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"? Thanks, Sumitro -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Tuesday, March 16, 2010 7:54 AM To: Sumitro Harjanto Cc: chimera-users@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. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> 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. Elaine 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
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... 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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