Hi there -
That error is indeed something totally misleading from python.
Somehow, the error messages get hard-coded at compilation time and
list the directories
that compilation took place at (in this case Gerrit's laptop).
We will try and suppress this message since its totally misleading.
The error message is in the parsing of the Refmac log file
(Garib ... we should indeed do the XML one of these days !)
I think we have seen it before, but if you could send us a gzip of
the whole run dir,
or at least the last refmac log file, we will be able to tell you
exactly.
In a similar case, getting the newest refmac5 from York solved the
problem.
Since I can almost guarantee that any such anomalies are genuine bugs
in ARP/wARP 7.0
(and especially in the 'new' flex-warp module) it might be best to
email directly the authors,
so we can deal with it asap ...
(I am on ccp4bb detox, I read it once a day to avoid shouting to too
many people)
Tassos
On Jul 23, 2007, at 16:24, Craig McElroy wrote:
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file
as it is"
option. When I run the program it quits after/during the first
REFMAC cycle
with the following message:
ERROR ('IndexError', ('list index out of range',), [' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CArc.py", line 78, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line 43, in
checkAndProcess\n', ' File
"/Users/gerrit/CProg/ARP_svn/pyWARP/CRefmacController.py", line
107, in
_parse\n'])
----------------------------------------------------------------------
----
ERROR => Ending JOB
----------------------------------------------------------------------
----
I'm relatively sure I have everything installed properly, but it
seems the
program is trying to reference scripts that do not exist (i.e.
there is no
/Users/gerrit on my system and therefore no python scripts in
/Users/gerrit/CProg/ARP_svn/pyWARP/).
Any help that you could provide would
be appreciated. Thanks in advance.
Craig
--
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
