Monday, 7 November 2011

WaterTidy fails in windows ccp4i

From: Jacob Keller

Dear CCP4ers,

I am trying to run watertidy from the windows gui to add waters, but
get the error message below. Since the gui is so short, I don't think
I am missing anything, so what I am doing wrong? Is there an
alternative water-picker in the gui? I used to use watpick, but I
believe that was in XPLOR...

Jacob


#CCP4I VERSION CCP4Interface 2.1.0#CCP4I SCRIPT LOG watertidy#CCP4I
DATE 19 Oct 2011  12:30:14#CCP4I USER 'UNKNOWN'#CCP4I PROJECT
Tues2bot#CCP4I JOB_ID 18#CCP4I SCRATCH C:/Ccp4Temp#CCP4I HOSTNAME
chloe#CCP4I PID 9820
<html> <!-- CCP4 HTML LOGFILE --><hr><pre>
###############################################################
###############################################################
############################################################### ###
CCP4 6.2: DISTANG                  version 6.2 : 02/04/08##
############################################################### User:
Jacob  Run date: 19/10/2011 Run time: 12:30:15

 Please reference: Collaborative Computational Project, Number 4.
1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta
Cryst. D50, 760-763. as well as any specific reference in the program
write-up.

  Logical name: XYZIN  File name:
C:/Users/Jacob/Desktop/Dallos_Lab/3MGL_Crystals/APS_10_10_2011/jacob/2botnr3/TuesProcessing/Tues2bot_4.1_buccaneer2_refmac1.pdb
 PDB file is being opened on unit 1 for INPUT.
  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE

             RF                                  RO
    0.012  -0.000  -0.000  -0.000       82.115   0.000   0.000  -0.000
  -0.000   0.012  -0.000   0.000        0.000  82.115   0.000   0.000
  0.000  -0.000   0.006  -0.000        0.000   0.000 159.320  -0.000
-0.000   0.000  -0.000   1.000       -0.000   0.000  -0.000   1.000
 ARSE  after CALL       RBSPGRP(SPGRP)P 43 21 2   Data line--- title
[No title given] Data line--- distance     vdw     intra Data line---
symmetry P43212
 Spacegroup information obtained from library file:  Logical Name:
SYMINFO   Filename: C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib
 Data line--- radii     CA 1.5     C 1.5     N 1.5     O 1.5     SG
1.5     OW 1.5 Data line--- from     atom 1 to 200000 Data line--- to
   atom  to  DISTANG:   *** Two  limits required***Times: User:
0.0s System:    0.0s Elapsed:     0:00
</pre></html>****************************************************************************
Information from CCP4Interface
script***************************************************************************The
program run with command: distang XYZIN
"C:/Users/Jacob/Desktop/Dallos_Lab/3MGL_Crystals/APS_10_10_2011/jacob/2botnr3/TuesProcessing/Tues2bot_4.1_buccaneer2_refmac1.pdb"
DISTOUT "C:/Ccp4Temp/Tues2bot_18_1_log_1.tmp" has failed with error
message DISTANG:   *** Two  limits
required******************************************************************************

#CCP4I TERMINATION STATUS 0 " DISTANG:   *** Two  limits
required***"#CCP4I TERMINATION TIME 19 Oct 2011  12:30:15#CCP4I
MESSAGE Task failed


--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
*******************************************

----------
From: Ed Pozharski


watertidy is not a water-picker

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

----------
From: Jacob Keller


Well, I see that it fixes/edits waters, but it seems to add them too,
according to the documentation

"Add/Tidy Waters - Watertidy

This task rationalises waters at the end of refinement.

See program documentation: Watertidy, Distang."

Is there a program in the gui that adds waters, if not this one? There
is of course arp/warp, but not in windows...

Jacob

----------
From: Ed Pozharski


Not sure where you quoting this from.  I am looking at the official
documentation here

http://www.ccp4.ac.uk/html/watertidy.html

which clearly states

This program has two purposes.

    1. It moves the H2O coordinates to the symmetry related position
       nearest to the host molecule.
    2. It attempts to design an H2O naming system which gives some
       information about the residue which a particular H2O is hydrogen
       bonded to. The user inputs chain IDs for host chains and assigns
       an output ID for the H2Os bonded to this chain.
There is an option in refmac gui to use coot to add waters.  If you
don't want to do extra refinement, just set the number of steps to 0.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

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

Hi Jacob,

to semi-answer your question: coot runs under windows, as far as I know,
but it may not be in the gui.

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


----------
From: Bernhard C. Lohkamp <bernhard@chem.gla.ac.uk>
Date: 20 October 2011 08:17
To: CCP4BB@jiscmail.ac.uk


Adding to Tim's comment. In Coot use:

Extensions->Modelling->"Arrange Waters Around Protein..."

B



No comments:

Post a Comment