from:"ClAuS Flensburg"

Re: [ccp4bb] xds crashes

2022-11-29 Thread ClAuS Flensburg

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> >>University of Thessaly
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> >>-
> >>Tel. +302410 565278
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> -- 
> ---
> Dr. Demetres D. Leonidas
> Professor in Biochemistry
> Department of Biochemistry & Biotechnology
> University of Thessaly
> Biopolis 41500 Larissa, Greece
> -
> Tel. +302410 565278
> Tel. +302410 565297 (Lab)
> Tel. +304210 565263 (X-ray)
> Fax. +302410 565290
> E-mail: ddleoni...@bio.uth.gr
> ORCID ID orcid.org/-0002-3874-2523
> ---
> 
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> 
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-- 

*--
* ClAuS Flensburg, Ph.D. claus AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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Re: [ccp4bb] dictionary conversion

2017-06-30 Thread ClAuS Flensburg

Hi Paul,

On Fri, Jun 30, 2017 at 02:00:14PM +0100, Paul Emsley wrote:
> Hi,
> 
> What is the best (or easiest) way to convert restraint information
> (and in particular torsion restraint information) from the mmcif
> output of privateer or acedrg to a dic file suitable for refinement
> with Buster/TNT?

the easiest is to not do it ;-)

BUSTER can use dictionaries from eg. $CCP4/lib/data/monomers/?/???.cif
directly ie. similar format to what Grade[1] produces.

You are welcome to write to buster-deve...@globalphasing.com if you
encounter problems in doing so.

Regards,

ClAuS & Andrew (for buster-develop)
[1]: http://grade.globalphasing.org/cgi-bin/grade/server.cgi

Re: [ccp4bb] ccp4 version in sharp

2013-12-11 Thread ClAuS Flensburg

Dear Lisa,

On Wed, Dec 11, 2013 at 07:48:24PM +0800, LISA wrote:
> Hi all,
> I tried to run autosharp and get the following error message about ccp4 
> version.
> 
> 
>  *WARNING* : Your CCP4 [1
> ]
> version (6.4.0) is newer than the
>supported ones (and therefore untested) - this might not work. 
> Please
>use a supported CCP4 version (4.2.2 up to 6.3.0 with the latest
>patches applied from the official CCP4 problems page)
> 
> 
> My computer installed both ccp4 6.3.0 and 6.4.0
> *. *
> How to change the ccp4 version for sharp without reinstall sharp? Thank you.

to change CCP4 settings for SHARP/autoSHARP you can run the script
$BDG_home/adm/bin/ccp4-setup to point to your CCP4-6.3.0 version.

The wiki-page at:

https://www.globalphasing.com/sharp/wiki/index.cgi?KnownProblems201306#ccp4640

details issues we have noticed sofar.

With best wishes,

ClAuS (for sharp-develop)

PS. You are welcome to write to the 
mailing list with SHARP/autoSHARP questions.

Re: [ccp4bb] Problem running Buster (mtzdump: Cannot open environ.def)

2012-09-11 Thread Claus Flensburg

Dear Rosa,

On Tue, Sep 11, 2012 at 04:51:44PM +0200, Rosa Grenha wrote:
> Dear all
> 
> I have been fighting to solve this problem in running buster and
> would appreciate any advice on the subject (errors shown below).
> 
> I have installed ccp4-6.3.0 and buster gives me now an error related
> to environ.def

when changing CCP4 installation (and removing the old) you should
re-run the ccp4-setup scriptlet from BUSTER. Eg.

===
cd /home/sylvie/buster
. setup.sh
./adm/bin/ccp4-setup
# specify new CCP4 location etc.
===

Does that make it run?


With best wishes,

ClAuS

Re: [ccp4bb] Sftools can not handle non-standard settings?

2010-09-01 Thread Claus Flensburg

Dear Herman,

please find attached a patch for sftools that will add support 
for the following non-standard space group settings:

A2, C21, I21, P2122, P2212, P21221, P22121

Note: the number for I21 follows the upcomming change to 
syminfo.lib: 3004 -> 5005.

diffstat -p0 < 
CCP4-20091104-src-sftools_-sftools.f-Add-some-non-standard-spgrps-v1.patch
 src/sftools_/sftools.f |   52 -
 1 files changed, 35 insertions(+), 17 deletions(-)

The patch applies equally well to series-6_1 and trunk.


Regards,

ClAuS

P.S. After applying the patch and compiling sftools, you can use it in BUSTER 
with this command line option:

% refine autoBUSTER_Exe_sftools=/path/to/patched-sftools/sftools ...

On Wed, Sep 01, 2010 at 12:29:55PM +0200, herman.schreu...@sanofi-aventis.com 
wrote:
> Dear CCP4,
> 
> In our automated data processing and refinement pipeline, phaser
> sometimes comes up with solutions in non-standard settings (e.g. P 21 2
> 21). These solutions subsequently fail in autobuster and it turned out
> that this is because autobuster invokes sftools and sftools apparently
> is not able to handle non-standard settings.
> 
> I am really puzzled. We upgraded to the latest CCP4 version (6.1.13) and
> the symmetry libraries have P 21 2 21 (space group 2018) in them. Other
> programs like reindex and coot handle this setting without any problems.
> Is sftools still supported by ccp4, or should we ask the buster people
> to switch to some other program?
> 
> Thank you for your help,
> Herman Schreuder
--- src/sftools_/sftools.f-orig 2008-09-19 09:12:11.0 +0100
+++ src/sftools_/sftools.f  2009-11-04 08:50:05.0 +
@@ -4169,8 +4169,9 @@
 
   implicit none
 
-  integer maxop, maxgrp
-  parameter (maxop=45, maxgrp=73)
+  integer maxop, maxgrp, maxops, maxcen
+  parameter (maxops=45, maxcen=5)
+  parameter (maxop=maxops+maxcen, maxgrp=80)
 
 c subroutine arguments
   integer spnum,klass,nsym,nprim
@@ -4267,7 +4268,15 @@
   data syminf( 70) /'  214 I4132   40   8  25   0   0'/
   data syminf( 71) /' 1146 R3R 25   0   0   0   0'/
   data syminf( 72) /' 1155 R32R25  26   0   0   0'/
-  data syminf( 73) /' 4005 I2   1   0   0   0   0'/
+  data syminf( 73) /' 2005 A2   1   0   0   0   0'/
+  data syminf( 74) /' 3005 C21 41   0   0   0   0'/
+  data syminf( 75) /' 4005 I2   1   0   0   0   0'/
+  data syminf( 76) /' 5005 I21 42   0   0   0   0'/
+  data syminf( 77) /' 1017 P21221  43   0   0   0'/
+  data syminf( 78) /' 2017 P22122  44   0   0   0'/
+  data syminf( 79) /' 2018 P21221   1   7   0   0   0'/
+  data syminf( 80) /' 3018 P22121   8  45   0   0   0'/
+c 5005 (I21) used to be 3004 in syminfo.lib!
 
 c the matrices for each generator
   data (g(n,  1),n=1,12) /-1, 0, 0, 0, 0, 1, 0, 0, 0, 0,-1, 0/
@@ -4310,12 +4319,17 @@
   data (g(n, 38),n=1,12) / 0,-1, 0,18, 1, 0, 0,18, 0, 0, 1, 6/
   data (g(n, 39),n=1,12) / 0,-1, 0,18, 1, 0, 0, 6, 0, 0, 1,18/
   data (g(n, 40),n=1,12) / 0,-1, 0, 6, 1, 0, 0,18, 0, 0, 1, 6/
+  data (g(n, 41),n=1,12) /-1, 0, 0,12, 0, 1, 0, 0, 0, 0,-1, 0/
+  data (g(n, 42),n=1,12) /-1, 0, 0,12, 0, 1, 0, 0, 0, 0,-1,12/
+  data (g(n, 43),n=1,12) / 1, 0, 0,12, 0,-1, 0, 0, 0, 0,-1, 0/
+  data (g(n, 44),n=1,12) / 1, 0, 0, 0, 0,-1, 0,12, 0, 0,-1, 0/
+  data (g(n, 45),n=1,12) / 1, 0, 0, 0, 0,-1, 0, 0, 0, 0,-1, 0/
 c centering operators
-  data (g(n, 41),n=1,12) / 1, 0, 0, 0, 0, 1, 0,12, 0, 0, 1,12/
-  data (g(n, 42),n=1,12) / 1, 0, 0,12, 0, 1, 0, 0, 0, 0, 1,12/
-  data (g(n, 43),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1, 0/
-  data (g(n, 44),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1,12/
-  data (g(n, 45),n=1,12) / 1, 0, 0,16, 0, 1, 0, 8, 0, 0, 1, 8/
+  data (g(n, maxops+1),n=1,12) / 1, 0, 0, 0, 0, 1, 0,12, 0, 0, 1,12/
+  data (g(n, maxops+2),n=1,12) / 1, 0, 0,12, 0, 1, 0, 0, 0, 0, 1,12/
+  data (g(n, maxops+3),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1, 0/
+  data (g(n, maxops+4),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1,12/
+  data (g(n, maxops+5),n=1,12) / 1, 0, 0,16, 0, 1, 0, 8, 0, 0, 1, 8/
 
 c point group names according to CCP4
   data pgnams / 'PG1'  ,'PG2'  ,'PG222', 'PG4'  ,'PG422', 'PG3',
@@ -4407,7 +4421,9 @@
 c monoclinic and rhombohedral use the cell parameters to distinguish settings
   if(spnum2.eq.1)then
 klass2 = 1
-  else if((spnum2.ge.3 .and. spnum2.le.5) .or. spnum2.eq.4005)then
+  else if( (spnum2.ge.3 .and. spnum2.le.5) .or. 
+ $ (spnum2.eq.2005 .or. spnum2.eq.3005 .or.
+ $  spnum2.eq.4005 .or. spnum2.eq.5005) ) then
 if(cell(4).ne.90.0)then
   write(*,*)' !!! Illegal, monoclinic A unique is not valid !!!'
   return
@@ -4424,7 +4440,9 @@
   write(*,*)' to work with C-unique (e.g. -3, -4 or -5)'
 endif

Re: [ccp4bb] purchasing heavy atom clusters

2009-09-09 Thread Claus Flensburg

Hi Engin,

On Tue, Sep 08, 2009 at 04:06:20PM -0700, Engin Ozkan wrote:
...
> On a related point, I would appreciate any pointers, especially on  
> software like shelx, sharp, solve, and mlphare, on treating clusters at  
> resolutions where the heavy atoms are not resolved (at 6A or worse).  
> Until now, I've had much better luck just working on the Patterson  
> myself, and heavy atom searches and heavy atom position refinement with  
> software seem to invariably mess up the sites. Treating heavy metal  
> clusters as point scatterers is the preferred way in the literature, but  
> this could be implemented a few different ways. Any opinions are  
> appreciated.

SHARP has a feature whereby a cluster can be treated like a point
scatterer with a scattering factor that is the spherical average
of the atoms. The usage is briefly described here:

http://www.globalphasing.com/sharp/manual/appendix3.html#generalSPHCLUSTER


Regards,

ClAuS

Re: [ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4 and CCP4 6.0.1

2007-10-30 Thread Claus Flensburg

Hi Justin,

On Mon, Oct 29, 2007 at 01:11:54PM +0100, Justin Schmitz wrote:
> Hello All!
> 
> I have a problem with the output there from CCP4 into the log files on a 
> dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1.
> 
> 
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM13   Ano   0.147 -0.001  0.7232.055 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM14   Ano   0.347  0.519  0.8950.939 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM15   Ano   0.232  0.498  0.9650.546 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM16   Ano   0.031  0.124  0.022   -2.575  MLPHARE:  Normal termination
> Times: User:  84.9s System:0.3s Elapsed: 1:27 
> 
> 
> 
> BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM17   Ano   0.027 -0.001  0.8592.450 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM18   Ano   0.102 -0.002  0.8703.247 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM19   Ano   0.025  0.107  0.0245.815 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> ATOM20   Ano   0.024  0.072  0.0695.565 BFAC   20.000
> ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> 
> 
> 
> Many Programs do this e.g. refmac. The Termination message is passed to 
> the log file before all other data is in it. This  breaks of ploting or 
> in case of mlphare of the whole process.
> 
> Does anybody know how to handle this? Is it related to the OS or to CCP4?

I have seen a similar problem with scaleit using a gfortran compiler
on a recent snapshot of the ccp4 tarball.

This was on an Intel T7500 equipped box running Fedora 8 (rawhide)
with these versions:  gfortran-4.1.2 and glibc-2.7-2.

If you are compiling with gfortran you can give the attached patch a try:

cd $CCP4
patch -p0 < yt-fixup-ccperr-flushing-buglet.patch
make


With best wishes,

ClAuS
diff -ru lib/src/ccp4_general_f.c~ lib/src/ccp4_general_f.c
--- lib/src/ccp4_general_f.c~   2005-09-08 17:27:26.0 +0100
+++ lib/src/ccp4_general_f.c2007-10-29 13:06:50.0 +
@@ -198,6 +198,12 @@
   strncpy(tmp_errstr,errstr,length);
   tmp_errstr[length]='\0';
 
+  /* work around a buglet: gfortran-4.1.2 glibc-2.7-2 (2.6.23.1-37.fc8 x86_64 
SMP)
+ Flush stdout using a Fortran call before printing further. C. Flensburg 
20071029. */
+#ifdef GFORTRAN
+  FORTRAN_CALL (CCP4_FFLUSH_STDOUT, ccp4_fflush_stdout, (), (), ());
+#endif
+
   if (abs(*istat) <= 2)
 FORTRAN_CALL (CCP4H_SUMMARY_BEG, ccp4h_summary_beg, (), (), ());
 
diff -ru lib/src/unix.m4~ lib/src/unix.m4
--- lib/src/unix.m4~2007-05-30 16:53:19.0 +0100
+++ lib/src/unix.m4 2007-10-29 13:08:34.0 +
@@ -123,6 +123,7 @@
 C options
 C UGTARG - Get command-line argument
 C hciftime - Time in cif format
+C ccp4_fflush_stdout - Flush buffers to stdout
 C
 C Functions:
 C
@@ -934,3 +935,12 @@
 
 C
 
+  subroutine ccp4_fflush_stdout()
+dnl   work around a buglet: : gfortran-4.1.2 glibc-2.7-2
+dnl   (2.6.23.1-37.fc8 x86_64 SMP) C. Flensburg 20071029.
+  implicit none
+ifelse(_gfort,1,
+[  call flush(6)
+],dnl (else)
+[  continue])
+  end

Re: [ccp4bb] xds crashes

Re: [ccp4bb] dictionary conversion

Re: [ccp4bb] ccp4 version in sharp

Re: [ccp4bb] Problem running Buster (mtzdump: Cannot open environ.def)

Re: [ccp4bb] Sftools can not handle non-standard settings?

Re: [ccp4bb] purchasing heavy atom clusters

Re: [ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4 and CCP4 6.0.1

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