[sharp-discuss] re: the problem with density modification

Tue, 29 Apr 2003 01:38:50 +0800

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Hello:
I have installed the Sharp in SGI IRIX64. But I was facing the problem =
while  running the density modification.

The problem is as follows:

#

# using binary dm

# arguments =3D hklin eden-unique.mtz=20

# hklout solo_57.0pc/t_dm_1.mtz=20

#

dm: Error in label assignments

dm 2.1

------

1###############################################################

###############################################################

###############################################################

### CCP4 4.2: dm version 4.2 : 26/11/98##

###############################################################

User: Run date: 5/ 1/03 Run time: 2:22:00

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.

<a href=3D"http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html">dm =
reference:</a>

<blockquote>

K. Cowtan (1994),

dm: An automated procedure for phase improvement by density =
modification.

Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, =
p34-38.

</blockquote><p>

Contents

--------

Command input

Comments

MTZ input

Data Checking

Data Scaling

Solvent Mask

First Cycle

Output

Command Input

-------------

Data line--- SOLCONT 0.5700 MEAN 0.32 0.43

Data line--- SOLMASK FRAC 0.5700 0.43

Data line--- MODE SOLV HIST

Data line--- COMBINE PERT REST 0.1

Data line--- RESOLUTI30.000 2.25

Data line--- NCYCLE AUTO

Data line--- SCHEME ALL

Data line--- LABIN FP=3DFP SIGFP=3DSIGFP PHIO=3DPHIB FOMO=3DFOM =
HLA=3DHLA HLB=3DHLB HLC=3DHLC HLD=3DHLD FOMDM=3DFOM PHIDM=3DPHIB

Data line--- LABOUT FDM=3DFDM FOMDM=3DFOMDM PHIDM=3DPHIDM HLADM=3DHLADM =
HLBDM=3DHLBDM HLCDM=3DHLCDM HLDDM=3DHLDDM

Comments

--------

Density modifications selected:<ul>

<li> Solvent flattening

<li> Histogram matching

</ul>

<h3>Number of cycles</h3>

You have chosen NCYCLE AUTO. This is a cautious mode which

runs few cycles of density modification and terminates at

the first indication of phase bias and FOM overestimation.

This is a good choice when you have weak data and no

averaging. However you must use SCHEME ALL (selected by

default).<p>

<h3>OK, continuing</h3></b>

MTZ Input

---------

(Q)QOPEN: file opened on unit 1 Status: READONLY

Logical Name: HKLIN Filename: eden-unique.mtz

HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1

* Title:

..

* Number of Columns =3D 6

* Number of Reflections =3D 28875

* Missing value set to NaN in input mtz file

* Column Labels :

H K L FUNI SIGFUNI FreeR_flag

* Column Types :

H H H F Q I

* Cell Dimensions :

83.7910 83.7910 165.9430 90.0000 90.0000 90.0000

* Resolution Range :

0.00018 0.19752 ( 74.536 - 2.250 A )

* Sort Order :

1 2 3 0 0

* Space group =3D P43212 (number 96)

*** Warning

>From LRASSN : User input label FP does not match any file label

*** Warning

>From LRASSN : User input label SIGFP does not match any file label

*** Warning

>From LRASSN : User input label PHIB does not match any file label

*** Warning

>From LRASSN : User input label FOM does not match any file label

*** Warning

>From LRASSN : User input label HLA does not match any file label

*** Warning

>From LRASSN : User input label HLB does not match any file label

*** Warning

>From LRASSN : User input label HLC does not match any file label

*** Warning

>From LRASSN : User input label HLD does not match any file label

*** Warning

>From LRASSN : User input label PHIB does not match any file label

*** Warning

>From LRASSN : User input label FOM does not match any file label

dm: Error in label assignments

Times: User: 0.0s System: 0.0s Elapsed: 0:00

Thank you,

with regards,

kumar Sundramurthy

Institute of Molecular and Cell Biology

#1, Research Link,

The National University Singapore=20

Singapore 117604

Phone : (65) 68727572

e-mail: kumar@imcb.nus.edu.sg

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<DIV>
<DIV>Hello:</DIV>
<DIV>I have installed the Sharp in SGI =
IRIX64. But I was=20
facing the problem while&nbsp; =
running the=20
density modification.</DIV>
<DIV>&nbsp;</DIV>
<DIV>
The problem is as follows:
#
# using binary dm
# arguments =3D hklin eden-unique.mtz 
# hklout solo_57.0pc/t_dm_1.mtz 
#
dm: Error in label assignments
&nbsp;
dm 2.1
------
&nbsp;
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: dm version 4.2 : 26/11/98##
###############################################################
User: Run date: 5/ 1/03 Run time: 2:22:00
&nbsp;
Please reference: Collaborative Computational Project, Number 4. =
1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. =
D50,=20
760-763.
as well as any specific reference in the program write-up.
&nbsp;
&nbsp;
&lt;a =
href=3D"http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html"&gt;dm=20
reference:&lt;/a&gt;
&lt;blockquote&gt;
K. Cowtan (1994),
dm: An automated procedure for phase improvement by density =
modification.
Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31,=20
p34-38.
&lt;/blockquote&gt;&lt;p&gt;
&nbsp;
&nbsp;
Contents
--------
Command input
Comments
MTZ input
Data Checking
Data Scaling
Solvent Mask
First Cycle
Output
&nbsp;
Command Input
-------------
Data line--- SOLCONT 0.5700 MEAN 0.32 0.43
Data line--- SOLMASK FRAC 0.5700 0.43
Data line--- MODE SOLV HIST
Data line--- COMBINE PERT REST 0.1
Data line--- RESOLUTI30.000 2.25
Data line--- NCYCLE AUTO
Data line--- SCHEME ALL
Data line--- LABIN FP=3DFP SIGFP=3DSIGFP PHIO=3DPHIB FOMO=3DFOM =
HLA=3DHLA HLB=3DHLB=20
HLC=3DHLC HLD=3DHLD FOMDM=3DFOM PHIDM=3DPHIB
Data line--- LABOUT FDM=3DFDM FOMDM=3DFOMDM PHIDM=3DPHIDM =
HLADM=3DHLADM HLBDM=3DHLBDM=20
HLCDM=3DHLCDM HLDDM=3DHLDDM
&nbsp;
Comments
--------
Density modifications selected:&lt;ul&gt;
&lt;li&gt; Solvent flattening
&lt;li&gt; Histogram matching
&lt;/ul&gt;
&lt;h3&gt;Number of cycles&lt;/h3&gt;
You have chosen NCYCLE AUTO. This is a cautious mode which
runs few cycles of density modification and terminates at
the first indication of phase bias and FOM overestimation.
This is a good choice when you have weak data and no
averaging. However you must use SCHEME ALL (selected by
default).&lt;p&gt;
&nbsp;
&lt;h3&gt;OK, continuing&lt;/h3&gt;&lt;/b&gt;
&nbsp;
MTZ Input
---------
&nbsp;
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: eden-unique.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1

* Title:

..

* Number of Columns =3D 6

* Number of Reflections =3D 28875

* Missing value set to NaN in input mtz file

* Column Labels :

H K L FUNI SIGFUNI FreeR_flag

* Column Types :

H H H F Q I

* Cell Dimensions :

83.7910 83.7910 165.9430 90.0000 90.0000 90.0000

* Resolution Range :

0.00018 0.19752 ( 74.536 - 2.250 A )

* Sort Order :

1 2 3 0 0

* Space group =3D P43212 (number 96)


*** Warning
From LRASSN : User input label FP does not match any file label


*** Warning
From LRASSN : User input label SIGFP does not match any file =
label


*** Warning
From LRASSN : User input label PHIB does not match any file label


*** Warning
From LRASSN : User input label FOM does not match any file label


*** Warning
From LRASSN : User input label HLA does not match any file label


*** Warning
From LRASSN : User input label HLB does not match any file label


*** Warning
From LRASSN : User input label HLC does not match any file label


*** Warning
From LRASSN : User input label HLD does not match any file label


*** Warning
From LRASSN : User input label PHIB does not match any file label


*** Warning
From LRASSN : User input label FOM does not match any file label

dm: Error in label assignments
Times: User: 0.0s System: 0.0s Elapsed: 0:00
&nbsp;
Thank you,
with regards,
&nbsp;
kumar Sundramurthy
Institute of Molecular and Cell Biology
#1, Research Link,
The National University Singapore 
Singapore 117604
Phone : (65) 68727572
e-mail: <A =
href=3D"mailto:kumar@imcb.nus.edu.sg">kumar@imcb.nus.edu.sg</A>
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