[Chimera-users] turning ksdssp off?

Sumitro Harjanto u0601918 at nus.edu.sg
Mon Mar 15 20:10:02 PDT 2010

Hi Elaine,

I am using "match" to calculate the rmsds. But the ksdssp algo was
automatically invoked when I opened my model. My models are generally
85% similar by sequence. Can I turn it off in this case..? and I will
have to weigh the same implication on accuracy if using "match"?


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, March 16, 2010 7:54 AM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] turning ksdssp off?

Hi Sumitro,

I thought you might be using the "matchmaker" command to superimpose  
structures and calculate RMSDs.

If so, be aware that matchmaker uses secondary structure assignments  
to help guide the alignment, unless you specify "ssFraction false".   
Without secondary structure information, it will use the sequences  
only, and the superposition might not be as good if the the sequences  
have low similarity.  If the sequences have high similarity it  
shouldn't make much difference, however.


On Mar 15, 2010, at 4:17 PM, Eric Pettersen wrote:

> Hi Sumitro,
> 	The shortest answer is no, there is no way (barring some Python

> shenanigans).  You could clear SS assignments afterward with:
> setattr r isHelix false #
> setattr r isStrand false #
> Can you describe why you want to turn off the SS computation?  We  
> might make it optional somehow if it was of general use.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Mar 14, 2010, at 6:54 AM, Sumitro Harjanto wrote:
>> Hi,
>> Is there any way to turn off automatic secondary structure  
>> assignment upon opening a pdb file that does not contain secondary  
>> assignments?
>> Cheers,
>> Sumitro
>> ...
>> Opening B-7301_SRWGYQVKH_1K5N.pdb...
>> Computing secondary structure assignments...
>> Computed secondary structure assignments (see reply log)
>> Model 2 (B-7301_SRWGYQVKH_1K5N.pdb) appears to be a protein without  
>> secondary structure assignments.
>> Automatically computing assignments using 'ksdssp' and parameter  
>> values:
>>   energy cutoff -0.5
>>   minimum helix length 3
>>   minimum strand length 3
>> Use command 'help ksdssp' for more information.
>> ...
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