There seem to be a couple of issues, but I'm working to narrow them down. These may be in part due to ways our computing people have messed with the bat files to avoid CCP4 clashing with other software (notably OLEX).
The refmac from console problem I haven't completely isolated, but it may be that refmac is manipulating file paths assuming slash rather than backslash somewhere. I can patch this by setting CLIBD_MON to something ending in a slash (not sure if backslash works or not). I'll experiment further. The second problem is running refmac from within WinCoot. This may be a local foulup, but I think Stuart had a similar problem in his test machine. Again, more work needed. On Thu, 14 Feb 2019 at 10:03, Charles Ballard - UKRI STFC < charles.ball...@stfc.ac.uk> wrote: > Hi Kevin > > just checked and refmac runs happy for me from the CCP4Console. > Differences are that mine is in the default location, and that machine has > not had an earlier version of ccp4 installed. > > Can you check "set" to see what is set in the environment. > > Charles > > On 13 Feb 2019, at 11:29, Kevin Cowtan wrote: > > Hi! Can anyone run refmac from the WINDOWS command prompt? > > I've been experimenting with various combinations of environment > variables, but I always get an error. The one instance of this error on > google is an unanswered CCP4BB question. > > Dictionary path has not been defined > Check the environment variable CLIBD_MON > Current value of CLIBD_MON is C:\Apps\CCP4-7\7.0\lib\data\monomers > It should be set to wherever_dict/dic/ > ===> Error: Wrong path for the dictionary files > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > Refmac: Wrong path for the dictionary files > Refmac: Wrong path for the dictionary files > > The directory C:\Apps\CCP4-7\7.0\lib\data\monomers contains the following: > > Directory of C:\Apps\CCP4-7\7.0\lib\data\monomers > > 12/02/2019 15:42 <DIR> . > 12/02/2019 15:42 <DIR> .. > 12/02/2019 15:38 <DIR> 0 > 12/02/2019 15:39 <DIR> 1 > 12/02/2019 15:39 <DIR> 2 > 12/02/2019 15:39 <DIR> 3 > 12/02/2019 15:39 <DIR> 4 > 12/02/2019 15:39 <DIR> 5 > 12/02/2019 15:39 <DIR> 6 > 12/02/2019 15:39 <DIR> 7 > 12/02/2019 15:40 <DIR> 8 > 12/02/2019 15:40 <DIR> 9 > 12/02/2019 15:40 <DIR> a > 12/02/2019 15:40 <DIR> b > 12/02/2019 15:40 <DIR> c > 28/11/2016 21:43 7,640 COPYING > 12/02/2019 15:40 <DIR> d > 28/11/2016 21:43 3,553 dnarna_basepairs.txt > 28/11/2016 21:43 3,553 dnarna_basepairs_2.txt > 28/11/2016 21:43 5,248 dnarna_params.txt > 12/02/2019 15:40 <DIR> e > 27/04/2018 10:59 105,193 ener_lib.cif > 28/11/2016 23:06 105,136 ener_one_lib.cif > 12/02/2019 15:40 <DIR> f > 12/02/2019 15:40 <DIR> g > 12/02/2019 15:41 <DIR> h > 12/02/2019 15:41 <DIR> i > 12/02/2019 15:41 <DIR> j > 12/02/2019 15:41 <DIR> k > 12/02/2019 15:41 <DIR> l > 12/02/2019 15:41 <DIR> list > 12/02/2019 15:41 <DIR> m > 28/11/2016 21:43 1,372,146 mon_lib_ind.cif > 28/11/2016 21:43 6,490,087 mon_lib_ind2.cif > 28/11/2016 23:06 120 mon_lib_one_ind.cif > 28/11/2016 23:06 396 mon_lib_one_ind2.cif > 12/02/2019 15:41 <DIR> n > 31/08/2018 15:52 35,312 new_entries.txt > 31/08/2018 15:52 23,685 not_replaced_entries.txt > 12/02/2019 15:41 <DIR> o > 12/02/2019 15:41 <DIR> p > 28/11/2016 21:43 2,490,954 pdb_alt_names.txt > 28/11/2016 21:43 7,794 pdb_v2to3.py > 12/02/2019 15:41 <DIR> q > 12/02/2019 15:41 <DIR> r > 31/08/2018 15:52 29,731 replaced_entries.txt > 31/08/2018 15:52 754 revert_list.txt > 12/02/2019 15:41 <DIR> s > 12/02/2019 15:42 <DIR> t > 28/11/2016 21:43 557 template_link.pdb > 12/02/2019 15:42 <DIR> u > 12/02/2019 15:42 <DIR> v > 12/02/2019 15:42 <DIR> w > 31/08/2018 15:52 24 windows_reserved_words.txt > 12/02/2019 15:42 <DIR> x > 12/02/2019 15:42 <DIR> y > 12/02/2019 15:42 <DIR> z > -- > Professor Kevin Cowtan > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, York, YO10 5DD, UK > https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/ > > EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- Professor Kevin Cowtan York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, York, YO10 5DD, UK https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/ EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
