Dear Vimal, Jayashankar, Madravi,
Thanks for your Emails. I don't really know what the problem might be;
perhaps some of you could send me the data and the input parameters so
that I can reproduce the error locally. ARP/wARP is definitely not
resolution-limited (well, within limits of its applicability).
Regarding the practicality, one thing I would suggest you to try with
CCP4i ARP/wARP GUI is to turn Rfree off and let me know if this helps.
Otherwise you should always be able to build the solvent structure
with two alternative ARP/wARP possibilities, which run the same
sequence of the programs anyway:
1. command line script: $warpbin/warp_solvent.sh
2. graphics front end: $warpbin/arpnavigator
I look forward to hearing from you.
With best regards,
Victor
Quoting "vimal parkash" <vimal.park...@helsinki.fi>:
Hi,
I faced the same problem with my 2.8Å structure. But it was
alright with high resolution structure - so I thought the program is
resolution limited.
Regards,
Vimal
Quoting Jayashankar <s.jayashan...@gmail.com>:
Dear Victor,
I faced the same problem and got the same error for arpwarp solvent module,
and I have even communicated you through my system admin for arp warp
classic module
giving some trouble.
sincerely
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Fri, Mar 5, 2010 at 7:40 PM, Victor Lamzin <vic...@embl-hamburg.de>wrote:
Dear Madravi,
Probably the buffer was not flashed out to the log file.
Does the error stay if you run it from the command line,
$warpbin/auto_solvent.sh ?
Best regards,
Victor
Nalam, Madhavi wrote:
Hello:
I am using CCP4i version 6.1.2
I am trying to run the job ARP/wARP solvent building within CCP4. I used
the default values for running the job. The log file after the
run is pasted
below.
I looked in the file (sm14b_unique1_warp_solvent_last.log) for an error
message but the file is empty. Can anyone suggest what/where I should be
looking into?
Thanks,
Madhavi
--------------------
5 ARP refinement cycles will be run in total
Atoms will be removed if below 1.0 sigmas in 2mFoDFc map
Atoms will be added if above 3.4 sigmas in mFoDFc map
Refmac Refinement Parameters:
1 REFMAC cycle(s) in each ARP cycle
Weight for restraints is set to AUTO
Scaling protocol SIMPLE LSSC ANIS
FreeR will be used for monitoring and sigmaa calculations
QUITTING ... ARP/wARP module stopped with an error message:
REFMAC5
*** Look for error message in the file:
sm14b_unique1_warp_solvent_last.log
[1] 6836
#CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 05 Mar 2010 11:00:42
#CCP4I TERMINATION OUTPUT_FILES
/home/nalamm/angie/struc_soln/6_arp_warp_solvent.par angie
#CCP4I MESSAGE Task completed successfully
