Thank you all for your help. Looks like both ProFit and rms_cur will do
just what I needed.
Thanks!
Tom
--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
On Fri, Jul 22, 2011 at 10:59 AM, Michael Lerner <mgler...@gmail.com> wrote:
> PyMOL's rms_cur command will do what you want. E.g.
>
> fetch 1rx1
> fetch 1ra1
>
> # reports "Executive: RMS = 34.329 (159 to 159 atoms)"
> # because the structures still need to be translated and rotated
> rms_cur (1rx1 and name CA), (1ra1 and name CA)
>
> # reports "Executive: RMS = 0.862 (159 to 159 atoms)"
> # because it calculates translated/rotated value, but does now
> # apply the translation/rotation to the molecules
> rms (1rx1 and name CA), (1ra1 and name CA)
>
>
> # reports "Executive: RMS = 0.391 (1026 to 1026 atoms)"
> # standard PyMOL align, which also translates and rotates
> align 1rx1, 1ra1
>
> # both of these report "Executive: RMS = 0.862 (159 to 159 atoms)"
> # because the structures have now been translated and rotated
> rms_cur (1rx1 and name CA), (1ra1 and name CA)
> rms (1rx1 and name CA), (1ra1 and name CA)
>
> Cheers,
>
> -Michael
>
>
> On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant <tgr...@hwi.buffalo.edu>wrote:
>
>> Dear all,
>>
>> I'm attempting to align a series of structures using the CEAlign plug-in
>> in PyMOL due to a lack of any detectable sequence homology. CEAlign does a
>> good job of aligning and the fits are very reasonable. However, the RMSD
>> that is calculated is based only on the c-alphas that were actually aligned,
>> not based on the total number of c-alphas in the structure. After searching
>> online I have been unable to find any software or servers that will simply
>> calculate the RMSD of two structures as is, without aligning them first. I
>> would think this would be a relatively straightforward thing to do, just to
>> calculate RMSD from two existing structures without translation or rotation
>> for alignment.
>>
>> Does anyone know of a way either in PyMOL or in general to simply
>> calculate the RMSD between all c-alphas of two structures? Obviously it
>> won't necessarily be a one-to-one ratio of c-alphas, but I can manually
>> curate the pdb to include only the equivalent and "aligned" residues, even
>> if not used in the CEAlign algorithm, so that there are the same number of
>> c-alphas in both structures.
>>
>> Thank you for any help and suggestions,
>>
>> Tom
>>
>>
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>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> as of August 15th:
>
> Department of Physics and Astronomy
> Earlham College
> 801 National Road West
> Richmond, IN 47374-4095
>
>
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Learn 10 ways to better secure your business today. Topics covered include:
Web security, SSL, hacker attacks & Denial of Service (DoS), private keys,
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http://www.accelacomm.com/jaw/sfnl/114/51426210/
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