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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Oct 1, 2014 at 3:21 PM, PC 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:* [email protected] *Sent:* Wed, 1 Oct 2014 15:04:54 -0700 *To:* [email protected] *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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Oct 1, 2014 at 2:36 PM, PC 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.

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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 : [email protected] Date : 02/10/2014 - 13:41 (GMTDT) To : [email protected] Cc : [email protected] Subject : Re: [phenixbb] Off Topic: Calculating accurately RMSD No I wanted the structure alignment RMSD but thank you. -----Original Message----- From: [email protected] Sent: Wed, 1 Oct 2014 15:47:09 -0700 To: [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Oct 1, 2014 at 3:21 PM, PC 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: [email protected] Sent: Wed, 1 Oct 2014 15:04:54 -0700 To: [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Oct 1, 2014 at 2:36 PM, PC 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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: [email protected] Sent: Thu, 02 Oct 2014 18:57:04 +0200 To: [email protected] 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 : [email protected] Date : 02/10/2014 - 13:41 (GMTDT) To : [email protected] Cc : [email protected] Subject : Re: [phenixbb] Off Topic: Calculating accurately RMSD No I wanted the structure alignment RMSD but thank you. -----Original Message----- From: [email protected] Sent: Wed, 1 Oct 2014 15:47:09 -0700 To: [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Oct 1, 2014 at 3:21 PM, PC 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: [email protected] Sent: Wed, 1 Oct 2014 15:04:54 -0700 To: [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Oct 1, 2014 at 2:36 PM, PC 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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