Re: [ccp4bb] Tcl error - Snow Leopard OSX

[William G. Scott]

Looks like ccp4 has a potential fix:

I'll try it and if it works will submit a fix:

http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html#blt_2.4z_problems



On Sep 15, 2009, at 10:17 PM, William G. Scott wrote:



On Sep 15, 2009, at 4:43 PM, José Trincão wrote:


Hello all,
I upgraded my Macbook Pro to snow leopard and followed William G.  
Scotts Crystallography on OSX wiki to install CCP4 using Fink. I  
used the 64bit install with full compilation, not the pre-compiled  
binaries. When I start ccp4i I get a warning:
Application initialization failed: version conflict for package  
"Tcl": have 8.5.7, need exactly 8.5
but everything seems to work until I try to see the log graphs,  
where I get the same error followed by:
Error in startup script: dlsym(0x1006c47f0, Blt_Unload): symbol not  
founddlsym(0x1006c47f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

  while executing
"load $library BLT"
  (procedure "LoadBLT" line 30)
  invoked from within
"LoadBLT 2.4 /sw64/lib/blt2.4"
  ("package ifneeded BLT 2.4" script)
  invoked from within
"package require BLT"
  (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/bin/loggraph.tcl" line 47)
  invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
  (file "/sw64/share/xtal/ccp4-6.1.2/bin/loggraph" line 5)




It looks like it is bltwish itself that is messed up for 64-bit.   
I'll complain.  To demonstrate:


cd /sw64/lib/blt2.4/demos
bltwish barchart1.tcl

Application initialization failed: version conflict for package  
"Tcl": have 8.5.7, need exactly 8.5
Error in startup script: dlsym(0x1006d11f0, Blt_Unload): symbol not  
founddlsym(0x1006d11f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

   while executing
"load $library BLT"
   (procedure "LoadBLT" line 30)
   invoked from within
"LoadBLT 2.4 /sw/lib/blt2.4"
   ("package ifneeded BLT 2.4" script)
   invoked from within
"package require BLT"
   (file "barchart1.tcl" line 3)


What can I do to get everything working?
Thanks

Jose

P.S. Special thanks to W.G.Scott for the wonderful Wiki!

Re: [ccp4bb] Tcl error - Snow Leopard OSX

[William G. Scott]

On Sep 15, 2009, at 4:43 PM, José Trincão wrote:


Hello all,
I upgraded my Macbook Pro to snow leopard and followed William G.  
Scotts Crystallography on OSX wiki to install CCP4 using Fink. I  
used the 64bit install with full compilation, not the pre-compiled  
binaries. When I start ccp4i I get a warning:
Application initialization failed: version conflict for package  
"Tcl": have 8.5.7, need exactly 8.5
but everything seems to work until I try to see the log graphs,  
where I get the same error followed by:
Error in startup script: dlsym(0x1006c47f0, Blt_Unload): symbol not  
founddlsym(0x1006c47f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

   while executing
"load $library BLT"
   (procedure "LoadBLT" line 30)
   invoked from within
"LoadBLT 2.4 /sw64/lib/blt2.4"
   ("package ifneeded BLT 2.4" script)
   invoked from within
"package require BLT"
   (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/bin/loggraph.tcl" line 47)
   invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
   (file "/sw64/share/xtal/ccp4-6.1.2/bin/loggraph" line 5)




It looks like it is bltwish itself that is messed up for 64-bit.  I'll  
complain.  To demonstrate:


cd /sw64/lib/blt2.4/demos
 bltwish barchart1.tcl

Application initialization failed: version conflict for package "Tcl":  
have 8.5.7, need exactly 8.5
Error in startup script: dlsym(0x1006d11f0, Blt_Unload): symbol not  
founddlsym(0x1006d11f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

while executing
"load $library BLT"
(procedure "LoadBLT" line 30)
invoked from within
"LoadBLT 2.4 /sw/lib/blt2.4"
("package ifneeded BLT 2.4" script)
invoked from within
"package require BLT"
(file "barchart1.tcl" line 3)


What can I do to get everything working?
Thanks

Jose

P.S. Special thanks to W.G.Scott for the wonderful Wiki!

Re: [ccp4bb] Tcl error - Snow Leopard OSX

[William G. Scott]

On Sep 15, 2009, at 4:43 PM, José Trincão wrote:


Hello all,
I upgraded my Macbook Pro to snow leopard and followed William G.  
Scotts Crystallography on OSX wiki to install CCP4 using Fink. I  
used the 64bit install with full compilation, not the pre-compiled  
binaries. When I start ccp4i I get a warning:
Application initialization failed: version conflict for package  
"Tcl": have 8.5.7, need exactly 8.5
but everything seems to work until I try to see the log graphs,  
where I get the same error followed by:
Error in startup script: dlsym(0x1006c47f0, Blt_Unload): symbol not  
founddlsym(0x1006c47f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

   while executing
"load $library BLT"
   (procedure "LoadBLT" line 30)
   invoked from within
"LoadBLT 2.4 /sw64/lib/blt2.4"
   ("package ifneeded BLT 2.4" script)
   invoked from within
"package require BLT"
   (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/bin/loggraph.tcl" line 47)
   invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
   (file "/sw64/share/xtal/ccp4-6.1.2/bin/loggraph" line 5)

What can I do to get everything working?
Thanks

Jose

P.S. Special thanks to W.G.Scott for the wonderful Wiki!


The version conflict thingie seems only to appear in 64-bit, oddly.   
As for the other, that looks much much worse.  Sorry.

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

[Pavel Afonine]

This is why phenix.refine by default outputs both maps: 2mFo-DFc 
"filled" and not "filled", and it is the best to look at both keeping in 
mind all pros and cons of each of them.


Pavel.


On 9/15/09 5:22 PM, Peter Zwart wrote:

Application of a elliptical resolution boundary is justified because the
resolution boundary from common integration programs (Denzo and Mosflm for
example) is spherical where diffraction for anisotropic data is ellipsoidal.
A spherical boundary would result in the inclusion of numerous poorly
measured reflections in the higher resolution shells which effectively makes
these data more noisy. Imposing an ellipsoidal resolution boundary is
equivalent to removing noise from the higher resolution bins and is simply
the anisotropic equivalent of the normal resolution limit truncation.



Hi Justin,

Please be careful in interpreting maps from elliptically truncated
maps, there is a potential for introducing some bias. In Refmac (as
well and Phenix) maps are produced that fill in missing amplitudes
with DFcalc. When your mtz file contains only a small fraction of
miller indices in the highest (spherical) shell, all the missing
reflections will be assigned DFcalc. Depending on your anisotropy,
this can be a significant number of reflections.

I'm not sure how serious this issue is, but it might be worthwhile
checking the 'unfilled' maps as well (both phenix.refine and Refmac
allow you to compute these).

HTH

Peter
  

Re: [ccp4bb] Seeding and protease questions

[Artem Evdokimov]

Stabilizing mother liquor is anything that (hopefully) will keep your seeds
'competent' (capable of nucleating single crystals). This may be anything
but typically what people start with is something on the lines of the well
solution supplemented perhaps with a bit extra precipitant.

 

As to when to add - this depends on how your drops behave. Specifically, if
your drops can sit for weeks w/o nucleating then you may be able to add the
seeds many days post-setup. However if you get showers of crystals in a few
days (or hours) post setup then of course you should add seeds right away,
or as soon as practical. The main goal is to have at least some of the seeds
survive the transfer and hopefully nucleate big fat crystals for you.

 

Incidentally if you just scrape a whisker or acupuncture needle across
existing crystal(s) and then quickly sweep the end of it across fresh (or
aged, whatever works) drops - you're likely to get seeds transferred.
Passing the tip through several drops in series will create a pretty
reliable dilution effect which I personally use quite often to seed - thus
avoiding (most of the time) the need to mess with stabilizing solutions,
crushed crystals and so forth.

 

Proteases and crystallization - this is a hard guess to make. Assuming that
what you see is indeed due to proteolysis and not some other effect
(oxidation for instance, or dephosphorylation, or just the quirky physical
chemistry of protein crystallization) then you could approach this in at
least two ways:

 

1.   try to figure out what sort of protease(s) is clipping your protein
and where the cut sites are. Typical experiments involve analysis of gels,
MS, selective inhibition of protease classes with chemical agents, etc.

2.   just pick up a dozen or so different proteases and go to town on
your protein - just make sure that you always set up a range of
protein/protease ratios (start from perhaps 200:1 and up to 10,000:1
although sometimes 100:1 is also OK)

 

Proteases to consider using in this case (by no means a complete list!) are:
trypsin, chymotrypsin, papain, thermolysin, subtilisin, Arg-C, Glu-C, Lys-C,
Asp-N, etc. In a pinch you can deliberately (gasp!) add a tiny amount of
bacterial lysate to your protein. Just make sure to use 'cloning' grade
cells rather than 'expression' strains which are commonly engineered to
contain knockouts of OmpT, Lon, Prc and other proteases. 

 

Cheers,

 

Artem

 

"Nothing is built on stone; all is built on sand, but we must build as if
the sand were stone" 

 Jorge Luis Borges

 

  _  

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Joseph
Brock
Sent: Tuesday, September 15, 2009 7:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Seeding and protease questions

 

Hi everyone,

I have two conditions that I want to try and improve by microseeding. I have
been reading the literature on the subject and am a bit confused as to what
exactly is the "stabilizing mother liquor" that is used in the serial
dilution of the seed stock. Is this just purified protein in its stabilizing
buffer? Or a mixture of this and crystallization solution? I would also like
to know what the general opinion is on WHEN to add these seed stocks to
crystallization drop. Is addition generally more effective upon setup or
after the drops have had a chance to equilibrate?

Also, one of these conditions takes a LONG time to produce crystals (about 3
months). I understand this may be due to the slow digestion of my protein by
low levels of co-purified proteases, whose slow nibbling eventually produce
a truncated form that is more conducive to forming crystals. Thus, the
process can be accelerated by the addition of something like pepsin to the
crystallization drop. I was hoping that someone could offer advice as to
what the optimal protease/concentration to use is such experiments?

Many thanks in advance for the advice and everything I have learnt from this
community in the past.

Best regards,

Joe
PhD Student
Research School of Chemistry
Australian National University

  _  

Find out how here Get
  Hotmail on your
iPhone

Re: [ccp4bb] backbone b-factor

[Charlie Bond]

Hi Salameh,
Not sure if you mean a graph of B-factor vs sequence, or a 3D structure 
plot.


Either way you can get such a plot using aline 
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ which can 
produce a sequence alignment (or single sequence) coloured by B-factor 
(CA, Main, Side or All) and also output a pymol script to use those 
colours in pymol on the structure.


Cheers,
Charlie


Salameh, Mohd A., Ph.D. wrote:

Dear All,

I would like to prepare a plot showing the b-factor of only the alpha 
carbon and/or the backbone atoms and I wonder if somebody knows a module 
or software that I can use, I tried the structure analysis/Temperature 
factor analysis module in CCP4 but it plots the average b-factor of all 
atoms which I’m not interested in. appreciate your help. Thanks, Mohd




*Mohd A. Salameh, Ph.D.*

Mayo Clinic Cancer Center

Griffin Cancer Research Building

4500 San Pablo Road

Jacksonville, FL 32224

Tel:(904) 953-0046

Fax:(904) 953-0277

*salameh.m...@mayo.edu*





--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
charles.b...@uwa.edu.au
+61 8 6488 4406

[ccp4bb] Seeding and protease questions

[Joseph Brock]

Hi everyone,

I have two conditions that I want to try and improve by microseeding. I have 
been reading the literature on the subject and am a bit confused as to what 
exactly is the "stabilizing mother liquor" that is used in the serial dilution 
of the seed stock. Is this just purified protein in its stabilizing buffer? Or 
a mixture of this and crystallization solution? I would also like to know what 
the general opinion is on WHEN to add these seed stocks to crystallization 
drop. Is addition generally more effective upon setup or after the drops have 
had a chance to equilibrate?

Also, one of these conditions takes a LONG time to produce crystals (about 3 
months). I understand this may be due to the slow digestion of my protein by 
low levels of co-purified proteases, whose slow nibbling eventually produce a 
truncated form that is more conducive to forming crystals. Thus, the process 
can be accelerated by the addition of something like pepsin to the 
crystallization drop. I was hoping that someone could offer advice as to what 
the optimal protease/concentration to use is such experiments?

Many thanks in advance for the advice and everything I have learnt from this 
community in the past.

Best regards,

Joe
PhD Student
Research School of Chemistry
Australian National University

_
Get Hotmail on your iPhone Find out how here
http://windowslive.ninemsn.com.au/article.aspx?id=845706

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

[Peter Zwart]

> Application of a elliptical resolution boundary is justified because the
> resolution boundary from common integration programs (Denzo and Mosflm for
> example) is spherical where diffraction for anisotropic data is ellipsoidal.
> A spherical boundary would result in the inclusion of numerous poorly
> measured reflections in the higher resolution shells which effectively makes
> these data more noisy. Imposing an ellipsoidal resolution boundary is
> equivalent to removing noise from the higher resolution bins and is simply
> the anisotropic equivalent of the normal resolution limit truncation.

Hi Justin,

Please be careful in interpreting maps from elliptically truncated
maps, there is a potential for introducing some bias. In Refmac (as
well and Phenix) maps are produced that fill in missing amplitudes
with DFcalc. When your mtz file contains only a small fraction of
miller indices in the highest (spherical) shell, all the missing
reflections will be assigned DFcalc. Depending on your anisotropy,
this can be a significant number of reflections.

I'm not sure how serious this issue is, but it might be worthwhile
checking the 'unfilled' maps as well (both phenix.refine and Refmac
allow you to compute these).

HTH

Peter

[ccp4bb] Tcl error - Snow Leopard OSX

[José Trincão]

Hello all,
I upgraded my Macbook Pro to snow leopard and followed William G.  
Scotts Crystallography on OSX wiki to install CCP4 using Fink. I used  
the 64bit install with full compilation, not the pre-compiled  
binaries. When I start ccp4i I get a warning:
Application initialization failed: version conflict for package "Tcl":  
have 8.5.7, need exactly 8.5
but everything seems to work until I try to see the log graphs, where  
I get the same error followed by:
Error in startup script: dlsym(0x1006c47f0, Blt_Unload): symbol not  
founddlsym(0x1006c47f0, Blt_SafeUnload): symbol not foundversion  
conflict for package "Tcl": have 8.5.7, need exactly 8.5

while executing
"load $library BLT"
(procedure "LoadBLT" line 30)
invoked from within
"LoadBLT 2.4 /sw64/lib/blt2.4"
("package ifneeded BLT 2.4" script)
invoked from within
"package require BLT"
(file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/bin/loggraph.tcl" line 47)
invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
(file "/sw64/share/xtal/ccp4-6.1.2/bin/loggraph" line 5)

What can I do to get everything working?
Thanks

Jose

P.S. Special thanks to W.G.Scott for the wonderful Wiki!

[ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

[Justin Hall]

Dear All;

In response to my "Anisotropic Diffraction In Refinement", which asked  
for suggestions for how best to proceed with refinement with an  
anisotropic data set, I received a large number of responses which  
overwhelmingly suggested using the UCLA Anisotropy Server  
().


The Anisotripy Server treats scaled/truncated data sets (I used Scala  
and the old Truncate program). Fo and SigFo are analyzed with respect  
to resolution in three dimensions and the data treated in three steps:

1) An elliptical resolution boundary is determined and applied.
2) A purely anisotropic B-factor is applied to the Fo and SigFo data  
to cause the data in all directions to fall off equally.
3) A negative isotropic B-factor is then applied to the structure  
factors to force the fall-off in the strongest direction to match that  
of the original data, effectively meaning that the data are not scaled  
to the mean but the weaker data are scaled up to match the strongest  
data.


Application of a elliptical resolution boundary is justified because  
the resolution boundary from common integration programs (Denzo and  
Mosflm for example) is spherical where diffraction for anisotropic  
data is ellipsoidal. A spherical boundary would result in the  
inclusion of numerous poorly measured reflections in the higher  
resolution shells which effectively makes these data more noisy.  
Imposing an ellipsoidal resolution boundary is equivalent to removing  
noise from the higher resolution bins and is simply the anisotropic  
equivalent of the normal resolution limit truncation.


However, I was confused by the second and third steps.  The second  
step of application of anisotropic scale factors is appropriate if the  
refinement program does not include anisotropic scaling in its  
calculation of Fc, however modern refinement programs do this. Pavel  
Afonine touched on this in his CCP4BB general posting in response to  
my original posting where he noted that "anisotropic scale factor[s]  
that [are] part of the total structure factor take care of this"  
().


For the third step, applying a negative isotropic B-factor to modify  
the Fo is equivalent to sharpening the peaks in your maps and this can  
be useful.  However, applying the correction to Fo will also result in  
an inappropriate decrease in the average temperature factor of the  
resulting model.  Since B-factors are used as a measure of the  
coordinate error of an atom, modifying your Fo means these low B  
factors will tend to confuse the users of that model
into thinking its quality is better than it really is. If a sharper  
map makes identification of model errors easier, the map can be  
sharpened when it is calculated, without affecting the parameters in  
the PDB file.  The latest versions of Coot, for example, allows you to  
sharpen any map that it calculates.


I brought these points to the attention of the Anisotropy Server  
director (Michael Sawaya), who is now working to provide an option to  
omit steps 2 and 3 for users who do not what their structure factors  
modified.


My thanks to everyone who responded to my original question, and to  
Dale Tronrud and Michael Sawaya in particular for valuable discussion.

[ccp4bb] Meeting Announcement for the 5th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods

[Wes Sundquist]

Dear Colleagues:

We are delighted to announce that the 5th International Conference on 
Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held 
from March 10-14, 2010 in Lake Tahoe, California at the Granlibakken Conference 
Center. We invite you to visit our Symposium website at: 
http://www.hybridmethods2010.com/index.html, register for the Symposium, submit 
an abstract, encourage all other interested parties to attend, and display the 
enclosed meeting poster.

This Symposium builds on a series of very successful previous meetings on the 
same theme from 2004-2008. As in previous years, the overall goal is to 
illustrate the power of combining state of the art methods to tackle important 
and challenging biological problems and to identify limitations and gaps in 
currently practiced hybrid methods. The central premise is that gaining a 
comprehensive understanding of the highly sophisticated machines, complexes, 
and organelles of the cell requires the coordinated application of a number of 
complementary biophysical approaches (hybrid methods). New innovations at the 
2010 meeting will include a special workshop on "Harnessing Different 
Wavelengths of Electromagnetic Radiation", which will feature the rapidly 
developing fields of subdiffraction light microscopy and other emerging imaging 
techniques (e.g., X-ray tomography), as well as new advances within more 
"traditional" hybrid approaches such as the interfaces between electron 
microscopy, X-ray crystallography, and computational biology.  Featured topics 
will also include other biophysical methods, proteomics and cell biology.


The meeting will be divided into seven Scientific Sessions
and one Special Methods Workshop

Session I: Hybrid Approaches to Macromolecular Filaments
Session II: Hybrid Approaches to Membrane Complexes
Session III: Hybrid Approaches to Dynamic Assemblies
Session IV: Computational Approaches to Hybrid Analyses
Session V: Hybrid Approaches to Global Analyses
Session VI: Hybrid Approaches to Cell Biology
Session VII: Hybrid Approaches to Nanomachines
Special Methods Workshop: Harnessing Different Wavelengths of Electromagnetic 
Radiation

We are fortunate to have recruited two outstanding Keynote Speakers: Stephen C. 
Harrison (Harvard) and Thomas D. Pollard (Yale), as well as a great program of 
platform speakers who utilize multiple approaches to investigate a variety of 
complex biological systems. Additional platform speakers and all of the 
speakers for the Special Methods Workshop will be selected from submitted 
abstracts.

Sincerely yours,

The Organizing Committee: Wes Sundquist, Chair, Phoebe Stewart, Co-Chair, Dorit 
Hanein, Nobutaka Hirokawa, Felix Rey, Alasdair Steven, and Bill Weis.
Rachel Bookman, Conference Secretariat.

[ccp4bb] Assistant Professor Position Available in Structural Biology

[Smith Steven]

FACULTY POSITION
Structural Biology and Biochemistry

Stony Brook University invites applications for a tenure-track position as
Assistant Professor in the Department of Biochemistry and Cell Biology in
the area of structural biology/biochemistry starting Fall 2010. Stony
Brook's proximity and unique access to facilities at Brookhaven National
Laboratory make this an ideal opportunity for crystallographers. Required:
Candidates must have a Ph.D. in biochemistry, chemistry, or a closely
related field, as well as postdoctoral experience. Candidates must have
demonstrated excellence in innovative research and have a strong commitment
to teaching at the undergraduate and graduate levels. Application review
will begin November 1, 2009, and will continue until the position is filled.

To apply submit a single PDF file containing a cover letter, curriculum
vitae, and proposed research plans. In addition, candidates should arrange
to have three letters of recommendation submitted on their behalf. All
application materials should be submitted to:
biochemfacsea...@notes.cc.sunysb.edu, JOBS Reference #: F-5996-09-08. For
more information about the Department, please visit
http://www.sunysb.edu/biochem/.  Equal Opportunity/Affirmative Action
Employer.

Re: [ccp4bb] backbone b-factor

[Pavel Afonine]

Hi Mohd,

here is how using PHENIX tools:

Step 1:

phenix.pdbtools model.pdb keep=backbone

Step 2:

phenix.pdbtools model_backbone_only.pdb  --show-adp-statistics

Please let me know if you have questions about the above tools.

Pavel.


On 9/15/09 9:37 AM, Salameh, Mohd A., Ph.D. wrote:


Dear All,

I would like to prepare a plot showing the b-factor of only the alpha 
carbon and/or the backbone atoms and I wonder if somebody knows a 
module or software that I can use, I tried the structure 
analysis/Temperature factor analysis module in CCP4 but it plots the 
average b-factor of all atoms which I'm not interested in. appreciate 
your help. Thanks, Mohd




*Mohd A. Salameh, Ph.D.*

Mayo Clinic Cancer Center

Griffin Cancer Research Building

4500 San Pablo Road

Jacksonville, FL 32224

Tel:(904) 953-0046

Fax:(904) 953-0277

*salameh.m...@mayo.edu*

Re: [ccp4bb] backbone B-factor

[Palm]

Dear Mohd, 
  to plot the B-factors, I would read the pdb file in Excel (or similar).
Take care that 5.45 is read as a number and not as a string, which 
happens at least in German versions because of the . instead of the 
German,.
Specify the decimal separator. 
The sort by Atmon name to get all CA atoms in one block. 
Then, all B-factors will be in one column and you can proceed to 
make a plot. 

greetings
  Gottfried



===
WEB-Mailer der Uni-Greifswald ( http://www.uni-greifswald.de/ )
===

[ccp4bb] backbone b-factor

[Salameh, Mohd A., Ph.D.]

Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon and/or the backbone atoms and I wonder if somebody knows a module
or software that I can use, I tried the structure analysis/Temperature
factor analysis module in CCP4 but it plots the average b-factor of all
atoms which I'm not interested in. appreciate your help. Thanks, Mohd


Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32224
Tel:(904) 953-0046
Fax:(904) 953-0277
salameh.m...@mayo.edu 

Re: [ccp4bb] Peg3350 model

[Dalibor Milic]

Hi!

On Pet, rujan 11, 2009 15:37, sajid akthar wrote:
> I have some density and I can fit a peg molecule in their. I am confused
> and when I search database for peg3350, I have no hit. How can I build a
> model for Peg 3350. I found some PDB's with peg; but they they have used
> peg400; Is there any difference in the model between peg3350 and peg400.

PEG 3350 (as other PEGs) is a mixture of many polymers with different
numbers of -CH2CH2O- mers, but with the average relative molecular mass of
3500. In electron density maps, one can usually see only a patch of PEG
polymeric chain bound to protein molecules, so one needs to find out (i.e.
to estimate) what is the proper length of the bound PEG fragment.

> Can any one define where the peg ion could bind.

Have a look at http://dx.doi.org/10.1524/zksu.2006.suppl_23.613. It might
give you an idea where PEG molecules usually bind on protein molecules.

Regards,
Dalibor


-- 
Dalibor Milic
Laboratory of General and Inorganic Chemistry
Department of Chemistry
Faculty of Science
University of Zagreb
Horvatovac 102a
HR-1 Zagreb
Croatia

phone:  +385 1 460 6377
fax:+385 1 460 6341
e-mail: dmi...@chem.pmf.hr

Re: [ccp4bb] attachments

[Ian Tickle]

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of William G. Scott
> Sent: 15 September 2009 15:15
> To: Ian Tickle
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] attachments
 
> jsMath provides a convenient and easy-to-use way to embed and render
> LaTeX in HTML:
> 
> http://www.math.union.edu/~dpvc/jsMath/examples/welcome.html
> 
> This has really helped me with web pages.

Yes I agree that's very nice but as you say it's designed for making web
pages not for pasting into e-mails.  I can't paste HTML into my e-mails
(it will come out looking like HTML!).

> (I'm also not a fan of formatted emails.)

The ones I send (privately) don't need to be formatted in the sense of
paragraphs, tables etc as in a web page, though use of italic and bold
fonts (for which of course you need HTML) is pretty essential for
equations involving vectors & matrices, otherwise ambiguity is likely.
The critical feature is that they make use of the MIME standard to
transmit non-ASCII characters (e.g. Greek & math symbols).  The problem
is that the only other sensible alternatives are (1) a link to a web
page (which takes much more time than an e-mail to set up) or (2) an
attachment - which is also deprecated on this BB, and in which case
we're back where we started!

I think the fundamental problem is that some people are still very much
attached (pun not intended) to their text-based e-mail client (Pine,
Pico or whatever), and I completely agree that on this BB we have to
cater for the lowest common denominator.  If communicating legible
equations by e-mail was a priority for them, you can be sure they would
move to a MIME-compliant e-mail client.

Cheers

-- Ian



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Re: [ccp4bb] Preparation of seed-stocks without seed-beads

[Magnus Alphey]

You can always make your own 'seed-bead' using a French Press nylon ball
(1/8") and an eppendorf.
Or in the absence of French Press consumables suppliers, just find your
local industrial gadget supplier (I found Dejay Distribution Ltd in the
UK via google). They quoted me £4.45 for 100 x 1/8" nylon balls.
That should keep you going for a while.

Apparently these type of balls are used in valves, bearings, and
flowmeters and are resistant to most chemical, oils and greases. They
can also supply balls of steel, teflon, polypropylene, glass, ceramic,
etc of the same size if you really, really want.

Magnus

p.s. I'm not a rep for them, just a google-searcher. Honest.

The University of Dundee is a registered Scottish charity, No: SC015096

Re: [ccp4bb] attachments

[Ian Tickle]

> Why do you say that?
> Typing non-ascii text is the same process whether it's wrapped in HTML or
> not.
> Here's your sigma: ∑

My e-mail client only allows me to insert non-ASCII characters into HTML (or 
RTF), not plain text: the option to insert symbols is greyed out in plain text 
mode.  If I type non-ASCII characters in HTML mode then switch to plain text 
the symbols are all converted to garbage, e.g. Greek lower case 'sigma' appears 
as '('.

Maybe that's a deficiency of my e-mail client but I have to work with the tools 
I'm given (working in a company I'm not at liberty to choose any e-mail client).

Cheers

-- Ian


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action in reliance upon it. If you have received this communication in error, 
please notify Astex Therapeutics Ltd by emailing 
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Astex Therapeutics Ltd monitors, controls and protects all its messaging 
traffic in compliance with its corporate email policy. The Company accepts no 
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attachments having left the Astex Therapeutics domain.  Unless expressly 
stated, opinions in this message are those of the individual sender and not of 
Astex Therapeutics Ltd. The recipient should check this email and any 
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accepts no liability for damage caused by any virus transmitted by this email. 
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basis that the Company is not liable for any such alteration or any 
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Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] attachments

[Ethan Merritt]

On Tuesday 15 September 2009, Ian Tickle wrote:
> Yes, obviously it doesn't provide full equation formatting capabilities,
> as in LaTeX for example, but at least one can type or paste in equations
> containing for example the Greek 'sigma' character (upper or lower case
> of course) or the 'square root' symbol instead of having to spell them
> all out!  For obvious reasons I'm unable to demonstrate non-ASCII text!

Why do you say that?
Typing non-ascii text is the same process whether it's wrapped in HTML or not.
Here's your sigma: ∑ 

In fact, your message complaining about non-ASCII text is itself using
in a non-ascii character set. Here is the header from the message you sent:

Content-Type: text/plain;  charset=WINDOWS-1252

I seriously suggest to use UTF8 instead, since you've already crossed the 
Rubicon :-)

> The Wikipedia article on MIME (http://en.wikipedia.org/wiki/MIME) that I
> quoted earlier says:
> 
> "The basic Internet e-mail transmission protocol, SMTP, supports only
> 7-bit ASCII characters (see also 8BITMIME).  This effectively limits
> Internet e-mail to messages which, when transmitted, include only the
> characters sufficient for writing a small number of languages, primarily
> English.  Other languages based on the Latin alphabet typically include
> diacritics not supported in 7-bit ASCII, meaning text in these languages
> cannot be correctly represented in basic e-mail.  MIME defines
> mechanisms for sending other kinds of information in e-mail.  These
> include text in languages other than English using character encodings
> other than ASCII, ...".

This article is seriously out of date.  Most mail transport now handles
8 bit characters just fine.  Actually it does say that in the last sentence
you quote.

> 
> -- Ian
> 
> > -Original Message-
> > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
> On
> > Behalf Of Phil Evans
> > Sent: 15 September 2009 12:42
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] attachments
> > 
> > On 15 Sep 2009, at 11:24, Ian Tickle wrote:
> > 
> > >
> > > Phil
> > >
> > > Nothing at all wrong with plain text for simple messages as you say,
> > > but
> > > if you want to communicate a complicated equation (particularly one
> > > containing a lot of Greek letters and math symbols not in the
> standard
> > > ASCII set!) the HTML version is much cleaner and easier to
> understand.
> > > Obviously I would never try to send such an equation to the BB, I'm
> > > talking about private messages.  The problem is remembering to
> switch
> > > back to plain text for run-of-the-mill messages (and knowing
> people's
> > > sensitivities I always try to do that!).  On my client admittedly
> the
> > > option for plain text/HTML sending is in clear view, in a previous
> > > version it was buried deep in the menu options and had to be
> selected
> > > before you started to compose the message, and the same may well be
> > > true
> > > for other clients.
> > 
> > I didn't know you could sensibly do equations & Greek letters in html,
> > but clearly html can be useful. I would have plain text as the
> > default, though
> > 
> > >
> > > The other point of course is that you're never going to be able to
> > > stem
> > > the tide!  There will always be people who will use HTML even for
> > > simple
> > > messages, mostly through ignorance, and it seems to me that if the
> > > HTML
> > > version causes problems as it seems to be doing in your client, then
> > > the
> > > easiest solution is to adapt and select the 'by default view as
> plain
> > > text' option.
> > >
> > 
> > I suppose I also don't understand why people composing html messages
> > would select a tiny font size, or is that a function of the Mail
> > reader rather than the writer (which would seem to defeat the purpose
> > of the writer formatting the message)?
> > 
> > Phil (confused as usual)
> > 
> 
> 

Re: [ccp4bb] attachments

[William G. Scott]

On Sep 15, 2009, at 5:07 AM, Ian Tickle wrote:


it doesn't provide full equation formatting capabilities,
as in LaTeX for example, but at least one can type or paste in  
equations


jsMath provides a convenient and easy-to-use way to embed and render  
LaTeX in HTML:


http://www.math.union.edu/~dpvc/jsMath/examples/welcome.html

This has really helped me with web pages.

(I'm also not a fan of formatted emails.)

Bill

Re: [ccp4bb] attachments

[William G. Scott]

On Sep 15, 2009, at 3:43 AM, Harry Powell wrote:

I googled and found something about editing ~/Library/Preferences/ 
com.apple.mail.plist (double click on the icon, don't try with emacs  
or vi...)and adding the following to the start of the first  
dictionary:-


PreferPlainText
 



Try this:

defaults write com.apple.mail PreferPlainText 1



(This must have been an accessible preference in previous  
incarnations, back when I set it.)


You can also set the composing preference in mail to always use plain  
text.

Re: [ccp4bb] Preparation of seed-stocks without seed-beads

[Hargreaves, David]

Take two siliconised glass cover slips. Place 2-5ul of mother liquor on one and 
transfer a single crystal to this solution. Place the other cover slip on top 
and press down. The two optically flat surfaces crush the crystal (best 
observed using a microscope). Slide the two cover slips apart and use 25-50ul 
of mother liquor to hoover up the carnage. This is your seed stock. Use neat or 
up to x10,000 dilution. Freezing this stock can increase its potency. Try more 
ore less grinding for bigger or smaller seed fragments.

David



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-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]on Behalf Of Ed
Pozharski
Sent: 14 September 2009 17:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Preparation of seed-stocks without seed-beads


You can use the glass cell disruption pestle

http://www.vwrsp.com/catjpg/mp0/mp0440.jpg

to grind them up.  They cost money, of course, and if you plan to buy
something, why not go for seed bead kit?  But if you want something very
cheap, then you'll find this amazing discovery interesting:

"Outer diameter of the bottom of a 0.5 mL "eppendorf" tube is the same
as the inner diameter of a 1.5 mL "eppendorf" tube."

This is known as "eppendorf mortar-pestle phenomenon" :)

On Sat, 2009-09-12 at 13:52 +0530, james09 pruza wrote:
> Dear CCP4bbers,
> 
> Can anyone suggests how to make seed-stocks if one is not having
> seed-beads... Is there any other methods to crush the crystals for the
> same purpose. What if it is simple vortexed. Off-course there wold be
> all sorts of sizes, the intact crystals as well. 
> Please suggest.
> 
> Thanks a lot more for previous help.
> James.
-- 

Re: [ccp4bb] attachments

[Ian Tickle]

> I suppose I also don't understand why people composing html messages
> would select a tiny font size, or is that a function of the Mail
> reader rather than the writer (which would seem to defeat the purpose
> of the writer formatting the message)?

Assuming your mail reader has correctly interpreted the message '' as '' (i.e. '=3D' is
the escaped '=' as Joachim pointed out earlier), the question is how is
your mail reader interpreting 'FONT SIZE=2'?  In mine it comes out as
about 9pt which is still quite readable (the default FONT SIZE=3
corresponds to 12pt).  This article which talks about font size in MacOS
may throw some light on this (scroll down the page, there are some
pictures of various font sizes):

http://style.cleverchimp.com/font_size_intervals/altintervals.html

Cheers

-- Ian


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Astex Therapeutics Ltd monitors, controls and protects all its messaging 
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Astex Therapeutics Ltd. The recipient should check this email and any 
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accepts no liability for damage caused by any virus transmitted by this email. 
E-mail is susceptible to data corruption, interception, unauthorized amendment, 
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Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] attachments

[Ian Tickle]

Yes, obviously it doesn't provide full equation formatting capabilities,
as in LaTeX for example, but at least one can type or paste in equations
containing for example the Greek 'sigma' character (upper or lower case
of course) or the 'square root' symbol instead of having to spell them
all out!  For obvious reasons I'm unable to demonstrate non-ASCII text!

The Wikipedia article on MIME (http://en.wikipedia.org/wiki/MIME) that I
quoted earlier says:

"The basic Internet e-mail transmission protocol, SMTP, supports only
7-bit ASCII characters (see also 8BITMIME).  This effectively limits
Internet e-mail to messages which, when transmitted, include only the
characters sufficient for writing a small number of languages, primarily
English.  Other languages based on the Latin alphabet typically include
diacritics not supported in 7-bit ASCII, meaning text in these languages
cannot be correctly represented in basic e-mail.  MIME defines
mechanisms for sending other kinds of information in e-mail.  These
include text in languages other than English using character encodings
other than ASCII, ...".

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phil Evans
> Sent: 15 September 2009 12:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] attachments
> 
> On 15 Sep 2009, at 11:24, Ian Tickle wrote:
> 
> >
> > Phil
> >
> > Nothing at all wrong with plain text for simple messages as you say,
> > but
> > if you want to communicate a complicated equation (particularly one
> > containing a lot of Greek letters and math symbols not in the
standard
> > ASCII set!) the HTML version is much cleaner and easier to
understand.
> > Obviously I would never try to send such an equation to the BB, I'm
> > talking about private messages.  The problem is remembering to
switch
> > back to plain text for run-of-the-mill messages (and knowing
people's
> > sensitivities I always try to do that!).  On my client admittedly
the
> > option for plain text/HTML sending is in clear view, in a previous
> > version it was buried deep in the menu options and had to be
selected
> > before you started to compose the message, and the same may well be
> > true
> > for other clients.
> 
> I didn't know you could sensibly do equations & Greek letters in html,
> but clearly html can be useful. I would have plain text as the
> default, though
> 
> >
> > The other point of course is that you're never going to be able to
> > stem
> > the tide!  There will always be people who will use HTML even for
> > simple
> > messages, mostly through ignorance, and it seems to me that if the
> > HTML
> > version causes problems as it seems to be doing in your client, then
> > the
> > easiest solution is to adapt and select the 'by default view as
plain
> > text' option.
> >
> 
> I suppose I also don't understand why people composing html messages
> would select a tiny font size, or is that a function of the Mail
> reader rather than the writer (which would seem to defeat the purpose
> of the writer formatting the message)?
> 
> Phil (confused as usual)
> 



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

Re: [ccp4bb] attachments

[Phil Evans]

On 15 Sep 2009, at 11:24, Ian Tickle wrote:



Phil

Nothing at all wrong with plain text for simple messages as you say,  
but

if you want to communicate a complicated equation (particularly one
containing a lot of Greek letters and math symbols not in the standard
ASCII set!) the HTML version is much cleaner and easier to understand.
Obviously I would never try to send such an equation to the BB, I'm
talking about private messages.  The problem is remembering to switch
back to plain text for run-of-the-mill messages (and knowing people's
sensitivities I always try to do that!).  On my client admittedly the
option for plain text/HTML sending is in clear view, in a previous
version it was buried deep in the menu options and had to be selected
before you started to compose the message, and the same may well be  
true

for other clients.


I didn't know you could sensibly do equations & Greek letters in html,  
but clearly html can be useful. I would have plain text as the  
default, though




The other point of course is that you're never going to be able to  
stem
the tide!  There will always be people who will use HTML even for  
simple
messages, mostly through ignorance, and it seems to me that if the  
HTML
version causes problems as it seems to be doing in your client, then  
the

easiest solution is to adapt and select the 'by default view as plain
text' option.



I suppose I also don't understand why people composing html messages  
would select a tiny font size, or is that a function of the Mail  
reader rather than the writer (which would seem to defeat the purpose  
of the writer formatting the message)?


Phil (confused as usual)
 

Re: [ccp4bb] attachments

[Phil Evans]

Thanks for that - it works!

Phil

On 15 Sep 2009, at 11:43, Harry Powell wrote:


Hi

Apple mail (which is what I think Phil uses) is a bit of a nuisance  
- there is no menu option to display plain text by default,  
apparently (IMWBW) - you have the option to view the current message  
in plain text, but you have to do this on a message-by-message basis.


There is a non-menu option however. In a UNIX shell (i.e. on the  
command line) when Mail isn't running (because apparently when it  
exits it resets the defaults to what they were when it started)   
type -


defaults write com.apple.mail PreferPlainText -bool TRUE

I googled and found something about editing ~/Library/Preferences/ 
com.apple.mail.plist (double click on the icon, don't try with emacs  
or vi...)and adding the following to the start of the first  
dictionary:-


PreferPlainText
 
But this is accompanied by a warning to make sure you know what you  
are "doing when playing around in the XML preference files". I  
don't, and I couldn't easily see what to do here.

On 15 Sep 2009, at 11:24, Ian Tickle wrote:


Phil

Nothing at all wrong with plain text for simple messages as you  
say, but

if you want to communicate a complicated equation (particularly one
containing a lot of Greek letters and math symbols not in the  
standard
ASCII set!) the HTML version is much cleaner and easier to  
understand.

Obviously I would never try to send such an equation to the BB, I'm
talking about private messages.  The problem is remembering to switch
back to plain text for run-of-the-mill messages (and knowing people's
sensitivities I always try to do that!).  On my client admittedly the
option for plain text/HTML sending is in clear view, in a previous
version it was buried deep in the menu options and had to be selected
before you started to compose the message, and the same may well be  
true

for other clients.

The other point of course is that you're never going to be able to  
stem
the tide!  There will always be people who will use HTML even for  
simple
messages, mostly through ignorance, and it seems to me that if the  
HTML
version causes problems as it seems to be doing in your client,  
then the

easiest solution is to adapt and select the 'by default view as plain
text' option.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk 
]

On

Behalf Of Phil Evans
Sent: 15 September 2009 10:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

There are two problems, I think

1. Sending a simple mail like this in anything other than plain text
is wasteful, and also enforces the sender's way of displaying it on
the reader, rather than following the reader's preference.
(That may of course be appropriate in some cases where formatting is
important, but not in this context)

2. Messages such as Norman's (and others), which seem to come from
Outlook Express or Exchange Server, specify a font size 3D2  
(whatever

that means) which comes out too small to read, at least for me

The html line is:-


 What's wrong with plain text? 

Phil

On 15 Sep 2009, at 10:34, Ian Tickle wrote:



Phil

I had this same problem a while ago, if you recall.  Modern e-mail
clients sending a message in HTML format will almost certainly send

it

in 2 parts, the first a version converted to plain text and the

second

the original HTML version (and possibly other versions of the same
message).  This is the 'MIME multipart alternative' e-mail standard
which is designed so that e-mail clients or users reading the

message

can choose the version they want to display.  To quote from
http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then
choose
the "best" representation they are capable of processing; in

general,

this will be the last part that the system can understand".

So assuming your mail client is MIME-compatible (I would have

thought

that all modern clients are) there should be an option on your mail
reader (as there is on mine) to always display the plain text

version.


Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-
ccp...@jiscmail.ac.uk]

On

Behalf Of Phil Evans
Sent: 15 September 2009 09:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

while we're on this topic, it would be nice also if messages were
sent
in plain text, not as html (like yours, Norman :-)), particularly

as

these ones  generally come out in a tiny font in my (Apple) mail
reader, for some reason

Phil


On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:


In the past month there have been several postings to the BB with
large
(100kB or more) attachments. Can I remind subscribers that it is

our

policy to discourage attachments as, amongst other things, they

can

cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment,

is

more appropriate.

Norman Stein

Re: [ccp4bb] attachments

[Harry Powell]

Hi

Apple mail (which is what I think Phil uses) is a bit of a nuisance -  
there is no menu option to display plain text by default, apparently  
(IMWBW) - you have the option to view the current message in plain  
text, but you have to do this on a message-by-message basis.


There is a non-menu option however. In a UNIX shell (i.e. on the  
command line) when Mail isn't running (because apparently when it  
exits it resets the defaults to what they were when it started)  type -


defaults write com.apple.mail PreferPlainText -bool TRUE

I googled and found something about editing ~/Library/Preferences/ 
com.apple.mail.plist (double click on the icon, don't try with emacs  
or vi...)and adding the following to the start of the first dictionary:-


PreferPlainText
  
But this is accompanied by a warning to make sure you know what you  
are "doing when playing around in the XML preference files". I don't,  
and I couldn't easily see what to do here.

On 15 Sep 2009, at 11:24, Ian Tickle wrote:


Phil

Nothing at all wrong with plain text for simple messages as you say,  
but

if you want to communicate a complicated equation (particularly one
containing a lot of Greek letters and math symbols not in the standard
ASCII set!) the HTML version is much cleaner and easier to understand.
Obviously I would never try to send such an equation to the BB, I'm
talking about private messages.  The problem is remembering to switch
back to plain text for run-of-the-mill messages (and knowing people's
sensitivities I always try to do that!).  On my client admittedly the
option for plain text/HTML sending is in clear view, in a previous
version it was buried deep in the menu options and had to be selected
before you started to compose the message, and the same may well be  
true

for other clients.

The other point of course is that you're never going to be able to  
stem
the tide!  There will always be people who will use HTML even for  
simple
messages, mostly through ignorance, and it seems to me that if the  
HTML
version causes problems as it seems to be doing in your client, then  
the

easiest solution is to adapt and select the 'by default view as plain
text' option.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner- 
ccp...@jiscmail.ac.uk]

On

Behalf Of Phil Evans
Sent: 15 September 2009 10:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

There are two problems, I think

1. Sending a simple mail like this in anything other than plain text
is wasteful, and also enforces the sender's way of displaying it on
the reader, rather than following the reader's preference.
(That may of course be appropriate in some cases where formatting is
important, but not in this context)

2. Messages such as Norman's (and others), which seem to come from
Outlook Express or Exchange Server, specify a font size 3D2 (whatever
that means) which comes out too small to read, at least for me

The html line is:-


 What's wrong with plain text? 

Phil

On 15 Sep 2009, at 10:34, Ian Tickle wrote:



Phil

I had this same problem a while ago, if you recall.  Modern e-mail
clients sending a message in HTML format will almost certainly send

it

in 2 parts, the first a version converted to plain text and the

second

the original HTML version (and possibly other versions of the same
message).  This is the 'MIME multipart alternative' e-mail standard
which is designed so that e-mail clients or users reading the

message

can choose the version they want to display.  To quote from
http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then
choose
the "best" representation they are capable of processing; in

general,

this will be the last part that the system can understand".

So assuming your mail client is MIME-compatible (I would have

thought

that all modern clients are) there should be an option on your mail
reader (as there is on mine) to always display the plain text

version.


Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-
ccp...@jiscmail.ac.uk]

On

Behalf Of Phil Evans
Sent: 15 September 2009 09:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

while we're on this topic, it would be nice also if messages were
sent
in plain text, not as html (like yours, Norman :-)), particularly

as

these ones  generally come out in a tiny font in my (Apple) mail
reader, for some reason

Phil


On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:


In the past month there have been several postings to the BB with
large
(100kB or more) attachments. Can I remind subscribers that it is

our

policy to discourage attachments as, amongst other things, they

can

cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment,

is

more appropriate.

Norman Stein
CCP4

--
Scanned by iCritical.





Disclaimer
This communication is confidential and may con

Re: [ccp4bb] attachments

[Ian Tickle]

Phil

Nothing at all wrong with plain text for simple messages as you say, but
if you want to communicate a complicated equation (particularly one
containing a lot of Greek letters and math symbols not in the standard
ASCII set!) the HTML version is much cleaner and easier to understand.
Obviously I would never try to send such an equation to the BB, I'm
talking about private messages.  The problem is remembering to switch
back to plain text for run-of-the-mill messages (and knowing people's
sensitivities I always try to do that!).  On my client admittedly the
option for plain text/HTML sending is in clear view, in a previous
version it was buried deep in the menu options and had to be selected
before you started to compose the message, and the same may well be true
for other clients.

The other point of course is that you're never going to be able to stem
the tide!  There will always be people who will use HTML even for simple
messages, mostly through ignorance, and it seems to me that if the HTML
version causes problems as it seems to be doing in your client, then the
easiest solution is to adapt and select the 'by default view as plain
text' option.

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phil Evans
> Sent: 15 September 2009 10:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] attachments
> 
> There are two problems, I think
> 
> 1. Sending a simple mail like this in anything other than plain text
> is wasteful, and also enforces the sender's way of displaying it on
> the reader, rather than following the reader's preference.
> (That may of course be appropriate in some cases where formatting is
> important, but not in this context)
> 
> 2. Messages such as Norman's (and others), which seem to come from
> Outlook Express or Exchange Server, specify a font size 3D2 (whatever
> that means) which comes out too small to read, at least for me
> 
> The html line is:-
> 
> 
>  What's wrong with plain text? 
> 
> Phil
> 
> On 15 Sep 2009, at 10:34, Ian Tickle wrote:
> 
> >
> > Phil
> >
> > I had this same problem a while ago, if you recall.  Modern e-mail
> > clients sending a message in HTML format will almost certainly send
it
> > in 2 parts, the first a version converted to plain text and the
second
> > the original HTML version (and possibly other versions of the same
> > message).  This is the 'MIME multipart alternative' e-mail standard
> > which is designed so that e-mail clients or users reading the
message
> > can choose the version they want to display.  To quote from
> > http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then
> > choose
> > the "best" representation they are capable of processing; in
general,
> > this will be the last part that the system can understand".
> >
> > So assuming your mail client is MIME-compatible (I would have
thought
> > that all modern clients are) there should be an option on your mail
> > reader (as there is on mine) to always display the plain text
version.
> >
> > Cheers
> >
> > -- Ian
> >
> >> -Original Message-
> >> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-
> >> ccp...@jiscmail.ac.uk]
> > On
> >> Behalf Of Phil Evans
> >> Sent: 15 September 2009 09:59
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] attachments
> >>
> >> while we're on this topic, it would be nice also if messages were
> >> sent
> >> in plain text, not as html (like yours, Norman :-)), particularly
as
> >> these ones  generally come out in a tiny font in my (Apple) mail
> >> reader, for some reason
> >>
> >> Phil
> >>
> >>
> >> On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:
> >>
> >>> In the past month there have been several postings to the BB with
> >>> large
> >>> (100kB or more) attachments. Can I remind subscribers that it is
our
> >>> policy to discourage attachments as, amongst other things, they
can
> >>> cause mailboxes to fill at an alarming rate. A link to a website
> >>> carrying the data which would otherwise appear in the attachment,
is
> >>> more appropriate.
> >>>
> >>> Norman Stein
> >>> CCP4
> >>>
> >>> --
> >>> Scanned by iCritical.
> >>>
> >
> >
> >
> > Disclaimer
> > This communication is confidential and may contain privileged
> > information intended solely for the named addressee(s). It may not
> > be used or disclosed except for the purpose for which it has been
> > sent. If you are not the intended recipient you must not review,
> > use, disclose, copy, distribute or take any action in reliance upon
> > it. If you have received this communication in error, please notify
> > Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com
> > and destroy all copies of the message and any attached documents.
> > Astex Therapeutics Ltd monitors, controls and protects all its
> > messaging traffic in compliance with its corporate email policy. The
> > Company accepts no liability or responsibility for any onward
> > transmissio

Re: [ccp4bb] attachments

[Joachim Reichelt]

=3D is the escaped "="

=xx were is the hex code of any 8bit char

Am 15.09.2009 11:46, schrieb Phil Evans:

There are two problems, I think

1. Sending a simple mail like this in anything other than plain text 
is wasteful, and also enforces the sender's way of displaying it on 
the reader, rather than following the reader's preference.
(That may of course be appropriate in some cases where formatting is 
important, but not in this context)


2. Messages such as Norman's (and others), which seem to come from 
Outlook Express or Exchange Server, specify a font size 3D2 (whatever 
that means) which comes out too small to read, at least for me


The html line is:-


 What's wrong with plain text? 

Phil

On 15 Sep 2009, at 10:34, Ian Tickle wrote:



Phil

I had this same problem a while ago, if you recall.  Modern e-mail
clients sending a message in HTML format will almost certainly send it
in 2 parts, the first a version converted to plain text and the second
the original HTML version (and possibly other versions of the same
message).  This is the 'MIME multipart alternative' e-mail standard
which is designed so that e-mail clients or users reading the message
can choose the version they want to display.  To quote from
http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then choose
the "best" representation they are capable of processing; in general,
this will be the last part that the system can understand".

So assuming your mail client is MIME-compatible (I would have thought
that all modern clients are) there should be an option on your mail
reader (as there is on mine) to always display the plain text version.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]

On

Behalf Of Phil Evans
Sent: 15 September 2009 09:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

while we're on this topic, it would be nice also if messages were sent
in plain text, not as html (like yours, Norman :-)), particularly as
these ones  generally come out in a tiny font in my (Apple) mail
reader, for some reason

Phil


On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:


In the past month there have been several postings to the BB with
large
(100kB or more) attachments. Can I remind subscribers that it is our
policy to discourage attachments as, amongst other things, they can
cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment, is
more appropriate.

Norman Stein
CCP4

--
Scanned by iCritical.





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





--
Joachim

Re: [ccp4bb] attachments

[Phil Evans]

There are two problems, I think

1. Sending a simple mail like this in anything other than plain text  
is wasteful, and also enforces the sender's way of displaying it on  
the reader, rather than following the reader's preference.
(That may of course be appropriate in some cases where formatting is  
important, but not in this context)


2. Messages such as Norman's (and others), which seem to come from  
Outlook Express or Exchange Server, specify a font size 3D2 (whatever  
that means) which comes out too small to read, at least for me


The html line is:-


 What's wrong with plain text? 

Phil

On 15 Sep 2009, at 10:34, Ian Tickle wrote:



Phil

I had this same problem a while ago, if you recall.  Modern e-mail
clients sending a message in HTML format will almost certainly send it
in 2 parts, the first a version converted to plain text and the second
the original HTML version (and possibly other versions of the same
message).  This is the 'MIME multipart alternative' e-mail standard
which is designed so that e-mail clients or users reading the message
can choose the version they want to display.  To quote from
http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then  
choose

the "best" representation they are capable of processing; in general,
this will be the last part that the system can understand".

So assuming your mail client is MIME-compatible (I would have thought
that all modern clients are) there should be an option on your mail
reader (as there is on mine) to always display the plain text version.

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner- 
ccp...@jiscmail.ac.uk]

On

Behalf Of Phil Evans
Sent: 15 September 2009 09:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] attachments

while we're on this topic, it would be nice also if messages were  
sent

in plain text, not as html (like yours, Norman :-)), particularly as
these ones  generally come out in a tiny font in my (Apple) mail
reader, for some reason

Phil


On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:


In the past month there have been several postings to the BB with
large
(100kB or more) attachments. Can I remind subscribers that it is our
policy to discourage attachments as, amongst other things, they can
cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment, is
more appropriate.

Norman Stein
CCP4

--
Scanned by iCritical.





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

Re: [ccp4bb] attachments

[Ian Tickle]

Phil

I had this same problem a while ago, if you recall.  Modern e-mail
clients sending a message in HTML format will almost certainly send it
in 2 parts, the first a version converted to plain text and the second
the original HTML version (and possibly other versions of the same
message).  This is the 'MIME multipart alternative' e-mail standard
which is designed so that e-mail clients or users reading the message
can choose the version they want to display.  To quote from
http://en.wikipedia.org/wiki/MIME#Alternative : "Systems can then choose
the "best" representation they are capable of processing; in general,
this will be the last part that the system can understand".

So assuming your mail client is MIME-compatible (I would have thought
that all modern clients are) there should be an option on your mail
reader (as there is on mine) to always display the plain text version.

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phil Evans
> Sent: 15 September 2009 09:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] attachments
> 
> while we're on this topic, it would be nice also if messages were sent
> in plain text, not as html (like yours, Norman :-)), particularly as
> these ones  generally come out in a tiny font in my (Apple) mail
> reader, for some reason
> 
> Phil
> 
> 
> On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:
> 
> > In the past month there have been several postings to the BB with
> > large
> > (100kB or more) attachments. Can I remind subscribers that it is our
> > policy to discourage attachments as, amongst other things, they can
> > cause mailboxes to fill at an alarming rate. A link to a website
> > carrying the data which would otherwise appear in the attachment, is
> > more appropriate.
> >
> > Norman Stein
> > CCP4
> >
> > --
> > Scanned by iCritical.
> >



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

Re: [ccp4bb] attachments

[Phil Evans]

while we're on this topic, it would be nice also if messages were sent  
in plain text, not as html (like yours, Norman :-)), particularly as  
these ones  generally come out in a tiny font in my (Apple) mail  
reader, for some reason


Phil


On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE) wrote:

In the past month there have been several postings to the BB with  
large

(100kB or more) attachments. Can I remind subscribers that it is our
policy to discourage attachments as, amongst other things, they can
cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment, is
more appropriate.

Norman Stein
CCP4

--
Scanned by iCritical.

[ccp4bb] attachments

[Stein, Norman (STFC,DL,CSE)]

In the past month there have been several postings to the BB with large
(100kB or more) attachments. Can I remind subscribers that it is our
policy to discourage attachments as, amongst other things, they can
cause mailboxes to fill at an alarming rate. A link to a website
carrying the data which would otherwise appear in the attachment, is
more appropriate.

Norman Stein
CCP4

-- 
Scanned by iCritical.