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

[vimal parkash]

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.dewrote:


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] refinement problem

[parkash]

Hi,
 I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when I 
refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high 
B-factors around 70. But if I do TLS refinement, the R-factors lower 
down and B-factors come down to 40.


My question is; Are TLS refined B-factors real?? Can I trust them?
or what else could be done to lower down the B.factors?

BR
vimal