Hi Everyone,
Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data:
1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region.
2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer.
Thanks
Sena
Methodist. Leading Medicine.
Recognized by U.S.News & World Report as an "Honor Roll" hospital
Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row
Designated as a Magnet hospital for excellence in nursing
Visit us at methodisthealth.com
Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital
***CONFIDENTIALITY NOTICE***
This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
Dear developers,
Does the new mechanism of secondary structure restraints apply to nucleic
acids as well ? Are the average bond distances similar and does DSSP works
well with RNA/DNA ?
Thank you in advance for clarifying this issue,
Peter.
Dear Phenix BB
When I tried to install the latest binary version (1.6.1), the
"install" script always stopped and dumped an error message as follows:
-----
/software/PHENIX/phenix-installer-1.6.1-357/bin/install-from-binary:
line 347: 10964 Floating point exception$PHENIX_BUILD/base/bin/python
$PHENIX_LOC/cctbx_project/libtbx/configure.py --
current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >>
$PHENIX_LOG/binary.log 2>&1
Error configuring: see /software/PHENIX/phenix-installer-1.6.1-357/
build-binary/intel-linux-2.6-x86_64/lupus/log/binary.log for details
-----
And this "binary.log" file looks like this;
==========
.
. After many lines...
.
./reduce/comment_out_carboxylate_H_v2.3.pl
./reduce/Makefile
./reduce/libtbx_refresh.py
==========
This never happened when I installed version 1.6-289.
Could anybody out there tell me how I can get around this?
Or anything important is missing?
The system I'm using is:
Linux crux 2.6.16.60-0.27-smp #1 SMP Mon Jul 28 12:55:32 UTC 2008
x86_64 x86_64 x86_64 GNU/Linux
SUSE Linux Enterprise Desktop 10 (x86_64)
VERSION = 10
PATCHLEVEL = 2
Thank you very much for your help in advance!
Best regards,
kami
Tatsuya KAMINISHI, Ph.D.
Fucini Laboratory
Institute for Organic Chemistry and Chemical Biology
Johann Wolfgang Goethe University
Max-von-Laue-Strasse 7, N160/B413
D-60438 Frankfurt am Main, Germany
Tel: +49 69 798-29165
Fax: +49 69 798-29268
Web: http://user.uni-frankfurt.de/~joharms/akfucini/
hi phenix-bb
in the standard phenix.refine scripts there are options for adding
user defined restraints on bonds and angles, but not on dihedrals. Is
this currently possible in phenix.refine? One application would be to
restrain the phi-psi angles of a low resolution structure to phi-psi
angles from a high-res structure of the same protein, an option
previously made possible for xplor in the USF program XPLO2D
gregers
Gregers Rom Andersen
Associate professor
Department of Molecular Biology
University of Aarhus
Gustav Wiedsvej 10C DK8000 Aarhus C
phone +45 89425024 fax +45 86123178
www.bioxray.au.dk/gra
