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
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
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