Re: [ccp4bb] Rigaku R-axis IIC X-ray diffraction system

[Jim Pflugrath]

The first Rigaku R-AXIS IIC in North America were installed in late 1990 at 
Yale University and McMaster University.  That's the same year the Hubble 
Telescope went into space and the first search engine Archie was released.

The last R-AXIS IIC shipped in 1994.  So these are really vintage systems if 
anyone is still using them.

Jim


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ng Chyan Leong 
[c...@mrc-lmb.cam.ac.uk]
Sent: Friday, April 13, 2012 11:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rigaku R-axis IIC X-ray diffraction system

Dear all,
Do you know is anyone still using Rigaku R-axis IIC X-ray diffraction
system with support services? It seems Rigaku no longer support this
systems.

Thank you in advance.

Best Regards,
Leong

Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?

[Richard Gildea]

They were hit by a lightning strike on Thursday evening which took out
their power:

https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx

Cheers,

Richard
On Apr 14, 2012 9:28 AM, "Bosch, Juergen"  wrote:

> neither the websites nor ssh works to any of the machines.
> Did they fall into a black hole ?
> e.g. http://www-ssrl.slac.stanford.edu
>
> Jürgen
>
> ..
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-2926
> http://web.mac.com/bosch_lab/
>
>
>
>
>

Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?

[Bosch, Juergen]

I guess I must have missed this, glad we collected our data yesterday at ALS 
(shameless advertisement).
Hopefully things will be restored soon though.

Jürgen

On Apr 14, 2012, at 12:33 PM, Richard Gildea wrote:


They were hit by a lightning strike on Thursday evening which took out their 
power:

https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx

Cheers,

Richard

On Apr 14, 2012 9:28 AM, "Bosch, Juergen" 
mailto:jubo...@jhsph.edu>> wrote:
neither the websites nor ssh works to any of the machines.
Did they fall into a black hole ?
e.g. http://www-ssrl.slac.stanford.edu

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/





..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

[ccp4bb] Anybody knows why SSRL is unaccessible ?

[Bosch, Juergen]

neither the websites nor ssh works to any of the machines.
Did they fall into a black hole ?
e.g. http://www-ssrl.slac.stanford.edu

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] [cnsbb] MTZ label

[Edward A. Berry]

Dear Sunil,

I think you can do this with the ccp4i gui-
In the category "Reflection Data Utilities"
select "Edit mtz file (sftools)"
One of the panels is "Change column labels and types" with options to
edit labels or add new label. But Surprise, there are no labels in the list!
This is because the list is labels you have selected for the output file.
You have to click "add another label" and you will get to choose from the
labels in the input file, and change the labe and/or (probably not a good
idea) change its type.

However I don't think you need to change labels to run Amore-
If you are running amore from the ccp4i gui, start the main amore task,
right under the box where you select mtz file with input data,there
are two drop-down menus labeled FP and Sigma. The items to select
are all the labels in the mtz file, so you select the ones corresponding
to FP and Sigma

If you still have trouble, I suggest to subscribe to ccp4bb

Phaser is another very useful molecular replacement program you should try.
You can run it from the CCP4 Gui if it is installed.

HTH!

sunil wrote:



Hi

I am facing the problem of putting correct label in the MTZ file.
Ctruncate (ccp4 GUI) programme uses some default label which is not
sufficient to run AMoRe. Does anyone face this problem of MTZ label?
How can we put labels in the MTZ that we want e.g FP or PHIC etc ?
If anybody has some clue to this this please help me overcome this problem.
I tried to search the google but not able to find any script that can
handle the problem of mtz label.

I appreciate any help in this regard

__._,_.___
Reply to sender
 | Reply
to group  |
Reply via web post

| Start a New Topic


Messages in this topic

(1)
Recent Activity:

Visit Your Group



List information at http://groups.yahoo.com/group/cnsbb.
Posting is only allowed for members of this list.

Yahoo! Groups


Switch to: Text-Only
, Daily Digest
 •
Unsubscribe
 • Terms
of Use 
.

__,_._,___

Re: [ccp4bb] wwPDB and CCDC

[Eleanor Dodson]

A jolly good thing - congratulations and thanks to the instigators...
Eleanor


On 13 April 2012 15:40, Gerard DVD Kleywegt  wrote:

> Hi Paul,
>
> You saw the wwPDB/CCDC JPG in my PPT at GSK :-)
>
> Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means,
> amongst a number of other things, that wwPDB will be allowed to use Mogul
> in its validation pipeline and that wwPDB will be allowed to incorporate
> and redistribute CSD coordinates of small molecules that occur in both PDB
> and CSD.
>
> --Gerard (K)
>
>
>
>
> On Fri, 13 Apr 2012, Paul Emsley wrote:
>
>  On 13/04/12 14:30, Tim Gruene wrote:
>>
>>> -BEGIN PGP SIGNED MESSAGE-
>>> Hash: SHA1
>>>
>>> Hi Paul,
>>>
>>> you are not referring to Gerard Bricogne's announcement for the
>>> grade-server, are you?
>>> http://www.mail-archive.com/**ccp4bb@jiscmail.ac.uk/**msg25770.html
>>>
>>
>> :) No.
>>
>>  If not - what type of agreement do you have in mind?
>>>
>>>
>> IIRC, I remember a picture of Gerard (K), Helen, Haruki and a smiling
>> Colin Groom sitting along a table signing something. I was wondering if
>> more details are available on the web.
>>
>> Paul.
>>
>>
>
> Best wishes,
>
> --Gerard
>
> **
>   Gerard J. Kleywegt
>
>  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
>   The opinions in this message are fictional.  Any similarity
>   to actual opinions, living or dead, is purely coincidental.
> **
>   Little known gastromathematical curiosity: let "z" be the
>   radius and "a" the thickness of a pizza. Then the volume
>of that pizza is equal to pi*z*z*a !
> **
>

Re: [ccp4bb] Disorder or poor phases?

[Eleanor Dodson]

  Nothing profound to add to this interesting discussion, but I too would
like to plug
FobsA - FobsB type maps - when A and B are similar but not quite the same..
It is prudent to omit the interesting parts of model A (or B) - whichever
you use to calculate the PHIC and FOM -
but the peaks and pits often clear up ambiguity  brilliantly.

You need to CAD the two data sets together, and make sure both Fobs are on
the same scale..
Eleanor

On 13 April 2012 19:50, Gloria Borgstahl  wrote:

> a recent experience in our lab with molecular replacement (wt and
> disordered point mutant; same space group and unit cell)
> was solved with a combination of two methods.
>
> 1.  We made omit maps in the disordered region at several lower
> resolutions.  The region became interpretable after suffereing through
> these maps, building residue by residue and refinement.
> 2.  Then we had the bright idea to make Fwt-Fmutant maps to confirm
> our interpretation.  Happily this map did confirm the unexpected large
> structural changed caused by a point mutant.
>
> On Fri, Apr 13, 2012 at 1:31 PM, James Holton  wrote:
> > Francis,
> >
> > I think in the cases you describe the region in question is disordered.
> >  Time and time again I have users coming to my beamline wanting to clean
> up
> > a "questionable region" by getting experimental phases.  Ahh!  If only I
> had
> > a nickle for each one.  Oh wait, I suppose I kind of do?  I take that
> back!
> >  Go MAD everyone!
> >
> > Much as I hate to discourage people from using my favorite technique,
> Tim is
> > right: phases are not region-specific in electron density maps.  Dale
> does
> > make a good point that there is such a thing as "model bias" and one can
> > argue that experimental phases don't have it.  But, this is only true if
> you
> > have not yet applied solvent flattening.  How long has it been since you
> > looked at a "raw" experimentally-phased map (before solvent flattening)?
> >  I'm willing to bet a while.  With very few exceptions, raw experimental
> > phases are lousy.  We have actually become quite dependent on density
> > modification to clean them up.  In fact, solvent flattening is the only
> > reason why SAD works at all.
> >
> > However, you CAN use anomalous differences to clear up disordered
> regions in
> > a different way.  Something I started calling "SeMet scanning" a number
> of
> > years ago.  A few of my users have done this, and a good example of it is
> > Figure 3 of Huang et al. 2004 (doi:10.1038/nsmb826).  Basically, you
> mutate
> > residues in the disordered region one at a time to SeMet, and look at
> phased
> > anomalous difference Fourier (PADF) maps.  These maps are surprisingly
> > clear, even when the anomalous difference signal is so weak as to make
> > experimental phasing hopeless.  Yes, the best phases to use for PADF maps
> > are model phases, but, as always, it is prudent to refine the model after
> > omitting the thing you are looking for before calculating such phases.
> >
> > Another way to get residue-specific labeling for low-resolution chain
> > tracing is radiation damage.  If you expose for the right amount of time,
> > Asp and Glu side chains will be specifically "burnt off", but not Asn and
> > Gln.  You will also see Met loosing its head, etc.  So, as long as you
> have
> > read Burmeister (2000), an Fo-Fo map of damaged vs undamaged can be used
> to
> > guide sequence assignment, even at 4.5 A and worse.
> >
> > Anyway, when it comes to the question of "is it disordered or is it model
> > bias?", I think it is usually the former.  It is very difficult to make
> > "model bias" suppress a region that is actually well-ordered.  Try it!
> >  After all, this is the whole reason why we bother looking at fo-fc maps.
> >  Then again, it is always possible to have a model so bad that the phase
> > error is enough to squash anything.  An excellent example of this can be
> > found in the Book of Fourier.  Taking amplitudes from the image of a cat,
> > you can see what happens when you use the phases of a duck:
> > http://www.ysbl.york.ac.uk/~cowtan/fourier/picduckcatfft.gif
> > as opposed to what happens if you use the phases of a manx:
> > http://www.ysbl.york.ac.uk/~cowtan/fourier/piccatmanx2.gif
> > A manx is a species of cat that doesn't have a tail, so no animals were
> > harmed in obtaining these phases.  My point here is that the cat's tail
> can
> > be seen quite readily in the 2fo-fc map if most of the structure is
> already
> > "right", but if your model is completely unrelated to the true structure
> > (fitting a duck into a cat-shaped hole), then everything is "in the
> noise".
> >
> > Real structures are usually somewhere between these two extremes, and I
> > think an important shortcoming in modern crystallography is that we don't
> > have a good quantitative description of this middle-ground.  We all like
> to
> > think we know what "model bias" is, but we don't exactly have "units" for
> > it.  Should we b

Re: [ccp4bb] Good way to check ion sites on Coot

[Eleanor Dodson]

And Marjorie Hardings results are nicely tabulated on a web site..
Google for it
Eleanor

On 13 April 2012 22:08, Marc Kvansakul  wrote:

>   Hi Andre,
>
>  Majorie Harding wrote a few nice papers on metal ion binding sites and
> their associated coordination geometry, examples are:
>
>  Harding MM (2006) Acta D vol. 62 pp. 678-82 or Harding MM (2004) Acta D
> vol. 60 pp. 849-59
>
>  Best
>
>  Marc
>
>  Dr. Marc Kvansakul
> Laboratory Head, NHMRC CDA Fellow
> Dept. of Biochemistry| La Trobe University | Bundoora
> Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia
> T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
>
>
>   From: Zhijie Li 
> Reply-To: Zhijie Li 
> Date: Fri, 13 Apr 2012 16:37:43 -0400
> To: 
> Subject: Re: [ccp4bb] Good way to check ion sites on Coot
>
>   Hi
> This is what I do:
> Validate>Highly coordinated waters
>
>
>  *From:* Andre Godoy 
> *Sent:* Friday, April 13, 2012 3:57 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Good way to check ion sites on Coot
>
>  Dear all.
> can someone tell me what is the best way to check for ion binding sites on
> my structure?
> I mean, a text with coordination examples, or maybe a tool on coot for it
> ...
>
>  best wishes
>
>  Andre
>

Re: [ccp4bb] Coot chain ID

[Eleanor Dodson]

Edit,  or use coot to reorder chains
If you read that edited pdb into pdbset
pdbset xyzin edited.pdb xyzout edited-and-renumbered.pdb
end

I think the renumbering happens automatically..

Eleanor


On 14 April 2012 09:46, Bernhard Lechtenberg  wrote:

> In Coot you can use
>
> Extensions -> Modelling -> Reorder Chains
>
> Bernahrd
> --
> Bernhard Lechtenberg
> PhD student
> Huntington lab
> University of Cambridge
> Department of Haematology
> Cambridge Institute for Medical Research
> Wellcome Trust/MRC Building, Hills Road
> Cambridge, CB2 0XY
> United Kingdom
>
>
> -Original Message-
> From: Dipankar Manna 
> Reply-to: Dipankar Manna 
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Coot chain ID
> Date: Sat, 14 Apr 2012 06:55:10 +
>
> Dear All,
>
>
>
> I fitted a ligand into a structure along with SO4 and waters (COOT).
> Then I did the “Merge Molecules” and did the refinement. In output PDB
> file the chain ID sequence is showing B, A, C( ligand, protein and SO4
> respectively) and the ATOM numbering is starting from ligand (Chain B
> instead of Chain A). How can I make the sequence A, B and C (Protein,
> ligand and SO4).
>
>
>
> Best wishes
>
>
>
> Dipankar
>
>
>
>
> 
>
> This e-mail and any files transmitted with it are for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information.If you are not the intended recipient, please contact the
> sender by reply e-mail and destroy all copies of the original
> message.Any unauthorized review, use, disclosure, dissemination,
> forwarding,printing or copying of this email or any action taken in
> reliance on this e-mail is strictly prohibited and may be unlawful.
>
> Visit us at http://www.aurigene.com
>

Re: [ccp4bb] Coot chain ID

[Bernhard Lechtenberg]

In Coot you can use

Extensions -> Modelling -> Reorder Chains

Bernahrd
-- 
Bernhard Lechtenberg
PhD student
Huntington lab
University of Cambridge
Department of Haematology
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building, Hills Road
Cambridge, CB2 0XY
United Kingdom


-Original Message-
From: Dipankar Manna 
Reply-to: Dipankar Manna 
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot chain ID
Date: Sat, 14 Apr 2012 06:55:10 +

Dear All,

 

I fitted a ligand into a structure along with SO4 and waters (COOT).
Then I did the “Merge Molecules” and did the refinement. In output PDB
file the chain ID sequence is showing B, A, C( ligand, protein and SO4
respectively) and the ATOM numbering is starting from ligand (Chain B
instead of Chain A). How can I make the sequence A, B and C (Protein,
ligand and SO4).

 

Best wishes

 

Dipankar






This e-mail and any files transmitted with it are for the sole use of
the intended recipient(s) and may contain confidential and privileged
information.If you are not the intended recipient, please contact the
sender by reply e-mail and destroy all copies of the original
message.Any unauthorized review, use, disclosure, dissemination,
forwarding,printing or copying of this email or any action taken in
reliance on this e-mail is strictly prohibited and may be unlawful.

Visit us at http://www.aurigene.com

Re: [ccp4bb] Coot chain ID

[Antony Oliver]

Dipankar,

A little bit of cut-and-paste in a good text editor will sort that out fairly 
easily.

Tony.

Sent from my iPhone

On 14 Apr 2012, at 07:54, "Dipankar Manna" 
mailto:dipanka...@aurigene.com>> wrote:

Dear All,

I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did 
the “Merge Molecules” and did the refinement. In output PDB file the chain ID 
sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM 
numbering is starting from ligand (Chain B instead of Chain A). How can I make 
the sequence A, B and C (Protein, ligand and SO4).

Best wishes

Dipankar



This e-mail and any files transmitted with it are for the sole use of the 
intended recipient(s) and may contain confidential and privileged 
information.If you are not the intended recipient, please contact the sender by 
reply e-mail and destroy all copies of the original message.Any unauthorized 
review, use, disclosure, dissemination, forwarding,printing or copying of this 
email or any action taken in reliance on this e-mail is strictly prohibited and 
may be unlawful.

Visit us at http://www.aurigene.com