No subject
Fri Sep 26 14:07:15 PDT 2014
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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rmsd command in chimera allows you to specify atoms in alternate conformati=
ons - <div>(https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rms=
d.html) there is a bit of a learning curve in getting the selection syntax =
right.</div><div>But I think it will only match the unique ones that you sp=
ecify - not include all of a complete set of alternative confs, which=
is maybe what you want.</div><div>rmsd takes the existing superimposition =
- match will do a superimposition<br><div> all the best</div><div>&nb=
sp; Martyn </div><div>Cambridge <br><blockquote style=3D"margin-=
right: 0px; margin-left:15px;">----Original message----<br>From : patrick.c=
ossins at inbox.com<br>Date : 02/10/2014 - 13:41 (GMTDT)<br>To : nwmoriarty at lb=
l.gov<br>Cc : phenixbb at phenix-online.org<br>Subject : Re: [phenixbb] Off To=
pic: Calculating accurately RMSD<br><br>
<div>No I wanted the structure alignment RMSD but thank you. </div><br=
><br><blockquote style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT:=
#0000ff 2px solid; MARGIN-RIGHT: 0px"><div class=3D"msgHeaders">-----Origi=
nal Message-----<br><b>From:</b> nwmoriarty at lbl.gov<br><b>Sent:</b> Wed, 1 =
Oct 2014 15:47:09 -0700<br><b>To:</b> patrick.cossins at inbox.com<br><b>Subje=
ct:</b> Re: [phenixbb] Off Topic: Calculating accurately RMSD<br><br></div>=
<div class=3D"oldBody"><div><div dir=3D"ltr">Patrick<div><br></div><div>If =
you do a refinement in Phenix you get a .geo which contains the geometry re=
straints information. It's a simple matter to calculate the rmsd of the geo=
metry restraints given that the model and ideal values are all listed.</div=
><div><br></div><div>Do you want a geometry restraints rmsd or a structure =
alignment rmsd?</div></div><div _class=3D"gmail_extra"><br clear=3D"all"><d=
iv><div dir=3D"ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---<=
/div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Divi=
sion<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br=
>Phone : 510-486-5709 Email : NWMoriarty at LBL.gov<br>Fax&=
nbsp; : 510-486-5909 Web : <a href=3D=
"http://CCI.LBL.gov">CCI.LBL.gov</a></div></div></div></div>
<br><div _class=3D"gmail_quote">On Wed, Oct 1, 2014 at 3:21 PM, PC <span di=
r=3D"ltr"><<a href=3D"mailto:patrick.cossins at inbox.com" target=3D"_blank=
">patrick.cossins at inbox.com</a>></span> wrote:<br><blockquote _class=3D"=
gmail_quote" _style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding=
-left:1ex"><u></u>
<div>
<div>Hi Nigel,</div><div><br></div><div>Could you tell me how you used the =
.geo file?</div><div><br></div><div>In this I case I don't have a geo file =
but this might be useful in the future </div><div><div _class=3D"h5"><=
br><br><blockquote _style=3D"PADDING-LEFT:5px;MARGIN-LEFT:5px;BORDER-LEFT:#=
0000ff 2px solid;MARGIN-RIGHT:0px"><div>-----Original Message-----<br><b>Fr=
om:</b> <a href=3D"mailto:nwmoriarty at lbl.gov" target=3D"_blank">nwmoriarty@=
lbl.gov</a><br><b>Sent:</b> Wed, 1 Oct 2014 15:04:54 -0700<br><b>To:</b> <a=
href=3D"mailto:patrick.cossins at inbox.com" target=3D"_blank">patrick.cossin=
s at inbox.com</a><br><b>Subject:</b> Re: [phenixbb] Off Topic: Calculating ac=
curately RMSD<br><br></div><div><div><div dir=3D"ltr">Patrick<div><br></div=
><div>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.</div=
><div><br></div><div>
<p>elbow.refine_geo_display model.geo</p>
<p>Time to parse 1.43</p>
<p><br></p>
<p>RMS results for model</p>
<p><br></p>
<p>RMS(D/Z)</p>
<p> d-all  =
; d-none d-alt  =
; z-all z-none  =
; z-alt </p>
<p> bond 0.001( 3550) 0.001( 3550) =
0.000( 0) 0.051( 3550) 0.051( 3550) 0.00=
0( 0)</p>
<p> angle 0.532( 6399) 0.532( 6399) =
0.000( 0) 0.182( 6399) 0.182( 6399) 0.00=
0( 0)</p>
<p><br></p>
<p><br></p></div></div><div><br clear=3D"all"><div><div dir=3D"ltr">Cheers<=
div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty=
<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley N=
ational Laboratory<br>Berkeley, CA 94720-8235<br>Phone : <a href=3D"tel:510=
-486-5709" value=3D"+15104865709" target=3D"_blank">510-486-5709</a> =
Email : NWMoriarty at LBL.gov<br>Fax : <a href=3D"tel=
:510-486-5909" value=3D"+15104865909" target=3D"_blank">510-486-5909</a>&nb=
sp; Web : <a href=3D"http://CCI.LBL.gov" target=
=3D"_blank">CCI.LBL.gov</a></div></div></div></div>
<br><div>On Wed, Oct 1, 2014 at 2:36 PM, PC <span dir=3D"ltr"><<a href=
=3D"mailto:patrick.cossins at inbox.com" target=3D"_blank">patrick.cossins at inb=
ox.com</a>></span> wrote:<br><blockquote><u></u>
<div>
Hi,<div>Off topic-sorry</div><div>Is there a way to calculate RMSD </d=
iv><div><br></div><div>1) Considering atoms in ALT conformations?</div><div=
>2) considering all atoms in the protein ?</div><div><br></div><div>PYMOL s=
eems to be throwing atoms away.</div><div><br></div><div>Thank you</div><hr=
size=3D"1px" noshade=3D"">
<div>
<a href=3D"http://mysecurelogon.com/manager" target=3D"_blank"><img src=3D"=
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ht:1px">
<div _style=3D"font:12px Verdana,sans-serif;color:Black;background:white;pa=
dding:3px;line-height:1.3em">
<a href=3D"http://mysecurelogon.com/password-manager" target=3D"_blank"><im=
g src=3D"http://my.inbox.com/img/ftrs/mlman3703.jpg" width=3D"424" height=
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x;">
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