On Tue, Jan 26, 2016 at 6:16 PM, Nigel Moriarty wrote:

Roger

The monomer library is available stand alone from CCP4 and you can use it with cctbx. It's a little hidden so you might ask on the ccp4bb.

it's on Garib's website https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/di... the latest changes are in bazaar: bzr checkout bzr+http://fg.oisin.rc-harwell.ac.uk/bzr/monomers/trunk/ monomers

Monomer library that comes with Phenix is a truncated version of original CCP4 monomer library. We filter out entries that are not useful for refinement. GeoStd is used to compliment monomer library (Nigel can tell more about GeoStd). Pavel On 1/26/16 10:16, Paul Adams wrote:

The monomer library is also part of the Phenix distribution.

...

On Jan 26, 2016, at 8:49 AM, Roger Martin wrote:

Hi,

looking at the prebuilts(http://cci.lbl.gov/cctbx_build/dev-565/cctbx-installer-dev-565-intel-linux-2...) for CentOS I see the dependency for mon_lib in verify_mon_lib_data.py. Is mon_lib available stand alone or comes in the full ccp4 package only?

Where do most of you get a copy of mon_lib? _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hello Everyone, I apologize for my message to the cctbxbb that was meant to go to Pavel. Pressed "reply" on the wrong mail. Please ignore the electronic noise. Lothar

Hi Pavel,

it is not often that I am trying to compile the source but on occasion I want to take advantage of openmp. So I am compiling dev 2303

with

./install --openmp --prefix=/home/local/progs/Phenix/MP --source --without-pymol --nproc=8

But it stops with

Installing lz4_plugin... log file is /home/local/progs/Phenix/MP/phenix-installer-dev-2303-source/base_tmp/lz4_plugin_install_log /bin/sh: git: command not found

Do I have to have git ?

Thanks,

Lothar

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Lothar, Thanks for the question--this is a new issue for us. Today you need git. However, we will fix the dependency on git sometime in the next few days, so if you check back on Tuesday-ish, the source package will no longer use git. Nick Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Fri, Jan 29, 2016 at 4:24 PM, wrote:

Hi Pavel,

it is not often that I am trying to compile the source but on occasion I want to take advantage of openmp. So I am compiling dev 2303

with

./install --openmp --prefix=/home/local/progs/Phenix/MP --source --without-pymol --nproc=8

But it stops with

Installing lz4_plugin... log file is

/home/local/progs/Phenix/MP/phenix-installer-dev-2303-source/base_tmp/lz4_plugin_install_log /bin/sh: git: command not found

Do I have to have git ?

Thanks,

Lothar

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And I forgot to mention that if you don't want either Phenix or CCP4 you can get an open-source restraints library that Phenix uses from SourceForge called GeoStd at svn co https://svn.code.sf.net/p/geostd/code/trunk geostd which will also work with cctbx. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Jan 26, 2016 at 10:16 AM, Paul Adams wrote:

The monomer library is also part of the Phenix distribution.

...

On Jan 26, 2016, at 8:49 AM, Roger Martin wrote:

Hi,

looking at the prebuilts( http://cci.lbl.gov/cctbx_build/dev-565/cctbx-installer-dev-565-intel-linux-2...) for CentOS I see the dependency for mon_lib in verify_mon_lib_data.py. Is mon_lib available stand alone or comes in the full ccp4 package only?

Where do most of you get a copy of mon_lib? _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

-- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --

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