Re: [ccp4bb] modelling with sad/mad data

[Peng Zhang]

Hi, Peter,

Does the radition damage have such a large effect? There are many positive
peaks seeing from the difference map, seems abnormal. But  I have seen
such difference maps before which are OK for modeling and refining.

Actually when I try to modelling the Se-met into the positive peaks, the R
and free_R factor goes up about 2%. Does the occupancy of the Se affect
the R factor, or should I change the occupancy?

Another problem is  f' andf f" prime, which I refine them when phasing
with Solve.

Actually, I did not use the same free set when refining with the native
data and peak data.I try to compare them because I want to make it clear
that the difference may be caused by the mad data while not the model
itself.

Thanks.


> Hi Peng Zhang,
>
> The presence of radiation damage might cause some problems.
> Do so see any obvious features in the difference map?
>
> Another problem (although I doubt it would cause such a big difference)
> might be the fact that f' andf f" prime are incorrect.
> Try and refine them (CNS or phenix.refine) maybe.
>
> Does your native data have the same free set as the peak data? if not, you
> are in trouble and have to start from scratch with your native data to be
> able to make a fair comparison. The 22/25 for 2.7 A seems awfully close
> together.
>
> procheck has not very up to date standards of what is good and what is
> not. Better use molprobity, available from:
>
> http://molprobity.biochem.duke.edu/
>
> HTH
>
> Peter
>
>
>
>
>
>
>
>
>
> - Original Message -
> From: Peng Zhang <[EMAIL PROTECTED]>
> Date: Tuesday, March 20, 2007 6:04 pm
> Subject: Re: [ccp4bb] modelling with sad/mad data
> To: CCP4BB@JISCMAIL.AC.UK
>
>> Maybe I did not make the questions clear, which leading to the
>> misleadings.Firstly, I have collected the mad data and get the
>> phase at synchrotron,
>> the phased Se is quite good for modelling, and get over 70% of the
>> molecule run with resolve autobuilding.The density seems also good for
>> building. But when finally refining the model, the gap between the
>> R(0.22)and free_R(0.32 )is big, even though modelled the Se-
>> methionine. Before
>> collecting the mad data at synchrotron, I already have another
>> native data
>> set collected at home diffractometer (rigku, with R-axis IV++). To my
>> surprise, when I using the same model(first model) and run with
>> this data
>> set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and
>> further refine to R=0.22 and Free_R=0.25), and I got the final
>> model.Thegeometry of the first model and final model(actually no
>> big difference of
>> the two models)is quite good with procheck.The omit map says good
>> enoughwith both of the two models.
>>
>> So I wondering what happened with the peak data? Did the anomolous
>> signalhave much effect on the data? and anyone have the similar
>> experience?
>>
>> > First it is always best to refine your model against the highest
>> > resolution good quality data that you have available. There was
>> > correspondence about the geometric weighting - could you have
>> weighted> the Xray data too high and have bad geometry - see
>> previous Emails!
>> >
>> > And the Free R seems rather low for the Se data.
>> > Did you transfer the same Free R set from the native to the Se data?
>> > Eleanor
>> >
>> >
>> > Peng Zhang wrote:
>> >> Dear friends,
>> >>
>> >> Recently, I have solved a structure using mad method. When
>> using the
>> >> peak
>> >> data(2.3A) as the native for structure refinement, the gap
>> between R
>> >> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the
>> >> selenomethionine but the gap still exists. When I changed the
>> data for a
>> >> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28.
>> >>
>> >> Does anyone have the similar experience?
>> >> what should I pay attention to when using the sad/mad data as
>> the native
>> >> one for modelling and refinement?
>> >>
>> >> Thanks in advance.
>> >>
>> >>
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> Peng Zhang, Ph.D. Student
>> Institute of Biochemistry and Cell Biology
>> Shanghai Institutes for Biological Sciences
>> Chinese Academy of Sciences
>>
>> 320 Yue-Yang Road
>> Shanghai 20031
>> P.R. China
>>
>>
>>
>> Tel: 021-5492-1117
>> Fax: 021-5492-1116
>> Email: [EMAIL PROTECTED]
>>
>
>


-- 
Peng Zhang, Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences

320 Yue-Yang Road
Shanghai 20031
P.R. China



Tel: 021-5492-1117
Fax: 021-5492-1116
Email: [EMAIL PROTECTED]

Re: [ccp4bb] a question about O

[Jiamu Du]

Got it.
Turn down the resolution of the monitor. The characters will be large enough
to see. But the map looks not so soomth as before.


On 3/20/07, Jiamu Du <[EMAIL PROTECTED]> wrote:


Dear All:
I have a question about the new version O.v11.
In the new version, the characters displayed on the terminal are really
smaller than in the old versions.
So, it is hard to see it clearly.
Does anyone know the command for setting the size of the
characters displayed on the terminal in O.v11.

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)





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

Re: [ccp4bb] modelling with sad/mad data

[Petrus H Zwart]

Hi Peng Zhang,

The presence of radiation damage might cause some problems.
Do so see any obvious features in the difference map?

Another problem (although I doubt it would cause such a big difference) might 
be the fact that f' andf f" prime are incorrect.
Try and refine them (CNS or phenix.refine) maybe.

Does your native data have the same free set as the peak data? if not, you are 
in trouble and have to start from scratch with your native data to be able to 
make a fair comparison. The 22/25 for 2.7 A seems awfully close together.

procheck has not very up to date standards of what is good and what is not. 
Better use molprobity, available from:

http://molprobity.biochem.duke.edu/

HTH

Peter









- Original Message -
From: Peng Zhang <[EMAIL PROTECTED]>
Date: Tuesday, March 20, 2007 6:04 pm
Subject: Re: [ccp4bb] modelling with sad/mad data
To: CCP4BB@JISCMAIL.AC.UK

> Maybe I did not make the questions clear, which leading to the 
> misleadings.Firstly, I have collected the mad data and get the 
> phase at synchrotron,
> the phased Se is quite good for modelling, and get over 70% of the
> molecule run with resolve autobuilding.The density seems also good for
> building. But when finally refining the model, the gap between the 
> R(0.22)and free_R(0.32 )is big, even though modelled the Se-
> methionine. Before
> collecting the mad data at synchrotron, I already have another 
> native data
> set collected at home diffractometer (rigku, with R-axis IV++). To my
> surprise, when I using the same model(first model) and run with 
> this data
> set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and
> further refine to R=0.22 and Free_R=0.25), and I got the final 
> model.Thegeometry of the first model and final model(actually no 
> big difference of
> the two models)is quite good with procheck.The omit map says good 
> enoughwith both of the two models.
> 
> So I wondering what happened with the peak data? Did the anomolous 
> signalhave much effect on the data? and anyone have the similar 
> experience?
> 
> > First it is always best to refine your model against the highest
> > resolution good quality data that you have available. There was
> > correspondence about the geometric weighting - could you have 
> weighted> the Xray data too high and have bad geometry - see 
> previous Emails!
> >
> > And the Free R seems rather low for the Se data.
> > Did you transfer the same Free R set from the native to the Se data?
> > Eleanor
> >
> >
> > Peng Zhang wrote:
> >> Dear friends,
> >>
> >> Recently, I have solved a structure using mad method. When 
> using the
> >> peak
> >> data(2.3A) as the native for structure refinement, the gap 
> between R
> >> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the
> >> selenomethionine but the gap still exists. When I changed the 
> data for a
> >> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28.
> >>
> >> Does anyone have the similar experience?
> >> what should I pay attention to when using the sad/mad data as 
> the native
> >> one for modelling and refinement?
> >>
> >> Thanks in advance.
> >>
> >>
> >>
> >
> >
> >
> 
> 
> -- 
> Peng Zhang, Ph.D. Student
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
> 
> 320 Yue-Yang Road
> Shanghai 20031
> P.R. China
> 
> 
> 
> Tel: 021-5492-1117
> Fax: 021-5492-1116
> Email: [EMAIL PROTECTED]
> 

Re: [ccp4bb] modelling with sad/mad data

[Peng Zhang]

Maybe I did not make the questions clear, which leading to the misleadings.
Firstly, I have collected the mad data and get the phase at synchrotron,
the phased Se is quite good for modelling, and get over 70% of the
molecule run with resolve autobuilding.The density seems also good for
building. But when finally refining the model, the gap between the R(0.22)
and free_R(0.32 )is big, even though modelled the Se-methionine. Before
collecting the mad data at synchrotron, I already have another native data
set collected at home diffractometer (rigku, with R-axis IV++). To my
surprise, when I using the same model(first model) and run with this data
set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and
further refine to R=0.22 and Free_R=0.25), and I got the final model.The
geometry of the first model and final model(actually no big difference of
the two models)is quite good with procheck.The omit map says good enough
with both of the two models.

So I wondering what happened with the peak data? Did the anomolous signal
have much effect on the data? and anyone have the similar experience?


> First it is always best to refine your model against the highest
> resolution good quality data that you have available. There was
> correspondence about the geometric weighting - could you have weighted
> the Xray data too high and have bad geometry - see previous Emails!
>
> And the Free R seems rather low for the Se data.
> Did you transfer the same Free R set from the native to the Se data?
> Eleanor
>
>
> Peng Zhang wrote:
>> Dear friends,
>>
>> Recently, I have solved a structure using mad method. When using the
>> peak
>> data(2.3A) as the native for structure refinement, the gap between R
>> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the
>> selenomethionine but the gap still exists. When I changed the data for a
>> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28.
>>
>> Does anyone have the similar experience?
>> what should I pay attention to when using the sad/mad data as the native
>> one for modelling and refinement?
>>
>> Thanks in advance.
>>
>>
>>
>
>
>


-- 
Peng Zhang, Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences

320 Yue-Yang Road
Shanghai 20031
P.R. China



Tel: 021-5492-1117
Fax: 021-5492-1116
Email: [EMAIL PROTECTED]

Re: [ccp4bb] ccp4i error Mac OS

[Ulrich Genick]

Hi

it seems I overestimated what's in my little mac mini.
Its a g4 not a g5, so the g5 binaries would not really
be expected to work.

Thanks for the responses

Ulrich

[ccp4bb] ccp4i error on Mac OS

[Ulrich Genick]

Hi,

I just installed ccp4 6.0.2 with ccp4i 1.4.4.2 on a mac mini.

no matter what little job I try to run (importing mmCIF file,
calculating structure factors from pdb), the execution fails
with a note in the log file saying:

has failed with error message
child killed: illegal instruction
*

The same input files work on one of our linux
boxes, so it does not seem that the input files
are to blame.

I searched the bulletin boards and did not find this
particular error message for CCP4.

Other people had similar error messages such as
child killed: segmentation fault.

I those cases people suggested changing limit settings
in the shell (limit datasize unlimited) from which
CCP4i is launched. In my case this
did not make a difference.

Any suggestions?


Thanks,

Ulrich

Re: [ccp4bb] Validate tool pdb structure

[Ibrahim M. Moustafa]

 Actually, the structure is not mine. I just wanted to check the 
structure before using it for my work!


 The unit of the structure is:  a = 141.59,  b = 141.59,  c = 43.68
  alpha = 90.00,   beta = 90.00,   gamma = 120.00

  So, it is H3 not R3!

  Checking the structure after editing the space group to H3 did not 
show any bad close contacts vs. R3 spg.


  thanks for those who replied.

  Ibrahim




At 01:50 PM 3/20/2007, [EMAIL PROTECTED] wrote:

are you mixing R3 with H3 ?

in the current pdb R3 has a=b=c, al=be=ga
 while H3 has a=b, al=90, be=90, ga=120
this was not consistently used in the earlier pdb

examples

REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3
REMARK 290  SYMOP   SYMMETRY
REMARK 290 NNNMMM   OPERATOR
REMARK 290   1555   X,Y,Z
REMARK 290   2555   Z,X,Y
REMARK 290   3555   Y,Z,X
CRYST1   40.430   40.430   40.430  80.25  80.25  80.25 R 3   3


REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290  SYMOP   SYMMETRY
REMARK 290 NNNMMM   OPERATOR
REMARK 290   1555   X,Y,Z
REMARK 290   2555   -Y,X-Y,Z
REMARK 290   3555   Y-X,-X,Z
REMARK 290   4555   X+2/3,Y+1/3,Z+1/3
REMARK 290      -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290   6555   Y-X+2/3,-X+1/3,Z+1/3
REMARK 290   7555   X+1/3,Y+2/3,Z+2/3
REMARK 290   8555   -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290   9555   Y-X+1/3,-X+2/3,Z+2/3
CRYST1   64.520   64.520   32.570  90.00  90.00 120.00 H 3   9


Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel  (814) 863 8703
Fax (814) 865 7927

Re: [ccp4bb] coot and stereochemistry

[Dale Tronrud]

   I'm not a big fan of restraining chiral volumes, except for models based
on low resolution data (maybe up to 2.7A).  In my experience, if a refinement
results in the flipping of a chiral center the true solution is almost never
to flip it back.  If a CA flips then probably a neighboring peptide bond
needs to be flipped.  If a threonine CB flips then the OG1 and CG2 labels
need to be swapped.

   I would prefer a visual indicator on the screen when a chiral center is
bad in addition to your tool for jumping directly to bad centers.  That
way, when I'm passing down the chain I would see, say, an icon with a
picture of a hand with a red circle and diagonal slash and know immediately
that there is a problem.  Of course I would also like to see visually the
bad bond lengths and angles, but marking the bad chiral centers would not
clutter the screen and be a good start.

Dale Tronrud

Paul Emsley wrote:

On Tue, 2007-03-20 at 08:57 +0100, Laurent Maveyraud wrote:

Dear list,
 
another question related to stereochemistry, but concerning coot.

When using the RSR zone button, which should "improve geometry and fit to
map", it seems that the geometry is not always improved : some chiral
centers can be inverted. 


That is not always a bad thing.


The surprising thing is that using the "regularize
zone" afterwards does not correct this, even if the chirality of the center
is not set to both, but to positive in the cif dictionary (ie should define
only one possible chirality). 
Has anybody else notices this behavior ? Is there a way to adjust the weight

between geometry and map terms in the RSR option ?


Chiral volumes are not part of the geometric target function in Coot[1],
so changing the weight will have no effect.

Currently what I do for chiral volumes (as a work-around) is use
Validate -> Incorrect Chiral Volumes to find the building errors.  They
are trivial to fix when you know where they are.  Often I use single
atom drag to move the chiral centre to the other side of the chiral
plane (made by the chiral neighbours).

Paul.

[1] They should be, I tried it but it made the minimization slow and
unstable.  I should try it again.

[ccp4bb] 2008 Gordon Research Conference on Diffraction Methods in Structural Biology

[Elspeth Garman]

Call For Speakers

Gordon Research Conference on Diffraction Methods in Structural Biology
  July 13-18, 2008   Bates College, Lewiston, Maine, USA

   Co-Chairs:   Elspeth Garman & Andrew Leslie


The 2008 Gordon Research Conference on Diffraction Methods in Structural
Biology will encompass advances in the methodology for macromolecular
X-ray crystallography, and other diffraction/scattering applications.
Particularly significant structural results will be highlighted during
the meeting.  All participants will be expected to contribute
extensively to discussion, to present either a talk or a poster, and to
attend the entire conference.

Suggestions for topics, specific speakers, and any other aspect of the
meeting are kindly requested from you.  Please feel free to email either
Elspeth Garman ([EMAIL PROTECTED] ) 
and/or Andrew Leslie
([EMAIL PROTECTED] ) with your 
ideas.

A sentence or two about the speaker or idea would be
most helpful.  You are encouraged to suggest yourself as a speaker or
anyone else.


--

-
Dr. Elspeth F. Garman,
Reader in Molecular Biophysics,
Department of Biochemistry,
Rex Richards Building,
University of Oxford,  Tel: (44)-1865-275398
South Parks Road,  FAX: (44)-1865-275182
OXFORD, OX1 3QU, U.K.  E-mail: [EMAIL PROTECTED]

-

Re: [ccp4bb] Validate tool pdb structure

[Kim Henrick]

are you mixing R3 with H3 ?

in the current pdb R3 has a=b=c, al=be=ga
 while H3 has a=b, al=90, be=90, ga=120
this was not consistently used in the earlier pdb

examples

REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3
REMARK 290  SYMOP   SYMMETRY
REMARK 290 NNNMMM   OPERATOR
REMARK 290   1555   X,Y,Z
REMARK 290   2555   Z,X,Y
REMARK 290   3555   Y,Z,X
CRYST1   40.430   40.430   40.430  80.25  80.25  80.25 R 3   3


REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290  SYMOP   SYMMETRY
REMARK 290 NNNMMM   OPERATOR
REMARK 290   1555   X,Y,Z
REMARK 290   2555   -Y,X-Y,Z
REMARK 290   3555   Y-X,-X,Z
REMARK 290   4555   X+2/3,Y+1/3,Z+1/3
REMARK 290      -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290   6555   Y-X+2/3,-X+1/3,Z+1/3
REMARK 290   7555   X+1/3,Y+2/3,Z+2/3
REMARK 290   8555   -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290   9555   Y-X+1/3,-X+2/3,Z+2/3
CRYST1   64.520   64.520   32.570  90.00  90.00 120.00 H 3   9

[ccp4bb] Validate tool pdb structure

[Ibrahim M. Moustafa]

Dear All,

   I wanted to check some structure using the validate server 
http://deposit.pdb.org/validate/


  In the validation summary file I got a list of close contacts 
based on crystal symmetry:


  
---

==> Close contacts in same asymmetric unit.  Distances smaller than 2.2
Angstroms are considered as close contacts.

  none


==> Close contacts based on crystal symmetry.  Distances smaller than 2.2
Angstroms are considered as close contacts.

   Chain AtomRes  Seq   Chain 
AtomRes  Seq   Symm_Code Distance

   -
   A  OD2ASP   58 
- A  O  PHE   70  (  2,  5,  5,  5)  Dist = 0.13
   A  CA PRO   18 
- A  N  LEU   82  (  2,  5,  5,  5)  Dist = 0.13
   A  C  THR   63 
- A  C  GLU   73  (  2,  5,  5,  5)  Dist = 0.23
   A  OH TYR  190 
- A  C  GLY  131  (  2,  5,  5,  5)  Dist = 0.24
   A  NE ARG  159 
- B  OE2GLU   20  (  2,  5,  5,  5)  Dist = 0.24
   A  CE1TYR  154 
- A  N  SER  130  (  2,  5,  5,  5)  Dist = 0.27
   B  OG SER  130 
- B  CB LYS  111  (  3,  5,  5,  5)  Dist = 0.33
   A  N  GLY  164 
- A  CG2VAL  167  (  2,  5,  5,  5)  Dist = 0.34
   B  CG2VAL  188 
- A  N  GLY  184  (  3,  5,  5,  5)  Dist = 0.35
   A  C  GLY   14 
- A  CG TYR   41  (  3,  5,  5,  5)  Dist = 0.35
   A  OE2GLU   50 
- A  CG2THR  147  (  2,  5,  5,  5)  Dist = 0.35
   A  C  LEU  127 
- A  OG SER  182  (  2,  5,  5,  5)  Dist = 0.36
   A  CB VAL  118 
- A  O  GLY  164  (  3,  5,  5,  5)  Dist = 0.37
   A  CG ASN  120 
- A  O  SER   83  (  2,  5,  5,  5)  Dist = 0.39


-

 Actually, the list is really long, a lot of such contacts.

 My question: why a crystal structure would have all these bad 
contacts?? Does it indicate that the space group (R 3) used to solve 
the structure was not right??


   I'd love to hear the comments from people having experiences with 
structures solved in R3 sg.


  regards,
Ibrahim



Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel  (814) 863 8703
Fax (814) 865 7927

[ccp4bb] Meeting: Micro-Crystals, Micro-Beams, and Multiple Crystals

[Richard Gillilan]

In case anyone here did not hear about our upcoming session on  
microcrystallography, here is some information.


Please note that the ACA has extended the deadline for abstract  
submission to April 1. We are still in the process of choosing final  
speakers, so if you have interesting science or engineering with  
small crystals, we would love to hear from you. The official link is  
www.biochem.utah.edu/aca2007/abstracts.html


Session 13.08. (Gerd Rosenbaum & Richard Gillilan, organizers).
Weds July 25, 2007 morning, (Salt Lake City, Utah)

---
"Micro-Crystals, Micro-Beams, and Multiple Crystals"

The aim of the session is to give crystallographers an account of the  
present state and experience with macromolecular microcrystallography  
at synchrotron radiation beamlines. The session will cover three  
topics: (i) x-ray optics for microfocused beams, (ii) endstation  
instrumentation for microcrystals and data acquisition and processing  
methods for multiple crystals, and (iii) scientific advances made  
possible with microcrystals. X-ray optics will cover methods of  
focusing high flux beams to focal sizes of 2-15 µm on the sample,  
beam stabilization, and reduction of instrumental scatter background.  
The 2nd topic, endstation instrumentation, will cover recognition of  
micrometer size samples and centering them to the microfocused beam,  
goniostat stability, reduction of scatter, and detectors with high  
detective quantum efficiency at very small intensities of diffraction  
peaks. Also invited are reports on improved software to efficiently  
achieve high completeness with the minimum number of multiple  
crystals, radiation damage compensation, and merging data from  
multiple crystals into a complete data sets. The 3rd topic,  
scientific advances with microcrystals, will cover scientific  
advances which were possible only with microcrystals, either because  
larger crystals were not obtainable even with great effort, or larger  
crystals didn't have the diffractive quality to solve the structure.


BioMacromolecules and Synchroton Radiation SIG

Also, feel free to contact me personally if you are interested or  
have suggestions.


Richard Gillilan
MacCHESS
Cornell University
Ithaca NY

[ccp4bb] Duration of a phaser job

[Michele Lunelli]

Dear all,

I am running a very long phaser job (using the keyword FINAL SELECT ALL). It 
found and refined 30370 solutions, and now it is in the very last stage (PRUNE 
DUPLICATES). How long could take this step on a machine with a xeon 3.2GHz cpu? 
Days, weeks, or months? I have no clue from the log file. The search model 
consists of a polyala of 42 residues.



Thank you,

Michele Lunelli
Department of Cellular Microbiology
Max Planck Institute for Infection Biology
Campus Charité Mitte
Charitéplatz 1
D-10117 Berlin









Chiacchiera con i tuoi amici in tempo reale! 
http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com 

Re: [ccp4bb] A bit of history: John W Backus obit

[Peter Keller]

On Tue, 20 Mar 2007, Robert Sweet wrote:


I'm pretty sure that the crystallographer was David Sayre.


Indeed it was. He is mentioned explicitly in this article:

http://inventors.about.com/od/bstartinventors/a/John_Backus_4.htm

Regards,
Peter.

Re: [ccp4bb] A bit of history: John W Backus obit [Broadcast]

[Soisson, Stephen Michael]

Regarding David Sayre,  Ed Lattman once opined in a Sayre's Equation
lecture to graduate students that if only David Sayre would focus his
attention on macromolecular crystallography again, that perhaps the
phase problem would be solved. 

Lofty praise indeed.

Thanks for the anecdote Bob.

Steve
  

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Robert Sweet
Sent: Tuesday, March 20, 2007 11:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A bit of history: John W Backus obit [Broadcast]

I'm pretty sure that the crystallographer was David Sayre.  I also
believe 
(not documented well enough for wikipedia, but perhaps for here)
that IBM were so pleased with this performance that they made David an
IBM 
Fellow, which meant that he could do anything he wanted for the rest of 
his life.  Here's what he decided to do:

He's known in crystallography for the Sayre Equation, a fundamental 
relationship in direct methods.  Also, maybe not so well known, he was a

major driving force behind the method of visualizing single molecules or

cells from diffraction patterns:  J. Miao, H. N. Chapman, J. Kirz, D. 
Sayre and K. O. Hodgson, TTaking X-ray Diffraction to the Limit: 
Macromolecular Structures from Femtosecond X-ray Pulses and Diffraction 
Microscopy of Cells with Synchrotron Radiation, Annu. Rev. Biophys. 
Biomol. Struct. 33, 157-176 (2004).

He and I used to use adjacent darkrooms at the NSLS for developing x-ray

films (the '80's).  I'd meet him on the long walk, ask what he was
doing, 
and smile sympathetically when he said he was going to image single
yeast 
cells.  Well, they're essentially doing it now.  One never want's to 
underestimate David Sayre's ability to find phases.

When David retired from IBM and his adjunct appointment at SUNY Stony 
Brook one of his old buddies from the FORTRAN project spoke at the 
symposium.  Perhaps it was Backus.  They both said that the period of 
developing that language in a small team was one of the happiest times
of 
their lives.

Don't take this as fact, but this is what I remember.

Bob


On Tue, 20 Mar 2007, Bart Hazes wrote:

> The storey also made it to the CNN business page and they add...
>
> The Fortran programming language, which was a huge leap forward in
easing the 
> creation of computer software, was released in 1957, said the report.
>
> Backus launched his research project at IBM (Charts) four years
earlier, 
> assembling a diverse team of 10, including a chess wizard, a
crystallographer 
> and a cryptographer, said the Times.
> 
>
> Full story @: 
>
http://money.cnn.com/2007/03/20/news/newsmakers/backus/index.htm?postver
sion=2007032008
>
> Bart
>
>
> P.Artymiuk wrote:
>> A bit of history: NY Times obituary for John W. Backus, 82, developer
of
>> Fortran, without which CCP4 and much else would not have been
possible. 
>>
http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=133204
3200&en=adde3ee5a1875330&ei=5124&partner=permalink&exprod=permalink
>> 
>> Pete A
>> 
>> 
>> 
>
>
>

-- 

=
 Robert M. Sweet E-Dress: [EMAIL PROTECTED]
 Group Leader, PXRR: Macromolecular   ^ (that's L
   Crystallography Research Resource at NSLSnot 1)
   http://px.nsls.bnl.gov/
 Biology Dept
 Brookhaven Nat'l Lab.   Phones:
 Upton, NY  11973631 344 3401  (Office)
 U.S.A.  631 344 2741  (Facsimile)

=




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Re: [ccp4bb] Generate Random phase set.

[Bart Hazes]

SFTOOLS has a random number generator that produces a uniform 
distribution between 0 and 1, which you can than use in different ways.


You could then select all non-centric reflections and asign their phase 
as RanU*360.
For the centric reflections you can first set them to the P-variable in 
the CALC command which substitutes the restricted phase value for 
centric reflections (0 or 90 degrees). Next you can use the random 
number to add 180 degrees to half of the centric reflections.


READ in.mtz
CALC col RanU = RAN_U
SELECT NOT CENTRO
CALC P col Phase = col RanU 360 *
SELECT INVERT
CALC col Phase = P
SELECT col RanU > 0.5
CALC col Phase = 180 +
SELECT ALL
WRITE out.mtz

This is clearly advanced use of the CALC/SELECT commands and even I had 
to check the help pages, but I thought it was a nice example of the 
flexibility.


Bart

Eleanor Dodson wrote:
You can do that to some extent by scattering random atoms about and 
calculating phases from them..

Then the centrics will be sensible.
That is how some direct methods programs get their "random starting set" 
of phases..

Depends on how flat you want the starting map to be
 Eleanor


David Briggs wrote:


Hi y'all.

Excuse that rather "noddy" question, but I've been googling this for 
hours now and I've finally lost patience...


How can I generate a random phase set for either a .mtz or .hkl (cns 
format) reflection file (if possbile with sensible values for centric 
reflections).


That's it.

Thanks in advance,

Dave

--
---
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net 
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on 
no account be allowed to do the job. - Douglas Adams 







--

==

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

==

Re: [ccp4bb] A bit of history: John W Backus obit

[Robert Sweet]

I'm pretty sure that the crystallographer was David Sayre.  I also believe 
(not documented well enough for wikipedia, but perhaps for here)
that IBM were so pleased with this performance that they made David an IBM 
Fellow, which meant that he could do anything he wanted for the rest of 
his life.  Here's what he decided to do:


He's known in crystallography for the Sayre Equation, a fundamental 
relationship in direct methods.  Also, maybe not so well known, he was a 
major driving force behind the method of visualizing single molecules or 
cells from diffraction patterns:  J. Miao, H. N. Chapman, J. Kirz, D. 
Sayre and K. O. Hodgson, TTaking X-ray Diffraction to the Limit: 
Macromolecular Structures from Femtosecond X-ray Pulses and Diffraction 
Microscopy of Cells with Synchrotron Radiation, Annu. Rev. Biophys. 
Biomol. Struct. 33, 157-176 (2004).


He and I used to use adjacent darkrooms at the NSLS for developing x-ray 
films (the '80's).  I'd meet him on the long walk, ask what he was doing, 
and smile sympathetically when he said he was going to image single yeast 
cells.  Well, they're essentially doing it now.  One never want's to 
underestimate David Sayre's ability to find phases.


When David retired from IBM and his adjunct appointment at SUNY Stony 
Brook one of his old buddies from the FORTRAN project spoke at the 
symposium.  Perhaps it was Backus.  They both said that the period of 
developing that language in a small team was one of the happiest times of 
their lives.


Don't take this as fact, but this is what I remember.

Bob


On Tue, 20 Mar 2007, Bart Hazes wrote:


The storey also made it to the CNN business page and they add...

The Fortran programming language, which was a huge leap forward in easing the 
creation of computer software, was released in 1957, said the report.


Backus launched his research project at IBM (Charts) four years earlier, 
assembling a diverse team of 10, including a chess wizard, a crystallographer 
and a cryptographer, said the Times.



Full story @: 
http://money.cnn.com/2007/03/20/news/newsmakers/backus/index.htm?postversion=2007032008


Bart


P.Artymiuk wrote:

A bit of history: NY Times obituary for John W. Backus, 82, developer of
Fortran, without which CCP4 and much else would not have been possible. 
http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=1332043200&en=adde3ee5a1875330&ei=5124&partner=permalink&exprod=permalink


Pete A









--
=
Robert M. Sweet E-Dress: [EMAIL PROTECTED]
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
=

Re: [ccp4bb] Warning messages from Refmac.

[Ian Tickle]

 
All - I'm refining some structures in SG P22121 and I lots of warning
msgs from Refmac: "===> Warning: No such space group in ASYLIM".

The job seems to run fine & I can't see anything untoward with the
results or the output files, so I was just wondering whether I need be
concerned about the messages?  It would be a pain to have to re-index
everything to P21212, particularly if it's not necessary!

Thanks a lot in advance.

-- Ian

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Re: [ccp4bb] Generate Random phase set.

[Eleanor Dodson]

You can do that to some extent by scattering random atoms about and 
calculating phases from them..

Then the centrics will be sensible.
That is how some direct methods programs get their "random starting set" 
of phases..

Depends on how flat you want the starting map to be
 Eleanor


David Briggs wrote:

Hi y'all.

Excuse that rather "noddy" question, but I've been googling this for 
hours now and I've finally lost patience...


How can I generate a random phase set for either a .mtz or .hkl (cns 
format) reflection file (if possbile with sensible values for centric 
reflections).


That's it.

Thanks in advance,

Dave

--
---
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net 
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on 
no account be allowed to do the job. - Douglas Adams 

Re: [ccp4bb] A bit of history: John W Backus obit

[Bart Hazes]

The storey also made it to the CNN business page and they add...

The Fortran programming language, which was a huge leap forward in 
easing the creation of computer software, was released in 1957, said the 
report.


Backus launched his research project at IBM (Charts) four years earlier, 
assembling a diverse team of 10, including a chess wizard, a 
crystallographer and a cryptographer, said the Times.



Full story @: 
http://money.cnn.com/2007/03/20/news/newsmakers/backus/index.htm?postversion=2007032008


Bart


P.Artymiuk wrote:

A bit of history: NY Times obituary for John W. Backus, 82, developer of
Fortran, without which CCP4 and much else would not have been possible. 


http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=1332043200&en=adde3ee5a1875330&ei=5124&partner=permalink&exprod=permalink

Pete A






--

==

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

==

[ccp4bb] [Fwd: Re: [ccp4bb] question about redundancy]

[Bart Hazes]

Hi Li, There is nothing wrong with your opinion the expected redundancy
is indeed 4 because, as you say, each reflection intersects the Ewald
sphere twice, once through the top and once through the bottom
(redundancy will actually be a bit less due to the missing cusp region).

Bart


yang li wrote:

Hi:
  I am confused by a idea for a long time, and it maybe an easy question.
That is, if a cryst with p1 spacegroup, after 360 degree data collection,
what the redundancy should be? I was told that it is 2, and the 2 are
F(h,k,l) and F(-h,-k,-l), but I think if the reciprocal lattice rotated 360
degree, it must intersect with the ewald sphere 2 times--for example,
go into the sphere and go out--then F(h,k,l) should be collected twice.
I donnot know what is wrong with my option. Anyone can tell me the
reason? Thanks!

Li Yang




--

==

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

==


--

==

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone:  1-780-492-0042
fax:1-780-492-7521

==

[ccp4bb] Generate Random phase set.

[David Briggs]

Hi y'all.

Excuse that rather "noddy" question, but I've been googling this for hours
now and I've finally lost patience...

How can I generate a random phase set for either a .mtz or .hkl (cns format)
reflection file (if possbile with sensible values for centric reflections).

That's it.

Thanks in advance,

Dave

--
---
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---
Anyone who is capable of getting themselves made President should on no
account be allowed to do the job. - Douglas Adams

[ccp4bb] A bit of history: John W Backus obit

[P.Artymiuk]

A bit of history: NY Times obituary for John W. Backus, 82, developer of
Fortran, without which CCP4 and much else would not have been possible. 

http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=1332043200&en=adde3ee5a1875330&ei=5124&partner=permalink&exprod=permalink

Pete A



-- 
 Prof Peter Artymiuk   
 Krebs Institute, Structural Studies Group 
 Department of Molecular Biology & Biotechnology 
 University of Sheffield   
 Sheffield S10 2TN,  U.K.   
Email: [EMAIL PROTECTED]   
 Tel: (+44) 114-222 4190  
 Fax: (+44) 114-272 8697 

Re: [ccp4bb] OS X Scala SCALES file weirdness

[pre]

The scales files is opened NEW, then overwritten by REWINDing for each
refinement cycle.

It is not explicitly closed, but relies on the compiler correctly flushing
& closing the file on exit.

This may be a compiler bug I suppose.

I can change Scala to close the file explicitly, which might fix the problem

Phil

> Hi Phil,
>
> Looking at the file it is clear that the end is missing - the files are
> identical to a certain point then the last few 0 values are missing and
> there is no newline at the end of the ppc version...
>
> I have just run it again on the firewire disk and got the same error,
> which is odd. So the problem looks like it is to do with the ppc mac not
> the file system. Any ideas anyone? It would seem like a major operating
> system fault to be missing (i.e. not writing) the end of a file...
>
> Thanks,
>
> Graeme
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> [EMAIL PROTECTED]
> Sent: 20 March 2007 10:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] OS X Scala SCALES file weirdness
>
> The SCALES file is plain text so you should be able to check it with an
> editor
> Phil
>
>> Hi Folks,
>>
>> Sorry this is slightly off topic. I have an OS X PPC mac mini and I
> have
>> noticed some very strange behaviour. When I run scala for one example
>> the scales file that is produced is exactly 16384 bytes, and when I
> try
>> and restore this scala dies. Now running the same scaling job on an
>> intel iMac the scales file is a few bytes larger and can be read
>> appropriately.
>>
>> This suggests to me that a few bytes are being "lost".
>>
>> Weirder still, if I run the *same* job on an external firewire disk on
>> the ppc mac it works fine and produces a slightly bigger than 16k
> scales
>> file. This suggests to me that there is something unhappy about the
> file
>> system on this device. This came with OS X 10.3 and an "upgrade" to
> 10.4
>> instead of a 10.4 fresh install, though I have no idea why this would
> be
>> a problem. On both machines I am running the job in my home
> directory...
>>
>> Has anyone noticed this behaviour? More usefully - has anyone got any
>> idea of how to prevent it?
>>
>> Thanks,
>>
>> Graeme
>>
>
>

Re: [ccp4bb] OS X Scala SCALES file weirdness

[Winter, G (Graeme)]

Hi Phil,

Looking at the file it is clear that the end is missing - the files are
identical to a certain point then the last few 0 values are missing and
there is no newline at the end of the ppc version...

I have just run it again on the firewire disk and got the same error,
which is odd. So the problem looks like it is to do with the ppc mac not
the file system. Any ideas anyone? It would seem like a major operating
system fault to be missing (i.e. not writing) the end of a file...

Thanks,

Graeme 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: 20 March 2007 10:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] OS X Scala SCALES file weirdness

The SCALES file is plain text so you should be able to check it with an
editor
Phil

> Hi Folks,
>
> Sorry this is slightly off topic. I have an OS X PPC mac mini and I
have
> noticed some very strange behaviour. When I run scala for one example
> the scales file that is produced is exactly 16384 bytes, and when I
try
> and restore this scala dies. Now running the same scaling job on an
> intel iMac the scales file is a few bytes larger and can be read
> appropriately.
>
> This suggests to me that a few bytes are being "lost".
>
> Weirder still, if I run the *same* job on an external firewire disk on
> the ppc mac it works fine and produces a slightly bigger than 16k
scales
> file. This suggests to me that there is something unhappy about the
file
> system on this device. This came with OS X 10.3 and an "upgrade" to
10.4
> instead of a 10.4 fresh install, though I have no idea why this would
be
> a problem. On both machines I am running the job in my home
directory...
>
> Has anyone noticed this behaviour? More usefully - has anyone got any
> idea of how to prevent it?
>
> Thanks,
>
> Graeme
>

Re: [ccp4bb] OS X Scala SCALES file weirdness

[pre]

The SCALES file is plain text so you should be able to check it with an
editor
Phil

> Hi Folks,
>
> Sorry this is slightly off topic. I have an OS X PPC mac mini and I have
> noticed some very strange behaviour. When I run scala for one example
> the scales file that is produced is exactly 16384 bytes, and when I try
> and restore this scala dies. Now running the same scaling job on an
> intel iMac the scales file is a few bytes larger and can be read
> appropriately.
>
> This suggests to me that a few bytes are being "lost".
>
> Weirder still, if I run the *same* job on an external firewire disk on
> the ppc mac it works fine and produces a slightly bigger than 16k scales
> file. This suggests to me that there is something unhappy about the file
> system on this device. This came with OS X 10.3 and an "upgrade" to 10.4
> instead of a 10.4 fresh install, though I have no idea why this would be
> a problem. On both machines I am running the job in my home directory...
>
> Has anyone noticed this behaviour? More usefully - has anyone got any
> idea of how to prevent it?
>
> Thanks,
>
> Graeme
>

[ccp4bb] question about redundancy

[yang li]

Hi:
  I am confused by a idea for a long time, and it maybe an easy question.
That is, if a cryst with p1 spacegroup, after 360 degree data collection,
what the redundancy should be? I was told that it is 2, and the 2 are
F(h,k,l) and F(-h,-k,-l), but I think if the reciprocal lattice rotated 360
degree, it must intersect with the ewald sphere 2 times--for example,
go into the sphere and go out--then F(h,k,l) should be collected twice.
I donnot know what is wrong with my option. Anyone can tell me the
reason? Thanks!

Li Yang

[ccp4bb] OS X Scala SCALES file weirdness

[Winter, G (Graeme)]

Hi Folks,

Sorry this is slightly off topic. I have an OS X PPC mac mini and I have
noticed some very strange behaviour. When I run scala for one example
the scales file that is produced is exactly 16384 bytes, and when I try
and restore this scala dies. Now running the same scaling job on an
intel iMac the scales file is a few bytes larger and can be read
appropriately.

This suggests to me that a few bytes are being "lost".

Weirder still, if I run the *same* job on an external firewire disk on
the ppc mac it works fine and produces a slightly bigger than 16k scales
file. This suggests to me that there is something unhappy about the file
system on this device. This came with OS X 10.3 and an "upgrade" to 10.4
instead of a 10.4 fresh install, though I have no idea why this would be
a problem. On both machines I am running the job in my home directory...

Has anyone noticed this behaviour? More usefully - has anyone got any
idea of how to prevent it?

Thanks,

Graeme

Re: [ccp4bb] ccp4 pdb format

[Martyn Winn]

CCP4 is a collaboration between many and varied authors, so the exact
answer depends on which bit of the ccp4 interface you are talking about!

Generally, most CCP4 programs will work with "standard" PDB files. The
spacegroup on the CRYST1 line is only needed if a program can't get the
symmetry information from elsewhere, such as MTZ file or program
keywords (for example, though not a heavy atom example, our distributed
example toxd.pdb doesn't have it).

Some CCP4 programs use the "HA" format for heavy atom input, see:
http://www.ccp4.ac.uk/dist/ccp4i/help/modules/exptphase.html#solution_files

HTH
Martyn


On Tue, 2007-03-20 at 15:06 +0800, yang li wrote:
> Hi:
>Now I need to input a heavy atom pdb file in the ccp4 interface, does
> ccp4 has a special format for all the programs in the package? I used
> heavy atom file from shelxd but it seemed not right. where can I get a
> model of such pdb file? Thanks!

Re: [ccp4bb] ccp4 pdb format

[Eleanor Dodson]

yang li wrote:

Hi:
  Now I need to input a heavy atom pdb file in the ccp4 interface, does
ccp4 has a special format for all the programs in the package? I used
heavy atom file from shelxd but it seemed not right. where can I get a
model of such pdb file? Thanks!



SHELX has its own interpretation of the PDB format
If you run
pdbset xyzin shelxl.pdb xyzoutout shelxl-a.pdb
CHAIN A
end

some things get corrected and you get a CHAIN ID added
But you will need to add your spacegroup to the CRYST1 line by hand I 
think..

Eleanor

Re: [ccp4bb] Sketcher and stereochemistry

[Eleanor Dodson]

Whatever you do it is good practice to do your first run of refinement as
Review Restraints"

Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list

Then run the job and you will get a list of violations of restraints
If your chirality ideal is -2 and the calculated value is +2 then think 
whether you have built the ligand wrongly or whetherthe sign is wrongly 
defined.


Eleanor

PS - you will also find the bad clashes ..


Garib Murshudov wrote:
Chiralities in refmac dictionaries are local just like in smile 
strings. You can of course put atoms by their priorities then
you will have correspondence to R/S assignments. However you do not 
have to do it.
In many case I find it useful to put chirality 'both' and then refine 
against this dictionary. This way you can handle severla stereoisomers

(configurations) with the same dictionary.

Regards
Garib

On 20 Mar 2007, at 00:49, Vu Thai wrote:


thanks for the link. I had already seen it and was using it to assign my
chirality. I guess I should clarify my question. In sketcher, does one
input the highest priority neighbor first, then the second, and 
finally the
third? The sketcher GUI has three columns list: B/3, F/4, & 1/5. Do 
these

columns have any significance?

Vu

On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud 
<[EMAIL PROTECTED]>

wrote:


Garib has documentation on his website that I presume matches what is
required by sketcher. It can be found at

http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html

(I did a Google of "ccp4 chiral" to find it.)

Dale Tronrud

Vu Thai wrote:

Hi All,

I was wondering how to properly define the stereochemistry for a 
new ligand
in sketcher. In the sketcher interface there are three columns 
after the
stereochem sign option. I would assume that the order in which you 
enter

the chiral neighbors would effect the sign that you choose for your
stereochemistry. Does any one know how sketcher reads these three 
columns

to determine the stereochemsitry?

Thanks in advance for your help.
Cheers,
Vu

Re: [ccp4bb] coot and stereochemistry

[Paul Emsley]

On Tue, 2007-03-20 at 08:57 +0100, Laurent Maveyraud wrote:
> Dear list,
>  
> another question related to stereochemistry, but concerning coot.
> When using the RSR zone button, which should "improve geometry and fit to
> map", it seems that the geometry is not always improved : some chiral
> centers can be inverted. 

That is not always a bad thing.

> The surprising thing is that using the "regularize
> zone" afterwards does not correct this, even if the chirality of the center
> is not set to both, but to positive in the cif dictionary (ie should define
> only one possible chirality). 
> Has anybody else notices this behavior ? Is there a way to adjust the weight
> between geometry and map terms in the RSR option ?

Chiral volumes are not part of the geometric target function in Coot[1],
so changing the weight will have no effect.

Currently what I do for chiral volumes (as a work-around) is use
Validate -> Incorrect Chiral Volumes to find the building errors.  They
are trivial to fix when you know where they are.  Often I use single
atom drag to move the chiral centre to the other side of the chiral
plane (made by the chiral neighbours).

Paul.

[1] They should be, I tried it but it made the minimization slow and
unstable.  I should try it again.

Re: [ccp4bb] ccp4 pdb format

[Tim Gruene]

You can run the pdb file through pdbset, supplying cell and spacegroup, 
that's probably the quickest way to fix it.

Tim

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

GPG Key ID = A46BEE1A


On Tue, 20 Mar 2007, yang li wrote:


Hi:
 Now I need to input a heavy atom pdb file in the ccp4 interface, does
ccp4 has a special format for all the programs in the package? I used
heavy atom file from shelxd but it seemed not right. where can I get a
model of such pdb file? Thanks!

[ccp4bb] coot and stereochemistry

[Laurent Maveyraud]

Dear list,
 
another question related to stereochemistry, but concerning coot.
When using the RSR zone button, which should "improve geometry and fit to
map", it seems that the geometry is not always improved : some chiral
centers can be inverted. The surprising thing is that using the "regularize
zone" afterwards does not correct this, even if the chirality of the center
is not set to both, but to positive in the cif dictionnary (ie should define
only one possible chirality). 
Has anybody else notices this behavior ? Is there a way to adjust the weight
between geometru and map terms in the RSR option ?
 
thanks for any ideas or advices
 
laurent
---
Laurent Maveyraud  laurent.maveyraud AT ipbs DOT fr
Université Paul Sabatier   Toulouse III
I.P.B.S. UMR 5089 Groupe de Biophysique Structurale
Département Mécanismes Moléculaires des Infections Mycobactériennes
205 route de Narbonne   31077 TOULOUSE Cedex FRANCE
Tél: +33 (0)561 175 435Fax : +33 (0)561 175 994
---


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