[ccp4bb] Secondary structure prediction for billions of sequences ?

[hari jayaram]

Hi all
It’s been a while since I posted on this group so apologies for a slightly
tangential, non CCP4 question.

I wanted to get secondary structure predictions for designing a library of
50-100 amino acid peptides. The library could get very large ( 10^9) and I
was wondering if there is a way to predict the secondary structure for this
large set of sequences that scales well.

I am currently using psipred which works well, but runs one sequences at a
time and generates the desired prediction with concurrent creation of many
temp files.

Although I realize this is solvable with the current approach, by
parallelizing the calls  I was wondering if there are other approaches that
are suitable for this.

Thanks for your help in advance
Hari Jayaram



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Re: [ccp4bb] Issues with Coot & XQuartz

[hari jayaram]

Hi All

I tried coot and pymol with OSX Sierra 10.12.2 and Xquartz 2.7.11 aall the
way through 2.7.8 after seeing this post.

Pymol ( self compiled 1.8.2 ) 80% of the time on two different machines
stops responding to the mouse.
Coot behaves the same way where smooth rotation my mouse is severely
affected.

Even tried with a new user profile and with no other programs running.

It seems that somethin in Xquartz and OSX Sierra with OpenGL applications
and mouse scrolling is affected.

IOf any Sierra users can confirm or let me know its consistently working (
I see "no issues" randomly 2 out of 10 times) ...let me know

 Thanks a tonne
Hari


On Tue, Nov 22, 2016 at 9:28 AM CROENEN, LAURA E.M. (Student) <
laura.croe...@durham.ac.uk> wrote:

> Hi all,
>
> I downloaded the 2.7.8 package and rebooted which has solved the problem.
> Thank you all so much for your help!
>
> Best wishes,
>
> Laura
> --
> *From:* CCP4 bulletin board  on behalf of Phil
> Evans 
> *Sent:* 22 November 2016 12:45:35
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Issues with Coot & XQuartz
>
> I can run coot locally (though not remotely) on Quartz 2.7.11 (OS X
> Yosemite 10.10.5)
> Phil
>
> > On 22 Nov 2016, at 12:39, Martin Montgomery 
> wrote:
> >
> > Hi,
> >
> > We have had these problems with coot and xquartz versions greater than
> 2.7.8.  This affects coot running locally on OSX and via ssh -XY from the
> mac to our linux workstations.  You should still be able to download the
> xquartz-2.7.8 package (https://www.xquartz.org/releases/XQuartz-2.7.8.html).
> Rebooting after the installation of a later xquartz has not made any
> difference on our macs.
> >
> > Regards
> >
> > MGM
> >
> >
> >
> >
> >> On 22 Nov 2016, at 12:32, Phil Evans  wrote:
> >>
> >> Something we [re]discovered at a recent workshop is that after
> installing Quartz you need to reboot (I believe to start the X11 launch
> daemon). Could this be the problem?
> >>
> >> Phil
> >>
> >>> On 22 Nov 2016, at 11:28, Laura Croenen 
> wrote:
> >>>
> >>> Hello all,
> >>>
> >>> I recently downloaded the CCP4 package on Mac (OS X Yosemite 10.10.2).
> With this I am using the latest update of XQuartz. Some aspects of the
> package (ccp4i2, QtMG) are working fine, but others, inc. Coot, are not
> working at all. When I try to open Coot, it appears to start opening (the
> icon appears at the bottom of my screen) and then disappears, with the
> message:
> >>>
> >>> "student-10-245-174-102:MacOS lauracroenen$ ./coot
> >>> 2016-11-21 17:07:40.946 coot[39004:3369025] script to run
> /Applications/ccp4-7.0/coot.app/../bin/coot
> >>>
> >>> (coot-bin:39010): Gtk-WARNING **: cannot open display:
> >>>
> >>> (coot-crash-catcher.scm:39011): Gtk-WARNING **: cannot open display:"
> >>>
> >>> Has anyone else had this problem? Am I missing something?
> >>>
> >>> Thank you in advance.
> >>>
> >>> Laura Croenen
> >
>

Re: [ccp4bb] Coot and XQuartz

[hari jayaram]

Hi Alexandra and Matt
I am using OSX Sierra 10.12.2 and Xquartz 2.7.11 and noticing severe
degradation in performance with coot and pymol. I can get the program to
load up and X11 window comes up. But if I try rotating even a small 30kd
protein , the rotation is smooth for two seconds and then the molecule
stops responding to the mouse.

I have tried this on a Macbook Pro and Macbook Air with different levels of
RAM ( 8GB and 16 GB ) and graphics card with same Xquartz and am close to
convinced there is something strange with Sierra and Xquartz ( a few months
before my Sierra upgrade -early Dec 2016 , I didnt see any issues with El
Capitaan ).

Wanted to add to your thread in case more people see this
Hari


On Thu, Dec 1, 2016 at 6:24 PM Matthew Bratkowski 
wrote:

> I recently upgraded to Sierra 10.12.1 and found that none of my
> crystallography programs (Coot, ccp4, phenix) worked.  I downloaded XQuartz
> again and that seemed to fix everything.  This is the only time that I
> upgraded my computer since probably 2013 or 2012, and the only reason that
> I did it was because I could not install Firefox on the old OS.  If you
> have the option to upgrade for free to the lastest OS, you could try doing
> that and then re-downloading XQuartz.
>
> Matt
>
> On Thu, Dec 1, 2016 at 5:09 PM, Deaconescu, Alexandra <
> alexandra_deacone...@brown.edu> wrote:
>
> Hello,
>
> I am having problems with running Coot on El Capitan 10.11.6. I have tried
> various versions of XQuartz from 2.7.7 to 2.7.9 with no success. As
> mentioned some time ago on the bb, I have also tried disabling rootless
> (System Integrity Protection) in OS X, but that also seemed to disable my
> ...keyboard.
>
> Does anyone have a solution to this, please?
>
> Thanks so much,
> Alexandra
>
>
>

[ccp4bb] broken loggraph on 64 bit redhat: new style refmac graph popup after refmac from inside coot?

[hari jayaram]

Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running ccp4
6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph pops up
and then crashes with an error complaining of the loggraph.tcl script( see
below).

This script nor associated scripts have not changed in ccp4 for a while,
and everything works on 64 bit Ubuntu, so I am scared the error may like
with some redhat component.

I tried to compile a native blt instead of using the ccp4 supplied one to
see if that fixed things. Digging through the blt forums etc it seems that
many are abandoning blt to something like a replacement called wize. Also
judging from the forums several things in the blt 2.4 and older seem
to have issues with newer  tk flavors  like 8.5.

Regardless , given all this , are there any ways to auto popup the new
style qt based graphs when running refmac from within coot upon completion.


Sorry I am cross posting to coot, ccp4bb.

thanks for your help in advance.
hari

the error I see in refmac : view log graphs OR in coot on refmac completion
says:

Error in startup script: syntax error in expression 10 11 12 + 12: extra
tokens at end of expression
while executing
expr [string trim $ele] + $data(NCOLUMNS) 
(procedure extract_tables_from_GRAPH line 44)
invoked from within
extract_tables_from_$filetype $input $arrayname
(procedure extract_tables_from_file line 31)
invoked from within
extract_tables_from_file $system(SCRIPT) $system(FORMAT) data
invoked from within
if { $system(SCRIPT) !=  } {
  if { ![ElementExists system FORMAT] || $system(FORMAT) ==  } {
 set system(FORMAT) [GetFileFormat $system(SCRI...
(file
/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl
line 2324)
invoked from within
source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]
(file
/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl line 83)

Re: [ccp4bb] loggraph not popping up after refmac5 ccp4-6.4

[hari jayaram]

Hi Ingo,
I tried replacing the loggraph script and also running the old ccp4 in its
entirety on the same machine
Both of them popup the blank graph window and then promptly crash with the
message we had posted.
Can anyone confirm if they are using Redhat 6.5 and blt with loggraph

Thanks for your suggestion

Hari

On Friday, April 4, 2014, Ingo P. Korndoerfer korndoer...@crelux.com
wrote:

  hi,

 i belive i have for quite a while simply copied loggraph from the last
 working installation into the active version of ccp4.

 might be worth a shot ...

 ingo


 hari jayaram wrote:

 Hi all ..
 loggraph seems to be broken on Redhat 6.5 . It may be a blt  error. Can
 someone confirm that they can get loggraph to work on Redhat Enterprise 6.5
 with the ccp4 provided binaries.

  Sadly Redhat nor Activestate provide blt replacements

  In all cases the loggraph starts a blank window ready to plot a graph
 and then fails with the error

  Error in startup script: syntax error in expression 10 11 12 + 12:
 extra tokens at end of expression
 while executing
 expr [string trim $ele] + $data(NCOLUMNS) 
 (procedure extract_tables_from_GRAPH line 44)
 invoked from within
 extract_tables_from_$filetype $input $arrayname
 (procedure extract_tables_from_file line 31)
 invoked from within
 extract_tables_from_file $system(SCRIPT) $system(FORMAT) data
 invoked from within
 if { $system(SCRIPT) !=  } {
   if { ![ElementExists system FORMAT] || $system(FORMAT) ==  } {
  set system(FORMAT) [GetFileFormat $system(SCRI...
 (file
 /home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl
 line 2324)
 invoked from within
  source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]
 (file
 /home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl line 83)
 

  Sadly We cannot go back to using Ubuntu where this was working.

  The CCP4 provided  blt, bltsh and wish binaries seem to work fine ..its
 only loggraph that fails .

  We are using the current ccp4 installed yesterday.

  I also tried using Activestate wish and combining it with ccp4 provided
 bltsh ..but in that case I get the error :

  package require blt

  Thanks

  Hari ( and Yong)




 On Wed, Apr 2, 2014 at 2:33 PM, Yong Tang liutan...@gmail.com wrote:

  Hello All,

 Further to my earlier email..I am running ccp4 6.4 , on 64 bit Redhat
 Linux 6.5

  I cannot see loggraphs with View-Files-From-Job - View Log Graphs--

  That throws an error in the shell. This is the same error  I see when
 coot finishes refmac5 as well.
 It seems that the loggraph tcl script is broken somehow.

  Any ideas on how to fix.
  Thank you for your help


  Yong


 Top level CCP4 directory is /home/yong/ccp4_root/ccp4-6.4.0
 Using CCP4 programs from /home/yong/ccp4_root/ccp4-6.4.0/bin
 Error in startup script: syntax error in expression 10 11 12 + 12: extra
 tokens at end of expression
 while executing
 expr [string trim $ele] + $data(NCOLUMNS) 
 (procedure extract_tables_from_GRAPH line 44)
 invoked from within
 extract_tables_from_$filetype $input $arrayname
 (procedure extract_tables_from_file line 31)
 invoked from within

 --
 CRELUX GmbH

 Dr. Ingo Korndoerfer
 Head of Crystallography

 Am Klopferspitz 19a
 82152 Martinsried
 Germany

 Phone: +49 89 700760210
 Fax: +49 89 700760222 korndoer...@crelux.com 
 javascript:_e(%7B%7D,'cvml','korndoer...@crelux.com');www.crelux.com

 Amtsgericht München HRB 165552 - Managing Directors: Dr. Michael Schäffer, 
 Dr. Ismail Moarefi

 This e-mail may contain confidential and/or privileged information. If you 
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 notify the sender immediately and destroy this e-mail. Any unauthorized 
 copying, disclosure or distribution of the material in this e-mail is 
 strictly forbidden.
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 irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und 
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 Weitergabe dieser Mail ist nicht gestattet.

Re: [ccp4bb] loggraph not popping up after refmac5 ccp4-6.4

[hari jayaram]

Hi all ..
loggraph seems to be broken on Redhat 6.5 . It may be a blt  error. Can
someone confirm that they can get loggraph to work on Redhat Enterprise 6.5
with the ccp4 provided binaries.

Sadly Redhat nor Activestate provide blt replacements

In all cases the loggraph starts a blank window ready to plot a graph and
then fails with the error

Error in startup script: syntax error in expression 10 11 12 + 12: extra
tokens at end of expression
while executing
expr [string trim $ele] + $data(NCOLUMNS) 
(procedure extract_tables_from_GRAPH line 44)
invoked from within
extract_tables_from_$filetype $input $arrayname
(procedure extract_tables_from_file line 31)
invoked from within
extract_tables_from_file $system(SCRIPT) $system(FORMAT) data
invoked from within
if { $system(SCRIPT) !=  } {
  if { ![ElementExists system FORMAT] || $system(FORMAT) ==  } {
 set system(FORMAT) [GetFileFormat $system(SCRI...
(file
/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl
line 2324)
invoked from within
source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]
(file
/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl line 83)


Sadly We cannot go back to using Ubuntu where this was working.

The CCP4 provided  blt, bltsh and wish binaries seem to work fine ..its
only loggraph that fails .

We are using the current ccp4 installed yesterday.

I also tried using Activestate wish and combining it with ccp4 provided
bltsh ..but in that case I get the error :

package require blt

Thanks

Hari ( and Yong)




On Wed, Apr 2, 2014 at 2:33 PM, Yong Tang liutan...@gmail.com wrote:

 Hello All,

 Further to my earlier email..I am running ccp4 6.4 , on 64 bit Redhat
 Linux 6.5

 I cannot see loggraphs with View-Files-From-Job - View Log Graphs--

 That throws an error in the shell. This is the same error  I see when coot
 finishes refmac5 as well.
 It seems that the loggraph tcl script is broken somehow.

 Any ideas on how to fix.
 Thank you for your help


 Yong


 Top level CCP4 directory is /home/yong/ccp4_root/ccp4-6.4.0
 Using CCP4 programs from /home/yong/ccp4_root/ccp4-6.4.0/bin
 Error in startup script: syntax error in expression 10 11 12 + 12: extra
 tokens at end of expression
 while executing
 expr [string trim $ele] + $data(NCOLUMNS) 
 (procedure extract_tables_from_GRAPH line 44)
 invoked from within
 extract_tables_from_$filetype $input $arrayname
 (procedure extract_tables_from_file line 31)
 invoked from within
 extract_tables_from_file $system(SCRIPT) $system(FORMAT) data
 invoked from within
 if { $system(SCRIPT) !=  } {
   if { ![ElementExists system FORMAT] || $system(FORMAT) ==  } {
  set system(FORMAT) [GetFileFormat $system(SCRI...
 (file
 /home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl
 line 2324)
 invoked from within
 source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]
 (file
 /home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl line 83)



 On Wed, Apr 2, 2014 at 2:22 PM, Yong Tang liutan...@gmail.com wrote:

 Hi ,
 I have just switched to a new computer with ccp4 6.4 and binary coot
 installed from Paul Emsleys nightlies.

 When I run refmac5 inside coot or run refmac5 inside ccp4,  the loggraph
 does not pop-up at the end of a refmac run. I looked everywhere in settings
 inside ccp4i or inside coot and could not re-enable loggraph popup.

 Can someone tell me what setting I need to change to have the old style
 loggraphs popup ? .

 Thanks

 Yong

 --
  Yong Tang

Re: [ccp4bb] Only refine Bs in Refmac?

[hari jayaram]

Hi Garib,

Thanks for your help. I read the document at this
locationhttp://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html
.

Without mixed keyword the default iso B's kick in, so this statement
below did not work. I took in a  pdb with ANISO B's and ran a B-factor
refinement and outputs a PDB without ANISOU records for every atom

# DId not work when I had anisou records for all atoms in input
refine-
bref bonly


*This works and does the full anisotropic only refinement *
refine-
bref aniso bonly


*This also works* ( I was just guessing before I saw your previoud
email)* but It probably is equivalent to the one above.
*
refine-
bref anisoonly

Thanks for your help
Hari







On Thu, Sep 5, 2013 at 11:24 AM, Garib N Murshudov
ga...@mrc-lmb.cam.ac.ukwrote:

 You do not need anisoonly. You need bref only. If input pdb has aniso card
 then refmac will assume that mixed refinement should be done. If you want
 to add aniso for some of the atoms then you can use instructions like:

 *brefine mixed aniso residue 100 A atoms FE S C**
 *
 *
 *
 *
 Please have a look documentation from the our LMB site for further details.

 Regards
 Garib


 On 5 Sep 2013, at 15:50, hari jayaram wrote:

 Thanks Garib for the new version.

 For only an anisotropic B refinement ..what are the keywords. The one
 below seems to work
 refi -
 type REST -
 resi MLKF -
 meth CGMAT -
 bref anisoonly
 ncyc 5

 As far as Bill Scotts question does coot not pick up refmac5 and libcheck
 from $CCP4_BIN ?

 Thanks
 Hari



 On Thu, Sep 5, 2013 at 10:15 AM, William G. Scott wgsc...@ucsc.eduwrote:

 On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk
 wrote:

  You may need to use the latest available version (5.8) from our LMB site

 Hi Garib:

 Would it be possible to add a link for the source code, so this could
 also be used with Coot?

 Thanks.

 Bill



 Dr Garib N Murshudov
 Group Leader, MRC Laboratory of Molecular Biology
 Francis Crick Avenue
 Cambridge Biomedical Campus
 Cambridge
 CB2 0QH UK
 Email: ga...@mrc-lmb.cam.ac.uk
 Web http://www.mrc-lmb.cam.ac.uk,
 http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

Re: [ccp4bb] Only refine Bs in Refmac?

[hari jayaram]

Thanks Garib for the new version.

For only an anisotropic B refinement ..what are the keywords. The one below
seems to work
refi -
type REST -
resi MLKF -
meth CGMAT -
bref anisoonly
ncyc 5

As far as Bill Scotts question does coot not pick up refmac5 and libcheck
from $CCP4_BIN ?

Thanks
Hari



On Thu, Sep 5, 2013 at 10:15 AM, William G. Scott wgsc...@ucsc.edu wrote:

 On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk
 wrote:

  You may need to use the latest available version (5.8) from our LMB site

 Hi Garib:

 Would it be possible to add a link for the source code, so this could also
 be used with Coot?

 Thanks.

 Bill

[ccp4bb] Only refine Bs in Refmac?

[hari jayaram]

Hi,
How does one only refine Bs in refmac without changing the model
coordinates .

Is this accomplished using a zero cycle refinement with b-refinement set.

I  have never had to do this till now and didnt know how to set it up.

Thanks

Hari

[ccp4bb] CCP4 package manager not available for 32 bit OSX?

[hari jayaram]

Hi ,
I am trying to use the CCP4 package manager on my 32 bit OSX 10.6.8 running
laptop and it complains

/bin/sh: Volume/setup/.pm/Setup.app/Contents/MacOS/Setup: Bad CPU type in
executable.

Is there a 32 bit package manager available...
Thanks
Hari
attachment: Screen shot 2013-07-10 at 10.57.53 AM.png

Re: [ccp4bb] deleted font settings for ccp4i--how to have ccp4i use Ubuntu fonts

[hari jayaram]

Thanks Installing those fonts did the trick.

sudo apt-get install xfonts-75dpi xfonts-100dpi xfs xfstt

Hari



On Tue, May 14, 2013 at 9:04 PM, Roger Rowlett rrowl...@colgate.edu wrote:

 In 12.04LTS I install X-fonts, and font servers e.g.,

 sudo apt-get install xfonts-75dpi xfonts-100dpi xfs xfstt

 This allows ccp4i to display the fonts I remember. X-fonts are not
 installed by default in Ubuntu 12.04 and probably 13.04 as well. There may
 be a more elegant way to customize ccp4i but this works for me and is
 legible.

 Roger Rowlett
 On May 14, 2013 6:49 PM, hari jayaram hari...@gmail.com wrote:

 After an Ubuntu 13.04 reboot I noticed that all my ccp4i fonts looked
 very jagged and illegible.

 The preferences have the font assigned to be

 -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-*

 Is there a way to have ccp4i use the Ubuntu fonts ?

 Thanks for your help

 Hari

[ccp4bb] deleted font settings for ccp4i--how to have ccp4i use Ubuntu fonts

[hari jayaram]

After an Ubuntu 13.04 reboot I noticed that all my ccp4i fonts looked very
jagged and illegible.

The preferences have the font assigned to be

-Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-*

Is there a way to have ccp4i use the Ubuntu fonts ?

Thanks for your help

Hari

[ccp4bb] ctruncate/scapepacktomtz : terminate called after throwing an instance of clipper::Message_fatal

[hari jayaram]

Hi All,
I am running the latest ccp4 ( auto-updated using the new autoupdate tool
built into ccp4i)

I was running what should be a routine scalepack to mtz conversion and I
got an error which I have never seen before with ctruncate.


When I run the same job with old truncate it succeeds.


Any ideas what may be causing this. I hope I snipped the correct part of
the error message.


Thanks
Hari



***
* Information from CCP4Interface script
***
The program run with command:
/home/hari/ccp4-6.3-download/ccp4-6.3.0/bin/ctruncate -hklin
/tmp/hari/B8-C7-A_P21_4_1_mtz.tmp -hklout
/tmp/hari/B8-C7-A_P21_4_3_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\]
-colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout B8-C7-A_P21 -nres 150
has failed with error message
CCP4MTZfile - internal error
terminate called after throwing an instance of 'clipper::Message_fatal'
***


#CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error terminate called
after throwing an instance of 'clipper::Message_fatal'
#CCP4I TERMINATION TIME 19 Nov 2012  16:50:26
#CCP4I MESSAGE Task failed

Re: [ccp4bb] sealing tapes

[hari jayaram]

Hello Flip,
I saw your post on the ccp4bb about UV transparent seals. Is it possible
for you to send me the compilation that formulatrix has put together

Thanks
Hari
Constellation Pharmaceuticals


On Mon, Mar 7, 2011 at 4:41 AM, Flip Hoedemaeker f...@formulatrix.comwrote:

 Hi Jean-Luc,

 We have complied a list of UV compatible cover media and plates. The list
 is by all means not complete yet, but the best seals we found are all
 sheets (that does not mean all sheets are UV compatible!). If you want I
 can send you a PDF file outside of the BB.

 Flip


 On 3/7/2011 10:31, ferrer wrote:

 Dear all,

 Sorry for this slightly off-topic email, but I am looking for a
 transparent sealing tape for 96-well crystallization plates, with the
 following properties:
 - high sealing performances
 - compatible with UV screening
 - optionally, available as rolls

 Thanks for your help

 JL

[ccp4bb] libcheck garbled small molecule in ccp4 6.3 but not in ccp4 6.2.2

[hari jayaram]

Hi,
I just upgraded to the newest CCP4  version 6.3 and noticed that libcheck
which coot uses to produce restraints from a SMILES string produces garbled
coordinates in ccp4 version 6.3 , but the same SMILES string works just
fine with CCP4 version 6.2.

I tried to get it to fail on public molecules , but couldnt find an
illustrative example.
But consistently the old version 6.2.2 succeeds but 6.3 garbles the phenyl
rings.


Anyone else seeing this.
Thanks

Hari

Re: [ccp4bb] Building coot from scratch

[hari jayaram]

I got the latest coot svn 4245 to build on Ubuntu 10.04 and Ubuntu 12.04 ,
64 bit using the  build-it-gtk2-simple python  after setting up the
environment as Tim and the docs indicate.
 The only change I had to make was to have the build-script force building
of the gtkglext library by modifying the flag in the build script for
build gtkglext from 0 to 1.

just my 2c

Hari




On Friday, June 22, 2012, Tim Gruene wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Hello Andre,

 what you see is not an error message, it is only a warning message. It
 is actually the last message before the remaining output is redirected
 to into the ${LOGS} directory.

 Paul set up a wrapper wrap-build-it for me:
 #!/bin/bash
 OS=$(uname)
 HOST=$(hostname)
 AUTOBUILD_BUILD=$HOME/public_html/coot_deb/autobuild/building
 AUTOBUILD_INSTALL=$HOME/public_html/coot_deb/autobuild/${OS}-${HOST}
 AUTOBUILD_INSTALLED=$HOME/public_html/coot_deb/autobuild/${OS}-${HOST}
 LOGS=$HOME/public_html/coot_deb/build-logs/${OS}-${HOST}
 NIGHTLY_DEST_DIR=$HOME/public_html/coot_deb/binaries/nightlies/pre-release
 STABLE_DEST_DIR=$HOME/public_html/coot_deb/binaries/stable


 . build-it-gtk2-simple python

 when you place it into $HOME/public_html/coot_deb together with
 build-it-gtk2-simple, call it as
bash wrap-build-it
 that seems to work reasonably well - we have not fixed all testing
 issues, but at least the resulting binary tree works for me.

 Good luck,

 Tim

 On 06/21/2012 10:17 PM, Andre Godoy wrote:
  Dear All
 
  I'm trying build_from_scratch my coot and it doesn't work... the
  following error appears, and I really don't know how to fix it:
 
 
  Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
  HTTP request sent, awaiting response... 200 OK Length: 7039 (6.9K)
  [text/plain] Saving to: `build-notes'
 
 
 100%[=]
  7,039   26.4K/s   in 0.3s
 
  2012-06-21 17:10:09 (26.4 KB/s) - `build-notes' saved [7039/7039]
 
  WARNING: timestamping does nothing in combination with -O. See the
  manual for details.
 
  WARNING: timestamping does nothing in combination with -O. See the
  manual for details.
 
  WARNING: timestamping does nothing in combination with -O. See the
  manual for details.
 
 
  If i try has root, an different error appears:
 
  Resolving coot.googlecode.com... 74.125.134.82, 2001:4860:800a::52
  Connecting to coot.googlecode.com|74.125.134.82|:80... connected.
  HTTP request sent, awaiting response... 200 OK Length: 111873
  (109K) [text/plain] Saving to: `build-it-gtk2-simple'
 
 
 100%[=]
  111,873  223K/s   in 0.5s
 
  2012-06-21 17:17:04 (223 KB/s) - `build-it-gtk2-simple' saved
  [111873/111873]
 
  .: 7: build-it-gtk2-simple: not found
 
 
  anyone know how to fix?
 
  thank you all
 
  Andre
 

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

 GPG Key ID = A46BEE1A
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 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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 BfQ/U61EdItMfRGp5mMAVak=
 =fj6v
 -END PGP SIGNATURE-

Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

[hari jayaram]

Thanks a lot Roger Rowlett for your  very detailed response. I got the
SG-Zn refinement to work exactly as you  detailed.
The key was to rebuild the Cysteines in coot keeping in mind the 2.3 Å
coordination distance and not get put off by coot SS bonding things
while I tried to get the Cys-SG's in place . So after some fixing in
coot -all Zns were 2.0 to 2.5 Å away from a Cys-SG going in to refmac
and then your approach worked perfectly.

So I had to:
Rebuild and put the Cys-SG within 2.3 A of the Zinc.
Remove the SSBOND definitions from the pdb file in an editor
Run the mock refinement with refmac to have it detect the SG-ZN coordination
Merge the cif file with my ligand cif file.
Run the restrained refinement in coot


I had just one question. I am imagining that the Cys SG-Zn restraint
can be added to the standard refmac  monomer dict or I should be able
to simply reuse this dummy run cif file everytime I refine a structure
with a SG-Zn coordination. Cif files are reside number agnostic is
that true.

Also since the refmac dict has the ZN defined , how come coot does not
have the cif defined?
I am assuming I can similarly make coot coordination and Zn ion aware


Regardless, thanks again for your detailed response I have the
refinement working flawlessly.

Hari

On Thu, May 13, 2010 at 8:53 PM, Roger Rowlett rrowl...@colgate.edu wrote:
 Hari,

 Before starting your dummy refmac job to write out the appropriate cif file,
 you will need to use Coot adjust the positions of the Cys and other
 Zn-ligand side chains to appropriate positions (consisatent with your
 electron density maps, of course) to coordinate to Zn. Typical Zn-S bonds
 are 2.3 A, Zn-O or Zn-N bonds are about 2.0 A. You have to do this in order
 to break the apparent S-S disulfide bond. You don't have to get the bond
 distances perfect for refmac to figure it out. You can't do a real-space
 refinement of the metal ligands in coot because it does not know about the
 metal ion you have separately added, and will instead try to insert the
 ligands into the electron density contributed by the zinc. Do the ligand
 readjustment manually to put everything in to a reasonable place for refmac
 to start from. Save this as your pdb file with your zinc ion merged in to
 start the refmac job. Before running refmac, ensure there are no disulfide
 or other undesired linkage records in your pdb file. Remove them in your
 favorite text editor as required. I can't remember at the moment if S-S
 bonds are listed as a LINKR, LINK or as some other type record, but it
 should be obvious in the PDB file. Just remove the offending S-S bond
 record. Then start your dummy refmac job, which will fail and generate a cif
 file with all the metal ligand linkage information. If you have positioned
 ligands properly, you should see in this cif file definitions for all
 Zn-ligand linkages and nothing else. Remove any blocks in the cif file that
 are not linkages you would like to incorporate into your refinement
 restraints, if necessary. Now run your refmac refinement, using the cif file
 as your input library with your metal ligand restraints. If the metal ligand
 distances are reasonable, refmac should pick them up and refine them with
 proper restraints. Refmac will write the necessary LINKR records into your
 PDB file for all future refinements of this file.

 We do this routinely for Zn-metalloenzymes and it works just fine with
 2.5-2.9A data. Coot doesn't make a real link between sulfurs: it is just
 adding a bond for any atoms that are within reasonable bonding distance of
 each other. If you rotate the sulfur atoms away from each other, Coot will
 break the bond for you. On the other hand, if you leave a linker record in
 the pdb file for a S-S bond, then refmac will restrain this bond throughout
 refinement no matter what else is present.

 Good luck. You should be able to get to to work out properly.

 Cheers, Roger Rowlett


 On 5/13/2010 7:31 PM, hari jayaram wrote:

 Hello Eleanor and Roger Rowlett and everyone,

 I am still having a tough time with coordinated metal refinements in
 refmac ( and coot )

 I followed Rogers suggestion of creating a pseudo refmac run and then
 using the output cif definition for Cys -SG Zn as an input for further
 refinement. Even If I did input this cif , I see that my
 tetra-coordinated Zinc is pushed aside and my Cysteine SG - are
 disulphide
 bonded to each other creating a tetrahedral arrangement.

 One caveat . The Resolution of the data is no all that spectacular
 (2.5) so the whole assembly appears rather blobby with three clear Zn
 spheres like I would expect in the DELFWT maps before I model in the
 Zn.

 The other un-related problem is that coot seems to also want to bond
 Cysteines to each other when I do the real space refinement, but I
 think thats because SG-Zn restraints are not part of the coot
 dictionary .So the problem may very well be in the lack of a record in
 the pdb output by coot that says ..dont

Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

[hari jayaram]

Hello Eleanor and Roger Rowlett and everyone,

I am still having a tough time with coordinated metal refinements in
refmac ( and coot )

I followed Rogers suggestion of creating a pseudo refmac run and then
using the output cif definition for Cys -SG Zn as an input for further
refinement. Even If I did input this cif , I see that my
tetra-coordinated Zinc is pushed aside and my Cysteine SG - are
disulphide
bonded to each other creating a tetrahedral arrangement.

One caveat . The Resolution of the data is no all that spectacular
(2.5) so the whole assembly appears rather blobby with three clear Zn
spheres like I would expect in the DELFWT maps before I model in the
Zn.

The other un-related problem is that coot seems to also want to bond
Cysteines to each other when I do the real space refinement, but I
think thats because SG-Zn restraints are not part of the coot
dictionary .So the problem may very well be in the lack of a record in
the pdb output by coot that says ..dont disulfide bond these Cys. I
did check there were no explicit disulphide links defined or LINK or
LINKR.


So  I am still nor refining these Cys-Zn links and have them mangled
in my pdb, so any pointers will be greatly appreciated.
Thanks for your help in advance

Hari



On Thu, May 13, 2010 at 12:50 PM, Eleanor Dodson c...@ysbl.york.ac.uk wrote:
 Has anyone answered this?
 Eleanor

 hari jayaram wrote:

 Hi

 Am trying to build coordinated Zn+2 by CYS -SG atoms and have it
 refine properly in refmac5.5

 I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually
 the coordination relations in a text editor using LINK records.
 the ions were placed in the same chain that was doing the coordination.

 LINK        ZN    ZN A1001                 SG  CYS A 487     1555   1555
  2.34

 I found that some of these ions refined well using refmac 5.5 and the
 resulting pdb had LINKR records in place indicating the coordinating
 interactions.

 For some of the Zn atoms however , the ions did refine , but coot
 still was covalently disulphide bonding the Cys to each other rather
 than coordinating the ZN and there were no LINKR records in the refmac
 refined pdb file. I know these interactions are legitimate because it
 is a known structure.Should I manually create LINKR records instead of
 LINK records after modeling in the ions?

 What is the correct procedure to model coordinating ions and have
 refmac treat them appropriately.
 Thanks in advance.

 Hari

[ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

[hari jayaram]

Hi

Am trying to build coordinated Zn+2 by CYS -SG atoms and have it
refine properly in refmac5.5

I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually
the coordination relations in a text editor using LINK records.
the ions were placed in the same chain that was doing the coordination.

LINKZNZN A1001 SG  CYS A 487 1555   1555  2.34

I found that some of these ions refined well using refmac 5.5 and the
resulting pdb had LINKR records in place indicating the coordinating
interactions.

For some of the Zn atoms however , the ions did refine , but coot
still was covalently disulphide bonding the Cys to each other rather
than coordinating the ZN and there were no LINKR records in the refmac
refined pdb file. I know these interactions are legitimate because it
is a known structure.Should I manually create LINKR records instead of
LINK records after modeling in the ions?

What is the correct procedure to model coordinating ions and have
refmac treat them appropriately.
Thanks in advance.

Hari

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[hari jayaram]

Hello Garib,
I was using the ouput from a refmac run for the next round and using what I
thought were the original fobs .
So I guess as you said at each round I was using the de-twinned result from
the previous round.

I will repeat these refinements with the original scala output mtz to get a
more accurate feel for the twin fraction.

I am using medium restraints with NCS ( I have four molecules in the asu)
and the data does also look like P43212 with fewer molecules in the ASU.

Thank you  for all your suggestions
Hari


On Fri, Apr 23, 2010 at 5:38 PM, Garib Murshudov ga...@ysbl.york.ac.ukwrote:

 You may be using output reflection data  from the previous cycle of
 refinement for the next session. After twin refinement output Fobs
 (confusingly) may be detwinned. You can try to use original reflection data
 file (e.g. after scala/truncate/freerflag) and  for refinement and it may
 clarify things a bit. If you are using original reflection data file for
 refinement then I do not knwo the reason of such peculiar behaviour.

 I have seen that twin fraction during refinement goes down but I am not
 sure that it would happen  substatioally if your R/Rfree were as you stated
 before twin refinement.

 regards
 Garib

 On 23 Apr 2010, at 22:28, hari jayaram wrote:

 I am refining a twinned dataset in possible spacegroup P212121 . Pointless
 thinks it is P43212 , but based on reading this posting (
 http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html)
 I think it is P212121.

 The starting R/Rfree after molecular replacement  ( single site mutant)
 was 34/38 to 2.2 A

 After an initial round of restrained refinement ( without twin refinement)
 and minimal rebuilding I got the R/Rfree to 30/34

 Then I did an amplitude based twin refinement - The twin fraction was 0.48
 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29

 After a little more rebuilding ( a few residues out of 800 residues in ASU)
 and another twin refinement I got an r/rfree of 22/27 . Now the twin
 fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)

 The maps looked a little better allowing me to fix a few more residues

 Finally the same twin refinement gives me no twin operators and the R/Rfree
 is 22/26


 All the twinning tests indicate a serious twinning in my crystal.  Any
 ideas why I am seeing this

 Hari

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

[hari jayaram]

, at 7:49 AM, hari jayaram hari...@gmail.com wrote:
  
   Hi Tim,
   Thanks a tonne Tim for the pointer on how bltwish is handled in
debian.
  
   A symlink from /usr/bin/wish to /usr/bin/bltwish.
  
   Seems to at-least start ccp4i. Now to see if it will also plot my
graphs
  
   Hari
  
  

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

 GPG Key ID = A46BEE1A




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

 GPG Key ID = A46BEE1A


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 Version: GnuPG v1.4.9 (GNU/Linux)

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 QaIPxdlYeCsr1xWzqX8X7+Q=
 =cc71
 -END PGP SIGNATURE-

[ccp4bb] blt2.4z in ubuntu 10.04

[hari jayaram]

Hi I installed ccp4-6.1.3 on an ubuntu 10.04 beta box.
It does not have bltwish and I was trying to install it using gcc 4.4.3 on a
64 bit ubuntu machine

The known patches for getting blt2.4z are already applied to the source ,
the documented problems on the ccp4i problems page are also as they should
be in the code .

When I configure

./configure --with-tcl=/usr/lib64/tcl8.5 --with-tk=/usr/lib64/tk8.5

ANd then make I get the following errors which are beyong my troubleshooting
abilities . Any help will be greatly appreciated
Thanks
Hari

h...@hari:~/tcltk++/blt2.4z$ make
(cd src; make all)
make[1]: Entering directory `/home/hari/tcltk++/blt2.4z/src'
gcc -c -Wall -O6   -I. -I.  -I/usr/include/tcl8.5/tk-private/generic
-I/usr/include/tcl8.5 bltAlloc.c
In file included from bltInt.h:80,
 from bltAlloc.c:1:
bltNsUtil.h:50: error: conflicting types for ‘Tcl_FindCommand’
/usr/include/tcl8.5/tclDecls.h:3123: note: previous declaration of
‘Tcl_FindCommand’ was here
bltNsUtil.h:67: error: conflicting types for ‘Tcl_CreateNamespace’
/usr/include/tcl8.5/tclDecls.h:3068: note: previous declaration of
‘Tcl_CreateNamespace’ was here
bltNsUtil.h:72: error: conflicting types for ‘Tcl_FindNamespace’
/usr/include/tcl8.5/tclDecls.h:3116: note: previous declaration of
‘Tcl_FindNamespace’ was here
bltNsUtil.h:75: error: conflicting types for ‘Tcl_Export’
/usr/include/tcl8.5/tclDecls.h:3086: note: previous declaration of
‘Tcl_Export’ was here
make[1]: *** [bltAlloc.o] Error 1
make[1]: Leaving directory `/home/hari/tcltk++/blt2.4z/src'
make: *** [all] Error 2

Re: [ccp4bb] blt2.4z in ubuntu 10.04

[hari jayaram]

Hi Tim,
Thanks a tonne Tim for the pointer on how bltwish is handled in debian.

A symlink from /usr/bin/wish to /usr/bin/bltwish.

Seems to at-least start ccp4i. Now to see if it will also plot my graphs

Hari



On Wed, Apr 14, 2010 at 10:23 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
 Dear Hari,

 blt is, as far as I know, pretty deprecated and probably not updated anymore.
 It also depends on tcl/tk version 8.4, not version 8.5 which is installed on
 your system.  Maybe you can try to downgrade and recompile.

 Another, simpler way might be the following which works on the last 4 PCs I
 installed with Debian stable recently:
 Debian comes with the package blt which provides blt as a library, probably 
 the
 same as with ubuntu. Since there is only a 'wish' binary on your system but
 not 'bltwish', you have to change all occurences of bltwish in the scripts in
 $CCP4/ccp4i/bin with 'wish'.

 With Debian stable this works, even - which surprised me - for the loggraphs 
 (it
 didn't work previously for the graphs which was, as far as I understand, the
 reason why blt was provided as package by Bill Scott).

 Good luck, Tim


 On Wed, Apr 14, 2010 at 09:49:50AM -0400, hari jayaram wrote:
 Hi I installed ccp4-6.1.3 on an ubuntu 10.04 beta box.
 It does not have bltwish and I was trying to install it using gcc 4.4.3 on a
 64 bit ubuntu machine

 The known patches for getting blt2.4z are already applied to the source ,
 the documented problems on the ccp4i problems page are also as they should
 be in the code .

 When I configure

 ./configure --with-tcl=/usr/lib64/tcl8.5 --with-tk=/usr/lib64/tk8.5

 ANd then make I get the following errors which are beyong my troubleshooting
 abilities . Any help will be greatly appreciated
 Thanks
 Hari

 h...@hari:~/tcltk++/blt2.4z$ make
 (cd src; make all)
 make[1]: Entering directory `/home/hari/tcltk++/blt2.4z/src'
 gcc -c -Wall -O6   -I. -I.  -I/usr/include/tcl8.5/tk-private/generic
 -I/usr/include/tcl8.5 bltAlloc.c
 In file included from bltInt.h:80,
                  from bltAlloc.c:1:
 bltNsUtil.h:50: error: conflicting types for ‘Tcl_FindCommand’
 /usr/include/tcl8.5/tclDecls.h:3123: note: previous declaration of
 ‘Tcl_FindCommand’ was here
 bltNsUtil.h:67: error: conflicting types for ‘Tcl_CreateNamespace’
 /usr/include/tcl8.5/tclDecls.h:3068: note: previous declaration of
 ‘Tcl_CreateNamespace’ was here
 bltNsUtil.h:72: error: conflicting types for ‘Tcl_FindNamespace’
 /usr/include/tcl8.5/tclDecls.h:3116: note: previous declaration of
 ‘Tcl_FindNamespace’ was here
 bltNsUtil.h:75: error: conflicting types for ‘Tcl_Export’
 /usr/include/tcl8.5/tclDecls.h:3086: note: previous declaration of
 ‘Tcl_Export’ was here
 make[1]: *** [bltAlloc.o] Error 1
 make[1]: Leaving directory `/home/hari/tcltk++/blt2.4z/src'
 make: *** [all] Error 2

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

 GPG Key ID = A46BEE1A


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 Version: GnuPG v1.4.9 (GNU/Linux)

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 =4dy/
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[ccp4bb] Refmac flag to keep intensities, DANO and other columns in mtz output

[hari jayaram]

Hi ,
A trivial procedural question.

When running refmac from ccp4i , is there someway that I can have it only
add or substitute columns in the output mtz . I am currently running cad
after refmac to add back in my DAno column and the anomalous intensities ,
but was wondering if there is someway I can have refmac not drop the DAnos
and other columns from my input mtz in the output Mtz.

I seem to remember that older versions ( I am running the lates 6.1.3
provided refmac) did not drop these columns.

Thanks for your help
Hari

Re: [ccp4bb] imosflm plot question?

[hari jayaram]

Just sending along the answers to my question about the imosflm crystal
missets and mosaicity plot from Ethan Meritt and Harry Powell.


Value of the parameter as a function of diffraction image number.
If the parameter didn't vary, it would show as a horizontal line.

phi(x), etc are the crystal orientation angles.
mosaicity is self-named.

Ethan


Hi Hari

phi(x) phi(y) and phi(z) are the crystal missetting angles - how much the
apparent orientation differs from the calculated one from indexing.
Historically, with crystals mounted in capillaries, the crystal would often
really slide about, but these days (with cryocooled crystals held rigidly in
loops) they account for things like the rotation axis not ebing
perpendicular to the X-ray beam.

Mosaic should be self explanatory...
-
 Show quoted text -

 - Show quoted text -
 Screen shot 2010-03-17 at 5.10.49 PMMar 17, 2010.png


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 0QH
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742



On Wed, Mar 17, 2010 at 5:17 PM, hari jayaram hari...@gmail.com wrote:

 Hello ,

 I had a question about the imosflm plots during data integration.

 I am attaching the plot for one of my datasets ...Just curious what the
 middle plot is plotting


 Thanks a lot for your help

 Hari

[ccp4bb] imosflm plot question?

[hari jayaram]

Hello ,

I had a question about the imosflm plots during data integration.

I am attaching the plot for one of my datasets ...Just curious what the
middle plot is plotting


Thanks a lot for your help

Hari
attachment: Screen shot 2010-03-17 at 5.10.49 PMMar 17, 2010.png

Re: [ccp4bb] coot.App from ccp4-6.1.3 release suddenly started segmentation-faulting and dumping core on OSX- how to troubleshoot

[hari jayaram]

Thanks a tonne Paul .

Once I deleted  the ~/.fontconfig directory the ccp4-6.1.3 provided coot.App
[0.6 (revision 2540)  [with guile 1.8.3 embedded]] launched right up.

So I guess this is a gtk2 or Xquartz peculiarity because the fink compiled
coot (0.6.1 (revision 2740) , guile 1.8.2)  launched up just fine on the
same hardware.

I had put the coot.App on all the lab macs and knew it had to be something
this strange , because it was not crashing on any other Leopard running mac
in the lab.

Also thanks Birrane G for suggestions to help troubleshoot.

Thanks again
Hari



On Tue, Mar 2, 2010 at 4:26 AM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:

 hari jayaram wrote:

 Hi I just started having segmentation faults with the coot downloaded from
 the ccp4 releases page for ccp4-6.1.3. This release was working quite well,
  and I even convinced a few people to stop fink-ing and just download the
 coot dmg  from ccp4.

 The problem started after I installed a bunch of unrelated packages
 yesterday.

 Now when I try to launch the coot Application I get a crash report :
 pasted below.

 Any ideas why?


 Delete your ~/.fontconfig directory?

 c.f.

 http://www.mail-archive.com/wireshark-b...@wireshark.org/msg16312.html

 Paul.

[ccp4bb] coot distributed by ccp4-6.1.3 and python scripting

[hari jayaram]

Hi,
I noticed that the coot distributed by ccp4-6.1.3 does not have python built
into it. Is there anyway to add in the python support post installation ?
I am running the ccp4 supplied coot on OSX Leopard 10.5.8

I am cc-ing the coot mailing list as well .

Thanks
Hari

Re: [ccp4bb] ccp4-6.1.3 phaser sigmaa weighted maps problem

[hari jayaram]

Here is Randy's reply:

Dear Hari,

Well, it turns out to be a combination of some bad data and a
poorly-considered feature in Phaser.

Something must have gone wrong with the data from 2.9 to 2.8A, because
the intensities are much too large.  I've been developing a new
relative Wilson plot tool to look at such things.  This plots the
logarithm of the mean value of the observed F^2 divided by the mean
value of the calculated F^2 in each resolution shell, as a function of
(sin(theta)/lambda)^2.  This is then scaled to an average curve from
something like 15000 data sets in the PDB.  The plot in the attached
file compares the curve from your data (blue line) with the average
from the PDB (black line, with grey shading for the variation within
the PDB).  Things go bad around 2.9A.

The single biggest reason that the map from Phaser is much worse than
maps from Refmac or SIGMAA is that Phaser assumes that the Fo values
are on the right scale; the Fc values in the high resolution shell end
up being scaled up, so you get very large map coefficients in this bad
resolution shell.  If you look at the map in coot but limit the
resolution to 2.9A, it looks much better.  (You can set resolution
limits in coot using the Expert Mode button in the open map from MTZ
window, but you have to give both low and high resolution limits.)  In
Refmac and SIGMAA, the SigmaA values will refine to zero for the high
resolution shells, so that the map coefficients are zero in that shell
as well.

Maps from Refmac will probably look much better for a second reason:
your data are very incomplete beyond about 5A resolution.  By default,
if you have hkl values in the MTZ file (e.g. if you've used uniquify),
Refmac fills in the missing data with D*Fc.

Apart from the highest resolution shell being severely downweighted,
the refinement of SigmaA values is probably relatively unimportant for
the rest of the data.

Thanks for bringing this up and sharing the data!  We'll have to
figure out how to make Phaser cope with cases like this, either
through the SigmaA refinement or by looking at the relative Wilson
plot.

Regards,

Randy


On Fri, Feb 5, 2010 at 6:33 AM, Randy Read rj...@cam.ac.uk wrote:
 In all versions of Phaser up to the currently distributed ones, the assumed 
 RMS error of the model is used to generate an a priori SigmaA curve for the 
 likelihood target.  At the end of the structure solution, the map 
 coefficients are computed by using those a priori SigmaA values to calculate 
 m and D.

 So it should indeed be better to go into SIGMAA, Refmac or phenix.refine and 
 generate a map, because the SigmaA values will be refined to reflect the 
 actual agreement between Fo and Fc, not the agreement that was guessed 
 beforehand.  Nonetheless, I'm surprised that the difference in quality can be 
 so noticeable.  That implies that the initial guess of model quality was far 
 off the actual value, so it would be good to know what Phaser was told about 
 model completeness and either expected RMS error or sequence identity, in 
 cases where the maps were bad.

 We (by which I mean Airlie) are currently working on putting a SigmaA 
 refinement into the end of the Phaser MR run, so future versions of Phaser 
 won't have this issue.  It would be useful if we could get an example or two 
 of where the current version gives really bad maps, so we can verify that the 
 new procedure fixes the problem.

 Regards,

 Randy Read

 On 5 Feb 2010, at 00:48, hari jayaram wrote:

 Hi ,
 I just switched to ccp4-6.1.3 and ran  the phaser which is bundled
 with the ccp4-6.1.3 release. After molecular replacement I get a
 pretty good solution (TFZ 59.2)  and output pdb and mtz files.
 I am then looking at the maps from the phaser output mtz i.e the FWT ,
 PHWT map and the FWT PHIC map . Both maps look very crappy and look
 like noise. I tried the fft inside of coot and separately as a FFT
 inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be
 off.

 However , if I take the phaser solution output model and do the sigmaa
 myself. The map looks normal and sensible.

 It seems like phaser inside of ccp4-6.1.3 is not generating the output
 mtz correctly .
 Anyone else seeing this or is there something wrong with my setup.


 Hari

 --
 Randy J. Read
 Department of Haematology, University of Cambridge
 Cambridge Institute for Medical Research      Tel: + 44 1223 336500
 Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
 Hills Road                                    E-mail: rj...@cam.ac.uk
 Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk


attachment: hjBr6_relwilson.png

[ccp4bb] ccp4-6.1.3 phaser sigmaa weighted maps problem

[hari jayaram]

Hi ,
I just switched to ccp4-6.1.3 and ran  the phaser which is bundled
with the ccp4-6.1.3 release. After molecular replacement I get a
pretty good solution (TFZ 59.2)  and output pdb and mtz files.
I am then looking at the maps from the phaser output mtz i.e the FWT ,
PHWT map and the FWT PHIC map . Both maps look very crappy and look
like noise. I tried the fft inside of coot and separately as a FFT
inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be
off.

However , if I take the phaser solution output model and do the sigmaa
myself. The map looks normal and sensible.

It seems like phaser inside of ccp4-6.1.3 is not generating the output
mtz correctly .
Anyone else seeing this or is there something wrong with my setup.


Hari

[ccp4bb] CCP4 study weekend 2010 video archive?

[hari jayaram]

Hi I am wondering if video of any of the talks presented at the
recently concluded CCP4 study weekend 2010 is available anywhere.

The pdf and other material at
http://www.ccp4.ac.uk/courses/stwk10/talk_files/  makes for some
excellent reading.

Thanks
Hari

Re: [ccp4bb] Measuring membrane proteins with Nanodrop photometer

[hari jayaram]

Hello Florian,
We routinely measure membrane protein samples in detergent with much problem
on the nanodrop. The concentration of detergent is often many times the CMC
. We have found the drop does form quite well as long as the surface is
clean.
Often this can be easily achieved by repeated buffing of the surface with
a kimwipe.
Also at moderate protein concentrations used with crystallography i.e the
6-25 mg/ml range with 5 to 20 mM detergent ( CMC around 0.7 mM) , the A280
measurement is seemless ..you put the drop there ( 3 to 5  µl ) and read the
A280. Only about one out of ten times , the drop collapses and fails to give
a good reading.  Then you just buff the surface , and repeat the reading.
So in summary , there is no problem. I would also read a ccp4bb discussion
on this topic which occurred on Dec 4th
2004http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg08490.html
.
Hope this helps
Hari

On Mon, Jan 25, 2010 at 6:14 AM, Florian BrŸueckner 
f.brueck...@imperial.ac.uk wrote:

 Dear all,

 can anyone share experience with measuring membrane protein
 concentration in detergent containing buffer with a nanodrop photometer
 e.g. Thermo Scientific ND2000. Specifically, does the reduction in
 surface tension caused by the detergent pose any problems?

 Thanks!

 Cheers

 Florian

 --
 ---

 Dr Florian Brueckner
 MPL Group (Prof So Iwata), Imperial College
 Diamond Light Source Ltd
 Diamond House, Harwell Science and Innovation Campus
 Didcot, Oxfordshire
 OX11 0DE
 England

 Phone (Office): +44-1235-77-8465
 Phone (Lab):+44-1235-77-8794
 Email: f.brueck...@imperial.ac.uk

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

[hari jayaram]

I uploaded an archive( pdf of emails plus text log files) of all the
conversations that took place around Eleanor Dodsons Original thread on
08/17/07  discussing the 2HR0  structure along with the attached log files
to an archive available at

http://harijaycrystdata.s3.amazonaws.com/ccp4bb_archive_thread_withlogfiles_08_17_07_2HR0.zip

I tried to get the threads with attached logs to a single link using other
email thread viewers , but in the end put it into the above file using gmail
.
Since I missed most of the original discussion, re-reading it was very
enlightening.

Hope this helps

Hari Jayaram


On Fri, Dec 11, 2009 at 4:19 AM, Tommi Kajander
tommi.kajan...@helsinki.fiwrote:

 Would the exact analysis of how each of these things were wrong and
 fabricated be somewhere
 available Would be fair (apart from the known case of C3b) to have the
 whole analysis available
 instead of just this kind of news feed. I suspect its not obvious by five
 minute check in all cases.

 Perhaps there needs to be ways within PDB in form of automated tools that
 would raise those red
 flags in suspicious cases (e.g. some data analysis --such as the
 contribution by solvent etc now that data beyond 8Å
 is by default used in refinement) - as it appears peer review/editing by
 journals isn't/cant always be(?) stringent enough.

 In any case, some type of  automated analysis of the whole data base might
 be a good idea, as there can be
 other cases (with another couple of thousand papers citing them..).

 tommi

 On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote:

  After a thorough examination of the available data, which included a
 re-analysis of each structure alleged to have been fabricated, the
 committee
 found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than
 not
 falsified and/or fabricated and recommended that they be removed from the
 public record, the university said in its statement this week.

Re: [ccp4bb] measure detergent concentration

[hari jayaram]

Also depending on the detergent , If you have a detergent like
decyl-maltopyranoside ( DM) or any other glycoside based detergent you
can use the reaction with sulfuric acid  and phenol followed by
Absorption  measurement to quantitate as detailed in

Anal Biochem. 2005 Jan 1;336(1):117-24.
A colorimetric determination for glycosidic and bile salt-based
detergents: applications in membrane protein research.
Urbani A, Warne T.

Using a standard curve against the same detergent  you can quantitate
your detergent concentration in your final protein sample


Hari




On Fri, Oct 23, 2009 at 4:35 PM, Michael Matho mma...@scripps.edu wrote:

 Weikai,

 We did it using NMR but you asked for a simple way so I guess I'm out of 
 topic.

 Anyway, since I believe it is the most accurate method, here it is: using a 
 high detergent concentration stock solution you can assign resonance peaks to 
 your detergent molecule bonds.

 Then you can set up a standard curve using different known detergent 
 concentrations (for example from 10% down to 0.1%) by calculating the surface 
 of your peak(s) which is directly related to your detergent concentration.

 Each time you need to know the concentration of a new sample, you just need 
 to record the peaks, and use the three-click rule to deduct the unknown value.

 As a colleague answered you earlier, we noticed that a 50kDa cutoff withheld 
 a lot of detergent during concentration process and consequently your final 
 concentration might increase significantly. For example we started with 0.25% 
 DES and noticed increases of above 1%. Of course this will depend on the 
 concentration factor.

 This did not happen when using a 100kDa cutoff, and DES concentration remain 
 pretty much constant.

 Now, it will depend on your system: what detergent you are using, since micel 
 size and CMC are obviously the critical parameters here -- but also what 
 maximal cutoff you can use w/o loosing your membrane protein in the flow 
 through...

 Good luck,
 Michael

 - Original Message -
 From: Patrick Loll
 To: CCP4BB@jiscmail.ac.uk
 Sent: Friday, October 23, 2009 1:12 PM
 Subject: Re: [ccp4bb] measure detergent concentration
 I'll second this.  We've done this as an exercise in NSLS Membrane Protein 
 Crystallization workshop for a few years, and it works like a charm. You can 
 stain in a warm iodine chamber and visualize by scanning the TLC plate on a 
 garden variety scanner (we use an inexpensive Canon LIDE that probably cost 
 less than USD 60 five years ago). We quantify the spot intensity with NIH 
 Image or equivalent, and get lovely linearity down to the CMC, spotting only 
 1 uL of sample--so we haven't seen any need to concentrate.
 On 23 Oct 2009, at 3:41 PM, Edward A. Berry wrote:

 Only easy if you happen to have silica gel TLC plates and
 a chromatography jar lying around, perhaps from some
 phospholipid analysis:

 A strategy for identification and quantification of
 detergents frequently used in the purification of membrane proteins
 Laura R. Eriks, June A. Mayor, and Ronald S. Kaplan
 Analytical Biochemistry 323 (2003) 234–241

 This paper recommends spotting on a TLC plate and running
 beside standard amounts of the same detergent. From intensity/size
 of the detergent spot after developing you can bracket the detergent
 concentration. (And by the way they found that detergents are concentrated by 
 ultrafiltration). To increase sensitivity, speedvac a volume too large to
 spot on the plate, dissolve the residue in Me0H.

 Ed
 wei...@crystal.harvard.edu wrote:

 Hi Folks:

 After concentrating a membrane protein, is there a (easy) way of measuring

 the detergent concentration in the sample?

 Regards,

 Weikai

 ---

 Patrick J. Loll, Ph. D.

 Professor of Biochemistry  Molecular Biology

 Director, Biochemistry Graduate Program

 Drexel University College of Medicine

 Room 10-102 New College Building

 245 N. 15th St., Mailstop 497

 Philadelphia, PA  19102-1192  USA

 (215) 762-7706

 pat.l...@drexelmed.edu

[ccp4bb] Gridzilla - A graphical tool to calculate crystal optimization screening grids

[hari jayaram]

Hello ,

I have written an application that makes it easy to design and calculate
protein crystallization optimization screens for 24 , 96 and 384 well plates
.

Starting with your stock solutions you can create any screening grid  using
many gridding operations for eg. gradient along X , gradient along Y ,
constant value , gradient as list , buffer pH gradient etc

The application outputs the summary of the screen created as a PDF  file
with reagents volumes and concentrations.
Although I wrote the application to create dispense lists for a formulatrix
liquid handling robot which we have in the lab, I am hoping it will be
useful to others to quickly design screens and calculate pipetting volumes
for manual screen preparation.

You can download a binary for Linux , Mac and Windows  from

http://www.code-itch.com/gridzilla

There is also a screencast video that hopefully tells you how the app works
at :

http://code-itch.com/gridzilla/GridZillaScreencast.swf

The source code is  available on the site and also on my github acount (
http://github.com/harijay). It can be easily adapted to support other liquid
handling input formats.

Please let me know if you find the app useful .
Feedback , suggestions etc are welcome.

Thanks

Hari Jayaram

[ccp4bb] configure.def not copied over with in-place update of ccp4

[hari jayaram]

Hi I just updated my ccp4 to 6.1.2 ( the August 13th 2009  release) and
thought I would pass on this feedback.

I used the source version and the built in install.sh script which worked
very well on ubuntu Linux 654 bit ( Hardy Heron)

However after the update the new ccp4i gui had lost the location of all my
projects , although it still remembered the names.

The installation script did not move my old configure.def into the  new
installation. So I had to manually copy the old configure.def over and
change the
value as mentioned in a previous post on ccp4bb

USE_DBCCP4I_ON_STARTUP_logical  0


Hope this helps someone
elsehttp://www.bioscreencastwiki.com/Installing_ccp4-6.1.2_from_source_on_Ubuntu_Linux
Hari

Re: [ccp4bb] imosflm with multiple data sets

[hari jayaram]

I didnt realize the following:

You read in images from the two wedges  collected with the same
crystal orientation.

mydata_1_###.img
mydata_101_###.img


Now when you index ,if you say use images from both datasets
mydata_1_###.img use image 1,90
mydata_101_###.img use image 30 , 120

The matrix for the second wedge (mydata_101_###.img)  is still marked unknown?
Isnt this different from the behaviour in the X- mosflm . SHould the
matrixes be the same since the orientation was calculated using images
from both.

Now , If I did not force the second wedge to have the same matrix ,
using the save to file and read from file method you just described ,
does the new imosflm use the last calculated matrix from the running
session or calculate a new matrix ?..I guess I have to check some of
the data I processed with my erroneous assumption to make sure that
the matrixes for the two wedges are the same .

Thanks for clarifying this..
hari




On Mon, Aug 17, 2009 at 9:13 AM, Andrew Leslieand...@mrc-lmb.cam.ac.uk wrote:
 Dear Tom,

                  There is a straightforward way to do what you want. It is
 probably simplest to start by reading in only the images from the first
 segment (0-180). Then do the indexing, cell refinement and integration in
 the usual way.

 Then read in the second segment of data. You will notice that in this second
 segment, underneath the Sector name, there is a line starting Matrix and
 this will be Unknown. If you go to the Matrix line of the first segment,
 the matrix will have a name (based on the image template).  Double click on
 the name of the matrix. A popup window (Matrix properties) will appear.
 Click on the save matrix file icon (a blue disc) and save the matrix with
 an appropriate filename.

 Now go to the Matrix line of the second segment, double click (on Unknown)
 as before and this time click on the Open matrix file icon (a folder) and
 read in the matrix that you saved from the first sector. You can now process
 the second segment using this matrix.

 It would be even nicer if you could drag and drop the matrix, this is on
 our to do list.

 Best wishes,

 Andrew

 On 17 Aug 2009, at 13:33, Brett, Thomas wrote:

 I am an imosflm novice and have a relatively simple question. I have a 360
 deg data set collected in two swathes of 180 deg (one with phi=0 and omega
 going 0-180 and the second with phi = 180 and omega going 0-180). What is
 the easiest way to process the two datasets using a matching orientation
 matrix (or one rotated by 180 deg as it were) so that all the data can be
 merged together. Is there an easy way to do it in imosflm or must one
 process the two sets separately and then manipulate later with pointless
 before scalling and merging everything together?
 Thanks in advance.
 -Tom

 Tom J. Brett, PhD
 Assistant Professor of Medicine
 Division of Pulmonary and Critical Care
 Washington University School of Medicine
 Campus Box 8052, 660 S. Euclid
 Saint Louis, MO 63110

[ccp4bb] mama/mapman converted CCP4 format in dmmulti gives logical*1 error

[hari jayaram]

Hi everyone
Dmmulti seems to not like masks converted in mapman to the CCP4 format.
I get the following error

 dmmulti:   domnin - Mask file is not logical*1


I know the masks are fine because I can display them fine in coot which
reads CCP4 masks .I can also get ncsmask to read them fine.
Now in  ncsmask run if I  ask ncsmask to do operations which I have already
done in mama and write out the mask . Now dmmulti  does not give me the
logical*1 error.

I am attaching the mapman statistics for  the mask which does not work (
mama to ccp4 in mapman)  and the working mask ( mama-to-ccp4-then-ncsmask)
here.
They seem very similar so I am wondering why I have to have ncsmask touch my
CCP4 mask file before dmmulti is happy with it.

Thanks for your help
Hari


##
Not working mask
##

  File name for input map file on unit   1 : nottedmask.msk
   file size =  261328  ;  logical name
nottedmask.msk


   Number of columns, rows, sections ...   51   29   44
   Map mode 2
   Start and stop points on columns, rows, sections21   71
-6   22 -227 -184
   Grid sampling on x, y, z    80  103  154
   Cell dimensions .  79.81400
102.63900 153.62700  82.46000  75.53000  73.45000
   Fast, medium, slow axes .YXZ
   Minimum density . 0.0
   Maximum density . 1.0
   Mean density  0.19175
   Rms deviation from mean density . 0.39367
   Space-group .1
   Number of titles 2

 Titles :


   Created by MAPMAN V. 080625/7.8.5 at Mon Jul 13 11:27:06 2009 for
hari


 Parameters as read from the map file
 Origin .. -621  -227
 Extent .. 295144
 Grid  80   103   154
 Cell axes ...  79.81102.64153.63
 Cell angles .  82.46 75.53 73.45
 UVW (fast, medium, slow)   Y X Z

 Header done
 Not in core
 Reading levels ...
 Level number : (  10)
 Level number : (  20)
 Level number : (  30)
 Level number : (  40)
 Closing BINARY CCP4 map on unit : (   1)
 Map read into memory - calculating statistics
 Sum of density in map : (  1.248E+04)
 Requested dynamic range :  0.E+00  1.E+00
 Value of Prod and Plus  :  2.5500E+02   0
 Actual dynamic range:  0.E+00  1.E+00

##
Working mask:
##

 Logical Name: nottedmask_mod1.msk  Filename: nottedmask_mod1.msk
!--SUMMARY_END--/FONT/B


  File name for input map file on unit   1 : nottedmask_mod1.msk
   file size =   66180  ;  logical name
nottedmask_mod1.msk


   Number of columns, rows, sections ...   44   29   51
   Map mode 0
   Start and stop points on columns, rows, sections  -227 -184
-6   22   21   71
   Grid sampling on x, y, z    80  103  154
   Cell dimensions .  79.81400
102.63900 153.62700  82.46000  75.53000  73.45000
   Fast, medium, slow axes .ZXY
   Space-group .1
   Number of titles 1

 Titles :




 Parameters as read from the map file
 Origin .. -621  -227
 Extent .. 295144
 Grid  80   103   154
 Cell axes ...  79.81102.64153.63
 Cell angles .  82.46 75.53 73.45
 UVW (fast, medium, slow)   Z X Y

 Header done
 Closing BINARY CCP4 map on unit : (   1)
 Map read into memory - calculating statistics
 Sum of density in map : (  1.248E+04)
 Requested dynamic range :  0.E+00  1.E+00
 Value of Prod and Plus  :  2.5500E+02   0
 Actual dynamic range:  0.E+00  1.E+00

Re: [ccp4bb] mama/mapman converted CCP4 format in dmmulti gives logical*1 error

[hari jayaram]

Hi Todd

Thanks for the pointer to mama2ccp4 . I just successfully used it to convert
a mama mask to ccp4 format and could successfully use this in dmmulti.

I thought that lx_mapman did indeed convert the mama mask to ccp4 format
since I could display and check the lx_mapman converted mask correctly in
COOT.

I didnt realize that the CCP4 format map from mapman as seen by dmmulti is
different from from the CCP4 format mask as generated by mama2ccp4 and
ncsmask.

So lesson learnt : to convert mama masks to ccp4 format use mama2ccp4 .

Thanks a tonne

Hari





On Mon, Jul 13, 2009 at 2:50 PM, Green, Todd gr...@cbse.uab.edu wrote:

 Hello Hari-

 I'm not following exactly what you have done because i can't see the
 commands that you have used. However to the best of my knowledge mapman will
 not convert to ccp4 mask format. if you have a mask from MAMA, then you can
 use mama2ccp4 to convert to ccp4 mask format, ie from the commandline:

 mama2ccp4 maskin input.mask maskout output.mask

 probably you are reading in a mask and writing out a ccp4 map but as i said
 before I don't know because you haven't provided the commands that you have
 used. see if the above command works, if not, give us a little more info on
 what you have done and it should be an easy fix.

 cheers-
 todd

 -Original Message-
 From: CCP4 bulletin board on behalf of hari jayaram
 Sent: Mon 7/13/2009 11:11 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] mama/mapman converted CCP4 format in dmmulti gives
 logical*1 error

 Hi everyone
 Dmmulti seems to not like masks converted in mapman to the CCP4 format.
 I get the following error

  dmmulti:   domnin - Mask file is not logical*1


 I know the masks are fine because I can display them fine in coot which
 reads CCP4 masks .I can also get ncsmask to read them fine.
 Now in  ncsmask run if I  ask ncsmask to do operations which I have already
 done in mama and write out the mask . Now dmmulti  does not give me the
 logical*1 error.

 I am attaching the mapman statistics for  the mask which does not work (
 mama to ccp4 in mapman)  and the working mask ( mama-to-ccp4-then-ncsmask)
 here.
 They seem very similar so I am wondering why I have to have ncsmask touch
 my
 CCP4 mask file before dmmulti is happy with it.

 Thanks for your help
 Hari


 ##
 Not working mask
 ##

  File name for input map file on unit   1 : nottedmask.msk
   file size =  261328  ;  logical name
 nottedmask.msk


   Number of columns, rows, sections ...   51   29   44
   Map mode 2
   Start and stop points on columns, rows, sections21   71
 -6   22 -227 -184
   Grid sampling on x, y, z    80  103  154
   Cell dimensions .  79.81400
 102.63900 153.62700  82.46000  75.53000  73.45000
   Fast, medium, slow axes .YXZ
   Minimum density . 0.0
   Maximum density . 1.0
   Mean density  0.19175
   Rms deviation from mean density . 0.39367
   Space-group .1
   Number of titles 2

  Titles :


   Created by MAPMAN V. 080625/7.8.5 at Mon Jul 13 11:27:06 2009 for
 hari


  Parameters as read from the map file
  Origin .. -621  -227
  Extent .. 295144
  Grid  80   103   154
  Cell axes ...  79.81102.64153.63
  Cell angles .  82.46 75.53 73.45
  UVW (fast, medium, slow)   Y X Z

  Header done
  Not in core
  Reading levels ...
  Level number : (  10)
  Level number : (  20)
  Level number : (  30)
  Level number : (  40)
  Closing BINARY CCP4 map on unit : (   1)
  Map read into memory - calculating statistics
  Sum of density in map : (  1.248E+04)
  Requested dynamic range :  0.E+00  1.E+00
  Value of Prod and Plus  :  2.5500E+02   0
  Actual dynamic range:  0.E+00  1.E+00

 ##
 Working mask:
 ##

  Logical Name: nottedmask_mod1.msk  Filename: nottedmask_mod1.msk
 !--SUMMARY_END--/FONT/B


  File name for input map file on unit   1 : nottedmask_mod1.msk
   file size =   66180  ;  logical name
 nottedmask_mod1.msk


   Number of columns, rows, sections ...   44   29   51
   Map mode 0
   Start and stop points on columns, rows, sections  -227 -184
 -6   22   21   71
   Grid sampling on x, y, z

[ccp4bb] uniquefy and CELL dimension swap

[hari jayaram]

I am using ccp4-6.1.1 on linux and OSX .

I have a problem with uniquefy adopting the cell dimensions of the wrong
data set during an rfree copy.

When I use uniquefy to copy an rfree column from one data set to another. Is
it normal for uniquefy to replace the cell dimensions in the data to the
cell dimensions from the mtz that should merely be providing the rfree
column.

Thank you for your help in advance
Hari

[ccp4bb] cad gives a fortran runtime error in line 869 : comparing phase sets

[hari jayaram]

Hi
I have multiple phase sets from separate sharp ( experimental phasing) and
phaser molecular replacement runs. I have the values as hendrickson latman
coeffs as output by phaser and sharp.
I am imagining i can use phistats to compare these phase sets which are
probably on different origins .

The first problem I have is that i need to combine the multiple HLA files
from a couple of mtz files into one mtz file for input to phistats .
I am trying this with cad and I get the error in ccp4-6.0.99e At line 869
of file /home/hari/ccp4-6.0.99e/src/cad.f
Fortran runtime error: End of record 

I am hoping that cad can blindly take mtz columns from these files and put
them into the same file .
My questions are :
How can I put these multiple sources of phases into one file . My second
question is what is a good way to compare these phase sets .

The detailed error from cad is reproduced below

Thanks for your help
hari


***
* Information from CCP4Interface script
***
The program run with command: /home/hari/ccp4-6.0.99e/bin/cad HKLIN1
/home/hari/newtry/gio_12.1.mtz HKLIN2
/home/hari/AdiC/eden_flat_75.0pc.mtz HKLOUT
/home/hari/newtry/phasereden.mtz
has failed with error message
At line 869 of file /home/hari/ccp4-6.0.99e/src/cad.f
Fortran runtime error: End of record
***

[ccp4bb] directory location for latest refmac5 dictionary

[hari jayaram]

Hi I just upgraded to the latest  refmac5 . I am looking to merge this
newest refmac5 and its associated dictionaries with my existing ccp4-6.1
installation .
I was wondering where do I copy the latest accompanying dictionary
downloaded from Garib Murshudovs page to.
Thanks in advance

Hari

[ccp4bb] refmac5 v5.5.0066 bug - CRYST angles swapped

[hari jayaram]

Hi we regularly update our intel mac refmac5 ( and ccp4)  installs from W.G
. Scotts fink packages

We just add an unusual error with refmac5 v5.5.0066 doing a routine rigid
body refinement.
The program v5.5.0066 seemed to be swapping the beta and gamma angles in the
mtz produced after the refinement.

We immediately downloaded the v5.5.0089 binaries from garibs refmac5 page
and replaced them in-place. Now the rigid body refinement works well and
all the CRYST and mtz CELL labels are correct.

Is anyone using refmac5 v5.5.0066 seeing this .

Thanks
Hari Jayaram
Brandeis University

Re: [ccp4bb] suggestions for UV spectrometer

[hari jayaram]

We too have a nano-drop. We really like it , but have not  yet fully
switched over.

I agree with all the good things said about it , but here are the few times
the nano drop falls short:

1) We still use the old spec ( 1 cm path length ) for things at a very low
concentration , i.e for the monitoring free thiols in protein with ellman
reagent , the absorbances are very low and give poor reproducibility on the
nanodrop because of small path-length . Of course this can be overcome by
using a lot of protein at a higher concentration and modifying the assay.
2) For very concentrated membrane protein samples which tend to have a large
concentration of detergent . The reproducibility is not very good because of
the high concentration of deteregent preventing a proper meniscus from
forming. The solution to this is to dilute your sample so the dteergent
concentration is manageable ( a few times the CMC instead of tens of times
the CMC

Other than for these issues we almost entirely use the nanodrop and would
gladly recommend it
Hari

On Thu, Dec 4, 2008 at 1:27 PM, Michael Giffin [EMAIL PROTECTED] wrote:

 We also like the Nanodrop.  Very fast, no cuvettes (breaking, washing,
 cleaning, uh nitric acid bath anyone?), and the .ndv data file is a
 delimited text file.  Open in a text editor, copy and paste into a
 spreadsheet, and you have a convenient record of all of your stocks,
 including date, sample name, concentration, and full spectra.

 It is expensive, but so are good cuvettes.


 Mike


 Michael Giffin
 The Scripps Research Institute
 Department of Molecular and Experimental Medicine
 10550 North Torrey Pines Road, MEM-131
 La Jolla, CA 92037
 email:  [EMAIL PROTECTED]
 lab:  858-784-7758

 On Thu, Dec 4, 2008 at 7:16 AM, Tim Gruene [EMAIL PROTECTED]
 wrote:
  Dear all,
 
  we would like to purchase a UV spectrometer for measuring protein
  concentrations (280nm), and I would like to here your comments and
  especially recommendations.
 
  We don't need anything fancy, a small, fast device would be sufficient.
 
  Tim
 
 
  --
  Tim Gruene
  Institut fuer anorganische Chemie
  Tammannstr. 4
  D-37077 Goettingen
 
  GPG Key ID = A46BEE1A
 

Re: [ccp4bb] Crystallographic computing platform recommendations?

[hari jayaram]

For future proofing your computing platform , I would go with a 64 bit
system. You will not regret it.  All crystallography applications live very
happily on a 64bit platform .

There were a few teething troubles , but nothing an email to ccp4bb ,
phenixbb , coot or pymol newsgroups cant fix.
We recently upgraded all our computers to 64bit

Here we use two Mac Pros running Leopard OSX -64bit , after a few teething
problems we are at equilibrium.

Our third machine is a 64bit dual - quad- core , 16GB workstation from Appro
Linux with a nvidia graphics card that they installed for us during the
build and it does stereo  ( Quadro 3450 bought from ebay for $250 OR Quadro
4600 newer version for a whole lot more $2300-major overkill) . It runs
Ubuntu Hardy-Heron 64 bit  , installed from downloaded iso image and almost
minimal tweaking.


Since most projects release builds for ubuntu , I am partial to Ubuntu . But
Gentoo is also a great distribution.

Just my two cents
Hari


On Tue, Nov 18, 2008 at 12:15 PM, [EMAIL PROTECTED] wrote:

  I followed Kay's advice (after deciding that I knew better, of course,
 but we won't elaborate on that :-) and I am very pleased AND have had no
 trouble (knock on wood) to get everything working just fine. We make sure we
 have both 64 bit and 32 bit libraries and so far everything has worked out
 of the box, no hassle. And that includes coot.

 Mark


  -Original Message-
 From: Kevin Cowtan [EMAIL PROTECTED]
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Tue, 18 Nov 2008 3:21 am
 Subject: Re: [ccp4bb] Crystallographic computing platform recommendations?

  And I would give exactly the opposite advice, unless you are or have a
 guru who can devote time to fixing all the little things which still don't
 work under 64 bit OSs.

 (Does anyone else have any clues on why 64-bit compiled coot can't
 calculate a map? I need to look into it, but have a huge backlog of work at
 the moment.)

 Kay Diederichs wrote:
  Dear Anna,
   you didn't ask about that, but I would definitely recommend a 64bit 
 operating system.
   My specific recommendations are mostly in the articles 
 Computer_hardware and CentOS, to be found under the more general  topic
 Xtal_computing of the CCP4 wiki  (
 http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Xtal_computing)
HTH,
   Kay
   Anna S Gardberg schrieb:
  Dear list,
  I haven't seen the crystallographic computing platform thread come 
 up for a while, and I've got a chance to upgrade my desktop to a 
 workstation, so I thought I'd ask the CCP4BB for advice on:
 
  1. Mac vs. Linux (which flavor?) vs. Windows
  2. Graphics cards
  3. Displays
  4. Processors - multiple processors, multiple cores? Speed?
 
  About half of what I do involves ~1.0 A X-ray structures - data 
 processing, rebuilding in Coot, refinement, and so forth - so my  current
 desktop (Optiplex GX745, Radeon X1300) machine drags on  graphics
 sometimes. I don't seem to need stereo these days, for what  it's worth.
 
  Anybody have suggestions or specs they'd like to share? Thanks in 
 anticipation of your advice.
 
  Regards,
  Anna Gardberg
  

 --
 Instant access to the latest  most popular FREE games while you browse
 with the Games Toolbar - Download 
 Now!http://pr.atwola.com/promoclk/10075x1212904500x1200818240/aol?redir=http://toolbar.aol.com/games/download.html?ncid=emlweusdown0004

[ccp4bb] mtz type labels different in ccp4-6.0.99e?

[hari jayaram]

Hi
Is it likely that the type labels for DANO and IMEAN have been changed in
the beta ccp4-6.0.99e from
DANO -type - D to DANO  type F
IMEAN - -type - Y to IMEAN  type J

I am using an old  sharp and it seems to be a little miffed at my DANO
columns from ccp4 6.0.99e being of type F

Thanks in advance

Hari

Re: [ccp4bb] Channel inside a protein

[hari jayaram]

Hi Priya ,

I would recommend MOLE from the list kindly compiled by Jiamudu on the
CCP4 wikiThe list is available at the link
belowhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Programs_for_representing_the_surface_of_a_channel_inside_protein

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Programs_for_representing_the_surface_of_a_channel_inside_protein


Hari


On Mon, Nov 10, 2008 at 9:16 AM, Priya Mudgal [EMAIL PROTECTED]wrote:

 Hello All,

 Is there any program that can find if there is a channel inside a protein?
 I also would like to know what are the alternative ways to find out a
 channel inside a protein.

 Thanks a lot.

 Priya

Re: [ccp4bb] Protein folding pattern schematic

[hari jayaram]

Hi CharuEspript is an excellent resource for this
It is particulary useful when you want a secondary structure schematic with
an alignment and other information relevant to the structure .. .It has a
friendly web interface at
http://espript.ibcp.fr/ESPript/ESPript/

Fr eg
http://espript.ibcp.fr/ESPript/ESPript/images/vp7.gif

Hope this Helps
Hari Jayaram


On Mon, Nov 10, 2008 at 1:53 PM, Charu Chaudhry [EMAIL PROTECTED]wrote:

 Hello,
 Does anyone know of a program that can automatically generate a folding
 pattern schematic diagram showing the arrangement of secondary structure
 elements for a protein ? Presumably one would have to feed it a PDB file
 with secondary structure assigned from DSSP.
 Thanks!
 Charu
 Mayer lab/NIH

Re: [ccp4bb] ccp4 6.0.99e test release

[hari jayaram]

Hello ccp4-ers
I have been happily running ccp4-6.0.99e,  which I self compiled on an
Ubuntu 64bit ( Version 8.04) box

Things have been going smoothly till I noticed a segmentation fault when I
tried to get a postscript file using xplot84driver .
The binary run from  a shell and the ccp4i gui give the following error

FROM SHELL
[EMAIL PROTECTED]:~/ccp4-6.0.99e/x-windows/XCCPJIFFY$ ./xplot84driver
~/yjchotmp/yjchotmp_2_1.plt
Warning: Representation size 1 must match superclass's to override
useStringInPlace
Segmentation fault

FROM CCP4 GUI
[EMAIL PROTECTED]:~$ Warning: Representation size 1 must match superclass's to
override useStringInPlace

Any ideas on how to overcome this

I am attaching the Makefile I used to compile this xplot84driver binary on
my system
Thank you for your help
Hari


On Fri, Jul 25, 2008 at 11:54 AM, Martyn Winn [EMAIL PROTECTED] wrote:

 Dear All

 the latest test version is on the ccp4 ftp server.

 ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-core-src.tar.gz- core
 ccp4, rapper, clipper
 ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-phaser-src.tar.gz  - cctbx and
 phaser
 ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-balbes_db.tar.gz   - balbes
 database only

 There is also the dependency of PyXML if you want to run balbes
 ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-PyXML.tar.gz

 for the first 3 tarballs unpack into the same directory, then
 configure...make...make install.
 For the PyXML, follow the instructions in the PyXML-0.8.4 directory.

 Major changes:
 refmac5.5 built by default.  This gives twinning and sad refinement.
 dbhandler. Many optimisations, so this should be much more responsive.

 For other updates see the CHANGES file.

 Still to come:
 downloads pages (under internal testing).
 documentation updates (lots of)

 Feedback to the usual locale ([EMAIL PROTECTED])

 Thanks

 Charles and the rest of us here at DL.


 --
 ***
 * *
 *   Dr. Martyn Winn   *
 * *
 *   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
 *   Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] *
 *   Fax: +44 1925 603825Skype name: martyn.winn   *
 * URL: http://www.ccp4.ac.uk/martyn/  *
 ***



Makefile
Description: Binary data

Re: [ccp4bb] Crystallogrphy today

[hari jayaram]

Speaking of good material to attempt to understand crystallographic concepts
with , there a  video link to the talk given by Airlie McCoy based on the
 Liking  likelyhood paper
Its on the phaser publications page or at this
linkhttp://erice2005.docking.org/vcourse/16mon/1145-McCoy/McCoy.wmv
http://erice2005.docking.org/vcourse/16mon/1145-McCoy/McCoy.wmv

There is also a talk from Randy reed at that
locationhttp://erice2005.docking.org/vcourse/18wed/0945-Read/Read.wmv

It would be great if other such talks could be made available as videos . ,
for all of us to benefit from . It will be great to have a youtube or google
video channel for such videos. That way google pays for the bandwidth
instead of erice2005   or ccp4.

Thanks for this thread..

Hari

On Tue, Sep 23, 2008 at 11:31 AM, Jacob Keller 
[EMAIL PROTECTED] wrote:
 Perhaps you could translate and annotate it, then send it to the CCP4BB?

 JPK

 ps seriously, why do you say no need for review--is it boring, not well
 written, obsolete, or what? James is still pretty useful, I think, and
that
 was put out only two years later

 ***
 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: [EMAIL PROTECTED]
 ***

 - Original Message - From: Marius Schmidt
 [EMAIL PROTECTED]
 To: Jacob Keller [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK

 Sent: Monday, September 22, 2008 8:42 PM
 Subject: Re: [ccp4bb] Crystallogrphy today


 i have a suggestion for a nice book for you,
 you will love it. it is in German, great!, has over
 400 pages and it IS THE SOURCE.

 M. von Laue
 Roentgenstrahlinterferenzen
 Physik und Chemie und Ihre Anwendungen, Band VI
 2. Auflage (1st edition burnt down by cannonizing at WWII)
 1948
 Akademische Verlagsgesellschaft, Geest  Portig K.-G., Leipzig


 everything is covered, even protein crystallography,
 however in a very skeptic way, no need for a review ever.

 Cheers
 Marius

 To understand the fundamentals of any discipline, I have always found
 it
 completely worthwhile to go back to the original source, where the
 idea was
 first discovered or presented. This is really, really valuable,
 although not
 always possible. I wonder whether others agree with me about
 this...but I
 feel pretty strongly about this matter. Often one can read many
 reviews on
 some subject, which never really get to the gist of the matter, but
 when one
 reads the original source, the subject is usually laid out clearly
 because
 guess what: nobody knew it yet, so it had to be explained clearly.
 Furthermore, one gets a sense of the excitement of discovery, and the
 unsurety about some new proposed hypothesis which has not yet become
 cannonized into fact. For this reason, it is sometimes even
 worthwhile to
 saunter down to the...library!

 Jacob Keller

 ***
 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: [EMAIL PROTECTED]
 ***

[ccp4bb] Phaser fails with malloc error

[hari jayaram]

Hello,
I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard ,
Mac Pro machine .
I get the rather ominous error given below .
We have gotten similar malloc errors with large datasets before on this
machine. In those cases the same jobs ran fine on regular linux.
Thought I would write in. I can send the mtz and search model over if needed
for testing/ reproducing this error

Thanks a lot for your help
Hari Jayaram
Postdoc , Brandeis Univerity



EXIT STATUS: SUCCESS


CPU Time: 0 days 0 hrs 9 mins 0.67 secs (540.67 secs)
Finished: Thu Aug 21 13:45:26 2008

/pre
/html
***
* Information from CCP4Interface script
***
The program run with command: /sw/share/xtal/ccp4-6.0.99e/bin/phaser
has failed with error message
phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
***


#CCP4I TERMINATION STATUS 0 phaser(36682) malloc: *** mmap(size=1999872000)
failed (error code=12) *** error: can't allocate region *** set a breakpoint
in malloc_error_break to debug
#CCP4I TERMINATION TIME 21 Aug 2008  13:45:26
#CCP4I MESSAGE Task failed

Re: [ccp4bb] Phaser fails with malloc error

[hari jayaram]

Hello Phil and thanks for your email..I was running  a VMware fusion Ubuntu
session which was grabbing onto a large chunk of memory ( entirely my
fault). I didnt realize that virtualized sessions can divert memory away
from even the OS and make it essentially unavailable.

I am waiting for my ubuntu job to finish to retry the phaser run. Sorry I
jumped the gun and emailed ccp4bb

Thanks again
hari

On Thu, Aug 21, 2008 at 2:55 PM, Phil Jeffrey [EMAIL PROTECTED]wrote:

 I would take a look at how much physical memory is on the machine, how much
 disk space there is on the system drive (often used as virtual swap), and
 what other processes are running.  This would seem to be a failure to
 allocate 2Gb of memory, which isn't the smallest chunk I've ever seen.

 Phil


 hari jayaram wrote:

 Hello,
 I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard ,
 Mac Pro machine .
 I get the rather ominous error given below .
 We have gotten similar malloc errors with large datasets before on this
 machine. In those cases the same jobs ran fine on regular linux.
 Thought I would write in. I can send the mtz and search model over if
 needed for testing/ reproducing this error

 Thanks a lot for your help
 Hari Jayaram
 Postdoc , Brandeis Univerity


 
 EXIT STATUS: SUCCESS
 

 CPU Time: 0 days 0 hrs 9 mins 0.67 secs (540.67 secs)
 Finished: Thu Aug 21 13:45:26 2008

 /pre
 /html

 ***
 * Information from CCP4Interface script

 ***
 The program run with command: /sw/share/xtal/ccp4-6.0.99e/bin/phaser
 has failed with error message
 phaser(36682) malloc: *** mmap(size=1999872000) failed (error code=12)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug

 ***


 #CCP4I TERMINATION STATUS 0 phaser(36682) malloc: ***
 mmap(size=1999872000) failed (error code=12) *** error: can't allocate
 region *** set a breakpoint in malloc_error_break to debug
 #CCP4I TERMINATION TIME 21 Aug 2008  13:45:26
 #CCP4I MESSAGE Task failed

[ccp4bb] ccp4i gui issues with ccp4-6.0.99e?

[hari jayaram]

Hi I am having a

can't read array(TEXTFRAME): no such variable 

error when I perform the following action with ccp4i .

View files from job- Select an mtz file - List more info - run Sftools - and
try and display reflections along any index say 0 , 0, l

The log entry is attached below.
I am using ccp4-6.0.99e and Active state TCL-TK as my $CCPI_TCLTK variable.
I also get the error with the default TCL-TK.
I am running this on a Leopard Mac Pro OSX 10.5.2 with XQUARTZ 2.3.0

Anybody else see this?
Thanks

Hari Jayaram


ERROR log...

can't read array(TEXTFRAME): no such variable
can't read array(TEXTFRAME): no such variable
while executing
$array(TEXTFRAME) configure -state normal
(procedure LoadTextWindow line 10)
invoked from within
LoadTextWindow $arrayname [list [list $text {} ] ]
(procedure mtz_info_review line 13)
invoked from within
$review $arrayname $job_id 
(procedure RunCompleted line 36)
invoked from within
RunCompleted 57 cy_p10_2 FINISHED
(eval body line 1)
invoked from within
eval [concat RunCompleted [lrange $line 1 end] ]
(RunCompleted arm line 2)
invoked from within
switch [lindex $line 0] {
DbReceive {
eval [concat DbReceive [lrange $line 1 end] ]
}
DbAddOutputFile {
eval [concat DbAddOutputFile [lra...
(procedure ServerAcceptInput line 13)
invoked from within
ServerAcceptInput sock6

[ccp4bb] Scaling multiple native datasets together

[hari jayaram]

Thanks to everyone who wrote in with advice on scaling multi-crystal P1
datasets together to increase redundancy for MAD/SAD/SAS phasing.

I have  a question about scaling and merging these multiple datasets in
scale/scaleit.

In our case we have the following
1) Crystal 1 - CNAME - C1

[ccp4bb] multiple XNAME scala? and changing DNAMEs

[hari jayaram]

Sorry for that incomplete last post

Thanks to everyone who wrote in with advice on scaling multi-crystal
spacegroup P1 datasets together to increase redundancy for MAD/SAD/SAS
phasing.

I have three questions about scaling and merging  multi crystal datasets in
scala

In our case we have the following
1) Crystal 1 - XNAME - C1 - DNAME peak1
  DNAME  inf1
2)Crystal 2 - XNAME- C2 DNAME peak1

The two crystals have cell dimensions within 1-2 % and I have cadded the
output from mosflm for each of the crystals into one giant mtz file. No two
batch numbers are the same .When we run scala the Job fails and We get
errors like Insufficient Data to determine parameters erros - Too few
reflections

Of course scala on each crystal separately works great and gives us
reasonable correlation coefficients ( 0.2 to 0.3 for Correlations within
half dataset for peak and inflection to 3.2 A. The overall redundancy is
around 6-8. Rpim around 0.05 )

My question is can scala scale mutli-crystal datasets as I am attempting to
do.


2) My second unrelated question is how can I DRENAME using cad on unmerged
data. If I have run mosflm and then want to change the DNAME of a dataset ,
CAD says it can DRENAME a dataset , but at the same time CAD has a problem
with unmerged mtz files. How can I edit the DNAME, XNAME, PNAME etc on an
mtzfile output from mosflm

Your help is greatly appreciated.

Hari Jayaram

Re: [ccp4bb] multiple XNAME scala? and changing DNAMEs

[hari jayaram]

Hello Phil Evans,
Thanks a lot for your reply. Pointless worked great to edit XNAME and DNAME
for unmerged mtz files.

We are now taking multiple crystal data as unmerged mosflm output mtzs ,
squishing them together into one pseudo-crystal mtz with the same XNAME and
DNAME using Pointless. The mtz header does have correctly 1 dataset. The
only issue I guess is the CELL parameters are from one of the two datasets.

This does seem to be  quite strange but we are trying to mimic the Scenario
4 as presented in the HKL-scalepack manual in the section combining
multiple native datasets together . In that scenario it asks you to take
multiple native data-sets together and combine their *.x files and fit one
a*, b* and c* and a batch mosaicity , rotx , roty .


Wondering what  is the correct way of getting the CELL parameters for this
multi-crystal dataset.


Hari




On Tue, Jul 29, 2008 at 5:06 PM, Phil Evans [EMAIL PROTECTED] wrote:

 The easiest way to combine multiple crystals and renaming datasets for
 Scala is to use Pointless, available from the CCP4 prerelease site. You
 can't use CAD on unmerged files: the older programs Rebatch  Sortmtz can
 also be used

 Note the if you are merging multiple crystals, you are essentially creating
 a composite crystal so all parts to be merged must have the same XNAME 
 DNAME

 Phil





 On 29 Jul 2008, at 20:56, hari jayaram wrote:

  Sorry for that incomplete last post

 Thanks to everyone who wrote in with advice on scaling multi-crystal
 spacegroup P1 datasets together to increase redundancy for MAD/SAD/SAS
 phasing.

 I have three questions about scaling and merging  multi crystal datasets
 in scala

 In our case we have the following
 1) Crystal 1 - XNAME - C1 - DNAME peak1
  DNAME  inf1
 2)Crystal 2 - XNAME- C2 DNAME peak1

 The two crystals have cell dimensions within 1-2 % and I have cadded the
 output from mosflm for each of the crystals into one giant mtz file. No two
 batch numbers are the same .When we run scala the Job fails and We get
 errors like Insufficient Data to determine parameters erros - Too few
 reflections

 Of course scala on each crystal separately works great and gives us
 reasonable correlation coefficients ( 0.2 to 0.3 for Correlations within
 half dataset for peak and inflection to 3.2 A. The overall redundancy is
 around 6-8. Rpim around 0.05 )

 My question is can scala scale mutli-crystal datasets as I am attempting
 to do.


 2) My second unrelated question is how can I DRENAME using cad on unmerged
 data. If I have run mosflm and then want to change the DNAME of a dataset ,
 CAD says it can DRENAME a dataset , but at the same time CAD has a problem
 with unmerged mtz files. How can I edit the DNAME, XNAME, PNAME etc on an
 mtzfile output from mosflm

 Your help is greatly appreciated.

 Hari Jayaram

[ccp4bb] Using multiple crystals for structure solution in P1 using MAD/SAS/SAD

[hari jayaram]

We are faced  with phasing a structure for a protein that refuses to
crystallize in any spacegroup but P1.
To add to the fun , the resolution for most selenomethionine  and heavy atom
soak datasets ranges from 3.8 to 4.2 A .

In order to increase the redundancy we have been taking many inverse beam
datasets from each crystal  by making sure the beam is significantly
attenuated.
We now have 360 times 6, ( i.e 6 passes) and in some case 8 passes, datasets
for a few crystals collected at the peak wavelength in the case of
Selenomethionine crystals. In some cases we even managed an inflection
dataset . Needless to say the anomolous signal seems quite week at these
resolutions and low redundancies for any single crystal dataset.

I was wondering if anyone could comment on combining datasets from multiple
P1 crystals to increase the redundancy even further for such heavy atom (
SAS / SAD ) or MAD experiments.

Thanks a lot for your help and suggestions in advance
hari

[ccp4bb] model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch

[hari jayaram]

First off sorry for the cross post across bbs

I have a molecular replacement solution for a single site mutant for data
that goes out to 2.8 A.
After molecular replacement in phaser I run the following and examine the
maps for bias from the model.

Option1: simluated annealing refinement in phenix using the phaser mtz

Option2: take the phaser mtz and then just run prime and switch in resolve
and look at the map

Option3: First part: take the phaser mtz and then run simulated annealing
and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s
model phases and modified Fs

I am observing that Option 1 and Option 2 the maps are indistinguishable
from each other and show very little bias from the model.
In Option 3 just cns simulated annealing does not go as far at removing bias
as cns simulated annealing plus prime-and-switch.

Although my estimate of model bias is just a look and see feeling. Since I
lack a thorough understanding of the relative merits of these algorithms
I have the following questions

1)Does simulated annealing refinement as implemented in phenix use a
prime-and-switch style approach to modify phases at any point to guide the
refinement

2) Am I wrong in assuming that just simulated annealing and sigma-aa
weighted maps for cns (Option 3 part 1) are not as good as  cns simulated
annealing + sigmaa+ prime_and_switch ( option3 part 2)

Hoping to get a better idea on how well these approaches fair at removing
model bias

Hari Jayaram
Postdoc , Brandeis University

[ccp4bb] phaser:- set a breakpoint in malloc_error_break to debug

[hari jayaram]

Hi
I was running phaser on an 8 core Mac pro using the fink 10.5 (intel) ccp4
binaries provided by W.G Scott .
Although the many phaser jobs I have run in the last month have successfully
phased my data.
Today I saw a very strange error and phaser FAILED.

I did rerun phaser and have it work after a slight change in the pdb ( I
removed the heteroatoms) , so I dont think there is something wrong with
phaser or the pdb.

But I thought I would send the error message along in case it is a Mac Pro
specific problem that crops ups every now and then.
Thanks
Hari Jayaram



EXIT STATUS: FAILURE


CPU Time: 0 days 0 hrs 8 mins 35.41 secs (515.41 secs)
Finished: Thu May  1 14:19:16 2008

/pre
/html
***
* Information from CCP4Interface script
***
The program run with command: phaser
has failed with error message
phaser(88098) malloc: *** mmap(size=1185792000) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
***


#CCP4I TERMINATION STATUS 0 phaser(88098) malloc: *** mmap(size=1185792000)
failed (error code=12) *** error: can't allocate region *** set a breakpoint
in malloc_error_break to debug
#CCP4I TERMINATION TIME 01 May 2008  14:19:16
#CCP4I MESSAGE Task failed

Re: [ccp4bb] phaser:- set a breakpoint in malloc_error_break to debug

[hari jayaram]

Hello Ethan Meritt,
Thanks for your reply,

I have only recently started using the 8 core Mac pro , and in the last
three days have faced many such issues with swapsize and running out of
memory (the machine has 4GB total).
Just Yesterday I had a problem on a different dataset with a cns simulated
annealing  run which stopped because of swapsize issues. I know that phenix
on this machine has a setting in the com file which uses  ulimit (csh tcsh)
to unlimit everything . On a related note,  I think Apple also changed its
csh such that unlimit requires an argument such as unlimit stacksize
etc..and not just unlimit

Since I am an OSX leopard  newbie, Should I ( or could I )  use ulimit or
unlimit as a systemwide shell setting and should I put this into the
ccp4.setup.sh and ccp4.setup or in /etc/bashrc or /etc/cshrc so that I dont
run into such problems. From the seetings it seems like I have a very small
swapsize of 8192 kbytes

At the present moment the limit command on this machine when run in csh
returns

cputime  unlimited
filesize unlimited
datasize 6144 kbytes
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256
memorylocked unlimited
maxproc  266

I am wondering  why I havent had to mess with similar settings on linux
while this multi-core machine with a massive disk and reasonable amount of
memory , seems a little touchy with its swap size and other settings.

Thank you for your help,

Hari


On Thu, May 1, 2008 at 2:49 PM, Ethan Merritt [EMAIL PROTECTED]
wrote:

 On Thursday 01 May 2008 11:37, hari jayaram wrote:
  Hi
  I was running phaser on an 8 core Mac pro using the fink 10.5 (intel)
 ccp4
  binaries provided by W.G Scott .
  Today I saw a very strange error and phaser FAILED.
 
  #CCP4I TERMINATION STATUS 0 phaser(88098) malloc: ***
 mmap(size=1185792000)
  failed (error code=12) *** error: can't allocate region *** set a
 breakpoint
  in malloc_error_break to debug

 This is telling you that you ran out of memory.
 Perhaps you had more jobs running than usual, and not enough swap space.
 Perhaps something in the Phaser run caused it to calculate a map with
 finer grid spacing than your other runs. Perhaps something else entirely.
 I would start by checking the swap space.

Ethan Merritt

 --
 Ethan A MerrittCourier Deliveries: 1959 NE Pacific
 Dept of Biochemistry   Regular Mail: Mailstop 357742
 Health Sciences Building
 University of Washington - Seattle WA 98195-7742

[ccp4bb] CNS 1.2.2 binary running out of memory

[hari jayaram]

Hi
Since I am not on the cnsbb yet I am posting this here.
I downloaded the cns 1.2.2 intel build and was trying to run a simulated
annealing refinement on my macbook pro ( Intel) running 10.5.2 .

However the annealing job crashes roughly 40 minutes into the refinement
with the following message

There is not enough memory available to the program.
 This may be because of too little physical memory (RAM)
 or too little swap space on the machine. It could also be
 the result of user or system limits. On most Unix systems
 the limit command can be used to check the current user
 limits. Please check that the datasize, memoryuse and
 vmemoryuse limits are set at a large enough value.

Unfortunately on Leopard it seems that unlimit and limit are not available
under bash
Further when I use csh , I get the following values for the limits

[mango:~/aps_04_21_2008/p10_2] hari% limit
cputime  unlimited
filesize unlimited
datasize 6144 kbytes
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256
memorylocked unlimited
maxproc  266

In the same csh shell unlimit returns

[mango:~/aps_04_21_2008/p10_2] hari% unlimit
unlimit: descriptors: Can't remove limit (Invalid argument)

How can I setup cns to have free reign and use up unlimited datasize and
stacksize for all cns jobs?

Thanks for your help in advance

Hari Jayaram


The detailed error is posted below



 ASSFIL: file /Users/hari/cns/cns_solve_1.2/libraries/toppar/torsionmdmods
opened.
 MESSage=NORM
 EVALUATE: symbol $MESSAGE_OLD_TMOD set to NORM (string)
 ECHO=FALSe {OFF}
 EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical)
 NEXTCD: condition evaluated as false
 Program version= 1.2 File version= 1.2
 SELRPN:  0 atoms have been selected out of   2380
cns_solve(93676) malloc: *** mmap(size=300512) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
 ALLHP: request for -1294967296 bytes
 -
 There is not enough memory available to the program.
 This may be because of too little physical memory (RAM)
 or too little swap space on the machine. It could also be
 the result of user or system limits. On most Unix systems
 the limit command can be used to check the current user
 limits. Please check that the datasize, memoryuse and
 vmemoryuse limits are set at a large enough value.
 -
 %ALLHP error encountered: not enough memory available
   (CNS is in mode: SET ABORT=NORMal END)
 *
 ABORT mode will terminate program execution.
 *
 Program will stop immediately.
  
   Maximum dynamic memory allocation:   139649464 bytes
   Maximum dynamic memory overhead:   944 bytes
   Program started at: 14:51:17 on 30-Apr-2008
   Program stopped at: 15:09:16 on 30-Apr-2008
   CPU time used:1077.7678 seconds
  

Re: [ccp4bb] Scala summary and log file- sometimes shortened

[hari jayaram]

Hello everyone,
It seems that the reason I get short summaries in scala is because the
Show Summary button is affected by a possible intermitently appearing
change in  scala log file formatting.

When I looked for the text Summary in the log file I did find the entire
table -intact.

SO just for completeness - here is what the Show summary gave . And below
this I have the intact summary in the log file. It seems like ccp4i  Show
summary button for scala log file viewing does not include the entire table
in the window everytime.



Summary data for Project: cy Crystal: P10_2 Dataset: P10_2

   Overall  InnerShell OuterShell

  Low resolution limit  102.06102.06  2.11
  High resolution limit   2.00  6.34  2.00

  Rmerge 0.252 0.112 5.247
  Rmeas (within I+/I-)   0.269 0.118 6.982
 Scala:  ** Normal termination **
Times: User: 403.8s System:7.8s Elapsed: 6:52
/pre
/html

 ###

INTACT summary:
When I do Full log file view : I get the entire summary



Summary data for Project: cy Crystal: P10_2 Dataset: P10_2

   Overall  InnerShell OuterShell

  Low resolution limit  102.06102.06  2.11
  High resolution limit   2.00  6.34  2.00

  Rmerge 0.252 0.112 5.247
  Rmeas (within I+/I-)   0.269 0.118 6.982
 Scala:  ** Normal termination **
Times: User: 403.8s System:7.8s Elapsed: 6:52
/pre
/html
  Rmeas (all I+  I-)0.269 0.118 6.982
  Rpim (within I+/I-)0.091 0.036 4.552
  Rpim (all I+  I-) 0.091 0.036 4.552
  Fractional partial bias   -0.113-0.122-1.163
  Total number of observations 1458009111004  8307
  Total number unique   212719  9864  4327
  Mean((I)/sd(I))  6.4  16.6   0.3
  Completeness67.9  99.6   9.4
  Multiplicity 6.9  11.3   1.9





 ###


 User: hari  Run date: 22/ 4/2008 Run time: 16:39:47
On Tue, Apr 22, 2008 at 4:14 PM, hari jayaram [EMAIL PROTECTED] wrote:

 For some reason scala does not output the same log file for me everytime. I
 got used to looking at the summary for my scala run, using the Show summary
 button in ccp4i after picking view log file.
 In most cases I get a detailed summary. For this particular dataset ,
 despite not changing any parameters in the GUI  I get a very shortened
 summary.
 Is it that I clicked some button by mistake, that shortens the log-summary.

 I am using the latest version of ccp4 6.2.2 and fink installed ccp4 on OSX
 Leopard.
 I am reproducing the short and long summary here.

 Thanks for your help
 Hari Jayaram


 BAD Case:

 Summary data for Project: cy Crystal: P10_2 Dataset: P10_2

Overall  InnerShell OuterShell

   Low resolution limit  102.06102.06  2.11
   High resolution limit   2.00  6.34  2.00

   Rmerge 0.252 0.112 5.247
   Rmeas (within I+/I-)   0.269 0.118 6.982
  Scala:  ** Normal termination **
 Times: User: 404.5s System:8.0s Elapsed: 6:53
 /pre
 /html

 GOOD case:

 Summary data for Project: cy Crystal: p10_1 Dataset: p10_1

Overall  InnerShell OuterShell

   Low resolution limit  102.60102.60  2.12
   High resolution limit   2.01  6.35  2.01

   Rmerge 0.164 0.053 3.283
   Rmeas (within I+/I-)   0.183 0.058 4.363
   Rmeas (all I+  I-)0.183 0.058 4.363
   Rpim (within I+/I-)0.080 0.021 2.835
   Rpim (all I+  I-) 0.080 0.021 2.835
   Fractional partial bias   -0.022-0.018-0.072
   Total number of observations  835420 73666  4479
   Total number unique   196397  9701  3022
   Mean((I)/sd(I))  2.2   4.2   0.2
   Completeness64.3  99.8   6.9
   Multiplicity

[ccp4bb] Scala summary and log file- sometimes shortened

[hari jayaram]

For some reason scala does not output the same log file for me everytime. I
got used to looking at the summary for my scala run, using the Show summary
button in ccp4i after picking view log file.
In most cases I get a detailed summary. For this particular dataset ,
despite not changing any parameters in the GUI  I get a very shortened
summary.
Is it that I clicked some button by mistake, that shortens the log-summary.

I am using the latest version of ccp4 6.2.2 and fink installed ccp4 on OSX
Leopard.
I am reproducing the short and long summary here.

Thanks for your help
Hari Jayaram


BAD Case:

Summary data for Project: cy Crystal: P10_2 Dataset: P10_2

   Overall  InnerShell OuterShell

  Low resolution limit  102.06102.06  2.11
  High resolution limit   2.00  6.34  2.00

  Rmerge 0.252 0.112 5.247
  Rmeas (within I+/I-)   0.269 0.118 6.982
 Scala:  ** Normal termination **
Times: User: 404.5s System:8.0s Elapsed: 6:53
/pre
/html

GOOD case:

Summary data for Project: cy Crystal: p10_1 Dataset: p10_1

   Overall  InnerShell OuterShell

  Low resolution limit  102.60102.60  2.12
  High resolution limit   2.01  6.35  2.01

  Rmerge 0.164 0.053 3.283
  Rmeas (within I+/I-)   0.183 0.058 4.363
  Rmeas (all I+  I-)0.183 0.058 4.363
  Rpim (within I+/I-)0.080 0.021 2.835
  Rpim (all I+  I-) 0.080 0.021 2.835
  Fractional partial bias   -0.022-0.018-0.072
  Total number of observations  835420 73666  4479
  Total number unique   196397  9701  3022
  Mean((I)/sd(I))  2.2   4.2   0.2
  Completeness64.3  99.8   6.9
  Multiplicity 4.3   7.6   1.5

[ccp4bb] DM - NCS averaging after phaser molecular replacement run-confused about coefficients

[hari jayaram]

Hi everyone,
I have a phaser molecular replacement solution for my membrane protein which
crystallized in spacegroup P3. The diffraction data is good to about 3.3 A.
The model I used had 39% homology to the given protein. A solvent content
analysis suggests that there probably are three dimers in the ASU ( to give
about 67% solvent)
Phaser sucessfuly found two dimers in the ASU with good density and a third
dimer with very weak almost non-existent density.
I am now trying to do some NCS-averaging using DM to see If I can improve
the desnity for dimer 3 and have a question about the different
co-efficients I should be using for the averaging DM run.

Question1:
The phaser output mtz file has a PHWT and a PHIC . For carrying out DM with
flattening, averaging and histogram matching which phases do I use PHIC or
PHWT along with observed Fo. Also for the weight do I use the FOM.

Question2:
The output mtz from DM run either way above , now has  a PHIDM and a PHWT
along with a FWT and FC. Which coefficients should I be using to get a map
after DM for building.

FWT and PHWT
or
Fo and PHIDM
or
FWT and PHIDM.


Thank you for your help
Hari

Re: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem

[hari jayaram]

Hi Phil,Thanks for your email. I did get it to work with the options you
suggested .
i.e
 Toggle ON Override automatic definition of runs to mark discontinuities in
data
 Toggle ON Define Runs
 Toggle OFF Use run 1 as reference run.

 Setup runs as follows ( intended to exclude batches 200 to 400 from a total
dataset of 1 to 720 )

 Run 1 from  1 to 200
 Run 2 from 400 to 720

This combination worked as you said it would.
Thank you for your help

Hari Jayaram
Postdoc
Brandeis University







On Sat, Mar 15, 2008 at 3:44 AM, Phil Evans [EMAIL PROTECTED] wrote:

 You are right: this is a bug I should fix sometime

 Assigning two runs should work though

 You should not assign a reference run, and you shouldn't need to
 reassign the datasets

 Best wishes
 Phil

 On 14 Mar 2008, at 21:45, hari jayaram wrote:

  Hi.
  I did try that beforehand  when I tried excluding  a range of
  batches with the ccp4i gui
 
  But I got an error
 
   Scala:  *** Gap in time (rotation) ***
 
  Sorry...both versions of the protocol for handling a bad internal
  wedge are giving me either a gap in rotation error or a Run 2
  has not been assigned to a dataset error
 
  I am still stuck.
 
  ( error and com file for the exclude data range option is attached
  below)
  Thanks for your help.
 
  Hari Jayaram
 
 
 
  
  Error
  ---
 
    Large gap in time (rotation) coordinate:3.5 
    See WARNING above 
    Smoothed B-factor impossible 
 
 
 ***
  * Information from CCP4Interface script
 
 ***
  The program run with command: scala HKLIN /Users/hari/aps_feb08/
  p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT /tmp/hari/p2_2_13_2_mtz.tmp
  SCALES /Users/hari/aps_feb08/p2-2/p2_2_13.scala ROGUES /Users/
  hari/aps_feb08/p2-2/p2_2_13_rogues.log NORMPLOT /Users/hari/
  aps_feb08/p2-2/p2_2_13_normplot.xmgr ANOMPLOT /Users/hari/
  aps_feb08/p2-2/p2_2_13_anomplot.xmgr PLOT /Users/hari/aps_feb08/
  p2-2/p2_2_13_surface_plot.plt CORRELPLOT /Users/hari/aps_feb08/
  p2-2/p2_2_13_correlplot.xmgr
  has failed with error message
   Scala:  *** Gap in time (rotation) ***
 
 ***
 
 
  #CCP4I TERMINATION STATUS 0  Scala:  *** Gap in time (rotation)
  ***
  #CCP4I TERMINATION TIME 14 Mar 2008  17:38:34
  #CCP4I TERMINATION OUTPUT_FILES  /Users/hari/aps_feb08/p2-2/
  p2-2_A1_1_0001_sorted.mtz p2_2
  #CCP4I MESSAGE Task failed
 
  
  The com script was
  
  ***
  /tmp/hari/p2_2_13_3_com.tmp
  ***
   title Scala anon and deleted batches 200_400b try with two run
  definitions
  name project p2_2 crystal p2-2_A1_1 dataset p2_2
  exclude EMAX -
  10.0
  exclude batch -
  400 to 540
  partials -
  check -
  test 0.95 1.05 -
  nogap
  intensities PROFILE -
  PARTIALS
  final PARTIALS
  scales -
  rotation SPACING 5 -
  secondary 6 -
  bfactor ON -
  BROTATION SPACING 20
  UNFIX V
  FIX A0
  UNFIX A1
  initial MEAN
  tie surface 0.001
  tie bfactor 0.3
  cycles 10 converge 0.3 reject 2
  anomalous on
  output AVERAGE
  print cycles nooverlap
  RSIZE 80
 
 
  ## This script run with the command   ##
  # scala HKLIN /Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz
  HKLOUT /tmp/hari/p2_2_13_2_mtz.tmp SCALES /Users/hari/aps_feb08/
  p2-2/p2_2_13.scala ROGUES /Users/hari/aps_feb08/p2-2/
  p2_2_13_rogues.log NORMPLOT /Users/hari/aps_feb08/p2-2/
  p2_2_13_normplot.xmgr ANOMPLOT /Users/hari/aps_feb08/p2-2/
  p2_2_13_anomplot.xmgr PLOT /Users/hari/aps_feb08/p2-2/
  p2_2_13_surface_plot.plt CORRELPLOT /Users/hari/aps_feb08/p2-2/
  p2_2_13_correlplot.xmgr
  
 
 
  On Fri, Mar 14, 2008 at 5:11 PM, Phil Evans [EMAIL PROTECTED]
  wrote:
  In ccp4i Scala task, click to open the Excluded data panel, click on
  Exclude selected batches
 
  There you can define one or more ranges of batches or lists to exclude
 
  If you just want to exclude the last part you can define a range eg
  301 to 999
 
  You don't need to explicitly define runs
 
  Phil
 
  On 14 Mar 2008, at 18:57, hari jayaram wrote:
 
   Hi I am trying to exclude a bad wedge  of data during scaling in
   scala in the newest ccp4
  
   ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so
   they should be version 6)
  
   The batches I need are
   1 to 200 and 400-720
   I have clicked the Override automatic definition of runs to mark
   discontinuities in data button as well as created two runs to
   contain the required data
  
   But I get a  Run 2 has not been assigned to a dataset error.
   How I can exclude a bad wedge

[ccp4bb] exclude range within data in scala , discontinuous run in scala problem

[hari jayaram]

Hi I am trying to exclude a bad wedge  of data during scaling in scala in
the newest ccp4
( fink install this morning from W.G Scotts sage.ucsc Binaries ..so they
should be version 6)
The batches I need are
1 to 200 and 400-720
I have clicked the Override automatic definition of runs to mark
discontinuities in data button as well as created two runs to contain the
required data

But I get a  Run 2 has not been assigned to a dataset error.
How I can exclude a bad wedge in the middle of my data from within scala
without going through the split and  sort route in mtzutils. I have attached
the com file generated by ccp4i and the error text below

Thanks for your help
Hari Jayaram
Postdoc , Miller Lab
Brandeis University


-
The error I get is
-
13714715716
 717718719720

  Run 2 has not been assigned to a dataset 

***
* Information from CCP4Interface script
***
The program run with command: scala HKLIN
/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT
/tmp/hari/p2_2_12_2_mtz.tmp SCALES
/Users/hari/aps_feb08/p2-2/p2_2_12.scala ROGUES
/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log NORMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr ANOMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr PLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt CORRELPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr
has failed with error message
 Scala:  * Error in input *
***


In the GUI and the com file  I can see that Run 2  has
been correctly assigned to the correct dataset , i.e the same as Run 1 , but
I still see this error
-
The ccp4i generated  com files is attached here


***
/tmp/hari/p2_2_12_3_com.tmp
***
 title Scala anon and deleted batches 200_400b try with two run definitions
run 1 -
INCLUDE batch 1 to 200
run 2 -
INCLUDE batch 400 to 720
RUN 1 reference
name run 1 project p2_2 crystal p2-2_A1_1 dataset p2_2
name run 2 project p2_2 crystal p2-2_A1_1 dataset p2_2
exclude EMAX -
10.0
exclude batch -
400 to 540
partials -
check -
test 0.95 1.05 -
nogap
intensities PROFILE -
PARTIALS
final PARTIALS
scales -
rotation SPACING 5 -
secondary 6 -
bfactor ON -
BROTATION SPACING 20
UNFIX V
FIX A0
UNFIX A1
initial MEAN
tie surface 0.001
tie bfactor 0.3
cycles 10 converge 0.3 reject 2
anomalous on
output AVERAGE
print cycles nooverlap
RSIZE 80
## This script run with the command   ##
# scala HKLIN /Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT
/tmp/hari/p2_2_12_2_mtz.tmp SCALES
/Users/hari/aps_feb08/p2-2/p2_2_12.scala ROGUES
/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log NORMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr ANOMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr PLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt CORRELPLOT
/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr

Re: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem

[hari jayaram]

Hi.
I did try that beforehand  when I tried excluding  a range of batches with
the ccp4i gui
But I got an error

 Scala:  *** Gap in time (rotation) ***

Sorry...both versions of the protocol for handling a bad internal wedge are
giving me either a gap in rotation error or a Run 2 has not been
assigned to a dataset error

I am still stuck.

( error and com file for the exclude data range option is attached below)
Thanks for your help.

Hari Jayaram




Error
---

  Large gap in time (rotation) coordinate:3.5 
  See WARNING above 
  Smoothed B-factor impossible 

***
* Information from CCP4Interface script
***
The program run with command: scala HKLIN
/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT
/tmp/hari/p2_2_13_2_mtz.tmp SCALES
/Users/hari/aps_feb08/p2-2/p2_2_13.scala ROGUES
/Users/hari/aps_feb08/p2-2/p2_2_13_rogues.log NORMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_normplot.xmgr ANOMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_anomplot.xmgr PLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_surface_plot.plt CORRELPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_correlplot.xmgr
has failed with error message
 Scala:  *** Gap in time (rotation) ***
***


#CCP4I TERMINATION STATUS 0  Scala:  *** Gap in time (rotation) ***
#CCP4I TERMINATION TIME 14 Mar 2008  17:38:34
#CCP4I TERMINATION OUTPUT_FILES
 /Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz p2_2
#CCP4I MESSAGE Task failed


The com script was

***
/tmp/hari/p2_2_13_3_com.tmp
***
 title Scala anon and deleted batches 200_400b try with two run definitions
name project p2_2 crystal p2-2_A1_1 dataset p2_2
exclude EMAX -
10.0
exclude batch -
400 to 540
partials -
check -
test 0.95 1.05 -
nogap
intensities PROFILE -
PARTIALS
final PARTIALS
scales -
rotation SPACING 5 -
secondary 6 -
bfactor ON -
BROTATION SPACING 20
UNFIX V
FIX A0
UNFIX A1
initial MEAN
tie surface 0.001
tie bfactor 0.3
cycles 10 converge 0.3 reject 2
anomalous on
output AVERAGE
print cycles nooverlap
RSIZE 80


## This script run with the command   ##
# scala HKLIN /Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT
/tmp/hari/p2_2_13_2_mtz.tmp SCALES
/Users/hari/aps_feb08/p2-2/p2_2_13.scala ROGUES
/Users/hari/aps_feb08/p2-2/p2_2_13_rogues.log NORMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_normplot.xmgr ANOMPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_anomplot.xmgr PLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_surface_plot.plt CORRELPLOT
/Users/hari/aps_feb08/p2-2/p2_2_13_correlplot.xmgr



On Fri, Mar 14, 2008 at 5:11 PM, Phil Evans [EMAIL PROTECTED] wrote:

 In ccp4i Scala task, click to open the Excluded data panel, click on
 Exclude selected batches

 There you can define one or more ranges of batches or lists to exclude

 If you just want to exclude the last part you can define a range eg
 301 to 999

 You don't need to explicitly define runs

 Phil

 On 14 Mar 2008, at 18:57, hari jayaram wrote:

  Hi I am trying to exclude a bad wedge  of data during scaling in
  scala in the newest ccp4
 
  ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so
  they should be version 6)
 
  The batches I need are
  1 to 200 and 400-720
  I have clicked the Override automatic definition of runs to mark
  discontinuities in data button as well as created two runs to
  contain the required data
 
  But I get a  Run 2 has not been assigned to a dataset error.
  How I can exclude a bad wedge in the middle of my data from within
  scala without going through the split and  sort route in mtzutils. I
  have attached the com file generated by ccp4i and the error text below
 
  Thanks for your help
  Hari Jayaram
  Postdoc , Miller Lab
  Brandeis University
 
 
  -
  The error I get is
  -
  13714715716
   717718719720
 
    Run 2 has not been assigned to a dataset 
 
 
 ***
  * Information from CCP4Interface script
 
 ***
  The program run with command: scala HKLIN /Users/hari/aps_feb08/
  p2-2/p2-2_A1_1_0001_sorted.mtz HKLOUT /tmp/hari/p2_2_12_2_mtz.tmp
  SCALES /Users/hari/aps_feb08/p2-2/p2_2_12.scala ROGUES /Users/
  hari/aps_feb08/p2-2/p2_2_12_rogues.log NORMPLOT /Users/hari/
  aps_feb08/p2-2/p2_2_12_normplot.xmgr ANOMPLOT /Users/hari/
  aps_feb08/p2-2/p2_2_12_anomplot.xmgr PLOT /Users/hari

Re: [ccp4bb] SORTMTZ error status = 256

[hari jayaram]

Hello Eleanor
I was using the ccp4i gui to run scala when I got the SORTMTZ detected
error on obtaining record from sort procedure in return phase, status =
 256 .
The error vanished when I upgraded from ccp4 6.0 to 6.0.2

In any case the old com file for sortmtz is pasted below. It seems quite
normal .
Thanks for your help
Hari

sortmtz HKLIN /home/hari/cy30_2/cy30_2_p3.mtz HKLOUT
/home/hari/cy30_2/cy30_2_p3_sorted.mtz

ASCEND
H K L M/ISYM BATCH
scala HKLIN /home/hari/cy30_2/cy30_2_p3_sorted.mtz HKLOUT
/tmp/hari/cy30_2_charlie_8_2_mtz.tmp SCALES
/home/hari/cy30_2/cy30_2_charlie_8.scala ROGUES
/home/hari/cy30_2/cy30_2_charlie_8_rogues.log NORMPLOT
/home/hari/cy30_2/cy30_2_charlie_8_normplot.xmgr ANOMPLOT
/home/hari/cy30_2/cy30_2_charlie_8_anomplot.xmgr PLOT
/home/hari/cy30_2/cy30_2_charlie_8_surface_plot.plt CORRELPLOT
/home/hari/cy30_2/cy30_2_charlie_8_correlplot.xmgr

title P3 proc on charlie scaling
name project cy crystal cy30_2 dataset cy30_2
exclude EMAX -
10.0
partials -
check -
test 0.95 1.05 -
nogap
intensities PROFILE -
PARTIALS
final PARTIALS
scales -
rotation SPACING 5 -
secondary 6 -
bfactor ON -
BROTATION SPACING 20
UNFIX V
FIX A0
UNFIX A1
initial MEAN
tie surface 0.001
tie bfactor 0.3
cycles 10 converge 0.3 reject 2
output AVERAGE
print brief nooverlap
RSIZE 80



On Nov 13, 2007 4:28 AM, Eleanor Dodson [EMAIL PROTECTED] wrote:

 Can you attach the input file to sortmtz - the error is cryptic! I
 suspect the input file is corrupted somehow, but it needs testing.

 eleanor


 hari jayaram wrote:
  Hi ,
  I have a low resolution dataset at 3.2 to 3.5 Å resolution , upon
 running
  scala I get the following rather cryptic error
 
  SORTMTZ detected error on obtaining record from sort procedure in return
  phase, status =  256
 
  I am slightly unsure of the spacegroup and have been trying to process
 and
  scale
  the mtz file from mosflm in the various possibilities.
 
  I get the error when I try to process this dataset with the other
  possibilities from mosflm ( P3 and weirdly enough C222).
  Is this telling me something about my data or is it a bug. Googling
 revealed
  only one unanswered post right here on ccp4bb
 
 
  The same set of images when processed as P1 give an rmerge of around
 0.13 to
  3.2 A
 
 
 
  Thanks
  hari Jayaram
  postdoc, Brandeis University
 
  The detailed error is given below
 
  a name=outSORTMTZh3Header Information For Output MTZ File
 /h3/a
  pre
   SORTMTZ detected error on obtaining record from sort procedure in
 return
  phase, status =  256
 
   SORTMTZ:  Sorting failed
  Times: User:   5.5s System:0.3s Elapsed: 0:11
  /pre
  /html
 
 

Re: [ccp4bb] Unmerged output from Scala

[hari jayaram]

Hello all,
Along the lines of SCALA options UNMERGED and NOSCALE.. I am a little
confused..

I wanted to get my data from mosflm  to be used for the anisotropic scaling
and ellipsoidal truncation server at
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/

I was wondering what SCALA/Truncate  options I need to use to obtain my F
and SIG F for the analysis
Thanks
Hari Jayaram
Postdoc, Brandeis University






On Nov 19, 2007 3:53 PM, Clemens Vonrhein [EMAIL PROTECTED]
wrote:

 Hi Graeme,

 even with these options (ONLYMERGE and SCALES CONSTANT) you will have
 the SCALE column applied again to the intensities (not good) - at
 least that's how I understood Phil. You need to use

 ONLYMERGE
 INSCALE OFF

 to use the already scaled intensities and avoid applying the SCALE
 column again - Phil was the one telling me that. I was scratching my
 head for a long time trying to understand those various
 INTIAL/ONLYMERGE/INSCALE/NOSCALE options and how they relate to each
 other ...

 Cheers

 Clemens

 On Mon, Nov 19, 2007 at 08:07:02PM -, Winter, G (Graeme) wrote:
  Hi Phil,
 
  I use this option but not these columns. The only time I feed the file
 back I use ONLYMERGE and SCALES CONSTANT, to remerge the reflections.
 
  Cheers,
 
  Graeme
 
  
 
  From: CCP4 bulletin board on behalf of Phil Evans
  Sent: Mon 19/11/2007 5:07 PM
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: [ccp4bb] Unmerged output from Scala
 
 
 
  Is anyone using the OUTPUT UNMERGED option in Scala?
 
  This file contains columns called SCALE  SIGSCALE which are the
  applied scale and its SD
 
  I propose to change the names of these columns  so that if you put
  the file back into Scala the scales do not get re-applied by default
  (which is wrong since they have been applied already)
 
  Will this cause anyone problems? I suspect that very few people or
  programs are using this file
 
  Phil Evans
 

 --

 ***
 * 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)
 ***

[ccp4bb] SORTMTZ error status = 256

[hari jayaram]

Hi ,
I have a low resolution dataset at 3.2 to 3.5 Å resolution , upon running
scala I get the following rather cryptic error

SORTMTZ detected error on obtaining record from sort procedure in return
phase, status =  256

I am slightly unsure of the spacegroup and have been trying to process and
scale
the mtz file from mosflm in the various possibilities.

I get the error when I try to process this dataset with the other
possibilities from mosflm ( P3 and weirdly enough C222).
Is this telling me something about my data or is it a bug. Googling revealed
only one unanswered post right here on ccp4bb


The same set of images when processed as P1 give an rmerge of around 0.13 to
3.2 A



Thanks
hari Jayaram
postdoc, Brandeis University

The detailed error is given below

a name=outSORTMTZh3Header Information For Output MTZ File /h3/a
pre
 SORTMTZ detected error on obtaining record from sort procedure in return
phase, status =  256

 SORTMTZ:  Sorting failed
Times: User:   5.5s System:0.3s Elapsed: 0:11
/pre
/html