buccaneer_pipeline failure (ccp4 6.2.0)

From: Frank von Delft
Date: 17 October 2011 20:30

Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer fails from the GUI.  Below is what shows up if you view the com file before execution; and below that the logfile.

Seems to me it's using the wrong python executable;  the first one on my path is certainly nothing to do with ccp4, so now wonder it can't import. 

Shouldn't python be invoked explicitly with its full path?  Where can I set this?  (Mind you, setting it in the Run&View didn't work.)
Cheers
phx



   
Run&View Com File:
python -u /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin


Logfile
#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT LOG buccaneer_pipeline
#CCP4I DATE 17 Oct 2011  18:45:20
#CCP4I USER loretta
#CCP4I PROJECT PROJECT
#CCP4I JOB_ID 13
#CCP4I SCRATCH /tmp/loretta
#CCP4I HOSTNAME hestia.sgc.ox.ac.uk
#CCP4I PID 13684

***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: python -u /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin
has failed with error message
Traceback (most recent call last):
  File "/usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline", line 3, in <module>
    from CCP4pipeline import Control
ImportError: No module named CCP4pipeline
***************************************************************************

----------
From: Tim Gruene 

Hi Frank,

it may not be the python binary itself but the PYTHONPATH which is
incorrectly set. After initialising ccp4, mine reads
       tg@slartibartfast:~$ echo $PYTHONPATH
       /xtal/Suites/CCP4/ccp4-6.2.0/share/python:
which is modified around line 231 in $CBIN/include/ccp4.setup

My python binary is /usr/bin/python, and I have used buccaneer without
errors.

Tim
> *Run&View Com File: *
> python -u /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin
>
>
> *Logfile*
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen




----------
From: Frank von Delft

Mine reads:
/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python:/usr/local/ccpnmr/ccpnmr1.0/python

That should work, right?  Where else can I look, for the failing import?  This is a lettuce-fresh install, pulled straight off web and installed with all defaults.

Cheers
phx.

----------
From: Tim Gruene


And you do have read access to
/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/CCP4pipeline.py
(on our installation, the mode is actually 755, but I suppose 644 should
be sufficient).
You can set PYTHONVERBOSE to 1 or higher in the shell you start ccp4i
from to see what python is doing ('man python').

Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, DLS, 14-16th March 2012

Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples will be held at the Diamond Light Source, UK from 13:00 March 14th to 13:00 March 16th 2012.

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It will consist of around 30 talks of 20-25 minutes each covering:

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Abstract submission will close on the 1st March.

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Dear PDBe users and depositors,

Due to essential maintenance of the computers in the campus data centre this coming weekend, all web, ftp and e-mail services of the Protein Data Bank in Europe (PDBe; pdbe.org), as well as most other EBI services, will be unavailable from Friday 21 October 11 am BST until Monday 24 October 11 am BST (*). This includes our deposition services for PDB (Autodep) and EMDB (Emdep). However, the other wwPDB and EMDB deposition sites will not be affected, so if you are in a hurry to deposit, please use the deposition services of one of our partners.

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---
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REMINDER : CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC 30th Nov. to 4th Dec.: deadline 21st Oct

CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC

Proposal Deadline 21st October 2011

There will be beam time available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS absorbance or fluorescence spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism:

_http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal _

and it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project.


A brief description of the device is given below however users are encouraged to consult the web pages for detailed information:

_http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide_

The device is also described in: McGeehan, J., Ravelli, R.B., Murray, J.W., Owen, R.L., Cipriani, F., McSweeney, S., Weik, M. and Garman, E.F. (2009) Colouring cryo-cooled crystals: online microspectrophotometry. J Synchrotron Radiat., 16, 163-172.

As this is not a standard set-up, it might take a significant amount of time to train users, align the device, and analyze the data in order to derive relevant data collection schemes. We will therefore schedule 24 hours for each project. The deadline for this specific application is Friday 21st October 2011.

It is strongly recommended to, beforehand, record an absorption (fluorescence) spectrum of the crystal on a home microspectrophotometer such as the 4dx one, or at an off-line facility such as the ESRF Cryobench, and to provide it in the application form. Such a spectrum would greatly help to determine the feasibility of the experiment. For optimal experimental conditions, crystals should be frozen in minimal amounts of cryosolution, especially when the crystals are small. Finally, please note that the ESRF sample changer cannot be operated at the same time as the on-line microspec.
The use of specific LASER is possible if the device is compliant with the beam line safety system (interlock on device power).

++++++++++++
Dates of beam-time: 30th November - 4th December 2011
Storage Ring: 7/8 + 1 (200mA)
Beamline: ID14-1
Energy: 13.27 keV (not tunable)


Specifications:
UV/VIS-range: 250-1100 nm
Light source: Mikropack DH-2000-BAL (Deuterium/Halogen)
Fluorescence/Actinic excitation wavelength: 405, 440, 473, 532, 561, 671 nm
ODmax for UV-vis absorbance spectra: 2-2.5
Monitoring light size: 0.03 (min) - 0.15mm(max)
Sampling freq (to disk): 10Hz or lower

--  

help me after several refmac

From: 王瑞 <wangrui704
Date: 2011/10/13

hello everyone:

    Excuse me, could anyone give me some suggestions? Afetr several cycles of refmac, it give me such a result:               

                                       Initial    Final

                    R factor    0.2540   0.2531

                       R free    0.3499   0.3500

     Rms BondLength    0.0151   0.0151

      Rms BondAngle    2.0266   2.0393

     Rms ChirVolume    0.1179   0.1188

 In fact, I have tried model building & continue refmac, but the R free is still above 0.34. The resolution is  43.728 to  2.088Å and space group is C 2 2 21 . What I should to do? 

Thanks

----------
From: Roger Rowlett
Possibility of twinning? A simple way to check this at this point is to turn on the twin option in refmac and examine the log file. Twinning can cause you to get stuck at high R values in unaccounted for.
Roger Rowlett

----------
From: Tim Gruene

Dear ,

- - how complete is your model compared to the sequence expected in the
crystal? If it is not very complete, yet, your R-values might diverge

- - Your RMS BondAngle is pretty high. Set the matrix weight manually to a
lower number (0.1 or less) until the BondAngle is around 1.6

- - try arp/warp or any other autobuilding tool. If your data are fine,
they should produce a decent model.

Having said that you might also go back and check your data processing:
did you cut the resolution appropriately? Otherwise you may include a
lot a noise during refinement which will destabilise the refinement.

Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen





----------
From: Eleanor Dodson

 In fact, I have tried model building&  continue refmac, but the R free is

Hard to say without seeing your map, model is probably correct.. Have you built waters? Are there errors? How good is your data?

 Eleanor

----------
From: Yuri Pompeu
Echoing whats been said:
1- Are you sure your crystal really is in C 2 2 21? If so How good is your data (completeness, Rmerge, etc...)
2-Could have twinning? I recently just got done working on a structure that could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 twin.
(of course in monoclinic there are certain conditions for twinning...)
3- How good is your model, is it complete, all the waters? Missing protein or DNA?
 HTH

Yuri

----------
From: Pete Meyer
Similar to Tim's suggestion, but your low resolution limit may be too low (check refmac's chart of R vs resolution to confirm this).

Pete

----------
From: Xiaopeng Hu
Dear Yuri,
Could you give out the details? Such as how you found the twins?

Xiaopeng

----------
From: 王瑞 <wangrui704

After L-test,the result are follows:

TWINNING ANALYSIS:

First principles calculation of potential twinning operators using code by Andrey Lebedev:

First principles calculation has found 0 potential twinning operators

No twinning detected

<!--SUMMARY_END--></FONT></B>

$TABLE: L test for twinning:

$GRAPHS: cumulative distribution function for |L|:0|1x0|1:1,2,3,4:

$$ |L| Observed Expected_untwinned Expected_twinned $$

$$

0.000000 0.000000 0.000000 0.000000

0.050000 0.054127 0.050000 0.074938

0.100000 0.101795 0.100000 0.149500

0.150000 0.148706 0.150000 0.223312

0.200000 0.196638 0.200000 0.296000

0.250000 0.244675 0.250000 0.367188

0.300000 0.293074 0.300000 0.436500

0.350000 0.342463 0.350000 0.503563

0.400000 0.390543 0.400000 0.568000

0.450000 0.440510 0.450000 0.629437

0.500000 0.489954 0.500000 0.687500

0.550000 0.541145 0.550000 0.741812

0.600000 0.592157 0.600000 0.792000

0.650000 0.643445 0.650000 0.837688

0.700000 0.695155 0.700000 0.878500

0.750000 0.747505 0.750000 0.914062

0.800000 0.802393 0.800000 0.944000

0.850000 0.856546 0.850000 0.967938

0.900000 0.909764 0.900000 0.985500

0.950000 0.961975 0.950000 0.996313

1.000000 1.000000 1.000000 1.000000

$$

在 2011年10月13日 下午11:42，Xiaopeng Hu

----------
From: Eleanor Dodson
This Ltest certainly doesnt look twinned.

But your R factors are indictive of "mostly correct but still problems".

Didnt someone suggest running Arp-Warp to rebuild the structure?
This might reinterpret any dodgy bits.

Eleanor

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