Re: [ccp4bb] Movements of domains

[Nicholas M Glykos]

Hi Filip,

Would it be a worth-while exercise to make a histogram of the absolute 
values of atomic displacements ? If the distribution is bimodal (as you 
indicated that it may), then indicating statistical significance should be 
much easier (and convincing ?).

My twocents,
Nicholas



On Mon, 21 Nov 2011, Filip Van Petegem wrote:

> Dear crystallographers,
> 
> I have a general question concerning the comparison of different
>  structures.  Suppose you have a crystal structure containing a few
> domains.  You also have another structure of the same, but in a different
> condition (with a bound ligand, a mutation, or simply a different
> crystallization condition,...).  After careful superpositions, you notice
> that one of the domains has shifted over a particular distance compared to
> the other domains, say  1-1.5 Angstrom.   This is a shift of the entire
> domain.  Now how can you know that this is a 'significant' change?  Say the
> overall resolution of the structures is lower than the observed distance
> (2.5A for example).
> 
> Now saying that a 1.5 Angstrom movement of an entire domain is not relevant
> at this resolution would seem wrong: we're not talking about some electron
> density protruding a bit more in one structure versus another, but all of
> the density has moved in a concerted fashion.  So this would seem 'real',
> and not due to noise.   I'm not talking about the fact that this movement
> was artificially caused by crystal packing or something similar. Just for
> whatever the reason (whether packing, pH, ligand binding, ...), you simply
> observe the movement.
> 
> So the question is: how you can state that a particular movement was
> 'significantly large' compared to the resolution limit?  In particular,
> what is the theoretical framework that allows you to state that some
> movement is signifcant? This type of question of course also applies to
> other methods such as cryo-EM.  Is a 7A movement of an entire domain
> 'significant' in a 10A map? If it is, how do we quantify the significance?
> 
> If anybody has a great reference or just an individual opinion, I'd like to
> hear about it.
> 
> Regards,
> 
> Filip Van Petegem
> 
> 

-- 


Nicholas M. Glykos, Department of Molecular Biology
 and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

[ccp4bb]

[Sampath Natarajan]

http://agoni.es/zine/wp-content/plugins/extended-comment-options/chivpld.htm

Re: [ccp4bb] CCP4BB Digest - 20 Nov 2011 to 21 Nov 2011 (#2011-322)

[Fabio Dall'Antonia]

Dear Filip,

as Roberto mentioned earlier, our program Escet, respectively the RAPIDO 
web server - http://webapps.embl-hamburg.de/rapido/ - is taking 
coordinate errors (as derived from DPI- or empirically scaled B-factors) 
into account when judging the significance of structural invariance 
(that is, in particular domain movement). As far as crystal structures 
are concerned, you may want to give it a try ... otherwise I agree on 
the suggestion to compare the "internal" rmsd of individually 
superimposed domains to the overall rmsd of superimposed multi-domain 
structures, or more specifically, to the concerted shift of a domain 
relative to the other(s), so to estimate the resolution-independent 
significance of movement.


Cheers,
Fabio

--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
Notkestraße 85, Bldg. 25a
D-22603 Hamburg

phone:  +49 (0)40 89902-170
fax:+49 (0)40 89902-149
e-mail: fabio.dallanto...@embl-hamburg.de



On 11/22/11 1:00 AM, CCP4BB automatic digest system wrote:
Date: Mon, 21 Nov 2011 15:56:40 -0700 From: James Stroud 
 Subject: Re: Movements of domains On Nov 21, 
2011, at 3:04 PM, Filip Van Petegem wrote:

>  So the question is: how you can state that a particular movement was 
'significantly large' compared to the resolution limit?
 

I can think of a different but related question. How significant is a 
particular movement compared to a measured coordinate error? One way to measure 
the coordinate error in this example is to least-squares superpose the two 
instances of the domain in question and calculate the rmsd.

This makes the calculation of significance independent of the resolution of the 
data set.

James
   

Re: [ccp4bb] Movements of domains

[Fabio Dall'Antonia]

** Sorry for posting again, but I wanted to replace the subject by the 
specific topic (my former subject was due to the dact that I use the 
CCP4BB digest only) **


Dear Filip,

as Roberto mentioned earlier, our program Escet, respectively the RAPIDO 
web server - http://webapps.embl-hamburg.de/rapido/ - is taking 
coordinate errors (as derived from DPI- or empirically scaled B-factors) 
into account when judging the significance of structural invariance 
(that is, in particular domain movement). As far as crystal structures 
are concerned, you may want to give it a try ... otherwise I agree on 
the suggestion to compare the "internal" rmsd of individually 
superimposed domains to the overall rmsd of superimposed multi-domain 
structures, or more specifically, to the concerted shift of a domain 
relative to the other(s), so to estimate the resolution-independent 
significance of movement.


Cheers,
Fabio

--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
Notkestraße 85, Bldg. 25a
D-22603 Hamburg

phone:  +49 (0)40 89902-170
fax:+49 (0)40 89902-149
e-mail: fabio.dallanto...@embl-hamburg.de

Date: Mon, 21 Nov 2011 15:56:40 -0700 From: James Stroud 
 Subject: Re: Movements of domains On Nov 21, 
2011, at 3:04 PM, Filip Van Petegem wrote:

>  So the question is: how you can state that a particular movement was 
'significantly large' compared to the resolution limit?

I can think of a different but related question. How significant is a 
particular movement compared to a measured coordinate error? One way to measure 
the coordinate error in this example is to least-squares superpose the two 
instances of the domain in question and calculate the rmsd.

This makes the calculation of significance independent of the resolution of the 
data set.

James

Re: [ccp4bb] sugar and coot

[Joel Tyndall]

You can also try Jligand to generate your cif file
J

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan van 
Agthoven
Sent: Tuesday, 22 November 2011 1:17 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] sugar and coot

Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan

Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase

[Eleanor Dodson]

If you run scala after data integration, ( and thats a good idea whether 
you have used any integration software - just get out the unmerged 
scaled file - feed it through pointless to get useful info there, and 
then scala/truncate to get more useful graphs and analysis)   there isa 
an option to extract the freeR set from a previous data set. That is 
highly recommended if you have such data.


Eleanor


On 11/21/2011 11:48 PM, Dale Tronrud wrote:

I'll jump in here, and avoid the question entirely.

Since running MR on an isomorphous crystal gives the same answer as just
stuffing in the model and running some rigid body refinement, however you decide
to handle your R free flags, you should do the same thing in both cases.  The
model is the same.

Dale Tronrud

On 11/21/11 14:47, Michael Thompson wrote:

- Forwarded Message -
From: "Michael Thompson"
To: "e dodson"
Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase

A question regarding the plea for less MR (which I support):

There have been several recent instances in which I have used the solution of an 
isomorphous structure to do rigid body refinement for a new crystal (as described by 
Eleanor). It has always produced good results. My question is about how to best handle 
the free set of reflections when doing this? I have heard a number of differing opinions 
about whether or not it is important to carry the freeR flags from the original structure 
over to the new data set. I have heard equally convincing arguments from both sides, so 
my young and impressionable mind does not know who to believe. I was hoping I could get 
an opinion from the "advocates for less MR."

Sorry for hijacking this thread, but hopefully it will provide some insight 
that is relevant to the original post.

Thanks!

Mike




- Original Message -
From: "Eleanor Dodson"
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, November 21, 2011 2:23:21 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase

Just a plea for less molecular replacement.

If you get a new crystal of a known protein with the  same cell
dimension as youur old crystal, the most likely scenario is that it has
the same group, and you really should not try MR - use the previous
solution as input to do rigid body refinement, and then
   a) the R factor will tell you if this is a reasonable hypothesis (it
usually is..) and
b) you dont have this awful problem of not being able to compare the
solutions..

   Eleanor

On 11/20/2011 03:57 PM, Napoleão Valadares wrote:

Thank you all for the replies. Felix Frolow, Dan Leahy, Hans
Brandstetter, Boaz Shaanan and Tim Gruene you really helped a lot.

I think I understand it now, I always thought the "one ring to rule them
all" translated in the crystallography realms to "one origin to rule
them all". That probably means I have a long road in front of me.

I'm still half confused, I definitely need to read more, as much as I
read about symmetry and space groups I never seem to improve or get a
better understanding, but I'll keep trying.

About the same origin:
The pdbs of both Solution-1 and Solution-2 present the same space group
and cell, as observed opening the pdbs as text files or in pymol. When I
open both maps on coot they are not superposed but present the same cell
and origin.

If I open both solutions on pymol they clash. If I generate the symmetry
mates of both solutions none of them are superposed, instead they clash.
But I think they are related as you all pointed, I'll check it out.

Thank you all for your kind answers and your patience with a beginner.
Regards from a sunny Brazil,
Napo


On 11/20/2011 2:58 AM, Felix Frolow wrote:

Napoleao,
It is so called alternative origins play a game with you. You do not
change your structure by shifting 1/2 translation (or even combination
of these translations)
into directions of the main axes of your unit cell. Structure factors
after this operation stay the same, however phases change
systematically, producing however the same
map features.
Would I be a begin crystallographer now, I would read a bit more old
fashioned books
on crystallography such as probably Jensen and Stout…
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Nov 20, 2011, at 07:42 , Napoleão Valadares wrote:


Hello,
I'm observing a very strange phenomena (at least to me, I'm a
beginner). It is related to symmetry (I think).

I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas<  35% in
the last shell) and a partially refined solution with R/Rfree 22/24,
166 aminoacids observed and around 30 solvent molecules. I'll call
this Solution

Re: [ccp4bb] sugar and coot

[Paul Emsley]

On 22/11/11 00:16, Jan van Agthoven wrote:

Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?



Such a tool (if I understand correctly what you want) does not yet 
exist. However, I believe that things are not in as poor a state as one 
might infer from other posts.


Using the pre-release, you can

1) ideally position a NAG onto ASN
2) use multi-residue torsion to position a NAG by rotation of ASN chi angles
3) use the Ligand builder to build new carbohydrate monomers (it is my 
experience that PRODRG respects the wedge bonds - but I have heard that 
this is not always the case)


Using latest stable or later you can

4) multi-residue refinement (or sphere refine), which does a link 
analysis based on the coordinates of the residue selection (note that 
bonding atoms have to be within 3A to be considered a real glycosidic 
linkage)
5) add addition pseudo plane restraints to encourage ideal chair (in my 
experience, at low resolution or with poor density, carbohydrates tend 
to wander off and twist up without these)


The JLigand-Coot interface has stalled a bit, but I hope should be 
available for the Study Weekend.


The Refmac-Coot link-up using LINKR is under discussion with Garib and 
Eugene.


I would recommend against making a synthetic disaccharide carbohydrate 
with PRODRG.


Regards,

Paul.

Re: [ccp4bb] Movements of domains

[Savvas Savvides]

Dear Filip
'Annoying' MR problems for which the answer often lies in relatively small 
differences between the search model and 'RB-shifted' domains and/or subdomains 
in the actual structure, are I think a good experimental indication of the 
significance of such issues.

To extrapolate from this, RB refinement of whole domains that are initially 
misplaced by 0.5-2 angstroms will show that X-ray data to 4-8 angstrom 
resolution are often sufficient to refine the model to a position that 
decisively agrees better with data as judged by crystallographic refinement 
R-factors and electron density. So, my reaction every time I see such behavior 
is that the observed domain shift must be significant and that I should do my 
crystallographic best to model and cross-validate it as well as the data 
quality and resolution will allow.

However, the biological interpretation and impact of such significant 
displacements are of course quite specific to the system under study.

Best regards,

Savvas


On 21 Nov 2011, at 23:04, Filip Van Petegem wrote:

> Dear crystallographers,
> 
> I have a general question concerning the comparison of different  structures. 
>  Suppose you have a crystal structure containing a few domains.  You also 
> have another structure of the same, but in a different condition (with a 
> bound ligand, a mutation, or simply a different crystallization 
> condition,...).  After careful superpositions, you notice that one of the 
> domains has shifted over a particular distance compared to the other domains, 
> say  1-1.5 Angstrom.   This is a shift of the entire domain.  Now how can you 
> know that this is a 'significant' change?  Say the overall resolution of the 
> structures is lower than the observed distance (2.5A for example).
> 
> Now saying that a 1.5 Angstrom movement of an entire domain is not relevant 
> at this resolution would seem wrong: we're not talking about some electron 
> density protruding a bit more in one structure versus another, but all of the 
> density has moved in a concerted fashion.  So this would seem 'real', and not 
> due to noise.   I'm not talking about the fact that this movement was 
> artificially caused by crystal packing or something similar. Just for 
> whatever the reason (whether packing, pH, ligand binding, ...), you simply 
> observe the movement.   
> 
> So the question is: how you can state that a particular movement was 
> 'significantly large' compared to the resolution limit?  In particular, what 
> is the theoretical framework that allows you to state that some movement is 
> signifcant? This type of question of course also applies to other methods 
> such as cryo-EM.  Is a 7A movement of an entire domain 'significant' in a 10A 
> map? If it is, how do we quantify the significance?
> 
> If anybody has a great reference or just an individual opinion, I'd like to 
> hear about it.
> 
> Regards,
> 
> Filip Van Petegem
> 
> -- 
> Filip Van Petegem, PhD
> Assistant Professor
> The University of British Columbia
> Dept. of Biochemistry and Molecular Biology
> 2350 Health Sciences Mall - Rm 2.356
> Vancouver, V6T 1Z3
> 
> phone: +1 604 827 4267
> email: filip.vanpete...@gmail.com
> http://crg.ubc.ca/VanPetegem/

Re: [ccp4bb] adxv

[Rajesh kumar]

I don't know if I need that installed on my windows computer terminal.On the 
server also I could run adxv. Thought of using other ccp4 utilities.
Thanks for everyone for the help. I give up.
Regards,Rajesh

> Date: Mon, 21 Nov 2011 11:36:14 -0500
> From: ber...@upstate.edu
> Subject: Re: [ccp4bb] adxv
> To: CCP4BB@JISCMAIL.AC.UK
> 
> yum install lesstif ?
> 
> but wouldn't the motif stuff be required for the X-server, i.e. your 
> terminal, not for the 
> server running adxv?
> 
> Rajesh kumar wrote:
> > Dear Mark,
> >
> > $ locate XKeysymDB - didnt come with any thing suggests probably openmotif 
> > lib is not
> > installed.
> > I linux server has Fedora and I am using latest version of Adxv so details 
> > on the sbgrid
> > suggest its same problem.
> >
> > So how would I fix this.
> >
> > Thanks for your time.
> >
> > Regards
> > Rajesh
> >
> >
> >  > Date: Sun, 20 Nov 2011 23:18:32 +
> >  > Subject: Re: [ccp4bb] adxv
> >  > From: mark.x.bro...@gmail.com
> >  > To: ccp4...@hotmail.com
> >  > CC: CCP4BB@jiscmail.ac.uk
> >  >
> >  > Dear Rajesh,
> >  > Are you using the Openmotif library? If so, do you
> >  > have an XKeysymDB file installed?
> >  > In as shell, issue:
> >  > $ locate XKeysymDB
> >  > You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
> >  > elsewhere [1].
> >  > I suspect you're not the only one to have seen this [2].
> >  >
> >  > I hope this helps.
> >  >
> >  > Mark
> >  > [1]
> > ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
> >  > [2] http://sbgrid.org/news/newsletters/2009/06 (search for the string 
> > "adxv")
> >  >
> >  >
> >  > On 20 November 2011 19:45, Rajesh kumar  wrote:
> >  > >
> >  > > Dear Tim,
> >  > > Thanks. Your suggestion of adding to PATH works and its not completely 
> > functional may
> > be due to the Ximg/ssh or some thing to do with display.
> >  > > All three windows opened but couldn't open any image as it didn't 
> > display in the list
> > of autoload window. Pattern shows *.0.
> >  > >
> >  > > $adxv pin8_1_180.img
> >  > >
> >  > > (standard_in) 1: parse error
> >  > > (standard_in) 1: parse error
> >  > > (standard_in) 1: parse error
> >  > > beam_center x = pixels , mm
> >  > > beam_center y = pixels , mm
> >  > > distance = mm
> >  > > overload = counts
> >  > > pixelsize = 0.172 mm
> >  > > wavelength = Angstroem
> >  > > Adxv Version 1.9.4-beta
> >  > > Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems 
> > Corporation
> >  > > Using 24-bit TrueColor visual
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfActivate
> >  > > Warning: ... found while parsing ':osfActivate: 
> > ManagerParentActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfBeginLine
> >  > > Warning: ... found while parsing ':osfBeginLine: 
> > ManagerGadgetTraverseHome()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: osfHelp
> >  > > Warning: ... found while parsing ':osfHelp: ManagerGadgetHelp()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfActivate
> >  > > Warning: ... found while parsing ':osfActivate: 
> > ManagerParentActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfActivate
> >  > > Warning: ... found while parsing ':osfActivate: 
> > PrimitiveParentActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: osfHelp
> >  > > Warning: ... found while parsing ':osfHelp: Help()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfActivate
> >  > > Warning: ... found while parsing ':osfActivate: 
> > PrimitiveParentActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: osfCancel
> >  > > Warning: ... found while parsing ':osfCancel: MenuEscape()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: osfSelect
> >  > > Warning: ... found while parsing ':osfSelect: ArmAndActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: translation table syntax error: Unknown keysym name: 
> > osfActivate
> >  > > Warning: ... found while parsing ':osfActivate: 
> > PrimitiveParentActivate()'
> >  > > Warning: String to TranslationTable conversion encountered errors
> >  > > Warning: Locale not supporte

Re: [ccp4bb] adxv

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Rajesh,

are you saying that the computer you are sitting in front of is a
windows computer?
Are you sure you have been using CCP4 and phenix through an
ssh-connection and not the respective windows-binaries?

I am not familiar with windows and the possible existence of
X11-clients, but I would think that most suggestions to you assumed that
your client computer was also a linux-machine.

Cheers,
Tim

On 11/22/2011 02:27 PM, Rajesh kumar wrote:
> 
> I don't know if I need that installed on my windows computer terminal.On the 
> server also I could run adxv. Thought of using other ccp4 utilities.
> Thanks for everyone for the help. I give up.
> Regards,Rajesh
> 
>> Date: Mon, 21 Nov 2011 11:36:14 -0500
>> From: ber...@upstate.edu
>> Subject: Re: [ccp4bb] adxv
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> yum install lesstif ?
>>
>> but wouldn't the motif stuff be required for the X-server, i.e. your 
>> terminal, not for the 
>> server running adxv?
>>
>> Rajesh kumar wrote:
>>> Dear Mark,
>>>
>>> $ locate XKeysymDB - didnt come with any thing suggests probably openmotif 
>>> lib is not
>>> installed.
>>> I linux server has Fedora and I am using latest version of Adxv so details 
>>> on the sbgrid
>>> suggest its same problem.
>>>
>>> So how would I fix this.
>>>
>>> Thanks for your time.
>>>
>>> Regards
>>> Rajesh
>>>
>>>
>>>  > Date: Sun, 20 Nov 2011 23:18:32 +
>>>  > Subject: Re: [ccp4bb] adxv
>>>  > From: mark.x.bro...@gmail.com
>>>  > To: ccp4...@hotmail.com
>>>  > CC: CCP4BB@jiscmail.ac.uk
>>>  >
>>>  > Dear Rajesh,
>>>  > Are you using the Openmotif library? If so, do you
>>>  > have an XKeysymDB file installed?
>>>  > In as shell, issue:
>>>  > $ locate XKeysymDB
>>>  > You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
>>>  > elsewhere [1].
>>>  > I suspect you're not the only one to have seen this [2].
>>>  >
>>>  > I hope this helps.
>>>  >
>>>  > Mark
>>>  > [1]
>>> ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
>>>  > [2] http://sbgrid.org/news/newsletters/2009/06 (search for the string 
>>> "adxv")
>>>  >
>>>  >
>>>  > On 20 November 2011 19:45, Rajesh kumar  wrote:
>>>  > >
>>>  > > Dear Tim,
>>>  > > Thanks. Your suggestion of adding to PATH works and its not completely 
>>> functional may
>>> be due to the Ximg/ssh or some thing to do with display.
>>>  > > All three windows opened but couldn't open any image as it didn't 
>>> display in the list
>>> of autoload window. Pattern shows *.0.
>>>  > >
>>>  > > $adxv pin8_1_180.img
>>>  > >
>>>  > > (standard_in) 1: parse error
>>>  > > (standard_in) 1: parse error
>>>  > > (standard_in) 1: parse error
>>>  > > beam_center x = pixels , mm
>>>  > > beam_center y = pixels , mm
>>>  > > distance = mm
>>>  > > overload = counts
>>>  > > pixelsize = 0.172 mm
>>>  > > wavelength = Angstroem
>>>  > > Adxv Version 1.9.4-beta
>>>  > > Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems 
>>> Corporation
>>>  > > Using 24-bit TrueColor visual
>>>  > > Warning: translation table syntax error: Unknown keysym name: 
>>> osfActivate
>>>  > > Warning: ... found while parsing ':osfActivate: 
>>> ManagerParentActivate()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: 
>>> osfBeginLine
>>>  > > Warning: ... found while parsing ':osfBeginLine: 
>>> ManagerGadgetTraverseHome()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: osfHelp
>>>  > > Warning: ... found while parsing ':osfHelp: ManagerGadgetHelp()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: 
>>> osfActivate
>>>  > > Warning: ... found while parsing ':osfActivate: 
>>> ManagerParentActivate()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: 
>>> osfActivate
>>>  > > Warning: ... found while parsing ':osfActivate: 
>>> PrimitiveParentActivate()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: osfHelp
>>>  > > Warning: ... found while parsing ':osfHelp: Help()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: 
>>> osfActivate
>>>  > > Warning: ... found while parsing ':osfActivate: 
>>> PrimitiveParentActivate()'
>>>  > > Warning: String to TranslationTable conversion encountered errors
>>>  > > Warning: translation table syntax error: Unknown keysym name: osfCancel
>>>  > > Warning: ... found while parsing ':osfCancel: MenuEscape()'
>>>  > > Warning: String to TranslationTable conversion encountered err

Re: [ccp4bb] help with the structures

[Rajesh kumar]

Dear Prof Dodson,
I agree with you. Instead of further refining mutant structure, right now I am 
looking in to Apo structure. Which is at 2.74A and has R/freeR  22.7/27.9. But 
I have a molprobity profile like this 
Clashscore, all atoms:  33.73   50th percentile* (N=185, 2.740Å ± 
0.25Å)GeometryPoor rotamers   8.11%   Goal: <1%Ramachandran outliers
  0.52%   Goal: <0.2%Ramachandran favored 95.19%  Goal: >98%Cβ 
deviations >0.25Å  2   Goal: 0MolProbity score^ 
   3.0453rd percentile* (N=5278, 2.740Å ± 0.25Å)Residues with bad bonds:
   0.00%   Goal: 0%Residues with bad angles:   0.34%   Goal: <0.1%
If i fix the all the possible outliers and refine the structure it wouldn't 
improve the molprobity scores. I am not happy about the above scores at all.  I 
am wondering if this is an indication of any wrong in the structure or is this 
common for an enzyme. I have reprocessed  the data to make sure space group is 
same C2221.Any help would help me understand this and learn more.
ThanksRaj
> Date: Mon, 21 Nov 2011 12:27:04 +
> From: c...@ysbl.york.ac.uk
> To: ccp4...@hotmail.com
> CC: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] help with the  structures
> 
> I think you are proving yet again that refinement at 3.3A is not easy.
> Indeed there are probably multiple conformations for parts of the 
> structure and that may well be why your data is at low resolution and 
> anisotropic.  Maybe this is the best you can do..
> 
> I think I would make sure the apo structure is as good as it can be, 
> then fit that to the 3.3A data set, and only use that 3.3A data to 
> deduce whatever features differ from the APO structure.
> 
>   Eleanor
> On 11/19/2011 12:09 PM, Rajesh kumar wrote:
> >
> > Dear All,
> >
> >
> >
> > We have an anisotropic dataset of 3.3 A  and it was solved (not by me) with 
> > P6522 with R/freeR
> > 29.1/37.3.
> >
> >
> >
> > I got the corrected
> > mtz file by plugging in the .HKL (P6122) file to anisotropy diffraction 
> > server at
> > 2.04 A. I reindexed this p6122 to p6522 and extended the resolution and 
> > refined
> > (refmac) the structure to R/freeR
> > 36.40/38.50. With aotoncs option, fixing all Ramachnadran and rotamer
> > outliers I got it 30/32. When I added waters and it went down to 27.5/31.2. 
> > At
> > this point I recognized that my new .mtz file from anisotropy server has
> > different R flag than the earlier one (3.3A) so I copied the R flag and did 
> > refinemnt  to get R/Rfree 0.2682/0.3247. When I looked at
> > the refined structure I found  more outliers
> > than I fixed in earlier round. I did fix all the outliers and without NCS 
> > and
> > waters it gives R/Rfree 0.2906/0.3325. At all the stages I look at outliers 
> > at
> > molprobity server which suggested structure is 10th percentile and after
> > refinement more outliers comes back. At stage-1 map looked far better so was
> > happy that anisotropy correction has worked for me (this was my first time
> > handling this type of dataset) but further refinement didn’t make it look 
> > any
> > better.I use both refmac and autoBuster for refinement. 
> > http://www.flickr.com/photos/rajesh_ccp4/sets/72157628048657095/
> > This protein is an human enzyme and a bacterial homologue
> > which has 38% identity has been used to solve the  Apo structure (2.7 A, 
> > pC2221, R/freeR
> > 23.03/27.96, molprobity is around 50th percentile). I looked in to this I 
> > try to fix all the outliers and try to improve
> > molprobity score but it just refused to improve as after refinement I get 
> > more
> > outliers. This Apo structure was used to solve the mutant structure at
> > 3.3 A.  I believe that both structure could
> > have better R/freeR and excellent molprobity scores than what they have 
> > now. I am not able to recognise
> > if there is any problem in Apo structure and if errors have come to mutant 
> > so
> > both of them refuse to improve.
> >
> >
> > I wondered if there is any model bias (I don’t know if it’s
> > the case but nothing was coming to my mind) so thought using ARP/wARP 
> > classic
> > to build model from existing model but it complained that "The wilson plot
> > is very bad and ARp/wARP is very unlikely to run in a sensible way. Please
> > check your data" .  
> > http://www.flickr.com/photos/rajesh_ccp4/sets/72157628048687955/
> >
> >
> >
> > At this point I dont know how to systematically dissect this problem. I 
> > know there could be wrong in several places but with my only '2-3 structure 
> > experience' I am not able to identify the regions to look for
> > error but I think something is not right. I really appreciate if you give me
> > some suggestions/ideas/directions/tips so that I could recognize problem and
> > improve structure and learn some more.
> > I appreciate your valuable time.
> > Regards,Rajesh  
> >  

Re: [ccp4bb] adxv

[Rajesh kumar]

Dear Tim,
Yes, I have windows 7 computer and use ccp4 and phenix through xming/putty and 
I run them over linux lab computer.Sorry if I have confused you all with 
insufficient information.On the lab linux system,  I installed everything you 
suggested in BASH and it works but not completely.Core manager kind of not 
interested to look in to it and I dont know much to understand everything you 
nice people saying here.So instead I used idiffdisp and it opens the image. But 
wanted adxv to work thats all.
ThanksRaj
> Date: Tue, 22 Nov 2011 14:41:00 +0100
> From: t...@shelx.uni-ac.gwdg.de
> To: ccp4...@hotmail.com
> CC: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] adxv
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Rajesh,
> 
> are you saying that the computer you are sitting in front of is a
> windows computer?
> Are you sure you have been using CCP4 and phenix through an
> ssh-connection and not the respective windows-binaries?
> 
> I am not familiar with windows and the possible existence of
> X11-clients, but I would think that most suggestions to you assumed that
> your client computer was also a linux-machine.
> 
> Cheers,
> Tim
> 
> On 11/22/2011 02:27 PM, Rajesh kumar wrote:
> > 
> > I don't know if I need that installed on my windows computer terminal.On 
> > the server also I could run adxv. Thought of using other ccp4 utilities.
> > Thanks for everyone for the help. I give up.
> > Regards,Rajesh
> > 
> >> Date: Mon, 21 Nov 2011 11:36:14 -0500
> >> From: ber...@upstate.edu
> >> Subject: Re: [ccp4bb] adxv
> >> To: CCP4BB@JISCMAIL.AC.UK
> >>
> >> yum install lesstif ?
> >>
> >> but wouldn't the motif stuff be required for the X-server, i.e. your 
> >> terminal, not for the 
> >> server running adxv?
> >>
> >> Rajesh kumar wrote:
> >>> Dear Mark,
> >>>
> >>> $ locate XKeysymDB - didnt come with any thing suggests probably 
> >>> openmotif lib is not
> >>> installed.
> >>> I linux server has Fedora and I am using latest version of Adxv so 
> >>> details on the sbgrid
> >>> suggest its same problem.
> >>>
> >>> So how would I fix this.
> >>>
> >>> Thanks for your time.
> >>>
> >>> Regards
> >>> Rajesh
> >>>
> >>>
> >>>  > Date: Sun, 20 Nov 2011 23:18:32 +
> >>>  > Subject: Re: [ccp4bb] adxv
> >>>  > From: mark.x.bro...@gmail.com
> >>>  > To: ccp4...@hotmail.com
> >>>  > CC: CCP4BB@jiscmail.ac.uk
> >>>  >
> >>>  > Dear Rajesh,
> >>>  > Are you using the Openmotif library? If so, do you
> >>>  > have an XKeysymDB file installed?
> >>>  > In as shell, issue:
> >>>  > $ locate XKeysymDB
> >>>  > You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
> >>>  > elsewhere [1].
> >>>  > I suspect you're not the only one to have seen this [2].
> >>>  >
> >>>  > I hope this helps.
> >>>  >
> >>>  > Mark
> >>>  > [1]
> >>> ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
> >>>  > [2] http://sbgrid.org/news/newsletters/2009/06 (search for the string 
> >>> "adxv")
> >>>  >
> >>>  >
> >>>  > On 20 November 2011 19:45, Rajesh kumar  wrote:
> >>>  > >
> >>>  > > Dear Tim,
> >>>  > > Thanks. Your suggestion of adding to PATH works and its not 
> >>> completely functional may
> >>> be due to the Ximg/ssh or some thing to do with display.
> >>>  > > All three windows opened but couldn't open any image as it didn't 
> >>> display in the list
> >>> of autoload window. Pattern shows *.0.
> >>>  > >
> >>>  > > $adxv pin8_1_180.img
> >>>  > >
> >>>  > > (standard_in) 1: parse error
> >>>  > > (standard_in) 1: parse error
> >>>  > > (standard_in) 1: parse error
> >>>  > > beam_center x = pixels , mm
> >>>  > > beam_center y = pixels , mm
> >>>  > > distance = mm
> >>>  > > overload = counts
> >>>  > > pixelsize = 0.172 mm
> >>>  > > wavelength = Angstroem
> >>>  > > Adxv Version 1.9.4-beta
> >>>  > > Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems 
> >>> Corporation
> >>>  > > Using 24-bit TrueColor visual
> >>>  > > Warning: translation table syntax error: Unknown keysym name: 
> >>> osfActivate
> >>>  > > Warning: ... found while parsing ':osfActivate: 
> >>> ManagerParentActivate()'
> >>>  > > Warning: String to TranslationTable conversion encountered errors
> >>>  > > Warning: translation table syntax error: Unknown keysym name: 
> >>> osfBeginLine
> >>>  > > Warning: ... found while parsing ':osfBeginLine: 
> >>> ManagerGadgetTraverseHome()'
> >>>  > > Warning: String to TranslationTable conversion encountered errors
> >>>  > > Warning: translation table syntax error: Unknown keysym name: osfHelp
> >>>  > > Warning: ... found while parsing ':osfHelp: ManagerGadgetHelp()'
> >>>  > > Warning: String to TranslationTable conversion encountered errors
> >>>  > > Warning: translation table syntax error: Unknown keysym name: 
> >>> osfActivate
> >>>  > > Warning: ... found while parsing ':osfActivate: 
> >>> ManagerParentActivate()'
> >>>  > > Warning: String to TranslationTable conversion encountered errors
> >>>  > > Warning:

Re: [ccp4bb] adxv

[Ian Tickle]

Rajesh

I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp etc)
over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat) server
with no problems at all.

I suspect your  xming either just doesn't have the requisite X11 libs
or somehow they have not gotten installed on your system.  Can you try
Cygwin/X11, it's very easy to install.

Cheers

-- Ian

On 22 November 2011 13:49, Rajesh kumar  wrote:
> Dear Tim,
> Yes, I have windows 7 computer and use ccp4 and phenix through xming/putty
> and I run them over linux lab computer.
> Sorry if I have confused you all with insufficient information.
> On the lab linux system,  I installed everything you suggested in BASH and
> it works but not completely.
> Core manager kind of not interested to look in to it and I dont know much to
> understand everything you nice people saying here.
> So instead I used idiffdisp and it opens the image. But wanted adxv to work
> thats all.
> Thanks
> Raj
>> Date: Tue, 22 Nov 2011 14:41:00 +0100
>> From: t...@shelx.uni-ac.gwdg.de
>> To: ccp4...@hotmail.com
>> CC: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] adxv
>>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Dear Rajesh,
>>
>> are you saying that the computer you are sitting in front of is a
>> windows computer?
>> Are you sure you have been using CCP4 and phenix through an
>> ssh-connection and not the respective windows-binaries?
>>
>> I am not familiar with windows and the possible existence of
>> X11-clients, but I would think that most suggestions to you assumed that
>> your client computer was also a linux-machine.
>>
>> Cheers,
>> Tim
>>
>> On 11/22/2011 02:27 PM, Rajesh kumar wrote:
>> >
>> > I don't know if I need that installed on my windows computer terminal.On
>> > the server also I could run adxv. Thought of using other ccp4 utilities.
>> > Thanks for everyone for the help. I give up.
>> > Regards,Rajesh
>> >
>> >> Date: Mon, 21 Nov 2011 11:36:14 -0500
>> >> From: ber...@upstate.edu
>> >> Subject: Re: [ccp4bb] adxv
>> >> To: CCP4BB@JISCMAIL.AC.UK
>> >>
>> >> yum install lesstif ?
>> >>
>> >> but wouldn't the motif stuff be required for the X-server, i.e. your
>> >> terminal, not for the
>> >> server running adxv?
>> >>
>> >> Rajesh kumar wrote:
>> >>> Dear Mark,
>> >>>
>> >>> $ locate XKeysymDB - didnt come with any thing suggests probably
>> >>> openmotif lib is not
>> >>> installed.
>> >>> I linux server has Fedora and I am using latest version of Adxv so
>> >>> details on the sbgrid
>> >>> suggest its same problem.
>> >>>
>> >>> So how would I fix this.
>> >>>
>> >>> Thanks for your time.
>> >>>
>> >>> Regards
>> >>> Rajesh
>> >>>
>> >>>
>> >>> > Date: Sun, 20 Nov 2011 23:18:32 +
>> >>> > Subject: Re: [ccp4bb] adxv
>> >>> > From: mark.x.bro...@gmail.com
>> >>> > To: ccp4...@hotmail.com
>> >>> > CC: CCP4BB@jiscmail.ac.uk
>> >>> >
>> >>> > Dear Rajesh,
>> >>> > Are you using the Openmotif library? If so, do you
>> >>> > have an XKeysymDB file installed?
>> >>> > In as shell, issue:
>> >>> > $ locate XKeysymDB
>> >>> > You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
>> >>> > elsewhere [1].
>> >>> > I suspect you're not the only one to have seen this [2].
>> >>> >
>> >>> > I hope this helps.
>> >>> >
>> >>> > Mark
>> >>> > [1]
>> >>>
>> >>> ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
>> >>> > [2] http://sbgrid.org/news/newsletters/2009/06 (search for the
>> >>> > string "adxv")
>> >>> >
>> >>> >
>> >>> > On 20 November 2011 19:45, Rajesh kumar  wrote:
>> >>> > >
>> >>> > > Dear Tim,
>> >>> > > Thanks. Your suggestion of adding to PATH works and its not
>> >>> > > completely functional may
>> >>> be due to the Ximg/ssh or some thing to do with display.
>> >>> > > All three windows opened but couldn't open any image as it didn't
>> >>> > > display in the list
>> >>> of autoload window. Pattern shows *.0.
>> >>> > >
>> >>> > > $adxv pin8_1_180.img
>> >>> > >
>> >>> > > (standard_in) 1: parse error
>> >>> > > (standard_in) 1: parse error
>> >>> > > (standard_in) 1: parse error
>> >>> > > beam_center x = pixels , mm
>> >>> > > beam_center y = pixels , mm
>> >>> > > distance = mm
>> >>> > > overload = counts
>> >>> > > pixelsize = 0.172 mm
>> >>> > > wavelength = Angstroem
>> >>> > > Adxv Version 1.9.4-beta
>> >>> > > Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems
>> >>> > > Corporation
>> >>> > > Using 24-bit TrueColor visual
>> >>> > > Warning: translation table syntax error: Unknown keysym name:
>> >>> > > osfActivate
>> >>> > > Warning: ... found while parsing ':osfActivate:
>> >>> > > ManagerParentActivate()'
>> >>> > > Warning: String to TranslationTable conversion encountered errors
>> >>> > > Warning: translation table syntax error: Unknown keysym name:
>> >>> > > osfBeginLine
>> >>> > > Warning: ... found while parsing ':osfBeginLine:
>> >>> > > ManagerGadgetTraverseHome()'
>> >>> > > Warning: String to TranslationTable conversion encoun

Re: [ccp4bb] adxv

[AFL]

Rajesh,

 I think there is a simpler explanation to your problems but we need to 
go back to the installation of adxv on your linux machine.


 How did you extract adxv binary from the *.gz file?

 I've actually learned yesterday that if you use graphic tools to 
extract the binary the resulting file will not be fully functional! 
Windows open but the file selection dialogue is locked and the selection 
pattern is 0.*.


 Use command line 'gunzip' to extract the binary.
 Don't forget to 'chmod +x' on the resulting file and you should have a 
working adxv.


Andrzej

On 11/22/11 3:07 PM, Ian Tickle wrote:

Rajesh

I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp etc)
over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat) server
with no problems at all.

I suspect your  xming either just doesn't have the requisite X11 libs
or somehow they have not gotten installed on your system.  Can you try
Cygwin/X11, it's very easy to install.

Cheers

-- Ian

On 22 November 2011 13:49, Rajesh kumar  wrote:

Dear Tim,
Yes, I have windows 7 computer and use ccp4 and phenix through xming/putty
and I run them over linux lab computer.
Sorry if I have confused you all with insufficient information.
On the lab linux system,  I installed everything you suggested in BASH and
it works but not completely.
Core manager kind of not interested to look in to it and I dont know much to
understand everything you nice people saying here.
So instead I used idiffdisp and it opens the image. But wanted adxv to work
thats all.
Thanks
Raj

Date: Tue, 22 Nov 2011 14:41:00 +0100
From: t...@shelx.uni-ac.gwdg.de
To: ccp4...@hotmail.com
CC: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] adxv

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Rajesh,

are you saying that the computer you are sitting in front of is a
windows computer?
Are you sure you have been using CCP4 and phenix through an
ssh-connection and not the respective windows-binaries?

I am not familiar with windows and the possible existence of
X11-clients, but I would think that most suggestions to you assumed that
your client computer was also a linux-machine.

Cheers,
Tim

On 11/22/2011 02:27 PM, Rajesh kumar wrote:


I don't know if I need that installed on my windows computer terminal.On
the server also I could run adxv. Thought of using other ccp4 utilities.
Thanks for everyone for the help. I give up.
Regards,Rajesh


Date: Mon, 21 Nov 2011 11:36:14 -0500
From: ber...@upstate.edu
Subject: Re: [ccp4bb] adxv
To: CCP4BB@JISCMAIL.AC.UK

yum install lesstif ?

but wouldn't the motif stuff be required for the X-server, i.e. your
terminal, not for the
server running adxv?

Rajesh kumar wrote:

Dear Mark,

$ locate XKeysymDB - didnt come with any thing suggests probably
openmotif lib is not
installed.
I linux server has Fedora and I am using latest version of Adxv so
details on the sbgrid
suggest its same problem.

So how would I fix this.

Thanks for your time.

Regards
Rajesh



Date: Sun, 20 Nov 2011 23:18:32 +
Subject: Re: [ccp4bb] adxv
From: mark.x.bro...@gmail.com
To: ccp4...@hotmail.com
CC: CCP4BB@jiscmail.ac.uk

Dear Rajesh,
Are you using the Openmotif library? If so, do you
have an XKeysymDB file installed?
In as shell, issue:
$ locate XKeysymDB
You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
elsewhere [1].
I suspect you're not the only one to have seen this [2].

I hope this helps.

Mark
[1]


ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt

[2] http://sbgrid.org/news/newsletters/2009/06 (search for the
string "adxv")


On 20 November 2011 19:45, Rajesh kumar  wrote:


Dear Tim,
Thanks. Your suggestion of adding to PATH works and its not
completely functional may

be due to the Ximg/ssh or some thing to do with display.

All three windows opened but couldn't open any image as it didn't
display in the list

of autoload window. Pattern shows *.0.


$adxv pin8_1_180.img

(standard_in) 1: parse error
(standard_in) 1: parse error
(standard_in) 1: parse error
beam_center x = pixels , mm
beam_center y = pixels , mm
distance = mm
overload = counts
pixelsize = 0.172 mm
wavelength = Angstroem
Adxv Version 1.9.4-beta
Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems
Corporation
Using 24-bit TrueColor visual
Warning: translation table syntax error: Unknown keysym name:
osfActivate
Warning: ... found while parsing ':osfActivate:
ManagerParentActivate()'
Warning: String to TranslationTable conversion encountered errors
Warning: translation table syntax error: Unknown keysym name:
osfBeginLine
Warning: ... found while parsing ':osfBeginLine:
ManagerGadgetTraverseHome()'
Warning: String to TranslationTable conversion encountered errors
Warning: translation table syntax error: Unknown keysym name:
osfHelp
Warning: ... found while parsing ':osfHelp:
ManagerGadgetHelp()'
Warning: String to TranslationTable conversion encountered errors
Warning: translation table syntax error: Unkno

Re: [ccp4bb] adxv

[David Waterman]

Hi Rajesh,

A simple thing I would try first is to try to open a different image. I'm a
bit suspicious about yours given the error messages you sent. Is this from
a Pilatus detector? The line "pixelsize = 0.172 mm" suggests this is so,
but at the bottom below all the warnings it looks like this value is being
treated as a file: "No such file: 0.172".

ADXV can be used to open Pilatus images, in CBF format, but as I remember
you need a special start up script to do it. To rule out the X display
stuff as the source of your problems, perhaps try opening some images that
we know should work with ADXV. Harry has a set of images as part of the
iMosflm tutorial that would do:
http://www.ccp4.ac.uk/autostruct/testdata/mosflm/hg_images.tar, linked from
http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver105/.

Cheers

-- David


On 22 November 2011 14:13, AFL  wrote:

> Rajesh,
>
>  I think there is a simpler explanation to your problems but we need to go
> back to the installation of adxv on your linux machine.
>
>  How did you extract adxv binary from the *.gz file?
>
>  I've actually learned yesterday that if you use graphic tools to extract
> the binary the resulting file will not be fully functional! Windows open
> but the file selection dialogue is locked and the selection pattern is 0.*.
>
>  Use command line 'gunzip' to extract the binary.
>  Don't forget to 'chmod +x' on the resulting file and you should have a
> working adxv.
>
> Andrzej
>
>
> On 11/22/11 3:07 PM, Ian Tickle wrote:
>
>> Rajesh
>>
>> I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp etc)
>> over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat) server
>> with no problems at all.
>>
>> I suspect your  xming either just doesn't have the requisite X11 libs
>> or somehow they have not gotten installed on your system.  Can you try
>> Cygwin/X11, it's very easy to install.
>>
>> Cheers
>>
>> -- Ian
>>
>> On 22 November 2011 13:49, Rajesh kumar  wrote:
>>
>>> Dear Tim,
>>> Yes, I have windows 7 computer and use ccp4 and phenix through
>>> xming/putty
>>> and I run them over linux lab computer.
>>> Sorry if I have confused you all with insufficient information.
>>> On the lab linux system,  I installed everything you suggested in BASH
>>> and
>>> it works but not completely.
>>> Core manager kind of not interested to look in to it and I dont know
>>> much to
>>> understand everything you nice people saying here.
>>> So instead I used idiffdisp and it opens the image. But wanted adxv to
>>> work
>>> thats all.
>>> Thanks
>>> Raj
>>>
 Date: Tue, 22 Nov 2011 14:41:00 +0100
 From: t...@shelx.uni-ac.gwdg.de
 To: ccp4...@hotmail.com
 CC: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] adxv

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Rajesh,

 are you saying that the computer you are sitting in front of is a
 windows computer?
 Are you sure you have been using CCP4 and phenix through an
 ssh-connection and not the respective windows-binaries?

 I am not familiar with windows and the possible existence of
 X11-clients, but I would think that most suggestions to you assumed that
 your client computer was also a linux-machine.

 Cheers,
 Tim

 On 11/22/2011 02:27 PM, Rajesh kumar wrote:

>
> I don't know if I need that installed on my windows computer
> terminal.On
> the server also I could run adxv. Thought of using other ccp4
> utilities.
> Thanks for everyone for the help. I give up.
> Regards,Rajesh
>
>  Date: Mon, 21 Nov 2011 11:36:14 -0500
>> From: ber...@upstate.edu
>> Subject: Re: [ccp4bb] adxv
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> yum install lesstif ?
>>
>> but wouldn't the motif stuff be required for the X-server, i.e. your
>> terminal, not for the
>> server running adxv?
>>
>> Rajesh kumar wrote:
>>
>>> Dear Mark,
>>>
>>> $ locate XKeysymDB - didnt come with any thing suggests probably
>>> openmotif lib is not
>>> installed.
>>> I linux server has Fedora and I am using latest version of Adxv so
>>> details on the sbgrid
>>> suggest its same problem.
>>>
>>> So how would I fix this.
>>>
>>> Thanks for your time.
>>>
>>> Regards
>>> Rajesh
>>>
>>>
>>>  Date: Sun, 20 Nov 2011 23:18:32 +
 Subject: Re: [ccp4bb] adxv
 From: mark.x.bro...@gmail.com
 To: ccp4...@hotmail.com
 CC: CCP4BB@jiscmail.ac.uk

 Dear Rajesh,
 Are you using the Openmotif library? If so, do you
 have an XKeysymDB file installed?
 In as shell, issue:
 $ locate XKeysymDB
 You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
 elsewhere [1].
 I suspect you're not the only one to have seen this [2].

 I hope this helps.

 Mark
 [1]

>>>
>

Re: [ccp4bb] adxv

[Andrew Purkiss]

Hi Rajesh,

That is a very old version (1.9.4) of ADXV.

Try the current version from here

http://www.scripps.edu/~arvai/adxv/

version 1.9.8 works fine for us and opens Pilatus data without modifying
the files. 

Hope this helps.

Andrew Purkiss

-- 
X-ray Laboratory Manager,
London Research Institute,
Cancer Research UK. 

On Tue, 2011-11-22 at 09:30 -0500, Rajesh kumar wrote:
> Hi Andrzej,
> 
> 
> I used exactly what you have suggested.
> Downloaded file adxv.i686FC2.tgz from some place.
> untar Gunzip  so I get a folder adxv.1686FC2 which has adxv and
>   adxv.1686FC2_static files.
> I made both executable using chmod.
> I put the PATH in .bashrc
> If I run this command in the folder where images are then
> it opens with "Windows open but the file selection dialogue is locked
> and the selection  pattern is 0.*."
> 
> 
> But not functional  and get  the error I posted recently
> 
> 
> pin8]$ adxv pin8_1_144.img
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> beam_center x = pixels , mm
> beam_center y = pixels , mm
> distance = mm
> overload = counts
> pixelsize = 0.172 mm
> wavelength = Angstroem
> 
> 
> Adxv Version 1.9.4-beta
> Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems
> Corporation
> Using 24-bit TrueColor visual
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  ManagerParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfBeginLine
> Warning: ... found while parsing ':osfBeginLine:
> ManagerGadgetTraverseHome()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfHelp
> Warning: ... found while parsing ':osfHelp:
>ManagerGadgetHelp()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  ManagerParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfHelp
> Warning: ... found while parsing ':osfHelp:
>  Help()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfCancel
> Warning: ... found while parsing ':osfCancel:  MenuEscape()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfSelect
> Warning: ... found while parsing ':osfSelect:
>  ArmAndActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: Locale not supported for XmbTextListToTextProperty
> Warning: Cannot convert XmString to compound text
> Warning: translation table syntax error: Unknown keysym name:
>  osfPrimaryPaste
> Warning: ... found while parsing ':m
> osfPrimaryPaste:cut-primary()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfActivate
> Warning: ... found while parsing ':osfActivate:
>  PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfSelect
> Warning: ... found while parsing ':osfSelect:
>  ArmAndActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfPrimaryPaste
> Warning: ... found while parsing ':m
> osfPrimaryPaste:cut-primary()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:
>  osfSelect
> Warning: ... found while parsing ':osfSelect:
>  ManagerGadgetSelect()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: U

[ccp4bb] BSG Winter BCA meeting - registration closes 2 Dec

[Robin Owen]

Dear all,

A brief email to let you know that registration for this meeting will close on 
Friday 2 Dec, so if you would like to attend you have a week and a bit to 
register.

Registration details and a full program can be found at the meeting webpage
http://www.diamond.ac.uk/Home/Events/BCA.html
There is a very strong scientific program this year so please do take a look 
and register if you can make it to Diamond on 14 Dec.

For those that have already registered please note that registration and coffee 
will now be in the Atrium of Diamond House not in the Research Complex as 
previously advertised.

All the best,
Robin



Dr Robin Owen
Beamline Scientist
Microfocus Macromolecular Crystallography
Diamond Light Source, UK
Tel: +44 1235 77 8522
email robin.o...@diamond.ac.uk
web http://www.diamond.ac.uk

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robin Owen
Sent: 10 October 2011 13:31
To: ccp4bb
Subject: [ccp4bb] BSG Winter BCA meeting @ Diamond/RCaH 14 Dec

Dear all,

The Biological Structures Group Winter BCA Meeting will be held on Wednesday 
December 14th 2011 at Diamond Light Source / the Research Complex at Harwell.

The general theme of the meeting is 'from macromolecular to supramolecular'. 
The aim of the meeting is to highlight challenges in structure solution of 
large assemblies from crystallisation to data collection and structure 
solution, as well as focusing on the biological insight such structures can 
provide.

The meeting will be held on Wednesday December 14th 2011. Registration starts 
from 10:00 am in the Research Complex foyer with talks starting at 11:00. For 
further details, speaker list and to register visit

http://www.diamond.ac.uk/Home/Events/BCA.html

If you have any questions regarding the meeting please contact me.

All the best,

Robin


Dr Robin Owen
Beamline Scientist
Microfocus Macromolecular Crystallography
Diamond Light Source, UK
Tel: +44 1235 77 8522
email robin.o...@diamond.ac.uk
web http://www.diamond.ac.uk

Re: [ccp4bb] help with the structures

[Eleanor Dodson]

It is hard to make sensible comments without seeing your maps.

In these cases I use coot to validate.

Run the ramachandran check - click on all outliers and see if what the 
electron density looks like. Sometimes you do see indicators on how to 
make corrections.  Sometimes you have a CIS peptide which has been 
forced to be TRANS - that can cause disturbances in neighbouring 
residues too.


For the clashes - I use the REFMAC listing to see where they are - again 
check the density - and rebuild if possible. Some residues may simply be 
invisible, then I put the occupancy to 0.00 .


Bad rotamers and angles can be caused by crystal packing but again check..

And remember that in most structures there are poorly ordered regions - 
if the offending residues are there you probably cant refine them..


2.74A is not high resolution, so you will have problems correcting 
everything

Eleanor


On 11/22/2011 01:41 PM, Rajesh kumar wrote:


Dear Prof Dodson,
I agree with you. Instead of further refining mutant structure, right now I am 
looking in to Apo structure. Which is at 2.74A and has R/freeR  22.7/27.9. But 
I have a molprobity profile like this
Clashscore, all atoms:  33.73   50th percentile* (N=185, 2.740Å ± 0.25Å)Geometry   
 Poor rotamers   8.11%   Goal:<1%Ramachandran outliers0.52%   
Goal:<0.2%Ramachandran favored   95.19%  Goal:>98%Cβ deviations>0.25Å 
 2   Goal: 0MolProbity score^3.0453rd percentile* (N=5278, 
2.740Å ± 0.25Å)Residues with bad bonds:   0.00%   Goal: 0%Residues with bad angles:   
0.34%   Goal:<0.1%
If i fix the all the possible outliers and refine the structure it wouldn't 
improve the molprobity scores. I am not happy about the above scores at all.  I 
am wondering if this is an indication of any wrong in the structure or is this 
common for an enzyme. I have reprocessed  the data to make sure space group is 
same C2221.Any help would help me understand this and learn more.
ThanksRaj

Date: Mon, 21 Nov 2011 12:27:04 +
From: c...@ysbl.york.ac.uk
To: ccp4...@hotmail.com
CC: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] help with the  structures

I think you are proving yet again that refinement at 3.3A is not easy.
Indeed there are probably multiple conformations for parts of the
structure and that may well be why your data is at low resolution and
anisotropic.  Maybe this is the best you can do..

I think I would make sure the apo structure is as good as it can be,
then fit that to the 3.3A data set, and only use that 3.3A data to
deduce whatever features differ from the APO structure.

   Eleanor
On 11/19/2011 12:09 PM, Rajesh kumar wrote:


Dear All,



We have an anisotropic dataset of 3.3 A  and it was solved (not by me) with 
P6522 with R/freeR
29.1/37.3.



I got the corrected
mtz file by plugging in the .HKL (P6122) file to anisotropy diffraction server 
at
2.04 A. I reindexed this p6122 to p6522 and extended the resolution and refined
(refmac) the structure to R/freeR
36.40/38.50. With aotoncs option, fixing all Ramachnadran and rotamer
outliers I got it 30/32. When I added waters and it went down to 27.5/31.2. At
this point I recognized that my new .mtz file from anisotropy server has
different R flag than the earlier one (3.3A) so I copied the R flag and did 
refinemnt  to get R/Rfree 0.2682/0.3247. When I looked at
the refined structure I found  more outliers
than I fixed in earlier round. I did fix all the outliers and without NCS and
waters it gives R/Rfree 0.2906/0.3325. At all the stages I look at outliers at
molprobity server which suggested structure is 10th percentile and after
refinement more outliers comes back. At stage-1 map looked far better so was
happy that anisotropy correction has worked for me (this was my first time
handling this type of dataset) but further refinement didn’t make it look any
better.I use both refmac and autoBuster for refinement. 
http://www.flickr.com/photos/rajesh_ccp4/sets/72157628048657095/
This protein is an human enzyme and a bacterial homologue
which has 38% identity has been used to solve the  Apo structure (2.7 A, 
pC2221, R/freeR
23.03/27.96, molprobity is around 50th percentile). I looked in to this I try 
to fix all the outliers and try to improve
molprobity score but it just refused to improve as after refinement I get more
outliers. This Apo structure was used to solve the mutant structure at
3.3 A.  I believe that both structure could
have better R/freeR and excellent molprobity scores than what they have now. I 
am not able to recognise
if there is any problem in Apo structure and if errors have come to mutant so
both of them refuse to improve.


I wondered if there is any model bias (I don’t know if it’s
the case but nothing was coming to my mind) so thought using ARP/wARP classic
to build model from existing model but it complained that "The wilson plot
is very bad and ARp/wARP is very unlikely to run in a sensible way. Please
check your da

Re: [ccp4bb] adxv-SOLVED

[Ian Tickle]

Hi Rajesh

The fonts have to be installed where they are needed, i.e. where the
display of the GUI is happening, on the X server (e.g. your Windows
PC), not on the compute server (your Linux box).  I had problems with
missing fonts in Cygwin when I first installed it.  Cygwin doesn't
install all the fonts by default, I had to specifically ask for them
(I just installed all the fonts I could find in the Cygwin software
installation menu).  Can't help you with xming though, I've no idea if
it has all the fonts that adxv is asking for.

According to Wikipedia "xming is described as simple and easier to
install though less configurable than other popular free choices like
Cygwin/X" so it may not be fully functional.

Cheers

-- Ian

On 22 November 2011 15:37, Rajesh kumar  wrote:
>
> Dear All,
>
> All the suggestions helped me to solve this problem on my unix server.
>
>  Earlier I had 1.9.4   downloaded from
> http://pilatus.web.psi.ch/datasets.htm.
> untar gunzip yielded two file adxv  and adxv.i686FC2_static and they were
> made xecutable.
> I wrote the path to .bashrc.
> So still had windows locking with out opening anything.
>
> I updated now to 1.9.8  and it had only one file adxv.i686FC2.
> Copied this file to the adxv folder and start opening the file with
> adxv.i686FC2 instead of adxv.
> Its working with  some font error. Running "adxv" gives same old error. I
> dont worry about this any more.
>
> Since it works on Linux server, I could open on my windows laptop through
> XMING without any problem.
>
> I want to thank Tim, Andrew, David, Ian, Andrzej, Mark, and Edward for their
> valubale time an dsuggestions.
>
> I still have some error but I guess its font error. I downloaded the fonts
> to my working directory and tried adxv -fp fonts/ and adxv.i686FC2 -fp
> fonts/ and it didnt woked I guess.
> But its not effecting my work so I dont worry.
>
> In case any one wanted to know, here it is.
> tmp]$ adxv.i686FC2 /home/rajesh/Download/ALS831_lyso_Gd_001.img
> Adxv Version 1.9.8
> Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation
> Using 24-bit TrueColor visual
> adxv: Can not open font:
> "-*-lucidatypewriter-medium-r-*-*-*-120-75-75-*-*-iso8859-1". Trying:
> "fixed"
> adxv: Can not open font: "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1".
> Trying: "-urw-urw bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"
> adxv: Can not open font: "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1".
> Trying: "fixed"
> Warning: Cannot convert string
> "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
> Warning: Cannot convert string
> "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
> adxv: Can not open font: "-*-lucida-bold-r-*-*-*-180-75-75-*-*-iso8859-1".
> Trying: "fixed"
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-180-75-75-m-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-180-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-medium-r-*-*-*-100-75-75-*-*-iso8859-1" Trying:
> "-urw-urw bookman l-medium-r-*-*-*-100-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-medium-r-*-*-*-80-75-75-*-*-iso8859-1" Trying:
> "-urw-urw bookman l-medium-r-*-*-*-80-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-120-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
> Loading /home/yogesha/Download/ALS831_lyso_Gd_001.img
> 3072 x 3072 pixels
> Distance: 250 mm, Lambda: 0.979 A
> MaxI: 32609, AvgI: 42
> 0 Overflows
> Scale factor: 0.19
>
>
>
>
> THANKS for the HELP
>
> Warm regards,
> rajesh
>
>
>> Subject: Re: [ccp4bb] adxv
>> From: a.purk...@mail.cryst.bbk.ac.uk
>> To: ccp4...@hotmail.com
>> CC: CCP4BB@JISCMAIL.AC.UK
>> Date: Tue, 22 Nov 2011 14:41:19 +
>>
>> Hi Rajesh,
>>
>> That is a very old version (1.9.4) of ADXV.
>>
>> Try the current version from here
>>
>> http://www.scripps.edu/~arvai/adxv/
>>
>> version 1.9.8 works fine for us and opens Pilatus data without modifying
>> the files.
>>
>> Hope this helps.
>>
>> Andrew Purkiss
>>
>> --
>> X-ray Laboratory Manager,
>> London Research Institute,
>> Cancer Research UK.
>>
>> On Tue, 2011-11-22 at 09:30 -0500, Rajesh kumar wrote:
>> > Hi Andrzej,
>> >
>> >
>> > I used exactly what you have suggested.
>> > Downloaded file adxv.i686FC2.tgz from some place.
>> > untar Gunzip so I get a folder adxv.1686FC2 which has adxv and
>> > adxv.1686FC2_static files.
>> > I made both executable using chmod.
>> > I put the PATH in .bashrc
>> > If I run this command in the folder where images are then
>> > it opens with "Windows open but the file s

Re: [ccp4bb] Coot, RH6.1 x86 linux

[Paul Emsley]

On 22/11/11 00:31, Santarsiero, Bernard D. wrote:

I just installed CCP4-6.2.0 and COOT on a Red Hat v6.1, x86, linux
workstation. Some of the menus, along the right edge, are gray buttons on
gray background. Where is the preferences file to change the colors of the
menu buttons? The menus across the top of the window are fine.



Hello Bernie,

The buttons icons to which you refer are svg icons.  There is something 
old/strange about your system that fails to load/convert svg icons (it 
may be the gtk/gdk pixbuf loader). I don't have further details.


Hope that helps...

Paul.

Re: [ccp4bb] Movements of domains

[Pete Meyer]

Filip Van Petegem wrote:


In a case I'm currently looking at, I'm particularly dealing with cryo-EM data, 
not X-ray structures, but with the same underlying principles: what are the 
odds that all pixels of the map move together in the same direction?


I suspect you may be better off asking an EM person (or on an EM list), 
due to the peculiarities of cryo-EM reconstruction.  If I'm recalling 
correctly, EM resolution is determined by Fourier shell correlation so 
it might not have a one-to-one relationship to optical resolution.  In 
addition, there usually is some uncertainty in converting voxel 
distances to physical distances - so an optical resolution in terms of 
Anstroms would need to be converted.


As a few others have pointed out, you'd also need to account for 
coordinate uncertainty.  For 3d reconstruction, you've got uncertainties 
from particle image classification, image alignment, possibly 
conformational heterogeneity, and possibly uncertainties in the voxel 
position (due to interpolation) and voxel values (and the voxel to 
Angstrom conversion).  My understanding of EM is limited to what I need 
to know to deal with EM data from collaborators, or how to use some EM 
software with low-resolution x-ray data - so I may be missing a few 
things (or pointing out problems that have been dealt with).


The short version, or at least my take on it, is that you may not be 
able to get a mathematically/statistically rigorous test for if the 
movement of a set of voxels is significant or not - but asking an EM 
person could probably give you a better answer.


Pete



As mentioned for X-ray structures, a Luzzati analysis may give information 
about the positional errors, but there should be an increased resolution when 
comparing domain movements, because it's unlikely for all atoms to have an 
error in the same direction.

Filip

On Mon, Nov 21, 2011 at 2:16 PM, Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>> wrote:
Just to clarify: I think the question is about the mathematical sense
of "significance," and not the functional or physiological
significance, right? If I understand the question correctly, wouldn't
the reasoning be that admittedly each atom in the model has a certain
positional error, but all together, it would be very unlikely for all
atoms to be skewed in the same direction?

Jacob



On Mon, Nov 21, 2011 at 4:04 PM, Filip Van Petegem
mailto:filip.vanpete...@gmail.com>> wrote:

Dear crystallographers,
I have a general question concerning the comparison of different
 structures.  Suppose you have a crystal structure containing a few domains.
 You also have another structure of the same, but in a different condition
(with a bound ligand, a mutation, or simply a different crystallization
condition,...).  After careful superpositions, you notice that one of the
domains has shifted over a particular distance compared to the other
domains, say  1-1.5 Angstrom.   This is a shift of the entire domain.  Now
how can you know that this is a 'significant' change?  Say the overall
resolution of the structures is lower than the observed distance (2.5A for
example).
Now saying that a 1.5 Angstrom movement of an entire domain is not relevant
at this resolution would seem wrong: we're not talking about some electron
density protruding a bit more in one structure versus another, but all of
the density has moved in a concerted fashion.  So this would seem 'real',
and not due to noise.   I'm not talking about the fact that this movement
was artificially caused by crystal packing or something similar. Just for
whatever the reason (whether packing, pH, ligand binding, ...), you simply
observe the movement.
So the question is: how you can state that a particular movement was
'significantly large' compared to the resolution limit?  In particular, what
is the theoretical framework that allows you to state that some movement is
signifcant? This type of question of course also applies to other methods
such as cryo-EM.  Is a 7A movement of an entire domain 'significant' in a
10A map? If it is, how do we quantify the significance?
If anybody has a great reference or just an individual opinion, I'd like to
hear about it.
Regards,
Filip Van Petegem

--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/





--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***



--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: fili

Re: [ccp4bb] dark progression of radiation damage

[James Holton]

Mark may or may not have meant what I think he meant, but it did remind 
me of the following passage from Blundell and Johnson (1976):
"The chain reaction initiated by fee radical formation probably accounts 
for the common observation that radiation damage effects in protein 
crystals continue, even after the X-ray shutter has been closed."


Perhaps for no other reason than it appears in The Book, this 
expectation of "dark progression" seems to continue to this day?  
However, I was recently challenged by a colleague to find a paper or a 
system that demonstrated dark progression of damage at "room" 
temperature, and I have to admit I can't find one.  Any help?



I myself once convinced myself that I had a crystal that had "healed" 
after sitting under lN2 for a week.  I had been "burning" it in a rad 
dam study, but ran out of time and had to dismount it and continue the 
experiment on my next staff shift.  I was quite excited to see that it 
diffracted better the second time!  Unfortunately, after repeating this 
experiment several times and making sure that I had the beam hitting 
exactly the same part of the crystal after the "delay" I was 
disappointed to find that the damage always "picked up where it left 
off".  So, the most likely explanation for my crystal "healing" was that 
my alignment was slightly off the second time and I was shooting some 
"fresh" crystal that had remained outside the beam for the first round 
of "burning".  I never did publish anything about that.  In fact, I'm 
not sure I could publish it if I tried!


I have now heard three anecdotal stories about "attenuation" making 
crystals endure more dose before it "dies", but all of these seem to 
have arisen from an error in the attenuation factor.  Attenuators not 
only absorb photons, but they can also blow up the beam size, making the 
photons/area smaller than the "% transmittance" in the GUI would lead 
you to believe.  Best way to check that the attenuation is what you 
think it is is to look at the scale factors when scaling the two runs 
together, they should be ~1 if the integrated photons/area, crystal 
volume, wavelength, etc. was the same.


However, that is a "dose rate effect", and although "dark progression" 
implies a dose-rate effect, the converse is not necessarily true.  There 
is much debate about this in the rad dam field, but it seems whenever a 
traditionally-held belief like "dark progression" is challenged, the 
rest of the MX community seems to dismiss it as "oh, you're just working 
on lysozyme".  Well, what should we be working on?


-James Holton
MAD Scientist


On 11/20/2011 5:22 PM, Sanishvili, Ruslan wrote:

Hi James,
I don't think the comment you referenced meant to imply "dark progression of radiation 
damage. If I remember from the recent thread, it was to say that if you can only collect few 
(3?) shots from one crystal before it's "too dead" and you use 1st of these shots to 
devise the strategy, then you are wasting your crystals and will never get you data. Of 
course, you don't have to use so much flux for the image which is meant only for defining the 
orientation but it was omitted from that comment.

Now back to the rest of your message. I can add another warning observation:
If a cryo-cooled crystal was exposed long enough (i.e. for data collection) then stored 
(by a robot) and then mounted again, some times one sees that it had 
"exploded". Such an explosion, presumably a hydrogen gas escape, can be seen 
almost always if a crystal is wormed up after long data collection. The fact that 
robot-stored crystals sometimes display same behavior, indicates that a crystal in the 
arms of the robot can worm up somewhat. Therefore, comparing diffraction before and after 
storage is not always valid.
Also beware of comparing diffraction quality from different parts of the 
crystal as large crystals are almost never homogeneous.
Cheers,
Nukri




-Original Message-
From: CCP4 bulletin board on behalf of James Holton
Sent: Sun 11/20/2011 2:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] dark progression of radiation damage


Mark's comment below reminded me of a quandary that is starting to
develop in the rad dam field.  The idea of the "free radical cascade"
continuing to damage protein crystals even after the beam has been
turned off seems to have originated on page 253 of Blundell and Johnson
(1976), and I think most of us have had the unpleasant experience of
loosing diffraction after a "delay" in data collection.  However, can
one be sure that the incident beam alignment was the same if the "delay
in data collection" was due to a storage ring dump, or a filament
change?  Can one be sure that a crystal stored under cryo never ever got
warmed up (like during mounts and dismounts, or perhaps a colleague
making an undocumented late-night rummage through the storage dewar)?
Can one be sure that a crystal at room temperature wasn't just drying
up?  Can one be sure that the damage did

Re: [ccp4bb] adxv-SOLVED

[Pius Padayatti]

Rajesh,
The fonts error please follow the guidelines from following link

http://www.scripps.edu/~arvai/adxv.html

see relevant parts under the heading questions
it did solve issues for me
cheers
psp

On Tue, Nov 22, 2011 at 10:37 AM, Rajesh kumar  wrote:
>
> Dear All,
>
> All the suggestions helped me to solve this problem on my unix server.
>
>  Earlier I had 1.9.4   downloaded from
> http://pilatus.web.psi.ch/datasets.htm.
> untar gunzip yielded two file adxv  and adxv.i686FC2_static and they were
> made xecutable.
> I wrote the path to .bashrc.
> So still had windows locking with out opening anything.
>
> I updated now to 1.9.8  and it had only one file adxv.i686FC2.
> Copied this file to the adxv folder and start opening the file with
> adxv.i686FC2 instead of adxv.
> Its working with  some font error. Running "adxv" gives same old error. I
> dont worry about this any more.
>
> Since it works on Linux server, I could open on my windows laptop through
> XMING without any problem.
>
> I want to thank Tim, Andrew, David, Ian, Andrzej, Mark, and Edward for their
> valubale time an dsuggestions.
>
> I still have some error but I guess its font error. I downloaded the fonts
> to my working directory and tried adxv -fp fonts/ and adxv.i686FC2 -fp
> fonts/ and it didnt woked I guess.
> But its not effecting my work so I dont worry.
>
> In case any one wanted to know, here it is.
> tmp]$ adxv.i686FC2 /home/rajesh/Download/ALS831_lyso_Gd_001.img
> Adxv Version 1.9.8
> Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation
> Using 24-bit TrueColor visual
> adxv: Can not open font:
> "-*-lucidatypewriter-medium-r-*-*-*-120-75-75-*-*-iso8859-1". Trying:
> "fixed"
> adxv: Can not open font: "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1".
> Trying: "-urw-urw bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"
> adxv: Can not open font: "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1".
> Trying: "fixed"
> Warning: Cannot convert string
> "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
> Warning: Cannot convert string
> "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
> adxv: Can not open font: "-*-lucida-bold-r-*-*-*-180-75-75-*-*-iso8859-1".
> Trying: "fixed"
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-180-75-75-m-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-180-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-medium-r-*-*-*-100-75-75-*-*-iso8859-1" Trying:
> "-urw-urw bookman l-medium-r-*-*-*-100-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-medium-r-*-*-*-80-75-75-*-*-iso8859-1" Trying:
> "-urw-urw bookman l-medium-r-*-*-*-80-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-120-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
> adxv: Unable to open font:
> "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw
> bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
> Loading /home/yogesha/Download/ALS831_lyso_Gd_001.img
> 3072 x 3072 pixels
> Distance: 250 mm, Lambda: 0.979 A
> MaxI: 32609, AvgI: 42
> 0 Overflows
> Scale factor: 0.19
>
>
>
>
> THANKS for the HELP
>
> Warm regards,
> rajesh
>
>
>> Subject: Re: [ccp4bb] adxv
>> From: a.purk...@mail.cryst.bbk.ac.uk
>> To: ccp4...@hotmail.com
>> CC: CCP4BB@JISCMAIL.AC.UK
>> Date: Tue, 22 Nov 2011 14:41:19 +
>>
>> Hi Rajesh,
>>
>> That is a very old version (1.9.4) of ADXV.
>>
>> Try the current version from here
>>
>> http://www.scripps.edu/~arvai/adxv/
>>
>> version 1.9.8 works fine for us and opens Pilatus data without modifying
>> the files.
>>
>> Hope this helps.
>>
>> Andrew Purkiss
>>
>> --
>> X-ray Laboratory Manager,
>> London Research Institute,
>> Cancer Research UK.
>>
>> On Tue, 2011-11-22 at 09:30 -0500, Rajesh kumar wrote:
>> > Hi Andrzej,
>> >
>> >
>> > I used exactly what you have suggested.
>> > Downloaded file adxv.i686FC2.tgz from some place.
>> > untar Gunzip so I get a folder adxv.1686FC2 which has adxv and
>> > adxv.1686FC2_static files.
>> > I made both executable using chmod.
>> > I put the PATH in .bashrc
>> > If I run this command in the folder where images are then
>> > it opens with "Windows open but the file selection dialogue is locked
>> > and the selection pattern is 0.*."
>> >
>> >
>> > But not functional and get the error I posted recently
>> >
>> >
>> > pin8]$ adxv pin8_1_144.img
>> > (standard_in) 1: parse error
>> > (standard_in) 1: parse error
>> > (standard_in) 1: parse error
>> > beam_center x = pixels , mm
>> > beam_center y = pixels , mm
>> > distance = mm
>> > overload = counts
>> > pixelsize = 0.172 mm
>> > wavelength = Angstroem
>> >
>> >
>> > Adxv Version 1.9.4-beta
>> > Copyright (C) 1994-2007 by Andrew Arvai, Ar

Re: [ccp4bb] adxv-SOLVED

[Ian Tickle]

On 22 November 2011 22:04, Pius Padayatti  wrote:
> Rajesh,
> The fonts error please follow the guidelines from following link
>
> http://www.scripps.edu/~arvai/adxv.html

OK the fonts you need are the ones mentioned above (in
http://www.scripps.edu/~arvai/adxv/fonts.tar.gz), BUT the installation
instructions there are for an X server running on Linux.  It won't do
you any good to install them on the Linux system disk, unless it
happens to be mounted on your Windows PC (possible though unlikely).
The logical place to install them is with the Xming X server on your
Windows PC (or you could put them on any disk that's mounted from your
Windows PC).  For that you need to follow these instructions:

http://www.straightrunning.com/XmingNotes/fonts.php

Cheers

Re: [ccp4bb] adxv-SOLVED WITH FONTS

[Rajesh kumar]

Dear Ian,
I installed the fonts from the link 
http://www.scripps.edu/~arvai/adxv.html.Everything works now on my linux 
system.There was no need of extra fonts on my xming  (I had already installed 
extra fonts from the link you have suggested) and it works just fine.
Thanks to your time to help.I also thank PSP for the valuable suggestions.
Thanks for everyone to help me to run adxv successfully.
Regards,Rajesh

> Date: Wed, 23 Nov 2011 00:19:36 +
> Subject: Re: [ccp4bb] adxv-SOLVED
> From: ianj...@gmail.com
> To: ccp4...@hotmail.com
> CC: CCP4BB@jiscmail.ac.uk; ppadaya...@gmail.com
> 
> On 22 November 2011 22:04, Pius Padayatti  wrote:
> > Rajesh,
> > The fonts error please follow the guidelines from following link
> >
> > http://www.scripps.edu/~arvai/adxv.html
> 
> OK the fonts you need are the ones mentioned above (in
> http://www.scripps.edu/~arvai/adxv/fonts.tar.gz), BUT the installation
> instructions there are for an X server running on Linux.  It won't do
> you any good to install them on the Linux system disk, unless it
> happens to be mounted on your Windows PC (possible though unlikely).
> The logical place to install them is with the Xming X server on your
> Windows PC (or you could put them on any disk that's mounted from your
> Windows PC).  For that you need to follow these instructions:
> 
> http://www.straightrunning.com/XmingNotes/fonts.php
> 
> Cheers
  

[ccp4bb] negative density in difference map

[Careina Edgooms]

Good morning CCP4 members

I have a question about a 2F0-Fc difference map that I calculated with Refmac. 
In some instances it gives me negative (red) density around part of a side 
chain and no positive density in sight. Furthermore the entire residue fits 
well into the blue density of the complete map, including the part with 
negative density. 

I am struggling to interpret this. Does the fact that it fits the blue density 
mean that the side chain is in the correct place or does the red blob on part 
of the side chain (eg on the sulphur in a Met residue) mean that something 
funky is happening with this side chain?

Thanks for any assistance
Careina