Alex,
With regard to scalepack, be sure you use NO MERGE ORIGINAL INDEX, not
just NO MERGE.
Marian Szebenyi
MacCHESS
> Dear all:
>
> I am trying to solve a structure from apparently a hexagonal crystal.
> I indexed and scaled data in P6 in Scalepack (with merging) then used
> Scalepack2mtz (with ensure unique reflections and add Rfree as well as
> the truncate procedure), and then attempted to run molecular
> replacement with Phaser. Now the problem appeared - Phaser immediately
> quits with the following error message "FATAL RUNTIME ERROR:
> Reflections are not a unique set by symmetry". I do not understand
> this at all.
>
> I also tried running scalepack using the NO MERGE macro as people have
> indicated earlier on this bb (thank you again!, I also checked the
> scl.in that is written out and it had the NO MERGE statement), and
> then tried to run pointless to verify the spacegroup but the program
> complained the reflections are merged (that is impossible, I checked
> the number of reflections in the unmerged and merged files and they
> were different as one would expect). I repeated the procedures several
> times and I always get the same errors. I can't make any sense of this
> and I can't move forward. Any ideas?
>
> Many thanks,
> Alex
>
>
>
>
>
>
> On Jul 30, 2009, at 7:03 PM, CCP4BB automatic digest system wrote:
>
>> 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
>>
>> ----------------------------------------------------------------------
>>
>> Date: Thu, 30 Jul 2009 10:50:13 GMT
>> From: Elad Binshtien <[log in to unmask]>
>> Subject: refmac failed message
>>
>> This is a multi-part message in MIME format.
>>
>>
>> ----8d5c55134e491a1d1bdd
>> Content-Type: text/plain; charset=utf-8
>> Content-Disposition: inline
>> Content-Transfer-Encoding: quoted-printable
>>
>> 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
>>
>> ----8d5c55134e491a1d1bdd
>> Content-Type: text/html; charset=utf-8
>> Content-Disposition: inline
>> Content-Transfer-Encoding: quoted-printable
>>
>> 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
>>
>> ----8d5c55134e491a1d1bdd--
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 13:25:43 +0100
>> From: "Stein, ND (Norman)" <[log in to unmask]>
>> Subject: Re: refmac failed message
>>
>> This is a multi-part message in MIME format.
>>
>> ------_=_NextPart_001_01CA1110.DB7CC0CB
>> Content-Type: text/plain;
>> charset="windows-1255"
>> Content-Transfer-Encoding: quoted-printable
>>
>> 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:[log in to unmask]] On Behalf
>> Of =
>> Elad Binshtien
>> Sent: 30 July 2009 11:50
>> To: [log in to unmask]
>> 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
>>
>> ------_=_NextPart_001_01CA1110.DB7CC0CB
>> Content-Type: text/html;
>> charset="windows-1255"
>> Content-Transfer-Encoding: quoted-printable
>>
>> <!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:[log in to unmask]] <B>On Behalf Of </B>Elad=20
>> Binshtien<BR><B>Sent:</B> 30 July 2009 11:50<BR><B>To:</B>=20
>> [log in to unmask]<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>
>>
>> ------_=_NextPart_001_01CA1110.DB7CC0CB--
>>
>> ------------------------------
>>
>> Date: Fri, 31 Jul 2009 00:00:25 +0800
>> From: Jiamu Du <[log in to unmask]>
>> Subject: question of extra high B factor
>>
>> --00221504874fd6c69c046fee6655
>> Content-Type: text/plain; charset=ISO-8859-1
>> Content-Transfer-Encoding: 7bit
>>
>> 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: [log in to unmask]
>>
>> --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:[log in to unmask]">[log in to unmask]</
>> a><br>
>>
>> --00221504874fd6c69c046fee6655--
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 09:32:26 -0700
>> From: Pavel Afonine <[log in to unmask]>
>> 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 <[log in to unmask]>
>> 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 <[log in to unmask]>
>> Subject: Re: question of extra high B factor
>>
>> --0022152d604d09ee86046fee6f07
>> Content-Type: text/plain; charset=ISO-8859-1
>> Content-Transfer-Encoding: 7bit
>>
>> I am using TLS refinement with Phenix for the structure refinement.
>>
>>
>> On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du <[log in to unmask]> 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: [log in to unmask]
>>>
>>
>>
>>
>> --
>> 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: [log in to unmask]
>>
>> --0022152d604d09ee86046fee6f07
>> Content-Type: text/html; charset=ISO-8859-1
>> Content-Transfer-Encoding: quoted-printable
>>
>> 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:[log in to unmask]">[log in to unmask]
>> =
>> </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:[log in to unmask]"
>> 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:[log in to unmask]">[log in to unmask]</
>> a><br>
>>
>> --0022152d604d09ee86046fee6f07--
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 10:24:25 -0700
>> From: Huiying Li <[log in to unmask]>
>> 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: [log in to unmask]
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 18:33:01 +0100
>> From: Paul Emsley <[log in to unmask]>
>> 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 <[log in to unmask]>
>> Subject: Re: question of extra high B factor
>>
>> This is a cryptographically signed message in MIME format.
>>
>> --------------ms000208020902090005010407
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> 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: [log in to unmask] 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 <[log in to unmask]>
>> 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 <[log in to unmask]>
>> Subject: Re: question of extra high B factor
>>
>> --/9DWx/yDrRhgMJTb
>> Content-Type: text/plain; charset=us-ascii
>> Content-Disposition: inline
>> Content-Transfer-Encoding: quoted-printable
>>
>> 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
>> Content-Type: application/pgp-signature
>> Content-Disposition: inline
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v2.0.11 (GNU/Linux)
>>
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>> =gKGd
>> -----END PGP SIGNATURE-----
>>
>> --/9DWx/yDrRhgMJTb--
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 17:53:15 -0400
>> From: Jim Fairman <[log in to unmask]>
>> 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 <[log in to unmask]>
>> 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 [log in to unmask] [log in to unmask]
>>
>> --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:[log in to unmask]">warren@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:[log in to unmask]">[log in to unmask]</a> <a
>> href=3D"mailto:jame=
>> [log in to unmask]">[log in to unmask]</a><br>
>>
>>
>> --0015174be078b3c278046ff354f1--
>>
>> ------------------------------
>>
>> Date: Thu, 30 Jul 2009 15:23:04 -0700
>> From: James Holton <[log in to unmask]>
>> 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)
>> *************************************************************
>
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