> Should I immediately fix that in the head and 40 branch?
>> Yes, please do.
>>
>>> Carsten
>>> -- 
>>> Dr. Carsten Kutzner
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical and Computational Biophysics
>>> Am Fassberg 11, 37077 Goettingen, Germany
>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>>> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>>> _______________________________________________
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the www  
>>> interface or send it to gmx-developers-request at gromacs.org.
>>
>>
>> -- 
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Professor of Biology
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>> phone:	46 18 471 4205		fax: 46 18 511 755
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>> ++++
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www  
>> interface or send it to gmx-developers-request at gromacs.org.
>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>
>
>
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use thewww  
> interface or send it to gmx-developers-request at gromacs.org.


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne