Re: [ccp4bb] The importance of USING our validation tools

[Eleanor Dodson]

ZO has a good point - it is a pain trying to get decent simulated 
material - maybe there is an employment opportunity here?


Eleanor

Zbyszek Otwinowski wrote:

James Holton wrote:

How MUCH do you want to bet?

;)



Any amount, as long as we are taking about real diffraction images
corresponding to the deposited file with "observed" structure factors.
I doubt that simulated diffraction images will be shown, because they
are easy to be recognized as such. Independently, I value the possibility
of data simulation in methods development and for teaching purposes.


Zbyszek Otwinowski
UT Southwestern Medical Center   
5323 Harry Hines Blvd., Dallas, TX 75390-8816

(214) 645 6385 (phone) (214) 645 6353 (fax)
[EMAIL PROTECTED]

Re: [ccp4bb] The importance of USING our validation tools

[Jon Wright]

Think this bounced last time I tried to mail it in, a simulator exists at:

http://fable.sourceforge.net/index.php/Farfield_Simulation

Jon

Eleanor Dodson wrote:
ZO has a good point - it is a pain trying to get decent simulated 
material - maybe there is an employment opportunity here?


Eleanor

Zbyszek Otwinowski wrote:

James Holton wrote:

How MUCH do you want to bet?

;)



Any amount, as long as we are taking about real diffraction images
corresponding to the deposited file with "observed" structure factors.
I doubt that simulated diffraction images will be shown, because they
are easy to be recognized as such. Independently, I value the possibility
of data simulation in methods development and for teaching purposes.


Zbyszek Otwinowski
UT Southwestern Medical Center   5323 Harry Hines Blvd., Dallas, TX 
75390-8816

(214) 645 6385 (phone) (214) 645 6353 (fax)
[EMAIL PROTECTED]

Re: [ccp4bb] contact density

[Eleanor Dodson]

Look at the MSDpisa page:  
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html


reached from http://www.ebi.ac.uk/msd/

It probably tells you much of what you wantt o know..
Eleanor

Mary Rorick wrote:

Hi,

I'm a evolution/genetics grad student trying to address protein 
questions.  I'd like to figure out the easiest way to extract contact 
density (and possibly higher order contact traces in the future) from 
PDB files or SCOP domains.  I'm wondering if there is a server or a 
list somewhere that might provide me with a measure of contact density 
or the contact matrix for the proteins I'm interested in.  Or, are 
there any programs for analyzing PDB files that might make it easier 
for me to calculate this kind of thing?


Thanks!

Molly

Mary "Molly" Rorick
PhD Student
Yale University Department of Genetics

Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622

[Eleanor Dodson]

If you have a high off origin peak at 0 0 0.5 you must have absences 
along the 00l axis also consistent with

P63 22.
So you need to test both P6322 and P6 22

And is the tetramer generated by crystal symmetry or is the whole thing 
in the asymmetric unit?


Eleanor

Jorge Iulek wrote:

Dear all,

Please, maybe you could give some suggestions to the problem below.

1) Images show smeared spots, but xds did a good job integrating them. 
The cell is 229, 229, 72, trigonal, and we see alternating strong and 
weak rows of spots in the images (spots near each other, but rows more 
separated, must be by c*). They were scaled with xscale, P622 (no 
systematic abscences), R_symm = 5.3 (15.1), I/sigI = 34 (14) and 
redundancy = 7.3 (6.8), resolution 2.8 A. Reciprocal space show strong 
spots at h, k, l=2n and weak spots at h, k, l=2n+1 (I mean, l=2n 
intensities are practically all higher than l=2n+1 intensities, as 
expected from visual inspection of the images). Within planes h, k, 
l=2n+1, the average intensity is clearly and "much" *higher at high 
resolution than at low resolution*. Also, within planes h, k, l=2n, a 
subjective observation is that average intensity apparently does not 
decay much from low to high resolution. The data were trucated with 
truncate, which calculated Wilson B factor to be 35 A**2.


2) Xtriage points a high (66 % of the origin) off-origin Patterson 
peak. Also, ML estimate of overall B value of F,SIGF = 25.26 A**2.


3) I suspect to have a 2-fold NCS parallel to a (or b), halfway the c 
parameter, which is "almost" crystallographic.


4) I submitted the data to the Balbes server which using 
pseudo-translational symmetry suggested some solutions, one with a 
good contrast to others, with a 222 tetramer, built from a structure 
with 40 % identity and 58% positives, of a well conserved fold.


5) I cannot refine below 49 % with either refmac5, phenix.refine or 
CNS. Maps are messy, except for rather few residues and short 
stretches near the active site, almost impossible for rebuilding from 
thereby. Strange, to me, is that all programs "freeze" all B-factors, 
taking them the program minimum (CNS lowers to almost its minimum). 
Might this be due to by what I observed in the reciprocal space as 
related in "1" ? If so, might my (intensity) scaling procedure have 
messed the intensities due to their intrinsic "property" to be 
stronger in alternating planes ? How to overcome this ?


6) I tried some different scaling strategies *in the refinement step*, 
no success at all.


7) A Patterson of the solution from Balbes also shows an off-origin 
Patteron at the same position of the native data, although a little 
lower.


8) Processed in P6, P312 and P321, all of course suggest twinning.

I would thank suggestions, point to similar cases, etc... In fact, 
currently I wondered why refinement programs take B-factor to such low 
values


Many thanks,

Jorge

Re: [ccp4bb] Strange diffraction images

[Eleanor Dodson]

Beware twinning tests with pseudo translation! Intensity stats are 
distorted..

What does SFCHECK suggest? It pre-selects data for testing..
 Eeanor

Green, Todd wrote:


I have a case that is similar to this, or at least visually similar by 
diffraction pattern(ie. strong/weak intensities). I think my situation 
is due to a pseudo-translation. I say this my defining of pseudo 
translation as basically something other than pure translation(ie. 
some translation and some degree (albeit slight) of rotation). In my 
case, the crystals (I THINK!) are P23(and i guess you would say pseudo 
I23). There are assemblies at 0,0,0  and 0.5,0.5,0.5. The "translated" 
assembly at 0.5,0.5,0.5 is slightly misaligned(by a small rotation) 
with the assembly at the origin but near to perfect. If it were 
perfect it'd be I23. But since it is not, it is reduced to the 
Primitive cell. When indexing, if you don't include the more diffuse, 
lower intensity spots, you will lock on the I-cell. If you include 
them then you get right cell, as you would suspect. I included 
pictures. These are 2 regions of a single diffraction pattern with 
spot predictions for the indicated  Bravais lattice. You can easily 
see the sharper more dense spots versus the more diffuse less intense 
ones. In the second shot, you can see that the orthorhombic cell fits 
much better than either of the cubic cells but that's another issue 
which is related to my questions last week. So to muddy the water a 
little, my case could be pseudo-cubic altogether. I'm still working on 
all of that. As a side note, Xtriage doesn't think things are twinned 
as was suggested for one some of the other diffraction patterns 
discussed earlier today.


-Todd




-Original Message-
From: CCP4 bulletin board on behalf of Jacob Keller
Sent: Mon 8/27/2007 10:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange diffraction images

What a beautiful and interesting diffraction pattern!

To me, it seems that there is a blurred set of spots with different 
cell dimensions, although
nearly the same, underlying the ordered diffraction pattern. A 
possible interpretation occurred to
me, that the ordered part of the crystal is supported by a 
less-ordered lattice of slightly
different dimensions, which, because the crystal is a like a 
layer-cake of 2-d crystals, need not
be commensurable in the short range with the ordered lattice. The 
nicely-ordered "cake" part of the
crystal you solved, but the "frosting" between is of a different, less 
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I 
would have to see more
images to know whether this apparent lattice-spacing phenomenon is 
consistent, but it at least
seems that way to me from the images you put on the web. I would 
shudder to think of indexing it,

however.

All the best,

Jacob Keller

ps I wonder whether a crystal was ever solved which had two 
interpenetrating, non-commensurable

lattices in it. That would be pretty fantastic.

==Original message text===
On Mon, 27 Aug 2007 5:57:45 am CDT "Mark J. van Raaij" wrote:

In general, I think we should be careful about too strong statements, 
while in general structures with high solvent diffract to low-res, 
there are a few examples where they diffract to high res. Obviously, 
high solvent content means fewer crystal contacts, but if these few 
are very stable?
Similarly, there are probably a few structures with a high percentage 
of Ramachandran outliers which are real and similarly for all other 
structural quality indicators. However, combinations of various of 
these probably do not exist and in any case, every unusual feature 
like this should be described and an attempt made to explain/analyse 
it, which in the case of the Nature paper that started this thread 
was apparently not done, apart from the rebuttal later (and perhaps 
in unpublished replies to the referees?).


With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather 
than faith, I think the structure is held together by a real 
mechanism, which however I can't explain. Like in the structure Axel 
Brunger mentioned, there is appreciable diffuse scatter, which imo 
deserves to be analysed by someone expert in the matter (to whom, or 
anyone else, I would gladly supply the images which I should still 
have on a tape or CD in the cupboard...). For low-res version of one 
image see
http://web.usc.es/~vanraaij/diff45kd.pngand 

http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo 
 possibilities I 
have been thinking about:
1. only a few of the "tails" are ordered, rather like a stack of 
identical tables in which four legs hold the table surfaces stably 
together, but the few ordered tails/legs do not contribute much to 
the diffraction. This raises the question why some tails should be 
"stiff" and others not; perhaps traces of a

Re: [ccp4bb] small molecule refinement GUI for Mac

[Miller, Mitchell D.]

What about Ton Spek's Platon / System-S package?
http://www.cryst.chem.uu.nl/platon/pl00.html 
It does not have precompiled mac OSX binaries (only
linux and windows), but it does have source code 
and instructions for compiling under unix and states
that it will compile without changes under macOSX.
It is free for academics.

Regards,
Mitch




From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kristof Van 
Hecke
Sent: Friday, August 31, 2007 5:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] small molecule refinement GUI for Mac


Dear all, 

I'm looking for a small molecule refinement GUI for shelxl under Mac OSX
(commercially or non-commercially available).
Any suggestions are very welcome!

Many thanks

Sincerely

Kristof 
  


--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327468
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more 
information. 

Re: [ccp4bb] Alternate indexing

[J.P. Rose]

Hi,

I think there is a good explanation of this  in  Volume F of the  
International Tables (on page 273 I think).


John Rose

[ccp4bb] small molecule refinement GUI for Mac

[Kristof Van Hecke]

Dear all,

I'm looking for a small molecule refinement GUI for shelxl under Mac OSX
(commercially or non-commercially available).
Any suggestions are very welcome!

Many thanks

Sincerely

Kristof



--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327468
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] small molecule refinement GUI for Mac

[Peter Zwart]

What about the very nice OLEX2 gui?

http://www.dimas.dur.ac.uk/olex

Groet,

Peter

2007/8/31, William Scott <[EMAIL PROTECTED]>:
> gfortran -o platon platon.f xdrvr.c -lX11 -L/usr/X11R6/lib  does the trick.
>
>  export NETEXE="open"
>
> lets you use your default web browser.
>
> That's one fugly interface.
>
>
> Miller, Mitchell D. wrote:
> > What about Ton Spek's Platon / System-S package?
> > http://www.cryst.chem.uu.nl/platon/pl00.html
> > It does not have precompiled mac OSX binaries (only
> > linux and windows), but it does have source code
> > and instructions for compiling under unix and states
> > that it will compile without changes under macOSX.
> > It is free for academics.
> >
> > Regards,
> > Mitch
> >
> >
> > 
> >
> > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> > Kristof Van Hecke
> > Sent: Friday, August 31, 2007 5:16 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] small molecule refinement GUI for Mac
> >
> >
> > Dear all,
> >
> > I'm looking for a small molecule refinement GUI for shelxl under Mac OSX
> > (commercially or non-commercially available).
> > Any suggestions are very welcome!
> >
> > Many thanks
> >
> > Sincerely
> >
> > Kristof
> >
> >
> >
> > --
> > Kristof Van Hecke, PhD
> > Biomoleculaire Architectuur
> > Celestijnenlaan 200 F
> > B-3001 Heverlee (Leuven)
> > Tel: +32(0)16327468
> > --
> >
> >
> >
> >
> >
> > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more
> > information.
> >
>

Re: [ccp4bb] small molecule refinement GUI for Mac

[Bryan W. Lepore]

On Fri, 31 Aug 2007, William Scott wrote:

That interface


in the grand modern bazaar of free software, we shall see (not from me) an 
elegant bleeding edge gui this afternoon... late this afternoon.. ok, an 
overnight build... in a CVS repository...  SOMEthing..


-bryan

Re: [ccp4bb] small molecule refinement GUI for Mac

[William Scott]

gfortran -o platon platon.f xdrvr.c -lX11 -L/usr/X11R6/lib  does the trick.

 export NETEXE="open"

lets you use your default web browser.

That's one fugly interface.


Miller, Mitchell D. wrote:
> What about Ton Spek's Platon / System-S package?
> http://www.cryst.chem.uu.nl/platon/pl00.html
> It does not have precompiled mac OSX binaries (only
> linux and windows), but it does have source code
> and instructions for compiling under unix and states
> that it will compile without changes under macOSX.
> It is free for academics.
>
> Regards,
> Mitch
>
>
> 
>
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> Kristof Van Hecke
> Sent: Friday, August 31, 2007 5:16 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] small molecule refinement GUI for Mac
>
>
> Dear all,
>
> I'm looking for a small molecule refinement GUI for shelxl under Mac OSX
> (commercially or non-commercially available).
> Any suggestions are very welcome!
>
> Many thanks
>
> Sincerely
>
> Kristof
>
>
>
> --
> Kristof Van Hecke, PhD
> Biomoleculaire Architectuur
> Celestijnenlaan 200 F
> B-3001 Heverlee (Leuven)
> Tel: +32(0)16327468
> --
>
>
>
>
>
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more
> information.
>

Re: [ccp4bb] How many twinned crystals?

[Ian Tickle]

 
In the past twinned crystals must have been much more frequent than
published twinned structures because the traditional reaction of
crystallographers to twinning has been either to find a way of
inhibiting it or chucking the crystals in the bin and finding a
non-twinned form.  But I guess that's changing now with better software
and we're becoming more adventurous - maybe that's why we're hearing
about more twinned crystals now.

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller
> Sent: 31 August 2007 18:32
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: How many twinned crystals?
> 
> Since I joined this list, I have seen many many issues with 
> twinned structures, but have never seen 
> any personally. Granted, problems with twinning induce people 
> to write to the list, making them
> seem more prominent, but does anyone have an idea what 
> percent of crystals are twinned, or know of
> a ref about this? I always thought it was an anomaly, but
> 
> All the best,
> 
> Jacob Keller
> 
> 
> 


Disclaimer
This communication is confidential and may contain privileged information 
intended solely for the named addressee(s). It may not be used or disclosed 
except for the purpose for which it has been sent. If you are not the intended 
recipient you must not review, use, disclose, copy, distribute or take any 
action in reliance upon it. If you have received this communication in error, 
please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy 
all copies of the message and any attached documents. 
Astex Therapeutics Ltd monitors, controls and protects all its messaging 
traffic in compliance with its corporate email policy. The Company accepts no 
liability or responsibility for any onward transmission or use of emails and 
attachments having left the Astex Therapeutics domain.  Unless expressly 
stated, opinions in this message are those of the individual sender and not of 
Astex Therapeutics Ltd. The recipient should check this email and any 
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accepts no liability for damage caused by any virus transmitted by this email. 
E-mail is susceptible to data corruption, interception, unauthorized amendment, 
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basis that the Company is not liable for any such alteration or any 
consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674

[ccp4bb] How many twinned crystals?

[Jacob Keller]

Since I joined this list, I have seen many many issues with twinned structures, 
but have never seen 
any personally. Granted, problems with twinning induce people to write to the 
list, making them
seem more prominent, but does anyone have an idea what percent of crystals are 
twinned, or know of
a ref about this? I always thought it was an anomaly, but

All the best,

Jacob Keller

[ccp4bb] Buried lysines!

[Ramaswamy Subramanian]

Hello all, 

Is there any recent paper that contains an analysis of buried lysines in the
PDB?

Thanks.

Rams.
-- 
Ramaswamy. S
Department of Biochemistry
Roy J and Lucille A Carver College of Medicine
The University of Iowa.

[ccp4bb] mrBUMP 0.4.1 questions

[Ricardo Aparicio]

Dear all,

I have a couple of questions concerning mrBUMP:

1) I cannot correctly fix E-values for Fasta search, e.g.,  6E-11, 
actually it seems

it accepts only 4 decimal places like 0.0001.  I also tried to edit scripts
by hand ("run & view com file").

2) I would like to use mrBUMP firstly in the "model search only" option 
and then
restart/continue the job (in this case, off-line) to do molecular 
replacement with the previously selected models.

Is there a way to do it without having to enter the selected models by hand?

3) I also would like to enter pre-determined pdb files for molecular 
replacement but I cannot understand

very well the "User specified search models" session in ccp4i.
What I understand is that I need to specify BOTH the pdb file AND the chain.
Thus, if I have a pdb with many chains, I need to define many lines to 
refer to only one
pdb file. Is there a way to only specify the path of the pdb files and 
left to mrBUMP the decision

of whether or not to select a particular chain?

4) ccp4i dbviewer is launched automatically when mrBUMP starts to run.
A task button at the bottom of the "Program List" was created but it does
not work (message:   "sh: bltwish: command not found").
Maybe problems with my installation?
Is there a way to launch dbviewer by command line?


Thank you very much in advance,

Ricardo


#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG mrbump
#CCP4I DATE 31 Aug 2007  16:13:17
#CCP4I USER aparicio
#CCP4I PROJECT PRS
#CCP4I JOB_ID 18
#CCP4I SCRATCH /tmp/aparicio
#CCP4I HOSTNAME minerva.iqm.unicamp.br
#CCP4I PID 27340

http_proxy not specified in environemnt

#
#
#
#  CCP4: MRBUMP - Automated Bulk Molecular Replacement (version 0.4.1)  #
#

[ccp4bb] water picking

[Jianghai Zhu]

Hi all,

I know there are a lot of criteria for water picking.  It depends on  
the resolution, data quality, etc...  Can somebody point me a good  
literature on this topic?  Thanks.


Jianghai

+++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++

Re: [ccp4bb] How many twinned crystals?

[George M. Sheldrick]

Since processing non-merohedrally twinned crystals became routine in 
small-molecule crystallography, the number of such twins has increased 
dramatically. The data are often as good as from normal crystals and 
there is the advantage of getting a higher redundancy and greater 
completeness by collecting data from two or more crystals in different 
orientations at the same time! At the moment non-meroderally twinned 
protein crystals are often thrown away (e.g. because they don't index 
with programs designed for untwinned crystals) or one tries not to 
notice that the other components are there. I predict that when
MOSFLM, XDS, HKL2000 etc. are able to index and integrate non-merodedral 
twins, they will suddenly become much more common for macromolecules 
too. At least there is no problem indexing and integrating merohedral 
twins, and some refinement programs can handle them, so most of the 
discussion in this list has been about merohedral twins so far.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Fri, 31 Aug 2007, Ian Tickle wrote:

>  
> In the past twinned crystals must have been much more frequent than
> published twinned structures because the traditional reaction of
> crystallographers to twinning has been either to find a way of
> inhibiting it or chucking the crystals in the bin and finding a
> non-twinned form.  But I guess that's changing now with better software
> and we're becoming more adventurous - maybe that's why we're hearing
> about more twinned crystals now.
> 
> -- Ian
> 
> > -Original Message-
> > From: [EMAIL PROTECTED] 
> > [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller
> > Sent: 31 August 2007 18:32
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: How many twinned crystals?
> > 
> > Since I joined this list, I have seen many many issues with 
> > twinned structures, but have never seen 
> > any personally. Granted, problems with twinning induce people 
> > to write to the list, making them
> > seem more prominent, but does anyone have an idea what 
> > percent of crystals are twinned, or know of
> > a ref about this? I always thought it was an anomaly, but
> > 
> > All the best,
> > 
> > Jacob Keller
> > 
> > 
> > 
> 
> 
> Disclaimer
> This communication is confidential and may contain privileged information 
> intended solely for the named addressee(s). It may not be used or disclosed 
> except for the purpose for which it has been sent. If you are not the 
> intended recipient you must not review, use, disclose, copy, distribute or 
> take any action in reliance upon it. If you have received this communication 
> in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] 
> and destroy all copies of the message and any attached documents. 
> Astex Therapeutics Ltd monitors, controls and protects all its messaging 
> traffic in compliance with its corporate email policy. The Company accepts no 
> liability or responsibility for any onward transmission or use of emails and 
> attachments having left the Astex Therapeutics domain.  Unless expressly 
> stated, opinions in this message are those of the individual sender and not 
> of Astex Therapeutics Ltd. The recipient should check this email and any 
> attachments for the presence of computer viruses. Astex Therapeutics Ltd 
> accepts no liability for damage caused by any virus transmitted by this 
> email. E-mail is susceptible to data corruption, interception, unauthorized 
> amendment, and tampering, Astex Therapeutics Ltd only send and receive 
> e-mails on the basis that the Company is not liable for any such alteration 
> or any consequences thereof.
> Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
> Cambridge CB4 0QA under number 3751674
> 

Re: [ccp4bb] pointless / batch number / axial hkl

[Phil Evans]

On 31 Aug 2007, at 21:52, Bryan W. Lepore wrote:

[1] is there a way to make pointless read only up to a certain  
batch number?




Not at present - I'll add it at some stage, it wouldn't be hard

You can use "rebatch" to select batches


[2] should pointless compare axial reflections along all axes  
regardless of input spacegroup?  i.e, is it a waste of time to  
permute axes when indexing?


e.g, if pointless reports this :
 Zone  Number  PeakHeight  SD  Probability   
ReflectionCondition

 1   screw axis 4(2) [c]No observations
 1   screw axis 4(1) [c]No observations
 2   screw axis 2(1) [a]   28   0.969   0.291   *** 0.917
h00: h=2n


... does that mean [b] was not inspected?



No this means that in pointgroup 422 [b] is equivalent to [a]

It does check all necessary axes in each accepted point (Laue) group

Phil

[ccp4bb] pointless / batch number / axial hkl

[Bryan W. Lepore]

[1] is there a way to make pointless read only up to a certain batch 
number?


[2] should pointless compare axial reflections along all axes regardless 
of input spacegroup?  i.e, is it a waste of time to permute axes when 
indexing?


e.g, if pointless reports this :
 Zone  Number  PeakHeight  SD  Probability  
ReflectionCondition
 1   screw axis 4(2) [c]No observations
 1   screw axis 4(1) [c]No observations
 2   screw axis 2(1) [a]   28   0.969   0.291   *** 0.917   h00: h=2n

... does that mean [b] was not inspected?

-bryan

[ccp4bb] phaser + phased-TF

[Bryan W. Lepore]

if it doesn't now, will phaser be able to run a phased translation 
function in the future?


-bryan

[ccp4bb] Best program to find whether a crystal is twinned ?

[Jobichen Chacko]

Dear All,
Can you please inform me the programs available to find whether a crystal is 
twinned and also the data reduction programs for twinned crystals.
Thanks in advance.
Jobi



From: CCP4 bulletin board on behalf of Ian Tickle
Sent: Sat 9/1/2007 1:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How many twinned crystals?




In the past twinned crystals must have been much more frequent than
published twinned structures because the traditional reaction of
crystallographers to twinning has been either to find a way of
inhibiting it or chucking the crystals in the bin and finding a
non-twinned form.  But I guess that's changing now with better software
and we're becoming more adventurous - maybe that's why we're hearing
about more twinned crystals now.

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller
> Sent: 31 August 2007 18:32
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: How many twinned crystals?
>
> Since I joined this list, I have seen many many issues with
> twinned structures, but have never seen
> any personally. Granted, problems with twinning induce people
> to write to the list, making them
> seem more prominent, but does anyone have an idea what
> percent of crystals are twinned, or know of
> a ref about this? I always thought it was an anomaly, but
>
> All the best,
>
> Jacob Keller
>
>
>


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Re: [ccp4bb] Best program to find whether a crystal is twinned ?

[William Scott]

Try

phenix.xtriage


Jobichen Chacko wrote:
> Dear All,
> Can you please inform me the programs available to find whether a crystal
> is twinned and also the data reduction programs for twinned crystals.
> Thanks in advance.
> Jobi
>
> 
>
> From: CCP4 bulletin board on behalf of Ian Tickle
> Sent: Sat 9/1/2007 1:46 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] How many twinned crystals?
>
>
>
>
> In the past twinned crystals must have been much more frequent than
> published twinned structures because the traditional reaction of
> crystallographers to twinning has been either to find a way of
> inhibiting it or chucking the crystals in the bin and finding a
> non-twinned form.  But I guess that's changing now with better software
> and we're becoming more adventurous - maybe that's why we're hearing
> about more twinned crystals now.
>
> -- Ian
>
>> -Original Message-
>> From: [EMAIL PROTECTED]
>> [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller
>> Sent: 31 August 2007 18:32
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: How many twinned crystals?
>>
>> Since I joined this list, I have seen many many issues with
>> twinned structures, but have never seen
>> any personally. Granted, problems with twinning induce people
>> to write to the list, making them
>> seem more prominent, but does anyone have an idea what
>> percent of crystals are twinned, or know of
>> a ref about this? I always thought it was an anomaly, but
>>
>> All the best,
>>
>> Jacob Keller
>>
>>
>>
>
>
> Disclaimer
> This communication is confidential and may contain privileged information
> intended solely for the named addressee(s). It may not be used or
> disclosed except for the purpose for which it has been sent. If you are
> not the intended recipient you must not review, use, disclose, copy,
> distribute or take any action in reliance upon it. If you have received
> this communication in error, please notify Astex Therapeutics Ltd by
> emailing [EMAIL PROTECTED] and destroy all copies of the
> message and any attached documents.
> Astex Therapeutics Ltd monitors, controls and protects all its messaging
> traffic in compliance with its corporate email policy. The Company accepts
> no liability or responsibility for any onward transmission or use of
> emails and attachments having left the Astex Therapeutics domain.  Unless
> expressly stated, opinions in this message are those of the individual
> sender and not of Astex Therapeutics Ltd. The recipient should check this
> email and any attachments for the presence of computer viruses. Astex
> Therapeutics Ltd accepts no liability for damage caused by any virus
> transmitted by this email. E-mail is susceptible to data corruption,
> interception, unauthorized amendment, and tampering, Astex Therapeutics
> Ltd only send and receive e-mails on the basis that the Company is not
> liable for any such alteration or any consequences thereof.
> Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science
> Park, Cambridge CB4 0QA under number 3751674
>