[ccp4bb] Competition organised by the Scientist: Proteopedia voted first place

[Vellieux Frederic]

Dear ccp4bb subscribers,

I have just learned that Proteopedia (the wikipedia-style encyclopedia 
of macromolecular structures) has been voted winner in this year's 
competition organized by "the Scientist" ( http://www.the-scientist.com/ 
, readers and judges choice).


So thanks to all who voted, this "only" shows the importance of our 
beautiful structures.


Some of the comments on the Scientist's web site:

"Very absorbing. Kept me looking (and learning) with it for a long time" 
(Holmes)


"Very informative and a good resource" (Kirby)

So thanks to all who voted for our lovely structures, anything that can 
make our structures understood by as many people as possible and 
(possibly) bring back some funding to our Science is always welcome.


Fred.

[ccp4bb] Sftools and Phaser compatibility issues - continued

[Herman . Schreuder]

Dear bulletin board,

After downloading and recompiling the complete CCP4 package (we had the
precompiled 32bits version on our 64bits machines) we were able to apply
the patches of Claus and the problem case P21221 went through without
problems. 

However, with the next problem case tested, things immediately went
wrong again. The space group was R3 and phaser had written the following
space group information in the mtz file: 146  'R 3 :H'. Attempts to
change the space group with sftools to 'H 3' failed because sftools does
not know 'H 3'. Resetting the space group 146 with sftools was
successful, however, the name written in the mtz was R3. This prompted
autobuster to try to reset the spacegroup to 'H 3' using sftools (with
the results described above).

I did a quick comparison of the space groups implemented in sftools and
the CCP4 library, I found the following discrepancies and there are
probably more:

SFTOOLS   CCP4 
number  name  number   namecomment
  -3P112   1003P112different space group numbers
  -4P1121  1004P1121   different space group numbers
  -5 A112  ?? not present in CCP4, probably
2005: A2
  146 R3146  H3different setting
   1146  R3146 setting of SFTOOLS
 -146R3R
 1146R3R   different entries with the same name
 -155R32R  different entries with the same name
 1155R32R  1155 R32different name
All non-chiral and origin shifted space groups are missing from SFTOOLS.

As Bart told us, sftools was made to ease the transition from the
groningen biomol package to ccp4 and he added a lot of options to
manipulate the reflection data. I find this options very useful e.g. to
simulate the effects of lattice translocation disorder. In a private
mail, Bart told me that he has currently little time to maintain sftools
and since the program does all he needs, there is little incentive for
him to put a lot of time in it.

This leaves me, and probably many other ccp4 users, with the problem
that sftools may produce incompatible mtz files, especially in problem
and non-standard settings. These are exactly the cases where one would
use a program like sftools. In my opinion, either sftools should be
fixed to use the ccp4 library (they really did a wonderful job to
implement all space groups and all settings!), or sftools should be
labeled an unsupported program to be used at ones own risk. For general
scripts like autobuster, one should then probably switch to supported
programs. E.g. I solved the R3/H3 problem by using the reindex program
to change the space group.

The other question is: why does phaser write 'R 3 :H' in the mtz? When
the problem with the P21221 space group first popped up last year, Randy
told me that space group numbers like 2018 are non-standard, and that
space group 18 with the name P21221 was the way to go. This is fair
enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
it in the international tables. Is it maybe a phenix standard? 

Best regards,
Herman

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Bart Hazes
Sent: Wednesday, September 01, 2010 5:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools can not handle non-standard settings?

Hi Herman,

As a former biomol user you might have guessed why. SFTOOLS found its
origin as a transitional program helping the Groningen group move to the
CCP4 mtz format. Since the Groningen MDF and CCP4 mtz had different
ideas about space group symmetry and, especially, asymmetric unit
definitions SFTOOLS needed to handle both. Since the biomol space group
routine was basically a very large spaghetti of nested if-then-elses to
accommodate all the peculiar choices I chose to reimplement using a
simple set of symmetry generators and a matrix to define the asymmetric
unit.

Since there is no longer need to support MDF, sftools could switch to
use the ccp4 library but my code is used for many other things,
determining if a reflection is (a)centric, on a symmetry axis, should be
systematically absent, expected intensity, convertion to standard
asymmetric unit etc. So this will be a major undertaking. Alternatively,
you can create a list of symmetry generators and add space groups as
Claus has apparently already done.

Bart

On 10-09-01 05:39 AM, herman.schreu...@sanofi-aventis.com wrote:
> Dear Claus,
>
> Thank you very much for this patch. We will install it, and I hope 
> CCP4 will install it quickly as well ;-). Still I do not understand 
> why sftools has all symmetry operations hardcoded, while most other 
> programs use the CCP4 libraries. In that way, sftools would always be 
> up to date and would not need to be patched.
>
> Best,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of 
> Claus Flensburg
> Sent: Wednes

Re: [ccp4bb] CCP4 6.1.13 and ARP/wARP 7.1

[Charles Ballard]

Dear All

hopefully the fix for modules.def is now in the source and binaries for ccp4 
6.1.13

Charles Ballard
CCP4

On 30 Aug 2010, at 18:06, ger...@embl-hamburg.de wrote:

> Dear Colleagues,
> 
> some of you might have noticed that ARP/wARP does not install cleanly with 
> the latest version of CCP4, 6.1.13. We did some experiments ourselves and can 
> confirm the observation of an incomplete installation that is only partly 
> functional, the lack of the possibility of manual deinstallation and the 
> following error message that appears at the time of running the ARP/wARP 
> 'install.sh' script:
> can't read "getcontentlist_array(TASK_MODULE,206)": no such element in array
> 
> NOTE: You can skip the next paragraph if you're not interested in how I 
> reproduced the error and proceed to a bug fix. Sorry for the long paragraph.
> Two scenarios of CCP4+ARP/wARP installation were tested: Mac OSX 10.5 and 
> Ubuntu Linux 9, x86_64. Both the latest versions of both softwares. The 
> download of CCP4 was made from ccp4.ac.uk, a typical installation chosen, 
> which included also the tclsh/bltwish components that the GUI depends on. The 
> dmg-installer was used on the Mac to install into the folder /Applications, 
> on Linux the downloaded file was just untarred in a folder of choice followed 
> by running CCP4's 'install.sh'. The 'ccp4.setup_sh/csh' file was placed into 
> the user's shell config file by sourcing it there: '.bashrc', '.cshrc', 
> '.tcshrc' depending on the shell used. Starting from a terminal that has the 
> new CCP4 environment setup, the ARP/wARP installation could be done. On the 
> Mac however it is more complicated because the superuser owns the 
> installation. Through 'sudo xterm' and in there 'source ~user/.cshrc' (to be 
> replaced by your settings) the ccp4 environment is setup for the superuser. 
> In both cases (on the Mac as superuser) 'cd' to the ARP/wARP folder, e.g. 
> arp_warp_7.1, and run ARP/wARP's 'install.sh'. This script tries to install 
> ARP/wARP into the CCP4 GUI automatically and this is where problems start. 
> The error message from above, the 'Program List' contains no buttons from the 
> installation, these are just in 'Model Building', manual deinstallation is 
> not possible, the new tasks don't seem to be registered with the CCP4 GUI.
> 
> The fix: The tcl-files that control the installation of a new software module 
> read the file '$CCP4I_TOP/etc/UNIX/modules.def'. This file seems to have a 
> line missing: In the block of 'TASK_MODULE' lines (around line 500) the entry 
> 'TASK_MODULE,206 programlist' is missing. Please add it there at about 
> the right place. Rerun the ARP/wARP installation and the error message should 
> be gone, the installation should be complete, i.e. ARP/wARP buttons in 
> 'program list', too, and the possibility of manual deinstallation.
> 
> I hope this is helpful.
> 
> Cheers,
> Gerrit.

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Phil Evans]

I'm sure it would be a good thing if SFTOOLS recognised all possible space 
groups, but I wonder why you are using SFTOOLS at all. I've almost never had 
the need to use it myself. Space group changes and many other things can be 
done with CAD for example

Phil


On 2 Sep 2010, at 13:31, herman.schreu...@sanofi-aventis.com wrote:

> Dear bulletin board,
> 
> After downloading and recompiling the complete CCP4 package (we had the
> precompiled 32bits version on our 64bits machines) we were able to apply
> the patches of Claus and the problem case P21221 went through without
> problems. 
> 
> However, with the next problem case tested, things immediately went
> wrong again. The space group was R3 and phaser had written the following
> space group information in the mtz file: 146  'R 3 :H'. Attempts to
> change the space group with sftools to 'H 3' failed because sftools does
> not know 'H 3'. Resetting the space group 146 with sftools was
> successful, however, the name written in the mtz was R3. This prompted
> autobuster to try to reset the spacegroup to 'H 3' using sftools (with
> the results described above).
> 
> I did a quick comparison of the space groups implemented in sftools and
> the CCP4 library, I found the following discrepancies and there are
> probably more:
> 
> SFTOOLS   CCP4 
> number  name  number   namecomment
>  -3P112   1003P112different space group numbers
>  -4P1121  1004P1121   different space group numbers
>  -5 A112  ?? not present in CCP4, probably
> 2005: A2
>  146 R3146  H3different setting
>   1146  R3146 setting of SFTOOLS
> -146R3R
> 1146R3R   different entries with the same name
> -155R32R  different entries with the same name
> 1155R32R  1155 R32different name
> All non-chiral and origin shifted space groups are missing from SFTOOLS.
> 
> As Bart told us, sftools was made to ease the transition from the
> groningen biomol package to ccp4 and he added a lot of options to
> manipulate the reflection data. I find this options very useful e.g. to
> simulate the effects of lattice translocation disorder. In a private
> mail, Bart told me that he has currently little time to maintain sftools
> and since the program does all he needs, there is little incentive for
> him to put a lot of time in it.
> 
> This leaves me, and probably many other ccp4 users, with the problem
> that sftools may produce incompatible mtz files, especially in problem
> and non-standard settings. These are exactly the cases where one would
> use a program like sftools. In my opinion, either sftools should be
> fixed to use the ccp4 library (they really did a wonderful job to
> implement all space groups and all settings!), or sftools should be
> labeled an unsupported program to be used at ones own risk. For general
> scripts like autobuster, one should then probably switch to supported
> programs. E.g. I solved the R3/H3 problem by using the reindex program
> to change the space group.
> 
> The other question is: why does phaser write 'R 3 :H' in the mtz? When
> the problem with the P21221 space group first popped up last year, Randy
> told me that space group numbers like 2018 are non-standard, and that
> space group 18 with the name P21221 was the way to go. This is fair
> enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
> it in the international tables. Is it maybe a phenix standard? 
> 
> Best regards,
> Herman
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Bart Hazes
> Sent: Wednesday, September 01, 2010 5:03 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Sftools can not handle non-standard settings?
> 
> Hi Herman,
> 
> As a former biomol user you might have guessed why. SFTOOLS found its
> origin as a transitional program helping the Groningen group move to the
> CCP4 mtz format. Since the Groningen MDF and CCP4 mtz had different
> ideas about space group symmetry and, especially, asymmetric unit
> definitions SFTOOLS needed to handle both. Since the biomol space group
> routine was basically a very large spaghetti of nested if-then-elses to
> accommodate all the peculiar choices I chose to reimplement using a
> simple set of symmetry generators and a matrix to define the asymmetric
> unit.
> 
> Since there is no longer need to support MDF, sftools could switch to
> use the ccp4 library but my code is used for many other things,
> determining if a reflection is (a)centric, on a symmetry axis, should be
> systematically absent, expected intensity, convertion to standard
> asymmetric unit etc. So this will be a major undertaking. Alternatively,
> you can create a list of symmetry generators and add space groups as
> Claus has apparently already done.
> 
> Bart
> 
> On 10-09-01 05:39 AM, herman.schreu...@sanofi-aventis.com

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Herman . Schreuder]

Dear Phil,

CAD would also be an excellent alternative. I used REINDEX which also
worked. The point I tried to make is that if people do not know that
SFTOOLS is not up to date, they may use it in good faith and get into
trouble. If they know it, they might use it to hack an mtz file when
neccessary, but use other program for more serious purposes.

Herman


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Phil Evans
Sent: Thursday, September 02, 2010 3:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues -
continued

I'm sure it would be a good thing if SFTOOLS recognised all possible
space groups, but I wonder why you are using SFTOOLS at all. I've almost
never had the need to use it myself. Space group changes and many other
things can be done with CAD for example

Phil


On 2 Sep 2010, at 13:31, herman.schreu...@sanofi-aventis.com wrote:

> Dear bulletin board,
> 
> After downloading and recompiling the complete CCP4 package (we had 
> the precompiled 32bits version on our 64bits machines) we were able to

> apply the patches of Claus and the problem case P21221 went through 
> without problems.
> 
> However, with the next problem case tested, things immediately went 
> wrong again. The space group was R3 and phaser had written the 
> following space group information in the mtz file: 146  'R 3 :H'. 
> Attempts to change the space group with sftools to 'H 3' failed 
> because sftools does not know 'H 3'. Resetting the space group 146 
> with sftools was successful, however, the name written in the mtz was 
> R3. This prompted autobuster to try to reset the spacegroup to 'H 3' 
> using sftools (with the results described above).
> 
> I did a quick comparison of the space groups implemented in sftools 
> and the CCP4 library, I found the following discrepancies and there 
> are probably more:
> 
> SFTOOLS   CCP4 
> number  name  number   namecomment
>  -3P112   1003P112different space group numbers
>  -4P1121  1004P1121   different space group numbers
>  -5 A112  ?? not present in CCP4, probably
> 2005: A2
>  146 R3146  H3different setting
>   1146  R3146 setting of SFTOOLS
> -146R3R
> 1146R3R   different entries with the same name
> -155R32R  different entries with the same name
> 1155R32R  1155 R32different name
> All non-chiral and origin shifted space groups are missing from
SFTOOLS.
> 
> As Bart told us, sftools was made to ease the transition from the 
> groningen biomol package to ccp4 and he added a lot of options to 
> manipulate the reflection data. I find this options very useful e.g. 
> to simulate the effects of lattice translocation disorder. In a 
> private mail, Bart told me that he has currently little time to 
> maintain sftools and since the program does all he needs, there is 
> little incentive for him to put a lot of time in it.
> 
> This leaves me, and probably many other ccp4 users, with the problem 
> that sftools may produce incompatible mtz files, especially in problem

> and non-standard settings. These are exactly the cases where one would

> use a program like sftools. In my opinion, either sftools should be 
> fixed to use the ccp4 library (they really did a wonderful job to 
> implement all space groups and all settings!), or sftools should be 
> labeled an unsupported program to be used at ones own risk. For 
> general scripts like autobuster, one should then probably switch to 
> supported programs. E.g. I solved the R3/H3 problem by using the 
> reindex program to change the space group.
> 
> The other question is: why does phaser write 'R 3 :H' in the mtz? When

> the problem with the P21221 space group first popped up last year, 
> Randy told me that space group numbers like 2018 are non-standard, and

> that space group 18 with the name P21221 was the way to go. This is 
> fair enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did 
> not find it in the international tables. Is it maybe a phenix
standard?
> 
> Best regards,
> Herman
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of 
> Bart Hazes
> Sent: Wednesday, September 01, 2010 5:03 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Sftools can not handle non-standard settings?
> 
> Hi Herman,
> 
> As a former biomol user you might have guessed why. SFTOOLS found its 
> origin as a transitional program helping the Groningen group move to 
> the
> CCP4 mtz format. Since the Groningen MDF and CCP4 mtz had different 
> ideas about space group symmetry and, especially, asymmetric unit 
> definitions SFTOOLS needed to handle both. Since the biomol space 
> group routine was basically a very large spaghetti of nested 
> if-then-elses to accommodate all the peculiar choices I c

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Nat Echols]

On Thu, Sep 2, 2010 at 5:31 AM,  wrote:

> The other question is: why does phaser write 'R 3 :H' in the mtz? When
> the problem with the P21221 space group first popped up last year, Randy
> told me that space group numbers like 2018 are non-standard, and that
> space group 18 with the name P21221 was the way to go. This is fair
> enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
> it in the international tables. Is it maybe a phenix standard?
>

No, it pre-dates Phenix - it's the "extended Hermann Mauguin symbol",
whatever that means:

http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's
supported by CCP4 programs, except those which are still using the older
symmetry information.  syminfo.lib has the correct information (space group
number 146), symop.lib does not.  As previously noted the last time this
discussion came up (December, if memory serves), Coot also uses this
notation:

http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Kevin Cowtan]

Well, CCP4 programs using the core libraries should ignore the 
spacegroup symbol and use the operators instead, which bypasses the 
whole problem. I would advise anyone using the CCP4 libraries in their 
own programs to do the same.


That works for mtz and map, but not for pdb files of course.

Kevin

Nat Echols wrote:
  On Thu, Sep 2, 2010 at 5:31 AM,  > wrote:


The other question is: why does phaser write 'R 3 :H' in the mtz? When
the problem with the P21221 space group first popped up last year, Randy
told me that space group numbers like 2018 are non-standard, and that
space group 18 with the name P21221 was the way to go. This is fair
enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
it in the international tables. Is it maybe a phenix standard?


No, it pre-dates Phenix - it's the " extended Hermann Mauguin symbol", 
whatever that means:


http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's 
supported by CCP4 programs, except those which are still using the older 
symmetry information.  syminfo.lib has the correct information (space 
group number 146), symop.lib does not.  As previously noted the last 
time this discussion came up (December, if memory serves), Coot also 
uses this notation:


http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat



--
EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Miller, Mitchell D.]

FYI --

The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G 
chapter 4.7) under _space_group.reference_setting where it states "For the
space groups where more than one setting is given in International
Tables, the following choices have been made. For monoclinic
space groups: unique axis b and cell choice 1. For space
groups with two origins: origin choice 2 (origin at inversion centre,
indicated by adding :2 to the Hermann-Mauguin symbol in
the enumeration list). For rhombohedral space groups: hexagonal
axes (indicated by adding :h to the Hermann-Mauguin symbol
in the enumeration list)."

http://it.iucr.org/Ga/ch4o7v0001/ch4o7.pdf 
http://www.iucr.org/resources/cif/dictionaries/cif_sym 

The H3 / H32 designations are PDB conventions/standards. In the PDB
format description it states that "For a rhombohedral space group in 
the hexagonal setting, the lattice type symbol used is H."  
>From an archive of the PDB documentation at the University of Washington,
there is list of changes by PDB version that suggests that the PDB
introduced the H designation with the release of PDB format v2.0 
(sometime around March 1997) see
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/guide2.2_frame.html 
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_6.html 
The RCSB's archive of the 2.2 format gives a file not found error.
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html 
 

Regards,
Mitch


-Original Message--
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nat Echols
Sent: Thursday, September 02, 2010 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

On Thu, Sep 2, 2010 at 5:31 AM,  wrote:
The other question is: why does phaser write 'R 3 :H' in the mtz? When
the problem with the P21221 space group first popped up last year, Randy
told me that space group numbers like 2018 are non-standard, and that
space group 18 with the name P21221 was the way to go. This is fair
enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
it in the international tables. Is it maybe a phenix standard?

No, it pre-dates Phenix - it's the "extended Hermann Mauguin symbol", whatever 
that means:

http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's 
supported by CCP4 programs, except those which are still using the older 
symmetry information.  syminfo.lib has the correct information (space group 
number 146), symop.lib does not.  As previously noted the last time this 
discussion came up (December, if memory serves), Coot also uses this notation:

http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat

[ccp4bb] How to automatically answer "NO" to SFTOOLS reading in a shell script?

[Hailiang Zhang]

Hi,

I am reading a ccp4 mtz file using SFTOOLS. It asked me" Is this an XPLOR
RFREE flag column?". First I assume the answer is NO, since the input is a
CCP4 mtz file although the colume is for free-flags. Then, I am wondering
what is the script to automatically answer "NO" in a shell script.

Thanks!

Best Regards, Hailiang

Re: [ccp4bb] How to automatically answer "NO" to SFTOOLS reading in a shell script?

[Bart Hazes]

Hi Hailiang

sftools was first and foremost designed to be used interactively, that 
is why it tends to follow a question and answer user interface. Of 
course you can use sftools in scripts but if it pops up a question that 
was not anticipated, the script it will crash. There could be a batch 
mode where you give sftools permission to make a best guess but guessing 
can be dangerous.


In your particular case, XPLOR uses a flag=1 for rfree reflections and 0 
for working set reflections while CCP4 MTZ by default uses a flag=0 for 
rfree reflections and non-zero for working set reflections. If sftools 
encounters an mtz that appears to use the XPLOR definition it gives a 
warning and suggests to convert to the CCP4 definition.


For proper MTZ files this should not happen and if it does happen maybe 
you should find out why.


Bart

On 10-09-02 02:00 PM, Hailiang Zhang wrote:

Hi,

I am reading a ccp4 mtz file using SFTOOLS. It asked me" Is this an XPLOR
RFREE flag column?". First I assume the answer is NO, since the input is a
CCP4 mtz file although the colume is for free-flags. Then, I am wondering
what is the script to automatically answer "NO" in a shell script.

Thanks!

Best Regards, Hailiang

   


--



Bart Hazes (Associate Professor)
Dept. of Medical Microbiology&  Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

Re: [ccp4bb] How to automatically answer "NO" to SFTOOLS reading in a shell script?

[Hailiang Zhang]

GOt it! Thanks!

Best REgards, Hailiang
> Hi Hailiang
>
> sftools was first and foremost designed to be used interactively, that
> is why it tends to follow a question and answer user interface. Of
> course you can use sftools in scripts but if it pops up a question that
> was not anticipated, the script it will crash. There could be a batch
> mode where you give sftools permission to make a best guess but guessing
> can be dangerous.
>
> In your particular case, XPLOR uses a flag=1 for rfree reflections and 0
> for working set reflections while CCP4 MTZ by default uses a flag=0 for
> rfree reflections and non-zero for working set reflections. If sftools
> encounters an mtz that appears to use the XPLOR definition it gives a
> warning and suggests to convert to the CCP4 definition.
>
> For proper MTZ files this should not happen and if it does happen maybe
> you should find out why.
>
> Bart
>
> On 10-09-02 02:00 PM, Hailiang Zhang wrote:
>> Hi,
>>
>> I am reading a ccp4 mtz file using SFTOOLS. It asked me" Is this an
>> XPLOR
>> RFREE flag column?". First I assume the answer is NO, since the input is
>> a
>> CCP4 mtz file although the colume is for free-flags. Then, I am
>> wondering
>> what is the script to automatically answer "NO" in a shell script.
>>
>> Thanks!
>>
>> Best Regards, Hailiang
>>
>>
>
> --
>
> 
>
> Bart Hazes (Associate Professor)
> Dept. of Medical Microbiology&  Immunology
> University of Alberta
> 1-15 Medical Sciences Building
> Edmonton, Alberta
> Canada, T6G 2H7
> phone:  1-780-492-0042
> fax:1-780-492-7521
>
> 
>
>
>

[ccp4bb] to back-soak or not to back-soak

[amit sharma]

Hi,

I recently collected a MAD dataset on one of my xtals soaked in ~7mM KAuCN2
for 1.5 days. I had backsoaked these xtals prior to freezing and the signal
seems to be faint. I was wondering if it would help not back-soaking xtals.

I would be grateful for any comments/suggestions.

thanks,
-- 
Amit Sharma,
Postdoctoral Fellow,
Department of Biophysics,
Johns Hopkins University,
Baltimore,
MD21218

Re: [ccp4bb] Practical MR advice

[Roger Rowlett]

  
  
Ding ding ding ding...we have a winner:

  A search model with 30% identity was submitted to the Phyre
server which returned a target sequence-corrected model
  The Phyre monomer was "dimerized" in Pymol using symmetry
operators from a previous MR solution using a dimer of the
original homolog protein
  The Phyre dimer was used in Phaser to find a new MR solution
using the dimer (4 dimers placed, as expected, packs well in
unit cell.)
  
  This solution was Chainsawed to poly-Ala and then subjected to
refinement with 8-fold NCS symmetry averaging in Refmac to
generate phases. R=0.466, Rfree=0.460, FOM=0.219
  This model was fed to Parrot for 5 rounds of density
modification with 8-fold NCS symmetry averaging, improving FOM
to 0.770
  Parrot phases were fed into Buccaneer for 5 rounds of
autobuilding using the full target gene sequence and strict
sequence probability matching. The final Buccaneer model had
R=0.313, Rfree=0.345, and FOM=0.848, and the maps are readily
interpretable.

Omitting the Chainsaw step resulted in a much less satisfactory
solution, although perhaps usable, with R=0.41 and FOM=0.75, but the
map was not as interpretable, and had many problem areas and
possible mis-registrations.

My second choice of approach was going to be DM with phase extension
(Keller et al., 2006, Acta Cryst., D62, 1564-1570) which was
suggested by David Lawson. The MR challenge described in that paper
is eerily similar to mine. I may yet try this for kicks to see how
well it works ( may need this trick someday) but was too lazy to
feed all the NCS matrices into DM. Parrot will extract NCS operators
directly from the MR model, which is nice. :)

Thanks for all the very helpful advice!

On 9/2/2010 7:10 AM, Dima Klenchin wrote:

  
  1. Chainsaw the currrent solution, and
attempt to identify and build in the correct register of the
side chains. after refinement.

2. Do a low resolution refinement of the poly-Ala/Gly model to
better thread the main chain?

3. Try EPMR with the Phyre model or the poly-Ala/Gly model

4. Give up and get real phases (but I'm so close now!?)

  
  
  Roger,
  
  
  Here is what I'd do if I were you:
  
  
  1. Try both with and without Chainsaw.
  
  2. Refine current solution with tight NCS averaging.
  
  3. Feed the resulting phases into Parrot.
  
  4. Feed the output to Buccaneer.
  
  
  Since Phaser built "correct" tetramer, I'd be very surprised if
  the above procedure won't resolve registration issue.
  
  
  Good luck,
  
  
  Dima
  
  

-- 
  

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
  

  

Re: [ccp4bb] microseeding SeMet drops with native xtal seeds

[Diana Tomchick]

See the following publication for an interesting method to resolve  
pseudo-merohedral twinning in SeMet crystals:


Cansizoglu, A. E. and Chook, Y. M. (2007) Conformational heterogeneity  
of Karyopherinβ2 is segmental. Structure, 15(11):1431-1441.


"In an effort to obtain single selenomethionine Kapβ2 crystals,  
mixtures of selenomethionine and native proteins were crystallized. A  
1:1 molar mixture of the two proteins gave single crystals..."


Diana

On Sep 1, 2010, at 10:37 PM, amit sharma wrote:


Dear All,

My SeMet protein crystals have a needle-like morphology, worse than  
that of the native xtals. Also, although the cell dimensions of both  
forms is very much similar, the SeMet xtals are twinned(as indicated  
by Ctruncate plots). I was wondering if such cases were commonly  
seen, also is it alright to microseed my SeMet protein drops with  
seeds from the native xtal. I would be grateful if someone could  
shed light on this.


thanks in advance,
--
Amit Sharma,
Postdoctoral Fellow,
Department of Biophysics,
Johns Hopkins University,
Baltimore,
MD21218


* * * * * * * * * * * * * * * * * * * * * * * * * * * *
Diana R. Tomchick
Associate Professor
University of Texas Southwestern Medical Center
Department of Biochemistry
5323 Harry Hines Blvd.
Rm. ND10.214B   
Dallas, TX 75390-8816, U.S.A.   
Email: diana.tomch...@utsouthwestern.edu
214-645-6383 (phone)
214-645-6353 (fax)

[ccp4bb] Confirming expression of a GPCR in HEK293

[Qing Lu]

Dear All,

Apologies for a non-ccp4 question. I am planning to express a GPCR in
HEK293T cell line by transfecting with the requisite cDNA for performing an
assay. I would like to confirm the expression of the protein in the cell
line by western blot or histochemical studies. Any pointers in this regard
would be helpful.

Thanks,

Qing Lu

Re: [ccp4bb] Confirming expression of a GPCR in HEK293

[Jacob Keller]

If I were you, I would just make a gfp-tagged construct--this is an easy way to 
make sure that the protein is there, and made it to the membrane. If necessary, 
you can blot for gfp, or add other tags in the process for alternative blotting 
(one on each side to make sure it is not cleaved, for example.)

Jacob

  - Original Message - 
  From: Qing Lu 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Thursday, September 02, 2010 7:42 PM
  Subject: [ccp4bb] Confirming expression of a GPCR in HEK293


  Dear All,

  Apologies for a non-ccp4 question. I am planning to express a GPCR in HEK293T 
cell line by transfecting with the requisite cDNA for performing an assay. I 
would like to confirm the expression of the protein in the cell line by western 
blot or histochemical studies. Any pointers in this regard would be helpful.

  Thanks,

  Qing Lu




***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Confirming expression of a GPCR in HEK293

[Pascal Egea]

Hi Qing,

I would recommend either the use of GFP as mentioned by Jacob or a his-tag
or a flag-tag. C-terminal tagging is preferred to prevent interference with
signal sequences at the N-terminus of the protein.
Flag tag is really good for detection , the commercial antibodies for
detection are really great, however it is not that great, in my hands, when
it comes to purification of a membrane protein (in presence of detergent) I
prefer his-tags to flag-tags in this case. You can use a his-flag to combine
both advantages.

Hope this helps



-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
314 Biomedical Sciences Research Building
office (310)-983-3515
lab  (310)-983-3516
email pe...@mednet.ucla.edu

[ccp4bb] fit a peptide in isolated density

In an isolated piece of density, I want to fit a 7AA peptide fragment from a 
protein.
Only the sequence of the whole protein (200AA) is known, and I don't know the 
peptide sequence.
I think it's best to try from the beginning of the whole sequence to the end.
So is there any software or scripts which can do this automatically? The 
resolution is 2.3A.
Waiting for your reply!
Thank you!