Re: [ccp4bb] problem with ARP/wARP module in CCP4

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: crystallization of a macromolecular complex
From: "Murray, Michael (NIH/NIEHS)" murrayms {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2010-03-05

Next message:
Subject: pi-pi R stacking
From: Phoebe Rice price {- at -} UCHICAGO {- dot -} EDU
Date: 2010-03-05

Subject: Re: problem with ARP/wARP module in CCP4
From: Victor Lamzin victor {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2010-03-05

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
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: crystallization of a macromolecular complex
From: "Murray, Michael (NIH/NIEHS)" murrayms {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2010-03-05

Next message:
Subject: pi-pi R stacking
From: Phoebe Rice price {- at -} UCHICAGO {- dot -} EDU
Date: 2010-03-05