There are 13 messages totalling 1026 lines in this issue.
Topics of the day:
1. refmac failed message (2)
2. question of extra high B factor (6)
3. Coot:findwaters in REFMAC (2)
4. Postdoctoral position in protein crystallography at Karolinska
Institutet
5. OpenGL Stereo 3D on 120 Hz LCDs, at last!
6. Foils for energy calibration
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Date: Thu, 30 Jul 2009 10:50:13 GMT
From: Elad Binshtien <[email protected]>
Subject: refmac failed message
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Dear all=2C
I am refining a structure in Refmac at 2=2E2 A in win OS=2E=C2=A0
Howeve=
r=2C
Refmac failed and send this message=3A =C2=A0 =C2=A0 =C2=A0=C2=A0
forrtl=
=3A error (72)=3A floating overflow=C2=A0 =
Thank you in advance for your any helpful suggestions=2E=C2=A0 =
Best=2C
Elad
Elad Binshtein
Ph=2ED student =
Department of Life Science =
Ben Gurion University of the Negev
Ph=3A 972-8-6461325=E2=80=8E
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Dear all=2C=3Cbr=3E=3Cbr=3E=3Cbr=3EI am refining a structure in
Refmac a=
t 2=2E2 A in win OS=2E=26nbsp=3B However=2C
Refmac failed and send this message=3A =26nbsp=3B =26nbsp=3B
=26nbsp=3B=26=
nbsp=3B forrtl=3A error (72)=3A floating overflow=26nbsp=3B
=3Cbr=3E=3Cb=
r=3E Thank you in advance for your any helpful
suggestions=2E=26nbsp=3B =
=3Cbr=3E=3Cbr=3E=3Cbr=3EBest=2C=3Cbr=3EElad=3Cbr=3E=3CBR=3E=3CBR=3EElad
=
Binshtein=3Cbr=3EPh=2ED student =3Cbr=3EDepartment of Life Science
=3Cbr=
=3EBen Gurion University of the Negev=3Cbr=3EPh=3A
972-8-6461325=3C/BR=3E=
=3C/BR=3E=E2=80=8E
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------------------------------
Date: Thu, 30 Jul 2009 13:25:43 +0100
From: "Stein, ND (Norman)" <[email protected]>
Subject: Re: refmac failed message
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Hi Elad
=20
You don't say which version of Refmac you are using but I think the =
first thing to do would be to try the latest version (5.5.0102). You
can =
pick this up from
=20
ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe
=20
Copy this exe file to the bin subdirectory of your CCP4 installation. =
(Probably wise to make a backup copy of the existing refmac5.exe first).
=20
Best wishes
=20
Norman Stein
CCP4
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of =
Elad Binshtien
Sent: 30 July 2009 11:50
To: [email protected]
Subject: [ccp4bb] refmac failed message
Dear all,
I am refining a structure in Refmac at 2.2 A in win OS. However,
Refmac =
failed and send this message: forrtl: error (72): floating =
overflow =20
Thank you in advance for your any helpful suggestions. =20
Best,
Elad
Elad Binshtein
Ph.D student=20
Department of Life Science=20
Ben Gurion University of the Negev
Ph: 972-8-6461325
=FD=20
-- =0AScanned by iCritical.=0A
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charset="windows-1255"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dwindows-1255">
<META content=3D"MSHTML 6.00.2900.3562" name=3DGENERATOR></HEAD>
<BODY>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>Hi Elad</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2></FONT></SPAN> </DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>You don't say which version of Refmac you are =
using but I=20
think the first thing to do would be to try the latest =
version (5.5.0102).=20
You can pick this up from</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2></FONT></SPAN> </DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2><A=20
href=3D"ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe";>ftp=
://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe</A></FONT></SPA=
N></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2></FONT></SPAN> </DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>Copy this exe file to the bin subdirectory
of=20
your CCP4 installation. (Probably wise to make a backup copy =
of the=20
existing refmac5.exe first).</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2></FONT></SPAN> </DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>Best wishes</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2></FONT></SPAN> </DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>Norman Stein</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D419481712-30072009><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>CCP4</FONT></SPAN></DIV><BR>
<DIV class=3DOutlookMessageHeader lang=3Den-us dir=3Dltr align=3Dleft>
<HR tabIndex=3D-1>
<FONT face=3DTahoma size=3D2><B>From:</B> CCP4 bulletin board=20
[mailto:[email protected]] <B>On Behalf Of </B>Elad=20
Binshtien<BR><B>Sent:</B> 30 July 2009 11:50<BR><B>To:</B>=20
[email protected]<BR><B>Subject:</B> [ccp4bb] refmac failed=20
message<BR></FONT><BR></DIV>
<DIV></DIV>Dear all,<BR><BR><BR>I am refining a structure in Refmac at =
2.2 A in=20
win OS. However, Refmac failed and send this message: =
=20
forrtl: error (72): floating overflow <BR><BR>Thank =
you in=20
advance for your any helpful suggestions. =20
<BR><BR><BR>Best,<BR>Elad<BR><BR><BR>Elad Binshtein<BR>Ph.D student=20
<BR>Department of Life Science <BR>Ben Gurion University of the =
Negev<BR>Ph:=20
972-8-6461325<BR><BR>=FD
<br>=
<p>-- =0A<BR>Scanned by iCritical.=0A</p>
<br>=
</BODY></HTML>
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------------------------------
Date: Fri, 31 Jul 2009 00:00:25 +0800
From: Jiamu Du <[email protected]>
Subject: question of extra high B factor
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Dear All,
I am refining a structure of a complex between of 50kD protein and a
20kD
glycosylated protien. The data is of 2.9 A resolution. The wilson B
factor
is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is
extra
high. For the 50kD part, the average B factor is 76.5 A^2. But the B
factor
of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
electron density looks fine, even the sugar chain is seen clearly.
My question is:
1. How to reduce the B factor to a reasonable level?
2. If it can not be redueced, when I published it, is this value
acceptable?
3. In the same of similar resolutionIs, is there some other
structures like
this situation? A component or a subunit of the protein has a extra
high B
factor as high as 130.
Thanks and best wishes.
--
Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: [email protected]
--00221504874fd6c69c046fee6655
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Dear All,<br>I am refining a structure of a complex between of 50kD
protein=
and a 20kD glycosylated protien. The data is of 2.9 A resolution. The
wils=
on B factor is as high as 86.3 A^2.<br>The refinement seems well with
R/Rf =
of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the
averag=
e B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated
protein =
is as high as 133.3 A^2. Although the electron density looks fine,
even the=
sugar chain is seen clearly.<br>
My question is:<br>1. How to reduce the B factor to a reasonable
level?<br>=
2. If it can not be redueced, when I published it, is this value
acceptable=
?<br>3. In the same of similar resolutionIs, is there some other
structures=
like this situation?=A0 A component or a subunit of the protein has a
extr=
a high B factor as high as 130.<br>
<br>Thanks and best wishes.<br><br clear=3D"all"><br>-- <br>Jiamu Du,
Ph.D.=
<br>State Key Laboratory of Molecular Biology<br>Institute of
Biochemistry =
and Cell Biology<br>Shanghai Institutes for Biological
Sciences<br>Chinese =
Academy of Sciences<br>
320 Yue-Yang Road<br>Shanghai 200031<br>P. R. China<br>Tel:
+86-21-5492-111=
7<br>E-mail: <a
href=3D"mailto:[email protected]";>[email protected]</a><br>
--00221504874fd6c69c046fee6655--
------------------------------
Date: Thu, 30 Jul 2009 09:32:26 -0700
From: Pavel Afonine <[email protected]>
Subject: Re: question of extra high B factor
Hi Jiamu,
My question is:
1. How to reduce the B factor to a reasonable level?
3. In the same of similar resolutionIs, is there some other structures
like this situation?
POLYGON tool is (one of) your friend(s) to answer this question (apart
from debatable one about "a reasonable level"):
Acta Cryst. D65, 297-300 (2009).
Now it is available in PHENIX (from the latest nightly builds):
http://www.phenix-online.org/
Please let me know if you have any questions about it.
Pavel.
------------------------------
Date: Thu, 30 Jul 2009 17:47:55 +0100
From: Clemens Vonrhein <[email protected]>
Subject: Re: question of extra high B factor
Dear Jiamu,
On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote:
I am refining a structure of a complex between of 50kD protein and a
20kD
glycosylated protien. The data is of 2.9 A resolution. The wilson B
factor
is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor
is extra
high. For the 50kD part, the average B factor is 76.5 A^2. But the B
factor
of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
electron density looks fine, even the sugar chain is seen clearly.
My question is:
1. How to reduce the B factor to a reasonable level?
How do you define 'reasonable'? And why would you want to reduce this
anyway?
( 50*76.5 + 20*133.3 ) / 70 = 92.7
which seems fairly close to the Wilson B of 86.3, right?
2. If it can not be redueced, when I published it, is this value
acceptable?
Better question: is it the right value? Remember it is
results -> publish
and not
publish <- results
;-)
If they're correct than they are acceptable (I would accept those
values).
3. In the same of similar resolutionIs, is there some other
structures like
this situation? A component or a subunit of the protein has a extra
high B
factor as high as 130.
I'm sure hundreds of them ... but I'm sure you want your structure to
stand on its own, so don't look too close at other structures and
repeat the various mistakes we've all made and that are now set in
stone in some old PDB file.
Cheers
Clemens
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
------------------------------
Date: Fri, 31 Jul 2009 00:02:42 +0800
From: Jiamu Du <[email protected]>
Subject: Re: question of extra high B factor
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I am using TLS refinement with Phenix for the structure refinement.
On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du <[email protected]> wrote:
Dear All,
I am refining a structure of a complex between of 50kD protein and a
20kD
glycosylated protien. The data is of 2.9 A resolution. The wilson B
factor
is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor
is extra
high. For the 50kD part, the average B factor is 76.5 A^2. But the B
factor
of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
electron density looks fine, even the sugar chain is seen clearly.
My question is:
1. How to reduce the B factor to a reasonable level?
2. If it can not be redueced, when I published it, is this value
acceptable?
3. In the same of similar resolutionIs, is there some other
structures like
this situation? A component or a subunit of the protein has a extra
high B
factor as high as 130.
Thanks and best wishes.
--
Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: [email protected]
--
Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: [email protected]
--0022152d604d09ee86046fee6f07
Content-Type: text/html; charset=ISO-8859-1
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I am using TLS refinement with Phenix for the structure
refinement.<br><br>=
<br><div class=3D"gmail_quote">On Fri, Jul 31, 2009 at 12:00 AM,
Jiamu Du <=
span dir=3D"ltr"><<a
href=3D"mailto:[email protected]";>[email protected]=
</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid
rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear
All,<br>I am=
refining a structure of a complex between of 50kD protein and a 20kD
glyco=
sylated protien. The data is of 2.9 A resolution. The wilson B factor
is as=
high as 86.3 A^2.<br>
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is
extra=
high. For the 50kD part, the average B factor is 76.5 A^2. But the B
facto=
r of the 20 kD glycosylated protein is as high as 133.3 A^2. Although
the e=
lectron density looks fine, even the sugar chain is seen clearly.<br>
My question is:<br>1. How to reduce the B factor to a reasonable
level?<br>=
2. If it can not be redueced, when I published it, is this value
acceptable=
?<br>3. In the same of similar resolutionIs, is there some other
structures=
like this situation?=A0 A component or a subunit of the protein has a
extr=
a high B factor as high as 130.<br>
<br>Thanks and best wishes.<br><br clear=3D"all"><br>-- <br>Jiamu Du,
Ph.D.=
<br>State Key Laboratory of Molecular Biology<br>Institute of
Biochemistry =
and Cell Biology<br>Shanghai Institutes for Biological
Sciences<br>Chinese =
Academy of Sciences<br>
320 Yue-Yang Road<br>Shanghai 200031<br>P. R. China<br>Tel:
+86-21-5492-111=
7<br>E-mail: <a href=3D"mailto:[email protected]";
target=3D"_blank">jiamudu=
@gmail.com</a><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jiamu Du,
Ph.D.<br>Stat=
e Key Laboratory of Molecular Biology<br>Institute of Biochemistry
and Cell=
Biology<br>Shanghai Institutes for Biological Sciences<br>Chinese
Academy =
of Sciences<br>
320 Yue-Yang Road<br>Shanghai 200031<br>P. R. China<br>Tel:
+86-21-5492-111=
7<br>E-mail: <a
href=3D"mailto:[email protected]";>[email protected]</a><br>
--0022152d604d09ee86046fee6f07--
------------------------------
Date: Thu, 30 Jul 2009 10:24:25 -0700
From: Huiying Li <[email protected]>
Subject: Coot:findwaters in REFMAC
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters to
the refined structure. Often for the well ordered water sites the
routine added two water molecules in single water site, with their
distance (~1 Angs) way shorter than allowed hydrogen bonding distance. I
have to remove the extra water molecules manually.
Is this a intended feature? It seems to only create extra work to the
user. What is the purpose of having different chain IDs for waters
output
from this routine?
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [email protected]
------------------------------
Date: Thu, 30 Jul 2009 18:33:01 +0100
From: Paul Emsley <[email protected]>
Subject: Re: Coot:findwaters in REFMAC
Huiying Li wrote:
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters
to the refined structure. Often for the well ordered water sites the
routine added two water molecules in single water site, with their
distance (~1 Angs) way shorter than allowed hydrogen bonding distance.
I have to remove the extra water molecules manually.
Sounds like an old version. Things have improved.
Is this a intended feature? It seems to only create extra work to the
user.
:-(
What is the purpose of having different chain IDs for waters output
from this routine?
I thought (at the time) that it was sensible to add waters to a
different chain ID to the protein atoms (I still do, in fact). There
are others (somewhat less involved in model-building I suspect) that
think otherwise.
Paul.
------------------------------
Date: Thu, 30 Jul 2009 20:56:14 +0200
From: Kay Diederichs <[email protected]>
Subject: Re: question of extra high B factor
This is a cryptographically signed message in MIME format.
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Content-Transfer-Encoding: 7bit
Jiamu Du schrieb:
Dear All,
I am refining a structure of a complex between of 50kD protein and a
20kD glycosylated protien. The data is of 2.9 A resolution. The
wilson B
factor is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is
extra high. For the 50kD part, the average B factor is 76.5 A^2. But
the
B factor of the 20 kD glycosylated protein is as high as 133.3 A^2.
Although the electron density looks fine, even the sugar chain is seen
clearly.
My question is:
1. How to reduce the B factor to a reasonable level?
Please check out
<http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#help.2C_my_protein_has_high_B-factors.21>
2. If it can not be redueced, when I published it, is this value
acceptable?
As there's nothing wrong with it, it can be published.
3. In the same of similar resolutionIs, is there some other structures
like this situation? A component or a subunit of the protein has a
extra high B factor as high as 130.
Just look at the B-factors of new PDB entries which have a a resolution
worse than 3 A (e.g., membrane proteins) - there are quite a few of
those.
HTH,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [email protected] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
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--------------ms000208020902090005010407--
------------------------------
Date: Thu, 30 Jul 2009 21:13:45 +0200
From: Luca Jovine <[email protected]>
Subject: Postdoctoral position in protein crystallography at
Karolinska Institutet
POSTDOCTORAL FELLOWSHIP IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA
INSTITUT=
ET
As part of a collaboration between the laboratories of Rune
Toftg=E5rd an=
d Luca Jovine at the =
KI Department of Biosciences and Nutrition and the Center for
Biosciences=
=2C a postdoctoral =
position is immediately available on structural studies of key
players in=
the Hedgehog =
signaling pathway=2E
The Department of Biosciences and Nutrition has state-of-the-art
equipmen=
t for protein =
expression=2C purification and in house X-ray data collection=3B
frequent=
access to synchrotron =
sites and excellent computational facilities are also available=2E
With t=
heir close integration of =
academic=2C clinical and industrial research=2C KI and the Center for
Bio=
sciences offer a highly =
international and collaborative environment for biomedical studies=2E
Highly motivated candidates with experience in protein expression
(partic=
ularly in insect =
and/or mammalian cells)=2C purification=2C crystallization and
structure =
determination=2C are =
encouraged to apply by e-mailing a curriculum vitae=2C summary of
researc=
h experience and =
interests=2C and names and contact information for two references to
Luca=
Jovine =
(luca=2Ejovine=40ki=2Ese)=2E Please note that=2C in order to be
eligible =
for this scholarship=2C candidates =
should be non-Swedish citizens who have obtained a doctorate or the
equiv=
alent outside =
Sweden=2E Deadline for application is 1 October 2009=2E
------------------------------------------------
Luca Jovine=2C Ph=2ED=2E
Group Leader=2C Protein Crystallography Unit
Karolinska Institutet
Department of Biosciences and Nutrition
H=E4lsov=E4gen 7=2C SE-141 57 Huddinge=2C Sweden
Voice=3A +46=2E(0)8=2E6083-301 FAX=3A +46=2E(0)8=2E6089-290
E-mail=3A luca=2Ejovine=40ki=2Ese
W3=3A http=3A//jovinelab=2Eorg
------------------------------------------------
------------------------------
Date: Thu, 30 Jul 2009 12:29:09 -0700
From: Donnie Berkholz <[email protected]>
Subject: Re: question of extra high B factor
--/9DWx/yDrRhgMJTb
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On 00:00 Fri 31 Jul , Jiamu Du wrote:
Dear All,
I am refining a structure of a complex between of 50kD protein and a
20kD
glycosylated protien. The data is of 2.9 A resolution. The wilson B
factor
is as high as 86.3 A^2.
The refinement seems well with R/Rf of 0.21/0.25. But the B-factor
is ext=
ra
high. For the 50kD part, the average B factor is 76.5 A^2. But the B
fact=
or
of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
electron density looks fine, even the sugar chain is seen clearly.
My question is:
1. How to reduce the B factor to a reasonable level?
2. If it can not be redueced, when I published it, is this value
acceptab=
le?
3. In the same of similar resolutionIs, is there some other
structures li=
ke
this situation? A component or a subunit of the protein has a extra
high=
B
factor as high as 130.
Our group published a paper a few years ago with an average B of 80
A^2=20
(JMB 328:893 (2003)). One referee had some objections to this, so we=20
performed analyses of the whole Protein Data Bank for proteins at=20
2.5-3.0 A (see Fig. 2D in the paper). You may find this figure useful
if=20
you need to convince anyone.
--=20
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
--/9DWx/yDrRhgMJTb
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--/9DWx/yDrRhgMJTb--
------------------------------
Date: Thu, 30 Jul 2009 17:53:15 -0400
From: Jim Fairman <[email protected]>
Subject: Re: OpenGL Stereo 3D on 120 Hz LCDs, at last!
--0015174be078b3c278046ff354f1
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Just got this working on a machine with a Quadro FX 3800. Stereo looks
great on both Pymol (v1.1) and the latest build of WinCoot (v0.6 build
2172).
On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano <[email protected]>
wrote:
FYI, for folks not subscribed to pymol-users:
nVidia today released beta drivers which at last enable OpenGL-based
stereo
3D visualization on 120 Hz LCDs using Quadro graphics cards. So
long as you
are willing to put up with Windows, you can finally abandon those
old CRTs
without spending a fortune and without sacrificing quality of the
stereo 3D
effect.
Details posted at http://www.pymol.org
Cheers,
Warren
--
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [email protected] [email protected]
--0015174be078b3c278046ff354f1
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Just got this working on a machine with a Quadro FX 3800.=A0 Stereo
looks g=
reat on both Pymol (v1.1) and the latest build of WinCoot (v0.6 build
2172)=
.<br><br><div class=3D"gmail_quote">On Fri, Jul 17, 2009 at 1:20 AM,
Warren=
DeLano <span dir=3D"ltr"><<a
href=3D"mailto:[email protected]";>war...@d=
elsci.com</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid
rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link=3D"blue" vlink=3D"purple" lang=3D"EN-US">
<div>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">FYI, for folks not subscribed to pymol-users:=A0
</span></font=
</p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">=A0</span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">nVidia today released beta drivers which at last enable
OpenGL=
-based
stereo 3D visualization on 120 Hz LCDs using Quadro graphics
cards.=A0 So l=
ong
as you are willing to put up with Windows, you can finally abandon
those ol=
d CRTs
without spending a fortune and without sacrificing quality of the
stereo 3D
effect.</span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">=A0</span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">Details posted at <a href=3D"http://www.pymol.org/";
target=3D"=
_blank">http://www.pymol.org</a></span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">=A0</span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">Cheers,</span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">Warren</span></font><font size=3D"2"
face=3D"Arial"><span styl=
e=3D"font-size: 10pt; font-family: Arial;"></span></font></p>
<p><font size=3D"2" face=3D"Arial"><span style=3D"font-size: 10pt;
font-fam=
ily: Arial;">=A0</span></font></p>
</div>
</div>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jim
Fairman<br>Graduate=
Research Assistant<br>Department of Biochemistry, Cellular, and
Molecular =
Biology (BCMB)<br>University of Tennessee --
Knoxville<br>216-368-3337 <a h=
ref=3D"mailto:[email protected]";>[email protected]</a> <a
href=3D"mailto:jame=
[email protected]">[email protected]</a><br>
--0015174be078b3c278046ff354f1--
------------------------------
Date: Thu, 30 Jul 2009 15:23:04 -0700
From: James Holton <[email protected]>
Subject: Re: Foils for energy calibration
At ALS, we have a box of foils from EXAFS Materials that seems to get=20
passed around from beamline to beamline. I ran absorption scans on
17=20
edges from the metals in the box one day, and found that there was=20
considerable scatter in the expected vs observed edge positions:
http://bl831.als.lbl.gov/~jamesh/pickup/mono_calib.png
Here I have plotted the "correct" position of each edge as determined
by=20
Bearden & Burr (1967), against the edge I determined using the
criterion=20
recommended in the "Reference Spectra" document in the=20
exafsmaterials.com website: the first inflection point in the
derivative=20
spectrum. I think a large amount of the scatter is because my mono=20
(like many PX/MX beamlines) is Si(111) and not Si(220) like the one
used=20
to determine the reference spectra. It is not hard to imagine how=20
blurring the spectrum with a wider energy spread of the incident beam=20
will shift the position of the "edge". One could try to use the=20
electron binding energy tabulated in the "little orange book":
http://xdb.lbl.gov/Section1/Sec_1-1.html
but these do not always take into account the "near edge" features
(like=20
the white line from SeMet) which change depending on the chemical=20
environment around the metal, radiation damage, etc. It would be
nice=20
if someone could calibrate some standard reference materials using a=20
Si(111) monochromator, but I don't know of anyone who has done this.
However, another way to get your x-ray wavelength is using Bragg's law:
lambda =3D 2*d*sin(theta)
and the d-spacing of silicon is known to be 5.43159 =B1 0.00020 A,
and=20
NIST will sell you certified Si powder:
https://www-s.nist.gov/srmors/view_detail.cfm?srm=3D640d
The problem here is that although you know d very accurately, the
error=20
in lambda is dominated by sin(theta), or rather the uncertainty in
your=20
detector distance. The pixel field on most detectors is actually
quite=20
accurate, as a NIST-traceable calibration is used to make the pinhole=20
calibration mask, and the encoder on most detector distance stages is=20
very accurate for relative moves (counting ticks on the encoder).
But=20
there is always an offset from the "zero" position predicted by the=20
encoder to the true center of rotation that is hard to know.=20
Nevertheless, all you really want is for the d-spacing of silicon
powder=20
rings to be right at all detector distances. You can use the program=20
FIT2D to refine the wavelength, distance, detector tilt, etc. or any=20
combination thereof for a given image, but you will find that the=20
repeatability of such a fit (using different starting parameters) is
not=20
great because the distance and wavelength are highly correlated. =20
However, there is a way around this:
Since we know that a relative move of the distance will be accurate,=20
there should be one and only one offset that you can add to the
recorded=20
value of distance of each image to make it the "right" distance. You=20
can define the "right" offset as the one where FIXing the resulting=20
"right" distance in FIT2D and refining everything else gives you the=20
same refined value for the wavelength from every image. You need to=20
manually "refine" this offset for a few rounds. What you will
generally=20
see is that the graph of fitted wavelength vs the distance is a
straight=20
line, and you want to make the slope of this line to be zero. =20
Eventually, you will arrive at some offset that gives you the
smallest=20
spread in refined wavelength values. The average refined wavelength
is=20
then the "true" wavelength. Should be able to get it within one or
two=20
eV. Perhaps more if you take a lot of silicon powder images.
At ALS beamlines 8.3.1 and 12.3.1 I have done both kinds of
calibration,=20
and I am fairly certain I get the wavelength accurate to within 1 eV
by=20
calibrating the half-way-up point of an absorption scan of a ~122
micron=20
thick copper metal foil to 8979.0 eV.
-James Holton
MAD Scientist
Richard Gillilan wrote:
In the past we've used elemental foils from exafsmaterials.com for=20
energy calibration of our MAD beamline. These standards are for
EXAFS=20
and XANES. Most are thin (5 micron) metal foils.
Has anyone had experience with other sources of standards or other=20
forms (such as compounds rather than pure elements)?
I notice that a number of companies offer XRF standard kits.
Richard Gillilan
MacCHESS
------------------------------
End of CCP4BB Digest - 29 Jul 2009 to 30 Jul 2009 (#2009-207)
*************************************************************
