[phenixbb] Off Topic: Calculating accurately RMSD

[PC]

Hi,

I am certainly after what you suggested but seems like there is no tool for it (as far as I can tell).

Patrick

> -----Original Message-----
> From: tg at shelx.uni-ac.gwdg.de
> Sent: Thu, 02 Oct 2014 18:57:04 +0200
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Off Topic: Calculating accurately RMSD
> 
> Hi all,
> 
> I was wondering if any of the suggested solutions calculate the
> contribution to the RMSD of an atom with alternate coordinate as mean
> weighted by occupancy? I would think this is what Mark is after. -Mark?
> 
> Best,
> Tim
> 
> On 10/02/2014 04:28 PM, MARTYN SYMMONS wrote:
>> rmsd command in chimera allows you to specify atoms in alternate
>> conformations -
>> (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html) there
>> is a bit of a learning curve in getting the selection syntax right.
>> But I think it will only match the unique ones that you specify - not
>> include all of a complete set of alternative confs,  which is maybe what
>> you want.
>> rmsd takes the existing superimposition - match will do a
>> superimposition
>>   all the best
>>   Martyn
>> Cambridge
>> ----Original message----
>> From : patrick.cossins at inbox.com
>> Date : 02/10/2014 - 13:41 (GMTDT)
>> To : nwmoriarty at lbl.gov
>> Cc : phenixbb at phenix-online.org
>> Subject : Re: [phenixbb] Off Topic: Calculating accurately RMSD
>> No I wanted the structure alignment RMSD but thank you.
>> -----Original Message-----
>> From: nwmoriarty at lbl.gov
>> Sent: Wed, 1 Oct 2014 15:47:09 -0700
>> To: patrick.cossins at inbox.com
>> Subject: Re: [phenixbb] Off Topic: Calculating accurately RMSD
>> Patrick
>> If you do a refinement in Phenix you get a .geo which contains the
>> geometry restraints information. It's a simple matter to calculate the
>> rmsd of the geometry restraints given that the model and ideal values
>> are all listed.
>> Do you want a geometry restraints rmsd or a structure alignment rmsd?
>> Cheers
>> Nigel
>> ---
>> Nigel W. Moriarty
>> Building 64R0246B, Physical Biosciences Division
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>> On Wed, Oct 1, 2014 at 3:21 PM, PC <patrick.cossins at inbox.com> wrote:
>> Hi Nigel,
>> Could you tell me how you used the .geo file?
>> In this I case I don't have a geo file but this might be useful in the
>> future
>> -----Original Message-----
>> From: nwmoriarty at lbl.gov
>> Sent: Wed, 1 Oct 2014 15:04:54 -0700
>> To: patrick.cossins at inbox.com
>> Subject: Re: [phenixbb] Off Topic: Calculating accurately RMSD
>> Patrick
>> If you have a .geo (optionally from the end of phenix.refine) you can
>> run a script I wrote to get the rmsd values for all, alt and not alt.
>> elbow.refine_geo_display model.geo
>> Time to parse 1.43
>> RMS results for model
>> RMS(D/Z)
>>              d-all          d-none         d-alt          z-all
>> z-none         z-alt
>>   bond       0.001( 3550)   0.001( 3550)   0.000(    0)   0.051( 3550)
>> 0.051( 3550)   0.000(    0)
>>   angle      0.532( 6399)   0.532( 6399)   0.000(    0)   0.182( 6399)
>> 0.182( 6399)   0.000(    0)
>> Cheers
>> Nigel
>> ---
>> Nigel W. Moriarty
>> Building 64R0246B, Physical Biosciences Division
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>> On Wed, Oct 1, 2014 at 2:36 PM, PC <patrick.cossins at inbox.com> wrote:
>> Hi,
>> Off topic-sorry
>> Is there a way to calculate RMSD
>> 1) Considering atoms in ALT conformations?
>> 2) considering all atoms in the protein ?
>> PYMOL seems to be throwing atoms away.
>> Thank you
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> 
>> 
>> 
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> 
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
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