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" <[log in to unmask]>:
> 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 <[log in to unmask]>:
>
>> 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 <[log in to unmask]>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
>>>>
>>>>
>>>>
>>>
>>
>
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