Re: [ccp4bb] CCP4 PATH variable
Dear Petr, I also source the setup script $CCP4/bin/ccp4.setup-sh as I use ccp4 from the command line quite a bit. In my case (v. 6.5), the PATH is set to PATH=$PATH:$CCP4/etc:$CCP4/bin:$CCP4/share/xia2/Applications: i.e. CCP4 is appended, not prepended. I don't think I edited the line so it seems the default setting. If it's not, you only need to swap it or, if you don't have write access, ask the person who does to do it for you. Best, Tim On 03/13/2015 08:42 PM, Petr Leiman wrote: Dear All, I have to apologize for my somewhat insinuating message about CCP4 behavior. In order to retain command line functionality of CCP4 programs, I always sourced CCP4 setup script in my bashrc file, and this is what caused a significant amount of grief for me later. However, sourcing CCP4 setup is unnecessary for the ccp4i interface, which is self-consistent and fully contained in terms of environmental variables, and this is how we are supposed to use CCP4 today anyway. Sincerely, Petr P.S. Many thanks to Ed Pozharski for giving me pointers to figure out this problem. On 03/12/2015 08:49 PM, Petr Leiman wrote: Dear Community, What is the reason of placing the CCP4 PATH and other path-related variables in front of existing variables? This forces a linux system to use CCP4-distributed wish in all applications by default. Note that the ccp4i script calls CCP4 distributed wish explicitly with its full path. This might be trivial, and the fix is also trivial, but trivial things like that cause a lot of lost time and head scratching when tcl/tk programs compile without errors and perform some operations correctly but segfault on others - all due to a mixup of libraries and wish executables caused by CCP4 wish. Would it be possible to append CCP4 path variables by default instead of rather rudely jumping in front of the queue? Thank you, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 http://lbbs.epfl.ch -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] CCP4 PATH variable
On Mar 13, 2015, at 12:42 PM, Petr Leiman petr.lei...@epfl.ch wrote:
this is how we are supposed to use CCP4 today anyway.
I’ve never been big on doing what I am told I am supposed to do, so I have been
using this:
use this to put it at the end of the path:
ccp4_first_in_path=0
or this to put it at the beginning:
ccp4_first_in_path=1
with the following for bash and zsh:
if [[ $ZSH_NAME != zsh ]];then
# This is specific to bash, so protect it from zsh users
# CCP4 executables and scripts live in $CBIN and $CETC respectively; put
them
# on the path in an appropriate order for scripts to be used as wrappers for
# binaries of the same name. Put ccp4 stuff after the current path to avoid
# confusion with `.' or whatever in the path:
#
# This construct prevents the path getting longer each time ccp4.setup is
# executed (A. Perrakis)
#
ccp4pathlist=${CCP4}/etc ${CBIN}
#
for dir in ${ccp4pathlist}; do
if [[ `expr :${PATH}: : .*:${dir}:` -eq 0 ]]; then
if [[ $ccp4_first_in_path -eq 1 ]]; then
export PATH=${dir}:${PATH}
else
export PATH=${PATH}:${dir}
fi
fi
done
else
# This is specific to zsh, so protect it from bash users
if [[ $ccp4_first_in_path == 1 ]]; then
PATH=${CCP4}/etc:${CBIN}:$PATH
else
PATH=$PATH:${CCP4}/etc:${CBIN}
fi
typeset -U path # This construct prevents the path getting longer
each time
# ccp4.setup is executed in zsh.
export PATH
fi
Re: [ccp4bb] CCP4 PATH variable
Dear All, I have to apologize for my somewhat insinuating message about CCP4 behavior. In order to retain command line functionality of CCP4 programs, I always sourced CCP4 setup script in my bashrc file, and this is what caused a significant amount of grief for me later. However, sourcing CCP4 setup is unnecessary for the ccp4i interface, which is self-consistent and fully contained in terms of environmental variables, and this is how we are supposed to use CCP4 today anyway. Sincerely, Petr P.S. Many thanks to Ed Pozharski for giving me pointers to figure out this problem. On 03/12/2015 08:49 PM, Petr Leiman wrote: Dear Community, What is the reason of placing the CCP4 PATH and other path-related variables in front of existing variables? This forces a linux system to use CCP4-distributed wish in all applications by default. Note that the ccp4i script calls CCP4 distributed wish explicitly with its full path. This might be trivial, and the fix is also trivial, but trivial things like that cause a lot of lost time and head scratching when tcl/tk programs compile without errors and perform some operations correctly but segfault on others - all due to a mixup of libraries and wish executables caused by CCP4 wish. Would it be possible to append CCP4 path variables by default instead of rather rudely jumping in front of the queue? Thank you, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 http://lbbs.epfl.ch
[ccp4bb] POSTDOCTORAL POSITION - Molecular machines Proteotoxic stress (IMP, Vienna)
POSTDOCTORAL POSITION - Molecular machines dealing with proteotoxic stresss A 3-year postdoctoral position is available in the laboratory of Dr. Tim Clausen at the Research Institute of Molecular Pathology (IMP) in Vienna to study molecular machines removing toxic protein aggregates. Our laboratory is interested in (i) protein quality control and stress response pathways, (ii) the role of specific protein modifications therein, and (iii) the networking of chaperones carrying out the assembly of multi-protein complexes. We recently discovered protease-chaperone machineries that are of fundamental importance for intercellular signaling (Cell, 2013, 155, 647) and for forming myosin filaments (Cell, 2013, 152, 183), and identified a novel post-translational protein modification (phospho-arginine; Science, 2009, 324, 1323) coordinating the bacterial stress response. Regarding the latter point, we developed mass spectrometric procedures to monitor the occurrence and turnover of pArg protein modification on the proteomic scale (Mol Cell Proteomics, 2014, 13, 537). For further information of the group, please have a look at http://clausen.imp.ac.at . By applying a novel methodology specialized for dynamic protein complexes, we will analyze the structure and function of molecular machines mediating the degradation and disaggregation of damaged proteins. To this end, we will use the proteasome and the Hsp104 disaggregase as model systems. Preliminary data from our lab point to novel regulatory and structural features that are critical for the various housecleaning activities and for taming the otherwise dangerous protein shredders. To pursue a further, in-depth mechanistic analysis, we are looking for a highly motivated postdoc candidate. The position will provide a unique and multi-disciplinary exposure to modern Structural Biology. Located at the IMP (http://imp.ac.at), a leading international research institute in one of the world's best cities, our lab has access to cutting-edge service facilities and benefits from the excellent research community at the Vienna Biocenter Campus (http://www.viennabiocenter.org). The ideal candidate will have a doctoral degree and a published expertise in Biochemistry, Structural Biology or related fields. We particularly welcome applications from candidates interested in working at the interface of protein crystallography, electron microscopy and mass spectrometry. Please send a letter of intent, your CV, and names of 3 referees to Tim Clausen (clau...@imp.univie.ac.at) .
Re: [ccp4bb] Basic Anomalous Scattering Theory
An account here http://www.ccp4.ac.uk/courses/proceedings/1997/j_helliwell/main.html Colin From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org] Sent: 12 March 2015 17:51 To: ccp4bb Subject: Re: [ccp4bb] Basic Anomalous Scattering Theory Note that this can lead to anomalous scattering of the incident soldiers. But it would unfortunately not be imaginary—it would be altogether too real! Ethan But yes, it works for pianos too. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
