Hello all,
rotamers are a popular subject, apparently.
Would it be possible to display the closest rotamer to the currently
selected residue in the status bar? This would be a luxury because I guess
similar information is in the "rotamer analysis" window. I must say that
I've been pining for this for a while, but I can't contain myself any
longer!
Thanks,
Mark
P.S. Does anyone else have problems finding Clipper from the COOT
./configure script even when one specifies the path, (c.f.
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT )
...or am I overlooking something?
I ended up using a Clipper pkg-config definition, using Tim Fenn's clipper
patches as a basis.
==========================
/usr/lib/pkgconfig/clipper.pc
==========================
prefix=/usr/local/xtal
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include
Name: clipper
Description: clipper C++ crystallographic library
Requires: mmdb
Version: 2.0
Libs: -L${exec_prefix}/lib -lclipper -lclipper-core -lclipper-contrib
-lclipper-phs -lclipper-mmdbold -lclipper-cns -lclipper-cif -lclipper-ccp4
-lclipper-minimol -lclipper-mmdb -lsrfftw -lsfftw -lm
Cflags: -I${prefix}/include
==========================
So that one can use it in a similar way to Gnome:
$ pkg-config clipper --cflags --libs
-I/usr/local/xtal/include -I/usr/local/include -L/usr/local/xtal/lib
-L/usr/local/lib -lclipper -lclipper-core -lclipper-contrib -lclipper-phs
-lclipper-mmdbold -lclipper-cns -lclipper-cif -lclipper-ccp4
-lclipper-minimol -lclipper-mmdb -lsrfftw -lsfftw -lm -lccp4c -lmmdb
==========================
Which can be tested with PKG_CHECK macros in COOT's configure.in:
==========================
dnl Check for Clipper. we exit if clipper is not found.
#
PKG_CHECK_MODULES(CLIPPER, clipper, have_clipper=true, have_clipper=false)
if test "x${have_clipper}" = "xfalse" ; then
AC_MSG_ERROR([Error locating Clipper - a shiny new version of
Clipper is required now])
fi
AC_SUBST(CLIPPER_CFLAGS)
AC_SUBST(CLIPPER_LIBS)
==========================
Is this sensible?
Otherwise, does someone have a gtk2 binary of 0.5-pre-1 running on Ubuntu
Hardy Heron?
Thanks in advance,
Mark
2008/7/4 Dirk Kostrewa <[EMAIL PROTECTED]>:
> Hi Paul,
>
> speaking about rotamers and also about Chi torsion angles: would it
> possible in one of the next Coot versions, maybe, to display the actual
> torsion angles close to those bonds about which the rotations take place? I
> find it always difficult to look back and forth from either the rotamers
> popup window or the top row of the graphics display where the rotamer or Chi
> torsion angle(s) are currently displayed, and the actual side chain that I'm
> modifying.
>
> Best regards,
>
> Dirk.
>
> Am 04.07.2008 um 12:46 schrieb Paul Emsley:
>
> john kryst wrote:
>>
>>> Hi all !!
>>> Is there any command equivalent of changing the rotamer to a given value.
>>> I would like to generate different rotamers of Leu chi1 -60, +60, +180 of
>>> two Leu residues nearby and write out the all combinations as a pdb file. If
>>> i can get the command line then i can script it to make all possibilities.
>>>
>>
>>
>> Hi John,
>>
>> There wasn't - but I liked the idea, so there is now. Implemented in
>> revision 1214.
>>
>>
>> Attached is a script of how you might exercise the functions.
>>
>>
>> Paul.
>>
>>
>>
>>
>>
>>
>> (let ((imol (handle-read-draw-molecule-with-recentre "xxx.pdb" 0)))
>>
>> (let ((chain-id-1 "A")
>> (resno-1 74)
>> (chain-id-2 "A")
>> (resno-2 51))
>>
>> (let ((n-rots-1 (n-rotamers imol chain-id-1 resno-1 ""))
>> (n-rots-2 (n-rotamers imol chain-id-2 resno-2 "")))
>>
>> (if (> n-rots-1 1)
>> (if (> n-rots-2 1)
>>
>> (map (lambda (rot-no-1)
>> (set-residue-to-rotamer-number imol chain-id-1 resno-1
>> "" rot-no-1)
>> (map (lambda (rot-no-2)
>> (set-residue-to-rotamer-number imol chain-id-2
>> resno-2 "" rot-no-2)
>> (let ((file-name (string-append "rots-"
>> (number->string rot-no-1)
>> "-"
>> (number->string rot-no-2)
>> ".pdb")))
>> (write-pdb-file imol file-name)))
>> (range n-rots-2)))
>> (range n-rots-1)))))))
>>
>>
>>
>>
>
> *******************************************************
> Dirk Kostrewa
> Gene Center, A 5.07
> Ludwig-Maximilians-University
> Feodor-Lynen-Str. 25
> 81377 Munich
> Germany
> Phone: +49-89-2180-76845
> Fax: +49-89-2180-76999
> E-mail: [EMAIL PROTECTED]
> *******************************************************
>
--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks
