Re: [ccp4bb] differences Rfactor calculations

[Dirk Kostrewa]

 ... yes, and this is the reason why sfcheck should be replaced by a 
more modern program at the Protein Data Bank!


Best regards,

Dirk.

Am 13.07.10 22:15, schrieb Ethan Merritt:

Should be in an FAQ somewhere:
Q: Why does sfcheck not reproduce my original R factors?
A: Because instead of using the Fc in your file, sfcheck tries to
re-calculate Fc using only your atom names, coordinates and isotropic
B factors.  This is bad, because it ignores any contributions to your
original Fc from things like F_partial, Anisotropic corrections,
TLS models, scattering factor corrections, riding hydrogens, etc.

My advice is to use sfcheck only to evaluate the Fobs file resulting from
your data collection. It is not a suitable tool for validating a refined
model.



The same happened when I used this final model as starting model for a
refinement with Refmac5. Again I got an Rfactor of 20.8%.

Probably you failed to describe the full model to refmac.
Refmac and phenix.refine can both handle all the contributing factors
listed above, but it may take some work to pick a the correct
corresponding set of options.


Ethan



As far as I know, Phenix uses different algorithms for the refinement
than other programs, which in some cases can make Phenix gets better
Rfactors. Could these differences be the reason for this large
difference in the calculated Rfactors? Or I have to recheck my procedure
for mistakes?

Thanks a lot in advanced.
Looking forward to hearing form you.

Cheers,
Ariel



--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] imosflm on MAC OSX

[Martin M. Ripoll]

Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the
following errors:

 

testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 142:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 149:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 156:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 165:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 172:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file

/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
/usr/local/ccp4-6.1.13/bin/wish: Unknown error: 0

 

We have in the lab two other MAC machines with the same OSX and running the
same ccp4 version, and unexpectedly  imosflm runs perfectly.

Does anybody have a solution for this?

 

Thanks in advance,

Martin



Dr. Martin Martinez-Ripoll

Research Professor

  xmar...@iqfr.csic.es

Department of Crystallography & Structural Biology

  www.xtal.iqfr.csic.es

Consejo Superior de Investigaciones Científicas

Spanish National Research Council

www.csic.es

  Sin título-1

 

<>

Re: [ccp4bb] imosflm on MAC OSX

[Tim Gruene]

Dear Martin,

the error message 'cannot execute binary file' probably means that this is a
binary for a different platform (maybe PC, or a 64bit binary while your OS is
32bit).

check out the result of 
 file /usr/local/ccp4-6.1.13/bin/wish
and if that 'wish' is a link, follow it until you get to the binary.

If the message does not tell you anything, post it to the board so that we can
assist.

Tim

On Wed, Jul 14, 2010 at 09:58:41AM +0200, Martin M. Ripoll wrote:
> Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the
> following errors:
> 
>  
> 
> testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 142:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 149:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 156:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 165:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 172:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
> /usr/local/ccp4-6.1.13/bin/wish: Unknown error: 0
> 
>  
> 
> We have in the lab two other MAC machines with the same OSX and running the
> same ccp4 version, and unexpectedly  imosflm runs perfectly.
> 
> Does anybody have a solution for this?
> 
>  
> 
> Thanks in advance,
> 
> Martin
> 
> 
> 
> Dr. Martin Martinez-Ripoll
> 
> Research Professor
> 
>   xmar...@iqfr.csic.es
> 
> Department of Crystallography & Structural Biology
> 
>   www.xtal.iqfr.csic.es
> 
> Consejo Superior de Investigaciones Científicas
> 
> Spanish National Research Council
> 
> www.csic.es
> 
>   Sin título-1
> 
>  
> 



-- 
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

[Martyn Winn]

Which is why I said "make available" rather than "post it" or "email
me" :)

And he has done just that  will go have a look 

m

On Tue, 2010-07-13 at 18:42 -0700, James Holton wrote:
> 
> The original poster just told me that the map file is 2.6 GB.  Please
> don't encourage him to attach it to a ccp4bb email!
> 
> -James Holton
> MAD Scientist
> 
> 
> On Tue, Jul 13, 2010 at 2:58 PM,  wrote:
> Actually, zero spacegroup should be tolerated by the CCP4
> library now.
> 
> We were recently alerted to another problem, caused by
> non-zero origin in the EM map header. But I think this is
> different to the problem of the original poster.
> 
> It's probably fair to say we haven't tested enough against
> real EM maps, and perhaps we should.
> 
> Perhaps the original poster could make their problem maps
> available??
> 
> Cheers
> Martyn
> 
> 
> -Original Message-
> From: CCP4 bulletin board on behalf of Christoph Best
> Sent: Tue 7/13/2010 10:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] conversion of cyroEM reconstruction from
> MRC to CCP4 format
> 
> Hello,
> 
> we have found that there are some minor issues in MRC files
> using in Em
> that can make them unpalatable to the CCP4 map library. You
> can easily
> look at header fields in Python - here is a sample program to
> quickly
> check some of the more common problems.
> 
>from struct import *
> 
>header=file('your_file_name.map').read(1024)
>print 'dimensions=',unpack_from('iii',header,0)
>print 'mode=',unpack_from('i',header,3*4)[0],'should be 0,
> 1, or 2'
>print 'space
> group=',unpack_from('i',header,22*4)[0],'should be 1'
>print 'magic=',unpack_from('',header,52*4),'should be
> (\'M\', \'A\', \'P\', \' \')'
>print 'machine stamp=','%x' %
> unpack_from('i',header,53*4),' should be 4144 or '
>print 'nsymbt=',unpack_from('i',header,23*4)[0],' should be
> 0'
> 
> The issues we typically encountered were bad space groups
> (zero), wrong
> machine stamps (they should be 0x or 0x4144), missing the
> "magic
> bytes" that spell "MAP ", or a value of nsymbt that indicates
> the
> presence of additional symmetry information following the
> header, which
> is then missing.
> 
> Chimera ignores most of these issues.
> 
> -Christoph
> 
> --
> | Christoph Best 
> http://www.ebi.ac.uk/~best
> | European Bioinformatics Institute, Cambridge, UK
> +44-1223-492649
> 
> 
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] imosflm on MAC OSX

[Martin M. Ripoll]

Dear Tim,

Thank you very much for your help. In fact, the answer to:

file /usr/local/ccp4-6.1.13/bin/wish

is not a link. It answers just the following:

/usr/local/ccp4-6.1.13/bin/wish: data

So I am posting it also to the board...

Martin

Dr. Martin Martinez-Ripoll
Research Professor
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
Consejo Superior de Investigaciones Científicas
Spanish National Research Council
www.csic.es



-Mensaje original-
De: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] En nombre de Tim
Gruene
Enviado el: miércoles, 14 de julio de 2010 10:27
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: Re: [ccp4bb] imosflm on MAC OSX

Dear Martin,

the error message 'cannot execute binary file' probably means that this is a
binary for a different platform (maybe PC, or a 64bit binary while your OS
is 32bit).

check out the result of
 file /usr/local/ccp4-6.1.13/bin/wish
and if that 'wish' is a link, follow it until you get to the binary.

If the message does not tell you anything, post it to the board so that we
can assist.

Tim

On Wed, Jul 14, 2010 at 09:58:41AM +0200, Martin M. Ripoll wrote:


> Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the 
> following errors:
> 
> testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 142:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 149:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 156:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 165:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 172:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
> /usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> 
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236:
> /usr/local/ccp4-6.1.13/bin/wish: Unknown error: 0
> 
>  
> 
> We have in the lab two other MAC machines with the same OSX and 
> running the same ccp4 version, and unexpectedly  imosflm runs perfectly.
> 
> Does anybody have a solution for this?
> 
>  
> 
> Thanks in advance,
> 
> Martin
> 
> 
> 
> Dr. Martin Martinez-Ripoll
> Research Professor
>  xmar...@iqfr.csic.es
> Department of Crystallography & Structural Biology
>  www.xtal.iqfr.csic.es
> Consejo Superior de Investigaciones Científicas
> Spanish National Research Council
> www.csic.es
> 


--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

Re: [ccp4bb] imosflm on MAC OSX

[harry powell]

Hi

As Tim says, the Wish you seem to have set to $MOSFLM_WISH can't be  
run on OSX 10.6.4 - further to what he suggests, it's always  
worthwhile trying in case of problems (at the command line) -


which $MOSFLM_WISH

(in your case I guess it's set to "/usr/local/ccp4-6.1.13/bin/wish")

then

$MOSFLM_WISH

just to make sure it runs.

BTW, on OSX 10.6 (i.e. "Snow Leopard") I strongly recommend changing  
the default ccp4i MOSFLM_WISH to /usr/bin/wish8.4 - i.e. the Apple- 
supplied Wish 8.4 (wish 8.5 seems to be missing a load of stuff in  
their set-up); that way everything should run correctly and you get a  
nice Aqua TclTk experience rather than the rather agricultural X11  
TclTk you'd otherwise get. An addendum to this is that you cannot use  
Apple's Aqua TclTk for ccp4i because blt hasn't been ported to Aqua  
and probably never will be.



On 14 Jul 2010, at 08:58, Martin M. Ripoll wrote:

Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the  
following errors:


testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 142: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 149: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 156: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 165: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 172: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236: / 
usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236: / 
usr/local/ccp4-6.1.13/bin/wish: Unknown error: 0


We have in the lab two other MAC machines with the same OSX and  
running the same ccp4 version, and unexpectedly  imosflm runs  
perfectly.

Does anybody have a solution for this?

Thanks in advance,
Martin

Dr. Martin Martinez-Ripoll
Research Professor
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
Consejo Superior de Investigaciones Científicas
Spanish National Research Council
www.csic.es




Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH

Re: [ccp4bb] imosflm on MAC OSX

[Martin M. Ripoll]

Hi Harry,

Your remark was the solution to our "wish" problem. We have change the line:


setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish
to
setenv MOSFLM_WISH /usr/bin/wish8.4

and now imosflm runs as expected. 

Thank you very much for your help!

Martin

Dr. Martin Martinez-Ripoll
Research Professor
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
Consejo Superior de Investigaciones Científicas
Spanish National Research Council
www.csic.es



-Mensaje original-
De: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] En nombre de harry
powell
Enviado el: miércoles, 14 de julio de 2010 12:04
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: Re: [ccp4bb] imosflm on MAC OSX

Hi

As Tim says, the Wish you seem to have set to $MOSFLM_WISH can't be  
run on OSX 10.6.4 - further to what he suggests, it's always  
worthwhile trying in case of problems (at the command line) -

which $MOSFLM_WISH

(in your case I guess it's set to "/usr/local/ccp4-6.1.13/bin/wish")

then

$MOSFLM_WISH

just to make sure it runs.

BTW, on OSX 10.6 (i.e. "Snow Leopard") I strongly recommend changing  
the default ccp4i MOSFLM_WISH to /usr/bin/wish8.4 - i.e. the Apple- 
supplied Wish 8.4 (wish 8.5 seems to be missing a load of stuff in  
their set-up); that way everything should run correctly and you get a  
nice Aqua TclTk experience rather than the rather agricultural X11  
TclTk you'd otherwise get. An addendum to this is that you cannot use  
Apple's Aqua TclTk for ccp4i because blt hasn't been ported to Aqua  
and probably never will be.


On 14 Jul 2010, at 08:58, Martin M. Ripoll wrote:

> Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the  
> following errors:
>
> testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 142: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 149: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 156: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 165: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 172: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236: / 
> usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
> /usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 236: / 
> usr/local/ccp4-6.1.13/bin/wish: Unknown error: 0
>
> We have in the lab two other MAC machines with the same OSX and  
> running the same ccp4 version, and unexpectedly  imosflm runs  
> perfectly.
> Does anybody have a solution for this?
>
> Thanks in advance,
> Martin
> 
> Dr. Martin Martinez-Ripoll
> Research Professor
> xmar...@iqfr.csic.es
> Department of Crystallography & Structural Biology
> www.xtal.iqfr.csic.es
> Consejo Superior de Investigaciones Científicas
> Spanish National Research Council
> www.csic.es
> 
>

Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH

Re: [ccp4bb] differences Rfactor calculations

[Eleanor Dodson]

Everything said is true, but one of the most important factors in 
calculating structure factors and hence Rvalues is the scaling and 
solvent model. All of these are pretty inadequate - probably all protein 
"crystals" have large volumes of multiply ordered atoms - water 
networks, alternate conformations etc - and our calculations try to take 
these into account in different ways.  Hence there can be quite big 
differences between R factors although the Fcalcs are very similar.


  Eleanor


. Dirk Kostrewa wrote:
 ... yes, and this is the reason why sfcheck should be replaced by a 
more modern program at the Protein Data Bank!


Best regards,

Dirk.

Am 13.07.10 22:15, schrieb Ethan Merritt:

Should be in an FAQ somewhere:
Q: Why does sfcheck not reproduce my original R factors?
A: Because instead of using the Fc in your file, sfcheck tries to
re-calculate Fc using only your atom names, coordinates and isotropic
B factors.  This is bad, because it ignores any contributions to your
original Fc from things like F_partial, Anisotropic corrections,
TLS models, scattering factor corrections, riding hydrogens, etc.

My advice is to use sfcheck only to evaluate the Fobs file resulting from
your data collection. It is not a suitable tool for validating a refined
model.



The same happened when I used this final model as starting model for a
refinement with Refmac5. Again I got an Rfactor of 20.8%.

Probably you failed to describe the full model to refmac.
Refmac and phenix.refine can both handle all the contributing factors
listed above, but it may take some work to pick a the correct
corresponding set of options.


Ethan



As far as I know, Phenix uses different algorithms for the refinement
than other programs, which in some cases can make Phenix gets better
Rfactors. Could these differences be the reason for this large
difference in the calculated Rfactors? Or I have to recheck my procedure
for mistakes?

Thanks a lot in advanced.
Looking forward to hearing form you.

Cheers,
Ariel

[ccp4bb] covalent bond

[Vandana Kukshal]

how to make covalent
bond between ligand and protein residue by using CCp4 package

Re: [ccp4bb] covalent bond

[Paul Emsley]

On 14/07/10 12:56, Vandana Kukshal wrote:
how to make covalent bond between ligand and protein residue by using 
CCp4 package 


JLigand

http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html

p.s. Don't "Reply" if you are not following the same thread - doing so 
causes confusion to threaded mail readers.

Re: [ccp4bb] covalent bond

[Garib Murshudov]

Better link with nice tutorial from Andrey is:

www.ysbl.york.ac.uk/mxstat/

In the JLigand section there are some tutorials from Andrey to  
demonstrate how covalent links can be generated and used.


Garib

On 14 Jul 2010, at 14:35, Paul Emsley wrote:


On 14/07/10 12:56, Vandana Kukshal wrote:
how to make covalent bond between ligand and protein residue by  
using CCp4 package


JLigand

http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html

p.s. Don't "Reply" if you are not following the same thread - doing  
so causes confusion to threaded mail readers.

Re: [ccp4bb] differences Rfactor calculations

[Ariel Talavera]

Thanks a lot for all the quick replays to my post. It seems to be a
controversial topic. Bellow are to replays which more or less summarize
the answers to my post.

Cheers,
Ariel 


On Wed, 2010-07-14 at 07:44 -0500, Eleanor Dodson wrote:
> Everything said is true, but one of the most important factors in 
> calculating structure factors and hence Rvalues is the scaling and 
> solvent model. All of these are pretty inadequate - probably all protein 
> "crystals" have large volumes of multiply ordered atoms - water 
> networks, alternate conformations etc - and our calculations try to take 
> these into account in different ways.  Hence there can be quite big 
> differences between R factors although the Fcalcs are very similar.
> 
>Eleanor
> 
> 
> . Dirk Kostrewa wrote:
> >  ... yes, and this is the reason why sfcheck should be replaced by a 
> > more modern program at the Protein Data Bank!
> > 
> > Best regards,
> > 
> > Dirk.
> > 
> > Am 13.07.10 22:15, schrieb Ethan Merritt:
> >> Should be in an FAQ somewhere:
> >> Q: Why does sfcheck not reproduce my original R factors?
> >> A: Because instead of using the Fc in your file, sfcheck tries to
> >> re-calculate Fc using only your atom names, coordinates and isotropic
> >> B factors.  This is bad, because it ignores any contributions to your
> >> original Fc from things like F_partial, Anisotropic corrections,
> >> TLS models, scattering factor corrections, riding hydrogens, etc.
> >>
> >> My advice is to use sfcheck only to evaluate the Fobs file resulting from
> >> your data collection. It is not a suitable tool for validating a refined
> >> model.
> >>
> >>
> >>> The same happened when I used this final model as starting model for a
> >>> refinement with Refmac5. Again I got an Rfactor of 20.8%.
> >> Probably you failed to describe the full model to refmac.
> >> Refmac and phenix.refine can both handle all the contributing factors
> >> listed above, but it may take some work to pick a the correct
> >> corresponding set of options.
> >>
> >>
> >> Ethan
> >>
> >>
> >>> As far as I know, Phenix uses different algorithms for the refinement
> >>> than other programs, which in some cases can make Phenix gets better
> >>> Rfactors. Could these differences be the reason for this large
> >>> difference in the calculated Rfactors? Or I have to recheck my procedure
> >>> for mistakes?
> >>>
> >>> Thanks a lot in advanced.
> >>> Looking forward to hearing form you.
> >>>
> >>> Cheers,
> >>> Ariel
> >>>
> > 

[ccp4bb] Positions Available in Electron Crystallography of Membrane Proteins

[Iban Ubarretxena]

Positions Available: Electron Crystallography of Membrane Proteins

A number of different positions are available with the  
Transcontinental Electron Microscopy Initiative for Membrane Protein  
Structure (TEMIMPS;http://temimps.nysbc.org). TEMIMPS is a new center  
funded by the NIH Protein Structure Initiative and is composed of five  
research groups with combined expertise in membrane protein  
production, 2D crystallization, electron microscopy, image processing,  
and structure determination. Our center will focus on the development  
and implementation of high-throughput and high-resolution approaches  
to structure determination of membrane proteins using cryo-electron  
microscopy and 2D crystals. We are seeking highly motivated  
individuals with good communication skills and ability to interact  
with an interdisciplinary group ranging from biochemists to  
mathematicians. Individual positions will be available in New York,  
Cleveland, Seattle and Houston, working in the laboratories of Drs.  
David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel  
Penczek. These positions include a project manager, postdoctoral  
associates, software engineers and technical staff;  up-to-date  
descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs 
. Further questions or applications should be sent to  
temi...@nysbc.org.  Applications should include a cover letter, a  
curriculum vitae and contact information for three referees.  
Applications will be reviewed as they are received and will continue  
until the positions are filled.


Iban Ubarretxena-Belandia, PhD
Assistant Professor
Dept. Structural and Chemical Biology
Mount Sinai School of Medicine
Icahn Medical Institute Bldg., Room 16-70E
1425 Madison Avenue, Box 1677
New York, NY 10029

Office: 212-659-5593
Fax: 212-849-2456
Email: iban.ubarretx...@mssm.edu
WWW: http://www.mssm.edu/physbio/

This e-mail is confidential and may well also be legally privileged.  
If you have received it in error, you are on notice of its status.  
Please notify us immediately by reply e-mail and then delete this  
message from your system. Please do not copy it or use it for any  
purposes, or disclose its contents to any other person: to do so could  
be a breach of confidence. Thank you for your co-operation

[ccp4bb] Positions Available in Electron Crystallography of Membrane Proteins

[Iban Ubarretxena]

Positions Available: Electron Crystallography of Membrane Proteins

A number of different positions are available with the  
Transcontinental Electron Microscopy Initiative for Membrane Protein  
Structure (TEMIMPS;http://temimps.nysbc.org). TEMIMPS is a new center  
funded by the NIH Protein Structure Initiative and is composed of five  
research groups with combined expertise in membrane protein  
production, 2D crystallization, electron microscopy, image processing,  
and structure determination. Our center will focus on the development  
and implementation of high-throughput and high-resolution approaches  
to structure determination of membrane proteins using cryo-electron  
microscopy and 2D crystals. We are seeking highly motivated  
individuals with good communication skills and ability to interact  
with an interdisciplinary group ranging from biochemists to  
mathematicians. Individual positions will be available in New York,  
Cleveland, Seattle and Houston, working in the laboratories of Drs.  
David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel  
Penczek. These positions include a project manager, postdoctoral  
associates, software engineers and technical staff;  up-to-date  
descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs 
. Further questions or applications should be sent to  
temi...@nysbc.org.  Applications should include a cover letter, a  
curriculum vitae and contact information for three referees.  
Applications will be reviewed as they are received and will continue  
until the positions are filled.


Iban Ubarretxena-Belandia, PhD
Assistant Professor
Dept. Structural and Chemical Biology
Mount Sinai School of Medicine
Icahn Medical Institute Bldg., Room 16-70E
1425 Madison Avenue, Box 1677
New York, NY 10029

Office: 212-659-5593
Fax: 212-849-2456
Email: iban.ubarretx...@mssm.edu
WWW: http://www.mssm.edu/physbio/

This e-mail is confidential and may well also be legally privileged.  
If you have received it in error, you are on notice of its status.  
Please notify us immediately by reply e-mail and then delete this  
message from your system. Please do not copy it or use it for any  
purposes, or disclose its contents to any other person: to do so could  
be a breach of confidence. Thank you for your co-operation

Re: [ccp4bb] metal-chelating affinity chromatography and FosCholine detergents

[Ho Leung Ng]

Hi Pascal,

 I suspect the protein is aggregating in the presence of
FosCholine. In addition to the suggestions made by others, you can
also try changing the salt concentration or including additives like
glycerol in your FosCholine buffer. This can make an enormous
difference in the stability of the protein in detergent.


ho

Re: [ccp4bb] Perfect crystals but Low resolution

[Mary Ho]

Welcome to crystallography and the PhD.  Expect a lot of failure before your
degree.  I know its frustrating but all of the challenges you encounter will
teach you and increase your skills.  I had crystals my first year, moderate
resolution around 3 A and it took until end of my 4th year to phase a DNA
binding domain bound to DNA and then another 1.5 years to refine, generate
mutants and test binding.

Dealing with lab misinformation, although unfortunate and annoying, is also
part of the process.

You don't say what your resolution was.  New crystals, protein or dna
constructs or even additives might make a difference.  Did you test a room
temp crystal to make sure it's not your cryo effecting resolutions?

Hang in there.  A phd is like climbing a mountain or a marathon, one step at
a time will eventually get you there even if it doesn't feel like you're
making progress.

Mary

Mary Ho
Postdoc
Arnold Lab

On Tue, Jul 13, 2010 at 5:36 PM, Xun Lu  wrote:

> Dear All,
>
>   I took over this project last September. Since the information in the
> lab are not well managed, it's kind of starting over (WRONG plasmids
> sequences; even WRONG oligo length/sequence in the complex which has been
> successfully crystallized. Those crystals only gave low resolution data.) My
> boss told me to mutate the Cys to Ser, see if it would help. I finally got
> many perfect-looking crystals, and sent them to synchrotron. We didn't get
> better data at all. I think it makes sense, because the crystallization
> condition is similar to the one they got previously (I have tried their
> condition first of course, but at that time, the DNA oligoes were wrong!)
>
>   I am trying MBP fusion now, but am very upset these days that I have
> made some stupid mistakes.  How to cheer up? And most importantly, what
> should I do to improve the resolution? I heard a talk on a conference about
> microbeam. AND, a student in another crystallography lab in the same
> department has tried microbeam and got VERY GOOD data which far far beyond
> her and all others' expectation. In our lab, we didn't even know they were
> going to try the microbeam in chicago. Also, anyone can share experience
> with dehydrating crystals?
>
>   Although I didn't get good data this time, I have to say that, I have
> learnt a LOT during crystal screening, cryo, and remote control of
> synchrontron beamline from people in other labs.
>
>
> Thanks,
>
> Xun
> first year PhD
>
>
>

[ccp4bb] How to summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)

[Hailiang Zhang]

Hi all:

Does CCP4 or Phenix provide any utilities which can summarize the data
statistics (particularly looking for the average Fo_sigma/Fo for each
resolution shell)? Truncate seems to be able to do that but didn't get the
desired answer. Any short script will be greatly appreciated!

Best Regards, Hailiang

Re: [ccp4bb] How to summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)

[Tim Gruene]

On Thu, Jul 15, 2010 at 01:02:30AM -0400, Hailiang Zhang wrote:
> Hi all:
> 
> Does CCP4 or Phenix provide any utilities which can summarize the data
> statistics (particularly looking for the average Fo_sigma/Fo for each
> resolution shell)? Truncate seems to be able to do that but didn't get the
> desired answer. Any short script will be greatly appreciated!

If truncate does what you want but does not provide the desired answer it might
be your data's fault, not the fault of truncate.


Maybe you could explain what exactly you are looking for since you seem to
indicate that truncate already does that.
If you have access to xprep you can use xprep to get F and F/sigF per resolution
shell, even with the shells you want. You can convert the mtz-file to hkl-format
with mtz2hkl. 

Considering that pointless is now the ccp4-equivalent to determine the space
group (rather than xprep), pointless might also produce the statistics you are
looking for.

Cheers, Tim

> 
> Best Regards, Hailiang

-- 
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



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