Re: [COOT] Coot 0.5.2 and Molprobity problem

2009-01-07 Thread Paul Emsley 

Hi Ben,

Ben Eisenbraun wrote:


I seem to be running into the same problem reported by other people with
Coot showing a blank clashes window.

I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with
probe 2.12 and reduce 3.13.  Probe/reduce seem to run correctly; I get a
coot-molprobity output directory with files and their exit status is 0, but
the dots are never drawn and the Molprobity Probe Clash Gaps window is
blank with just a single OK button.


I am using 2.12.071128 and that works fine on my Ubuntu machine.

On my FC4 machine that causes an immediate crash.  However, 2.12.070727 
doesn't crash but behaves in the same manner as you describe.


look at probe-dots.out.  If you have (something like)
:1-1:wc:A   6 VAL HG13 :A  92 ILE  HA  :
that fails.

If you have
:1-1:wc: A   6 VAL HG13 : A  92 ILE  HA  :
that works.

Or so I think.  If that is not the issue, then I don't know what it is. 
(The format change is to support hybrid_36 pdb files).


An email in a similar thread from Bernhard Lohkamp on 11/18 suggested that 
if the window was blank, the version of probe was too old, but I don't see

a more recent version.


We encouraged them to make a new version for Windows.  It would be nice 
if I could have a version that worked on FC4 too.



Any clues on what I'm doing wrong would be much appreciated.


HTH?

See you soon,

Paul.

Re: [COOT] Coot 0.5.2 and Molprobity problem

2009-01-07 Thread Mark Brooks 
Hi,

The Phenix Molprobity binaries work for me on Coot 0.5 pre1 rev 1563 and 0.5
rev 1444. I can't say for Coot 5.2. I should do an update I guess, but I'm
having a pause after CCP4 6.1, and Phenix 1.4.3.

Updating Phenix also updates molprobity binaries too, which is handy:
(define *probe-command* /usr/local/phenix/phenix-1.4-
3/build/intel-linux-2.6/bin/phenix.probe)
(define *reduce-command*
/usr/local/phenix/phenix-1.4-3/build/intel-linux-2.6/bin/phenix.reduce)

These are the phenix versions, which work for me.
probe.2.12.071128
reduce.3.14.080821

...whereas these don't work and just give the blank windows and no pink
clashes.
probe.2.12.070727
reduce.3.10.080107

so be careful with the minor, minor version numbers!

HTH,

Mark


2009/1/7 Paul Emsley paul.ems...@bioch.ox.ac.uk

 Hi Ben,

 Ben Eisenbraun wrote:

  I seem to be running into the same problem reported by other people with
 Coot showing a blank clashes window.

 I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with
 probe 2.12 and reduce 3.13.  Probe/reduce seem to run correctly; I get a
 coot-molprobity output directory with files and their exit status is 0,
 but
 the dots are never drawn and the Molprobity Probe Clash Gaps window is
 blank with just a single OK button.


 I am using 2.12.071128 and that works fine on my Ubuntu machine.

 On my FC4 machine that causes an immediate crash.  However, 2.12.070727
 doesn't crash but behaves in the same manner as you describe.

 look at probe-dots.out.  If you have (something like)
 :1-1:wc:A   6 VAL HG13 :A  92 ILE  HA  :
 that fails.

 If you have
 :1-1:wc: A   6 VAL HG13 : A  92 ILE  HA  :
 that works.

 Or so I think.  If that is not the issue, then I don't know what it is.
 (The format change is to support hybrid_36 pdb files).

  An email in a similar thread from Bernhard Lohkamp on 11/18 suggested that
 if the window was blank, the version of probe was too old, but I don't see
 a more recent version.


 We encouraged them to make a new version for Windows.  It would be nice if
 I could have a version that worked on FC4 too.

  Any clues on what I'm doing wrong would be much appreciated.


 HTH?

 See you soon,

 Paul.




-- 
Mark Brooks,
IBBMC,
UMR8619 - Bâtiment 430,
Université de Paris-Sud,
91405 Orsay CEDEX.
Tel: 0169157968
Fax: 0169853715
Skype: markabrooks

[COOT] no way to calculate an E map

2009-01-07 Thread Eleanor Dodson 
At present the only way to calculate an E map via  the input option to 
read an MTZ file is to redefine the COLUMN type of E to that of F


Could this be fixed please?
Eleanor

Re: [COOT] no way to calculate an E map

2009-01-07 Thread Paul Emsley 
In message 4964b4e6.4000...@ysbl.york.ac.uk e.dod...@ysbl.york.ac.uk writes:
 At present the only way to calculate an E map via  the input option to 
 read an MTZ file is to redefine the COLUMN type of E to that of F

Bleugh.
 
  Could this be fixed please?

Certainly.

Paul.