[Chimera-users] turning ksdssp off?

Sumitro Harjanto u0601918 at nus.edu.sg
Wed Mar 17 01:33:49 PDT 2010

Hi Elaine, Eric,

Actually I now don't need to do that anymore. Initially I wanted to do
that to reduce the screen output lines (OK, bad reason!!) since I
couldn't find a way to retrieve the replylog other than copying it from
the console, and the console has a limit of 9999 lines. But now I can
redirect the output to a file so I no longer have to worry about the
number of lines output by chimera.

Of course, I kinda overlook the possible implications on alignment by
"match" when I turn ksdssp off. But anyway, thanks for the prompt reply.
And I admire your sincere interest in improving the program! Thanks


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 16 March 2010 1:29 PM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] turning ksdssp off?

Hi Sumitro,
No, currently you can't turn that off, as Eric said in his previous  
reply. I was only mentioning matchmaker in case you were using it.   
The match command is not affected by this issue; it only uses whatever  
atoms you tell it to use.

Why do you want to avoid the ksdssp calculation?  Let us know so we  
can consider adding an option to control that.

On Mar 15, 2010, at 8:10 PM, Sumitro Harjanto wrote:

> 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 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.
> <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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