Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32113
Modified Files:
ccp4.info ccp4.patch
Log Message:
ccp4 patch update 10.4 sci
Index: ccp4.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- ccp4.info 15 May 2005 16:09:21 -0000 1.4
+++ ccp4.info 8 Jun 2005 23:59:16 -0000 1.5
@@ -1,9 +1,9 @@
Package: ccp4
Version: 5.0.2
-Revision: 202
+Revision: 203
#
# Revision 200 is specific to 10-4 transitional and includes these
-# post-release patches obtained from CCP4 web site March 15, 2005.
+# post-release patches obtained from CCP4 web site 7 June, 2005.
#
# CCP4_utils-25Aug2004.tcl.diff cmtzlib_f-10Aug2004.c.diff
lsqkab-9Aug2004.f.diff
# abs.f-18Aug2004.f dmmulti-12Aug2004.f.diff
refmac5-13Aug2004.tcl.diff
@@ -12,7 +12,9 @@
# ccp4i/templates/mapmask.com ccp4i mail interface fixed to work with OSX
Mail.app
# autosnd-15Nov2004.f cmtzlib_f-24Dec2004.c.diff
cmtzlib_f-14Jan2005.c
# ncsref-26Jan2005.script.diff truncate-02Mar2005.com.diff
truncate-02Mar2005.def.diff
-# truncate-02Mar2005.tcl.diff`
+# truncate-02Mar2005.tcl.diff` mtzutils-11May2005.f.diff
mok-harvest-src.patch
+# mok-harvest-includes.patch refmac5-19May2005.com.diff
sftools-25May2005.f.diff
+# local-20Apr2005.tcl.diff
#
#
Source: ftp://ftp.%n.ac.uk/%n/current/packed/%n-%v.tar.gz
@@ -162,7 +164,7 @@
License agreement is part of configure file -- print out form and mail in,
additional comments at http://chemistry.ucsc.edu/~wgscott/xtal/page5.html
CCP4 files will be installed under /sw/share/xtal/ccp4-5.0.2
-This revision includes all available CCP4 patches as of March 15, 2005,
+This revision includes all available CCP4 patches as of June 7, 2005
and new bash and zsh command completions specific to ccp4.
<<
DocFiles: README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps
ccp4i_installation.html academic_software_licence.pdf
academic_software_licence.ps.gz academic_software_licence.rtf
Index: ccp4.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- ccp4.patch 15 May 2005 16:09:21 -0000 1.4
+++ ccp4.patch 8 Jun 2005 23:59:16 -0000 1.5
@@ -241,7 +241,7 @@
set MTZ_file_data(CHANGED) $changed
diff -ruN ccp4-5.0.2-orig/ccp4i/src/local.tcl ccp4-5.0.2/ccp4i/src/local.tcl
--- ccp4-5.0.2-orig/ccp4i/src/local.tcl 2004-01-26 02:37:16.000000000
-0800
-+++ ccp4-5.0.2/ccp4i/src/local.tcl 2005-05-07 07:04:25.000000000 -0700
++++ ccp4-5.0.2/ccp4i/src/local.tcl 2005-06-07 22:34:52.000000000 -0700
@@ -28,13 +28,13 @@
#----------------------------------------------------------------
proc SendMail { subject tmp_file mail_address } {
@@ -258,6 +258,46 @@
}
#d_index_title Interaction with Netscape
+@@ -178,16 +178,32 @@
+ } else {
+ set viewer_cmd "poll_netscape file 500 0 $url"
+ }
+- }
++ }
+
+- } else {
+- if { $tcl_platform(os) == "Darwin" } {
+- # for IE on make open only opens pages
+- set viewer_cmd "exec open -a {$configure(HYPERTEXT_VIEWER)} [lindex
[split $url # ] 0 ]"
++ } elseif { $tcl_platform(os) == "Darwin" } {
++ # for IE on make open only opens pages
++ set viewer_cmd "exec open -a {$configure(HYPERTEXT_VIEWER)} [lindex
[split $url # ] 0 ]"
++
++ } elseif { [regexp "mozilla" $configure(HYPERTEXT_VIEWER) ] || \
++ [regexp "firefox" $configure(HYPERTEXT_VIEWER)] } {
++ # This seems to be necessary for Mozilla
++ if { !$remote } { set url "file://$url" }
++ # Check if browser already open cf. Netscape version above
++ catch { exec $configure(HYPERTEXT_VIEWER) -remote ping() }
mozilla_message
++ if { [regexp "Error" $mozilla_message ] } {
++ # Command to open requested URL in new Mozilla browser
++ set viewer_cmd "exec $configure(HYPERTEXT_VIEWER) $url &"
+ } else {
+- # Command to open requested URL in non-netscape browser
+- set viewer_cmd "exec $configure(HYPERTEXT_VIEWER) $url &"
++ # Command to open requested URL in existing Mozilla browser
++ set viewer_cmd "exec $configure(HYPERTEXT_VIEWER) -remote
openURL($url) &"
+ }
++ } elseif { [regexp "konqueror" $configure(HYPERTEXT_VIEWER) ] } {
++ # This seems to be necessary for Konqueror
++ if { !$remote } { set url "file://$url" }
++ set viewer_cmd "exec $configure(HYPERTEXT_VIEWER) $url &"
++ } else {
++ # Command to open requested URL in other browser
++ set viewer_cmd "exec $configure(HYPERTEXT_VIEWER) $url &"
+ }
+ }
+
diff -ruN ccp4-5.0.2-orig/ccp4i/tasks/refmac5.tcl
ccp4-5.0.2/ccp4i/tasks/refmac5.tcl
--- ccp4-5.0.2-orig/ccp4i/tasks/refmac5.tcl 2004-06-10 03:33:39.000000000
-0700
+++ ccp4-5.0.2/ccp4i/tasks/refmac5.tcl 2005-05-07 07:04:25.000000000 -0700
@@ -351,6 +391,49 @@
$IFBORDER BORDER $BORDER
{ ![StringSame $EXTEND_MODE DEFAULT] } EXTEND $EXTEND_MODE
+diff -ruN ccp4-5.0.2-orig/ccp4i/templates/refmac5.com
ccp4-5.0.2/ccp4i/templates/refmac5.com
+--- ccp4-5.0.2-orig/ccp4i/templates/refmac5.com 2004-01-26
03:27:56.000000000 -0800
++++ ccp4-5.0.2/ccp4i/templates/refmac5.com 2005-05-22 13:11:57.000000000
-0700
+@@ -6,7 +6,7 @@
+ # A copy of the CCP4 licence can be obtained by writing to the
+ # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
+ #
+-#CCP4i_cvs_Id $Id$
++#CCP4i_cvs_Id $Id$
+ ########################################################################
+ # REFMAC5 - KEYWORD TEMPLATE
+ ########################################################################
+@@ -52,7 +52,7 @@
+
+ 1 refi
+ - 1 type $REFINE_TYPE
+- -- {[StringSame $INPUT_PHASE PHASE HL] } PHASE SCBL $PHASE_SCBLUR BBLU
$PHASE_BBLUR
++ - {[StringSame $INPUT_PHASE PHASE HL] } PHASE SCBL $PHASE_SCBLUR BBLU
$PHASE_BBLUR
+ - 1 resi MLKF
+ - 1 meth $MINIMISATION
+ IF { [StringSame $REFINE_TYPE IDEA RIGID] }
+@@ -95,7 +95,7 @@
+ - 1 LSSC
+ - $SCALING_ANISO ANISO
+ - $SCALING_IF_FIXB FIXB bvalue $SCALING_FIXB_BBULK
+- - SCALING_EXPE_SIGMA EXPE
++ - $SCALING_EXPE_SIGMA EXPE
+ - { [StringSame $SCALING_REF_SET FREE ] } FREE
+ - { [StringSame $SCALING_APPLY NO ] } appl $SCALING_APPLY
+
+@@ -109,9 +109,9 @@
+ # SOLVENT MASK
+ ######################################
+ $IF_SOLVENT solvent YES | solvent NO
+-- VDWProb $SOLVENT_VDWPROB
+-- IONProb $SOLVENT_IONPROB
+-- RSHRink $SOLVENT_RSHRINK
++- 1 VDWProb $SOLVENT_VDWPROB
++- 1 IONProb $SOLVENT_IONPROB
++- 1 RSHRink $SOLVENT_RSHRINK
+
+ # Always use MATRIX weighting
+ 1 weight
diff -ruN ccp4-5.0.2-orig/ccp4i/templates/truncate.com
ccp4-5.0.2/ccp4i/templates/truncate.com
--- ccp4-5.0.2-orig/ccp4i/templates/truncate.com 2004-01-26
03:27:58.000000000 -0800
+++ ccp4-5.0.2/ccp4i/templates/truncate.com 2005-05-07 07:04:26.000000000
-0700
@@ -5013,6 +5096,300 @@
CALL LWSORT(MTZOUT,MSORTX_OUT)
MLOOP = 1
+diff -ruN ccp4-5.0.2-orig/src/sftools_/sftools.f
ccp4-5.0.2/src/sftools_/sftools.f
+--- ccp4-5.0.2-orig/src/sftools_/sftools.f 2004-04-05 02:36:05.000000000
-0700
++++ ccp4-5.0.2/src/sftools_/sftools.f 2005-06-07 22:33:15.000000000 -0700
+@@ -1862,7 +1862,7 @@
+ endif
+
+ do 400, j=1,newcol
+- if(index('HSJKFGDQLMPMWBIRAY',type2(j)) .eq. 0)then
++ if(index('HSJKFGDQLMPWBIRAYE',type2(j)) .eq. 0)then
+ write(*,'(//,1x,a)')' !!! WARNING, unknown column type !!!'
+ write(*,'(/,1x,a,a)')' For column : ',label2(j)(1:30)
+ write(*,'(2x,43(''=''))')
+@@ -1875,8 +1875,9 @@
+ write(*,*)' L = Sigma for F+/F- M = sigma for I+/I-'
+ write(*,*)' W = weight factor B = batch number'
+ write(*,*)' I = any integer R = any real'
+- write(*,*)' A = phase prob. coeff. (Hendrickson/lattmann)'
++ write(*,*)' A = phase prob. coeff. (Hendrickson/Lattman)'
+ write(*,*)' Y = M/ISYM, partial/reject flag and symm. number'
++ write(*,*)' E = normalized structure factor'
+ write(*,*)
+ read(*,'(a1)')type2(j)
+ call upper(type2(j))
+@@ -3398,11 +3399,11 @@
+ c set to A B C or D for the four H/L coefficients
+ type2(l)=char(ichar('A')-1+numbhl)
+ if(numbhl.eq.4) numbhl = 0
+- write(*,*)' Hendrickson/Lattmann column',l,' is updated'
++ write(*,*)' Hendrickson/Lattman column',l,' is updated'
+ else if(numbhl.ne.0)then
+ write(*,*)' !!! WARNING, less then 4 H/L coeffs !!!'
+ write(*,*)
+- write(*,*)numbhl,' Hendrickson/Lattmann coefficients found'
++ write(*,*)numbhl,' Hendrickson/Lattman coefficients found'
+ write(*,*)' Four H/L columns expected. Check your column'
+ write(*,*)' labels. They should be set to A.'
+ return
+@@ -5822,6 +5823,8 @@
+ + gt_int,is_col,gt_col,lstline,ll
+ real dstarsq,conv(maxcl),celvol
+ logical input,done,is_int,missing
++ integer lenstr
++ external lenstr
+
+ done=.false.
+ card=incard
+@@ -5890,8 +5893,10 @@
+ else if(option(1:3).eq.'CEL')then
+ done=.true.
+ write(*,*)
+- write(*,*)' cell dimensions are:'
+- write(*,*)' ===================='
++ write(*,*)
++ $ ' global cell dimensions (obsolete - use crystal cells)'
++ write(*,*)
++ $ ' ====================================================='
+ write(*,*)
+ write(*,'(a,f8.3,5x,a,f7.2)')' a =',cell(1),'alpha =',cell(4)
+ write(*,'(a,f8.3,5x,a,f7.2)')' b =',cell(2),'beta =',cell(5)
+@@ -5899,6 +5904,49 @@
+ write(*,*)
+ write(*,'(A,F12.0,A)')' The cell volume is: ',
+ $ celvol(cell),' A**3'
++ else if(option(1:3).eq.'DCE')then
++ done=.true.
++ write(*,*)
++ write(*,*)' crystal cell dimensions are:'
++ write(*,*)' ============================'
++ write(*,*)
++ write(*,'(4x,a,8x,a,8x,a,6x,a,4x,a,3x,a,4x,a)')
++ $ 'a','b','c','alpha','beta','gamma','xname'
++ write(*,*)
++ do l=1,ndatasets
++C skip base dataset
++ if (xname(l)(1:lenstr(xname(l))).eq.'HKL_base') goto 110
++C skip if more than one dataset in a crystal
++ if (l.gt.1) then
++ do j=1,l-1
++ if (xname(l)(1:lenstr(xname(l))).eq.
++ $ xname(j)(1:lenstr(xname(j)))) goto 110
++ enddo
++ endif
++ write(*,
++ $ '(f10.4,x,f10.4,x,f10.4,x,f10.4,x,f10.4,x,f10.4,2x,a)')
++ $ dcell(1,l),dcell(2,l),dcell(3,l),
++ $ dcell(4,l),dcell(5,l),dcell(6,l),
++ $ xname(l)(1:lenstr(xname(l)))
++ 110 continue
++ enddo
++ else if(option(1:3).eq.'DWA')then
++ done=.true.
++ write(*,*)
++ write(*,*)' dataset wavelengths are:'
++ write(*,*)' ========================'
++ write(*,*)
++ write(*,'(4x,a,5x,a,7x,a)')
++ $ 'lambda','xname','dname'
++ write(*,*)
++ do l=1,ndatasets
++C skip base dataset
++ if (xname(l)(1:lenstr(xname(l))).eq.'HKL_base') goto 120
++ write(*,'(f10.5,3x,a,3x,a)')
++ $ dwavel(l),xname(l)(1:lenstr(xname(l))),
++ $ dname(l)(1:lenstr(dname(l)))
++ 120 continue
++ enddo
+ else if(option(1:3).eq.'TIT')then
+ done=.true.
+ write(*,*)' Title cards:'
+@@ -9311,7 +9359,7 @@
+ write(*,*)' ================================'
+ write(*,*)
+ write(*,*)' Command to reduce reflections to the asymmetric'
+- write(*,*)' unit. Phases & Hendrickson/Lattmann coefficients'
++ write(*,*)' unit. Phases & Hendrickson/Lattman coefficients'
+ write(*,*)' (if present) will be updated'
+ write(*,*)
+ write(*,*)' SILENT Keyword to supress output'
+@@ -9363,11 +9411,11 @@
+ c set to A B C or D for the four H/L coefficients
+ type2(l)=char(ichar('A')-1+numbhl)
+ if(numbhl.eq.4) numbhl = 0
+- write(*,*)' Hendrickson/Lattmann column',l,' is updated'
++ write(*,*)' Hendrickson/Lattman column',l,' is updated'
+ else if(numbhl.ne.0)then
+ write(*,*)' !!! WARNING, less then 4 H/L coeffs !!!'
+ write(*,*)
+- write(*,*)numbhl,' Hendrickson/Lattmann coefficients found'
++ write(*,*)numbhl,' Hendrickson/Lattman coefficients found'
+ write(*,*)' Four H/L columns expected. Check your column'
+ write(*,*)' labels. They should be set to A.'
+ return
+@@ -9783,7 +9831,7 @@
+ if(card .eq. ' ')then
+ nline = 1
+ else
+- nline = gt_int(card)
++ nline = gt_int(card(1:80))
+ if(nline .eq. -9999) return
+ endif
+
+@@ -10117,6 +10165,8 @@
+ c read all header items in temporary variables
+ call lrtitl(1,info2,n1)
+
++c n1 set to maximum number of history lines than can be returned
++ n1 = 30
+ call lrhist(1,info2(2),n1)
+
+ C---- Get dataset info (this is not included in chkhdr).
+@@ -11118,8 +11168,11 @@
+ character*(*) incard
+ integer l, j, k, gt_int, nspace, batnum, ncl
+ integer ncuse(maxcol), is_col, gt_col
+- real gt_real, rtmp
++ real gt_real, rtmp, tmp_dcell(6), tmp_dwave
++ character*64 tmp_xname, tmp_dname
+ logical input, is_int, is_real, yes
++ integer lenstr
++ external lenstr
+
+ card=incard
+ call upper(card)
+@@ -11156,7 +11209,10 @@
+ write(*,*)' -items is a list of header items to be changed'
+ write(*,*)' ALL = all header items, TITLE = title cards,'
+ write(*,*)' LABELS = column labels, TYPES = column types,'
+- write(*,*)' CELL = unit cell parameters, SORT = sort order,'
++ write(*,*)' CELL = unit cell parameters (not used by MTZ),'
++ write(*,*)' DCELL = crystal-specific unit cell parameters,'
++ write(*,*)' DWAVE = dataset-specific wavelength,'
++ write(*,*)' SORT = sort order,'
+ write(*,*)' SPACEGROUP = space group related data'
+ write(*,*)
+ write(*,*)' The program will list the old header information.'
+@@ -11169,7 +11225,7 @@
+ write(*,*)' ID for that column'
+ write(*,*)
+ write(*,*)' Examples:'
+- write(*,*)' SET CELL'
++ write(*,*)' SET DCELL'
+ write(*,*)' SET TYPES'
+ write(*,*)' SET TYPES COL 5'
+ write(*,*)
+@@ -11215,9 +11271,10 @@
+ write(*,*)' L = Sigma for F+/F- M = sigma for I+/I-'
+ write(*,*)' W = weight factor B = batch number'
+ write(*,*)' I = any integer R = any real'
+- write(*,*)' A = phase prob. coeff. (Hendrickson/lattmann)'
++ write(*,*)' A = phase prob. coeff. (Hendrickson/Lattman)'
+ write(*,*)
+ $ ' Y = M/ISYM, partial/reject flag and symm. number'
++ write(*,*)' E = normalized structure factor'
+ write(*,*)
+ write(*,*)' give the new type (or return) for column :',
+ $ ncuse(l)
+@@ -11226,7 +11283,7 @@
+ read(*,'(a1)')newtyp
+ if(newtyp.ne.' ')then
+ call upper(newtyp)
+- if(index('HSJKFGDQLMPWBIRAY',newtyp).eq.0)then
++ if(index('HSJKFGDQLMPWBIRAYE',newtyp).eq.0)then
+ write(*,*)' !!! error, unknown type given !!!'
+ write(*,*)' the old value will be kept'
+ else
+@@ -11269,6 +11326,88 @@
+ c determination
+ call list('CELL')
+ call rescnst
++ else if(option(1:3).eq.'DCE')then
++ write(*,*)' Current crystal cell dimensions are:'
++ call list('DCE')
++ write(*,*)
++ write(*,*)' To keep these cells: Type <return>'
++ write(*,'(a,a)')' To update cell dimensions for one crystal,',
++ $ ' type new dimensions followed by crystal name.'
++ read(*,'(a80)')newinfo
++ do 450,l=1,6
++ rtmp=-9.99E+11
++ if(input(newinfo,option,frmat).eqv.present)then
++ if(is_int(frmat))then
++ rtmp= real(gt_int(option))
++ else if(is_real(frmat))then
++ rtmp=gt_real(option)
++ endif
++ endif
++ if(rtmp.lt.-9.9E+11)then
++ write(*,*)' !!! WARNING, error in reading cell !!!'
++ write(*,*)' Parameters not updated.'
++ goto 460
++ endif
++ tmp_dcell(l)=rtmp
++ 450 continue
++ if(input(newinfo,option,frmat).eqv.absent)then
++ write(*,*)' !!! WARNING, no crystal name given !!!'
++ write(*,*)' Parameters not updated.'
++ goto 460
++ endif
++ do l=1,ndatasets
++ if (xname(l)(1:lenstr(xname(l))).eq.option) then
++ do j=1,6
++ dcell(j,l) = tmp_dcell(j)
++ enddo
++ endif
++ enddo
++ changed = .true.
++ 460 continue
++ call list('DCE')
++ else if(option(1:3).eq.'DWA')then
++ write(*,*)' Current dataset wavelengths are:'
++ call list('DWA')
++ write(*,*)
++ write(*,*)' To keep these wavelengths: Type <return>'
++ write(*,'(a,a)')' To update wavelength for one dataset,',
++ $ ' type new wavelength followed by crystal and dataset names.'
++ read(*,'(a80)')newinfo
++ rtmp=-9.99E+11
++ if(input(newinfo,option,frmat).eqv.present)then
++ if(is_int(frmat))then
++ rtmp= real(gt_int(option))
++ else if(is_real(frmat))then
++ rtmp=gt_real(option)
++ endif
++ endif
++ if(rtmp.lt.-9.9E+11)then
++ write(*,*)' !!! WARNING, error in reading wavelength !!!'
++ write(*,*)' Parameter not updated.'
++ goto 480
++ endif
++ tmp_dwave=rtmp
++ if(input(newinfo,option,frmat).eqv.absent)then
++ write(*,*)' !!! WARNING, no crystal name given !!!'
++ write(*,*)' Parameter not updated.'
++ goto 480
++ endif
++ tmp_xname=option
++ if(input(newinfo,option,frmat).eqv.absent)then
++ write(*,*)' !!! WARNING, no dataset name given !!!'
++ write(*,*)' Parameter not updated.'
++ goto 480
++ endif
++ tmp_dname=option
++ do l=1,ndatasets
++ if (xname(l)(1:lenstr(xname(l))).eq.tmp_xname .and.
++ $ dname(l)(1:lenstr(xname(l))).eq.tmp_dname) then
++ dwavel(l) = tmp_dwave
++ endif
++ enddo
++ changed = .true.
++ 480 continue
++ call list('DWA')
+ else if(option(1:3).eq.'TIT')then
+ write(*,*)
+ write(*,*)' To keep the old title card : Type <return>'
diff -ruN ccp4-5.0.2-orig/src/topp_/autosnd.f ccp4-5.0.2/src/topp_/autosnd.f
--- ccp4-5.0.2-orig/src/topp_/autosnd.f 2004-03-31 05:40:28.000000000
-0800
+++ ccp4-5.0.2/src/topp_/autosnd.f 2005-05-07 07:04:53.000000000 -0700
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