[ccp4bb] rotating a map

[Kianoush Sadre-Bazzaz]

Dear CCP4 community,

I am trying to rotate a map from one particular crystal form (spacegroup #19) 
into another (#4). Ultimately I like to compare two maps superimposed. 

I tried using the "Edit/Rotate Maps & Masks" and it's really close to doing it, 
but it's not right. I computed NCS operators from one crystal form into another 
(and vice versa) and both times the maps are shifted. Any help is appreciated.

Thanks in advance,
Kianoush

   
-
Choose the right car based on your needs.  Check out Yahoo! Autos new Car 
Finder tool.

[ccp4bb] Daresbury SRS 10.1

[Moody, Dr P.C.E.]

There has been some doubt about the availability of 10.1 in 2008.  
 
Users of SRS will be relieved to know that station 10.1 should be operating to 
the end of 2008, when the SRS closes, and Tracy Turner (Associate Director 
,SRD) has told me that  PX users will be able to apply for time in AP50 
(April-December 2008).
 
 
Peter Moody
Henry Wellcome Laboratories of Structural Biology
Department of Biochemistry
Henry Wellcome Building
University of Leicester
LE1 9HN
0116 229 7097

Re: [ccp4bb] Twinning in C2 ?

[Eleanor Dodson]

Oh dear - this is tricky!
You could have a dimer in the asymmetric unit, or two monomers in the 
asymm unit which generate dimers using the crystallographic 2 folds.


Things worth checking -
What does the self rotation show? Is there a clear 2 fold axis which is 
different from the crystallographic one?
If so you can use all of MOLREPs cleverness to use the self rotation 
definition and the pseudo translation.
(Under search parameters you can give the self rotation list of 
solutions - just use self rotation with 1 or 2 solutions and edit out 
the top one which will be the crystallographic 2 fold)


It will find the pseudo trans vector automatically.

If the only 2 fold is the cryst one then you need to search for 2 
molecules with the pseudo translation.


Eleanor

What is the solvent content of the native - the mutant has a smaller 
volume so less solvent - is that feasible?





I think I would generate P1 data Demetres D. Leonidas wrote:

Dear Eleanor,

Yes the native is a dimer and we did the search using the dimer as a 
model but we had similar results (i.e. all programs find one 
molecule). The graphs from TRUNCATE show rather "normal" and I am 
attaching a gif file with the plot for the cumulative intensity.


As for pseudo-translation running the "Analyse Data for MR" option in 
ccp4 in the patterson map we are getting a significant peak at 
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we 
need to apply this pseudo translation to the solution we are getting 
from molrep ?


many thanks

Demetres

P.S. I will summarize for the members of the list all the suggestions 
I will get at the end



Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer - 
if so I would search with that (you may need to turn off the packing 
search)


Or whether there is a pseudo translation vector in the mutant form..

Or what the data analysis graphs from TRUNCATE show - are they "normal"?

Eleanor

Demetres D. Leonidas wrote:

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native 
(C2) but the unit cell dimensions are different. These for the 
native structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 
160.4 32.3 107.0 90 125.7 90. As a result the mutant structure has  
four molecules in the asymmetric unit while the native had two. When 
we run molecular replacement all programs (CNS, molrep, and amore) 
find only two molecules. Phaser finds four but when we try to refine 
the Rfree does not drop below 0.44 if we use four molecules and 0.53 
if we only use two no matter how well we built the molecule and 
regardless of any addition of water molecules (the resolution of the 
data is 2.1). The interesting thing is that in the electron density 
map we can clearly see density for a substrate analog that was 
included in the crystallization media. Do you thing  that we have a 
case of twinning here ? We have to mention that Tod Yates served did 
not indicate any perfect merohedral twinning (partial merohedral 
twinning for this space group is not possible).


We would appreciate any comments

Many thanks

Demetres

Re: [ccp4bb] Twinning in C2 ?

[Peter Zwart]

Hi Demetres,

not sure if this is going to be usefull, but here I go.

Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.


There is no obvious 'perfect' relation between two unit cells. The
ratio between the two unit cell volumes is about 1.8 and a sublattice
of your native cell that comes close to the lattice of your mutant
does exist. iotbx.explore_metric_symmetry tries to find you  possible
relations. It uses niggli settings though and the output is not very
user (or even developer) friendly:

--
Mutant niggli cell :  32.3  81.8  90.1  76.8  79.7  78.6
Native niggli cell :   33.1  53.2  73.4  90.3  90.0 108.1

   /   100  \
matrix :  M =  |   021  |
   \   001  /

(matrix M acts on the real space basis vectors of the Native niggli cell)

Additional Niggli transform:  x-y,-y-z,y
Additional similarity transform:  x,y,z
Resulting unit cell :   33.1  90.5  90.9  67.8  79.5  79.5
Deviations :-2.5 -10.6  -0.8   8.9   0.2  -0.8
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.
--

Details of what the matrix M means is found in
http://www.ccp4.ac.uk/newsletters/newsletter44/articles/explore_metric_symmetry.html


It is too early for me to understand if the pseudo translation you see
at (1/2,0,1/2) is related to the transfomration shown above, but if
you multiply this translation in C2, you do end up with a smaller unit
cell. why don't you try this:

run xtriage (a latest version) on your mutant data and see what the
patterson analyses tells you what it thinks the unit cell is if the
patterson peak were a true crystallographic operator.
Take that unit cell and compare it to your native
(iotbx.explore_metric_symmetry might be usefull).

Again, I am not sure that a relation is there, but if it is real, you
can get the coordinates for your mutant structure almost directly from
your native structure.

The relations one sees can be deceiving though, it could be
crystallographic numerology.

Cheers

Peter








2007/7/13, Demetres D. Leonidas <[EMAIL PROTECTED]>:

Dear all,

we have encountered a problem in solving one mutant structure. The
mutant protein crystallizes in the same space group as the native (C2)
but the unit cell dimensions are different. These for the native
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3
107.0 90 125.7 90. As a result the mutant structure has  four molecules
in the asymmetric unit while the native had two. When we run molecular
replacement all programs (CNS, molrep, and amore) find only two
molecules. Phaser finds four but when we try to refine the Rfree does
not drop below 0.44 if we use four molecules and 0.53 if we only use two
no matter how well we built the molecule and regardless of any addition
of water molecules (the resolution of the data is 2.1). The interesting
thing is that in the electron density map we can clearly see density for
a substrate analog that was included in the crystallization media. Do
you thing  that we have a case of twinning here ? We have to mention
that Tod Yates served did not indicate any perfect merohedral twinning
(partial merohedral twinning for this space group is not possible).

We would appreciate any comments

Many thanks

Demetres

--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
 +30 210 7273895 (lab)
Fax. +30 210 7273831
E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

Re: [ccp4bb] Missing scatter deffinition in CNS

[Phil Jeffrey]

According to the error message your offending atom has a type:
chemical=FPAF

scatter.lib assigns scattering factors based on chemical type, and there 
are ones for "F" and "F-1" but of course not "FPAF" - this would likely 
be the source of your problem.  The quick fix is to make your own copy 
of scatter.lib and edit the files that reference it to pick up the local 
copy.


Phil Jeffrey
Princeton



Jian Wu wrote:

Dear all,
I am refining a structure in which there is an fluorine atom in the 
inhibtor. When I go on the energy minimization in CNS, an unusual error 
happened to this atom:


 Program version= 1.1 File version= 1.1
 CONNECt: selected atoms form  9 covalently disconnected set(s)

 list of isolated (non-covalently bonded) atoms:
 --none--

 list of isolated (non-covalently bonded) di-atomic molecules:
 --none--
 %XRASSOC-ERR: missing SCATter definition for ( $RX4  300  FAF  ) 
chemical=FPAF

 %XRASSOC error encountered: missing SCATter definition for SELEcted atoms.
   (CNS is in mode: SET ABORT=NORMal END)
 *
 ABORT mode will terminate program execution.
 *
 Program will stop immediately.
 
I have check the topology file, the paramter file, and the scatter.lib 
file, but found nothing is unusual in these files. Had anyone ever 
encountered this problem before?

Any suggestion would be welcome and thank you in advance!
Best Regards,
Jian Wu

--
Jian Wu

Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)
Tel: 0086-21-54921117
Email: [EMAIL PROTECTED] 

Re: [ccp4bb] Twinning in C2 ?

[Demetres D. Leonidas]

Dear Eleanor,

Yes the native is a dimer and we did the search using the dimer as a 
model but we had similar results (i.e. all programs find one molecule). 
The graphs from TRUNCATE show rather "normal" and I am attaching a gif 
file with the plot for the cumulative intensity.


As for pseudo-translation running the "Analyse Data for MR" option in 
ccp4 in the patterson map we are getting a significant peak at 
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we need 
to apply this pseudo translation to the solution we are getting from 
molrep ?


many thanks

Demetres

P.S. I will summarize for the members of the list all the suggestions I 
will get at the end



Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer - 
if so I would search with that (you may need to turn off the packing 
search)


Or whether there is a pseudo translation vector in the mutant form..

Or what the data analysis graphs from TRUNCATE show - are they "normal"?

Eleanor

Demetres D. Leonidas wrote:

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native 
(C2) but the unit cell dimensions are different. These for the native 
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 
32.3 107.0 90 125.7 90. As a result the mutant structure has  four 
molecules in the asymmetric unit while the native had two. When we 
run molecular replacement all programs (CNS, molrep, and amore) find 
only two molecules. Phaser finds four but when we try to refine the 
Rfree does not drop below 0.44 if we use four molecules and 0.53 if 
we only use two no matter how well we built the molecule and 
regardless of any addition of water molecules (the resolution of the 
data is 2.1). The interesting thing is that in the electron density 
map we can clearly see density for a substrate analog that was 
included in the crystallization media. Do you thing  that we have a 
case of twinning here ? We have to mention that Tod Yates served did 
not indicate any perfect merohedral twinning (partial merohedral 
twinning for this space group is not possible).


We would appreciate any comments

Many thanks

Demetres






--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

<>

Re: [ccp4bb] Twinning in C2 ?

[Eleanor Dodson]

You dont say whether the molecules in the native cell form a dimer - if 
so I would search with that (you may need to turn off the packing search)


Or whether there is a pseudo translation vector in the mutant form..

Or what the data analysis graphs from TRUNCATE show - are they "normal"?

Eleanor

Demetres D. Leonidas wrote:

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native (C2) 
but the unit cell dimensions are different. These for the native 
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3 
107.0 90 125.7 90. As a result the mutant structure has  four 
molecules in the asymmetric unit while the native had two. When we run 
molecular replacement all programs (CNS, molrep, and amore) find only 
two molecules. Phaser finds four but when we try to refine the Rfree 
does not drop below 0.44 if we use four molecules and 0.53 if we only 
use two no matter how well we built the molecule and regardless of any 
addition of water molecules (the resolution of the data is 2.1). The 
interesting thing is that in the electron density map we can clearly 
see density for a substrate analog that was included in the 
crystallization media. Do you thing  that we have a case of twinning 
here ? We have to mention that Tod Yates served did not indicate any 
perfect merohedral twinning (partial merohedral twinning for this 
space group is not possible).


We would appreciate any comments

Many thanks

Demetres

[ccp4bb] Missing scatter deffinition in CNS

[Jian Wu]

Dear all,
I am refining a structure in which there is an fluorine atom in the
inhibtor. When I go on the energy minimization in CNS, an unusual error
happened to this atom:

Program version= 1.1 File version= 1.1
CONNECt: selected atoms form  9 covalently disconnected set(s)

list of isolated (non-covalently bonded) atoms:
--none--
list of isolated (non-covalently bonded) di-atomic molecules:
--none--
%XRASSOC-ERR: missing SCATter definition for ( $RX4  300  FAF  )
chemical=FPAF
%XRASSOC error encountered: missing SCATter definition for SELEcted atoms.
  (CNS is in mode: SET ABORT=NORMal END)
*
ABORT mode will terminate program execution.
*
Program will stop immediately.

I have check the topology file, the paramter file, and the scatter.lib file,
but found nothing is unusual in these files. Had anyone ever encountered
this problem before?
Any suggestion would be welcome and thank you in advance!
Best Regards,
Jian Wu

--
Jian Wu

Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)
Tel: 0086-21-54921117
Email: [EMAIL PROTECTED]

Re: [ccp4bb] Asking help about refmac5?

[Eleanor Dodson]

Some answers:
Re FreeR increasing?
1) Have you been careful to keep the same FreeR set for the REFMAC and
CNS refinements?
I suspect not and that explains why your first FreeR is unrealistically
low, and then increases to a more realistic value.

If you use the GUI and select "Create mtz file" from the Reflection
Utilities you can ask to import a CNS and preserve the FreeR flags.

An easier way is to use this new program from

Kevin Cowtan:
He says in an earlier email
Here's an updated version of cns2mtz. The new version automatically
merges anomalous data, generates a full set of CCP4-style free sets from
the CNS test column, completes the data (unless you tell it not to), and
can take the cell and spacegroup information from a pdb file as well as
from the command line.

It converts every file I have automatically, but I haven't tested the
output extensively. More testing would be good. Mail me with any problems.

x86 Linux binary available from here:
http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html

Q2) Then re TLS - you must select and define your own TLS groups
Ethan Merritt has a informative paper about how to do this, and a server
which make suggestions:

Email from Ethan:

On Thursday 21 December 2006 10:39, U Sam wrote:

> > I would like to know
> > (a) how TLS parameters are calculated.
>   

Willis, B. T. M. & Pryor, A. W. (1975). 
Thermal Vibrations in Crystallography. 
Cambridge University Press.

Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). 
Use of TLS parameters to model anisotropic displacements in 
macromolecular refinement
Acta Cryst. D57, 122�C133.

J Painter & E A Merritt (2006)  Acta Cryst. D62, 439-450
Optimal description of a protein structure in terms of multiple groups 
undergoing TLS motion



Q3) I distrust the stt - R and Rfree should differ by < 3% - this depends on 
the data you are using as well as the quality of your model..

If you have very high resolution that is likely.
If you have NCS you may achieve it but it is somewhat unrealistic
If you have 2.6A data you would expect a greater difference..
and so on..


Eleanor





zhongzhou chen wrote:
> Dear Sir or madam,
>
>  I have some questions about refmac5.
>
>  I am new to Refmac. I optimized the structure with CNS (Rwork: 23%, Rfree: 
> 25%).
>
> Cell :71.48071.480   151.81390.00090.00090.000
> Space group p43212
> resolution 100 1.97
>
> protein contain 350 amino acids.
> Nmol/asym: 1
>
> number of amino acids built: 330
> number of  waters:330
> three glycerols 
> six sulfate ions.
>
>
>
> My friends told me that refmac5 will get lower Rfree and Rfactor.
>  
>  I refined the pdb structure from CNS using restrained refinement.
>
>   Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
> $$
>
> using TLS:
>  0   0.215   0.2210.763  165320.60.0061.2500.092
>  1   0.189   0.2300.751  162623.70.0221.6800.116
>  2   0.187   0.2330.751  162500.20.0221.7240.119
>  3   0.185   0.2390.747  162269.00.0221.7900.123
>  4   0.185   0.2410.748  162314.80.0221.8090.124
>  5   0.185   0.2440.744  162248.10.0231.8310.126
>  6   0.185   0.2450.744  162353.00.0231.8390.126
>  7   0.185   0.2470.743  162226.20.0231.8580.128
>  8   0.186   0.2480.741  162430.40.0231.8520.128
>  9   0.185   0.2480.741  162300.20.0231.8570.128
> 10   0.185   0.2490.740  162317.20.0231.8610.129
>
>
> without TLS:
>   Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
> $$
>  0   0.217   0.2230.764  166172.20.0061.2500.092
>  1   0.192   0.2340.752  163514.50.0221.6760.116
>  2   0.190   0.2370.752  163400.60.0221.7150.119
>  3   0.188   0.2420.747  163218.20.0221.7830.124
>  4   0.188   0.2440.747  163276.60.0221.8020.125
>  5   0.188   0.2480.744  163167.90.0231.8280.127
>  6   0.188   0.2480.744  163271.00.0231.8320.127
>  7   0.188   0.2510.743  163144.50.0231.8490.128
>  8   0.189   0.2510.742  163331.20.0231.8450.129
>  9   0.188   0.2520.741  163209.30.0231.8500.129
> 10   0.188   0.2530.741  163249.60.0231.8540.129
>
>
> May I ask some questions?
>
> 1. Can I use the structure in zero cycle to deposit in pdb bank?
>Because its rfree is lowest  and it just come from CNS result without any 
> change of B 
>
> factor?
>
> 2. Why Rfree increase during refinement?
>
> 3. Usually,   delta(Rwork,Rfree) is lower 

[ccp4bb] Twinning in C2 ?

[Demetres D. Leonidas]

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native (C2) 
but the unit cell dimensions are different. These for the native 
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3 
107.0 90 125.7 90. As a result the mutant structure has  four molecules 
in the asymmetric unit while the native had two. When we run molecular 
replacement all programs (CNS, molrep, and amore) find only two 
molecules. Phaser finds four but when we try to refine the Rfree does 
not drop below 0.44 if we use four molecules and 0.53 if we only use two 
no matter how well we built the molecule and regardless of any addition 
of water molecules (the resolution of the data is 2.1). The interesting 
thing is that in the electron density map we can clearly see density for 
a substrate analog that was included in the crystallization media. Do 
you thing  that we have a case of twinning here ? We have to mention 
that Tod Yates served did not indicate any perfect merohedral twinning 
(partial merohedral twinning for this space group is not possible).


We would appreciate any comments

Many thanks

Demetres

--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

[ccp4bb] about Procheck

[Jiamu Du]

Dear All:
I am refining a structure with TLS parameters in REFMAC5.
When I run the Procheck, some warning appear like below:

--- generate density   ---
  WARNING: Determinant(U) =< 0 : -0.000475003297
   for atom: C   , res: 18, CHAIN: 1
  U:  0.08410  0.31220  0.17130  0.02360  0.04920 -0.20800
   atom will not be used
  WARNING: Determinant(U) =< 0 : -0.000683392049
   for atom: O   , res: 18, CHAIN: 1
  U:  0.08280  0.32110  0.15860  0.01930  0.05420 -0.20470
   atom will not be used
  WARNING: Determinant(U) =< 0 : -0.000691463996
   for atom: N   , res: 19, CHAIN: 1
  U:  0.07950  0.30660  0.17030  0.01890  0.04760 -0.21570
   atom will not be used

What does this warning mean? Does this mean something about the model
quality?
But I have found nothing unusual in this position, when I look at this part
of my strucutre model with its well defined density.

Is there anyone who have met the same warning? How to deal with it?

Thanks

--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)