Re: [ccp4bb] flow rate for cooling stream?

[Ian Clifton]

Hello Patrick,

On 02/07/2020 21:03, Patrick Loll wrote:

[...]


Does anyone have an estimate for the flow rate one would typically
use for the cold nitrogen stream passing over a protein crystal in a
standard data collection?


[...]

A Cryostream 700 works at 5 litres per minute (gas), I believe. (10 in 
“turbo” mode.)


--
Ian.



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[ccp4bb] “Bound ligand” versus “modified residue”

[Ian Clifton]

Hello everyone,

PDB structure 4qdu contains a “modified residue”, 30V. This is joined
into the rest of the main chain by means of LINK records. In 5kwj, a
similar type of modification is described as a cysteine with a
side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
two clear examples we found to illustrate the question.)

Is there any reason to prefer one of these approaches over the other?
Does it just depend on what ligands are already in the PDB?

Thanks,
-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University : ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK




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Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

[Ian Clifton]

On 27/11/2018 12:52, Pierre Rizkallah wrote:
> Hi Harry,
> 
> Please find attached a picture of the FAST that was installed on its 
> side, at SRS Station 9.6. The polarisation of the synchrotron beam meant 
> we had to move the theta angle in the vertical plane to get to high 
> resolution. Enjoy.

Hi Pierre,

Ah, memory lane! Can you remember how long the FAST was in use on 9.6? I 
guess it was replaced by an early Mar.

-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University : ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK



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Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

[Ian Clifton]

I  wrote:

> Frank von Delft  writes:
>
>> No, the point is: uniqueify manages to not always do this. 
>
> The “uniqueify” script depends on the “unique” program, which seems to
> contain a built‐in low‐resolution limit of 50Å. Could it be this isn’t
> always low enough?

No, scrub that—the low resolution limit of the file that comes out
depends on the cell that you put in (that’ll teach me to use round
numbers for my test cell).
-- 
Ian ◎

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

[Ian Clifton]

Frank von Delft <frank.vonde...@sgc.ox.ac.uk> writes:

> No, the point is: uniqueify manages to not always do this. 

The “uniqueify” script depends on the “unique” program, which seems to
contain a built‐in low‐resolution limit of 50Å. Could it be this isn’t
always low enough?
-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University : ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK

Re: [ccp4bb] Any suggestions?

[Ian Clifton]

"Dr. Isabel  De Moraes"  writes:

> Any suggestions regarding to the positive densities?
>
Your pictures didn’t seem to make it as attachments, at least as
received here.

BW,
-- 
Ian ◎

Re: [ccp4bb] cif-file macro?

[Ian Clifton]

Edwin Pozharski <pozharsk...@gmail.com> writes:

> I expect this not to exist, but is there a way to define a variable in
> a cif-file (e.g. a global esd target for, say, angles)?

No, I don’t think either CIF or CIF2 have such variables/macros, I’m
afraid.
-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University : ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK

Re: [ccp4bb] P3212--1's in Space Group Names?

[Ian Clifton]

Laurent Maveyraud laurent.maveyr...@ipbs.fr writes:

 this is explained in details in table 2.2.4.1 of vol A of
 International Tables of Crystallography (p 18 in my edition).

 For trigonal/hexagonal, the primary direction is along c, along the
 3-fold (6-fold axis). It's the same in tetragonal (obviously for the
 4-fold axis !)..

 The secondary directions for trigonal/hexagonal are [100], the a
 vector, [010], the b vector, and [-1-10] the diagonal direction
 between -a and -b vectors (and therefore of between the a and b
 vectors).
 In tetragonal, the secondary directions are only [100], a, and [010], b.

 The tertiary direction for trigonal/hexagonal are [120] and [-2-10]
 which are directions perpendicular to a and to b, respectively, and
 [1-10]. None of these directions are the diagonal of a and b vectors.
 In tetragonal, the tertiary directions are [110], the diagonal of the
 a and b vectors, and [1-10], the diagonal of the a and -b vectors.


I find it less confusing in these cases—not everyone might agree—to use
three equivalent axes ⟂ to Z: X, Y and U, and hence four‐index
denotations for directions, h k i l where h + k + i = 0. Someone has
borrowed my copy of McKie and McKie, and not brought it back, but I’ve
made the enclosed badly‐drawn diagram from memory.


-- 
Ian ◎

Re: [ccp4bb] question about powder diffraction

[Ian Clifton]

Edward A. Berry ber...@upstate.edu writes:

 The plane will scatter, and all atoms in the plane will scatter in phase
 if angle of incidence equals angle of reflection. this is how a mirror
 reflects. Furthermore all the parallel planes will also reflect at this angle.
 Trouble is the beams scattered from the different parallel planes are
 systematically out of phase with each other unless Bragg's law is met
 for that set of planes, so interference is destructive and adds up to nothing.
 At least that's how I understand it,
 eab

Yes, the way I like to think of it as a double condition, the
reflection‐in‐a‐mirror condition *plus* the special condition imposed
by Bragg’s Law. This is why I often prefer the unfashionable spelling
“reflexion”.

-- 
Ian ◎

Re: [ccp4bb] Www

[Ian Clifton]

avinash singh avns.si...@gmail.com writes:

 wwdwwwy

Wow, imagine the fluorescence from that…

-- 
Ian ◎

Re: [ccp4bb] mmCIF as working format?

[Ian Clifton]

On 05/08/13 09:03, Tim Gruene wrote:


having read Gerard Kleywegt's latest announcement on the wwPDB Workshop
(1st August) made me wonder whether it is planned to introduce mmCIF as
working format to users in addition to using it at e.g. the PDB, because
I think that would make life unnecessarily complicated.


There’s nothing to stop you using your /own/ working format—it’s easy to 
extract a simpler file from the full archive file—but the archive file 
obviously has to contain the full set of metadata, and to be useful, 
that metadata has to be easily parsable.




The example mmCIF file for GroEL is about 7.5 times bigger than its PDB
file.
I know that disk space is 'cheap' nowadays, but that does not make it fast.

And personally I find mmCIF very awkward to work with, since it is not
line-oriented. 'grep', 'awk', 'perl' etc. do not work well on XML-like
files.
Instead of using mmCIF, one could, e.g. introduce a free format PDB
format, with space holders for non-assigned entities, and maybe a line
continuation character.


Are you sure you’re talking about the CIF‐based mmCIF format here, not 
the XML‐based PDBx format? mmCIF shouldn’t be much bigger than PDB.



If mmCIF is not going to be the working format for MX (refinement)
programs I would be happy for a reassurance, and otherwise I would
appreciate some comments about the benefits of an XML file format over a
line-oriented free format for the scientists that work with structural data.
I my opinion, using XML (or mmCIF) for structural information is an
attempt of programmers to make themselves more indespensable to
scientists, rather than scientifically needed.


Even when searching the “simple” PDB format, you’re likely to encounter 
problems with line endings. Imagine trying to find all files containing 
PEG, your script must reliably recognise something like:


REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M LITHIUM SULPHATE, 100MM POLY
REMARK 280   ETHYLENE GLYCOL

—in fact this sort of thing is much /easier/ to do, given the proper 
tools, in a format like XML.


With file formats, the devil is always in the details. If you set out to 
create a “line‐oriented, free format” PDB replacement, and you carefully 
ironed out all the potential ambiguities and awkward corner cases, I bet 
you’d come up with something close to mmCIF.

--
Ian ◎

Re: [ccp4bb] Why the name aimless

[Ian Clifton]

Martyn Winn martyn.w...@stfc.ac.uk writes:

 I think Phil saw something nasty in the woodshed ...

 HTH
 Martyn

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Roberto Battistutta
 Sent: 02 May 2013 11:07
 To: ccp4bb
 Subject: [ccp4bb] Why the name aimless
 
 Hi everyone,
 just a curiosity, why the name aimless for the recent data reduction
 and analysis program in CCP4? You know, my students are curious ...
 Thank you,
 Roberto.

We mustn’t forget, we already have a name, due to Zbigniew Dauter, for a
future combination of pointless + aimless—“hopeless”.
-- 
Ian ◎

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Ian Clifton]

Hi Fred,

vellieux frederic.velli...@ibs.fr writes:


[...]

 I get errors (at run time) of the type:

 At line 138 of file program.f (unit = 6, file = 'stdout')
 Fortran runtime error: Missing initial left parenthesis in format


[...]

Mmm, that kind of error rings a bell … is the relevant format a string
rather than given in a FORMAT statement? If so, you need round brackets
INSIDE the format string, i.e.

   write (*, '(i5)') 123

rather than

   write (*, 'i5') 123

—this can manifest itself at run‐time, especially if the format is in a
character variable.
-- 
Ian ◎

[ccp4bb] How to make an unnatural amino acid ligand?

[Ian Clifton]

I need to make dictionaries for a ligand that includes an unnatural
amino acid (D chirality, and unnatural side‐chain) amongst a short
sequence of natural amino acids. Sounds easy, but how to do it? I’m
thinking of first making my unnatural amino acid in isolation, then
using an editor to fix up the generated dictionaries to have the correct
partial charges etc. for the main‐chain atoms, using standard dictionary
entries as a template. Is there a better or sounder way to do it?

Thanks,
-- 
Ian ◎

Re: [ccp4bb] Today ...

[Ian Clifton]

Tom Murray-Rust tom.murray.r...@gmail.com writes:

 Hi Juergen,

 Your scheme as printed has two J's - so January and July are
 indistinguishable! I would suggest the letters should instead be
 JFMAYULGSOND. 

 Happy apocalypse!

 Tom

 On 21 Dec 2012, at 01:52, Bosch, Juergen jubo...@jhsph.edu wrote:


 May I introduce you to another fool proof way:
 12d12
 year-month-day
 This is in particular useful in a mixed lab with american and
 europeans labeling Eppendorf tubes differently. The month has a
 defined letter, like this you know that your buffer was made on
 June 9th and not September 6th 
 J, F,M,A,Y,J,U,G,S,O,N,D for the months, simply first letter, but
 if taken move to the second letter etc.

Or there’s the Japanese system, using characters which unambiguously
identify which field is which. Happy 21日12月24年!

 I'm sure you guys know about the two Bohemian mathematicians who
 figured out that the Apocalypse as predicted by the Mayan
 calendar is due in 104 years because the alignment of events was
 done incorrectly.

Will there be egg on their faces in 104 year’s time!

Wishing everyone a Merry Christmas, Happy New Year, and a sober 
instructive CCP4.

-- 
Ian ◎

Re: [ccp4bb] hkl2000 install

[Ian Clifton]

王瑞 wangrui...@gmail.com writes:

   I'm sorry for a little off-topic! I want to install HKL2000 on
 ubuntu11.10 32bits, but it produces a file named info not cr_info
 after  run the access_prod program.And when I put info to

 /usr/local/lib directory and typingHKL2000 in terminal, it display:
 root@ubuntu:/usr/local/bin# HKL2000
 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found
 Error code: -1

 So could anyone tell me how to do it ?

Yes, you use your “info” file to obtain a “cr_info” file from HKL
Research:

http://www.hkl-xray.com/

Regards,
-- 
Ian ◎

Re: [ccp4bb] AW: [ccp4bb] Postdoctoral position - University of Edinburgh

[Ian Clifton]

Froehlich, Chris chris.froehl...@mdc-berlin.de writes:

 is there any program enclosed in CCP4 to convert a *.brix file or a
 *.mrc file into a CCP4.map file?

 If not, is there any other way to do so?`

MAPMAN from Uppsala (http://xray.bmc.uu.se/usf/) can read BRIX (and
write CCP4), not sure about .mrc format though.
-- 
Ian ◎

Re: [ccp4bb] Question on Symmetry Axis Notation Convention

[Ian Clifton]

Ethan Merritt merr...@u.washington.edu writes:

 On Thursday, June 14, 2012 12:06:13 pm James Stroud wrote:
 Hello All,
 
 I would like to discuss symmetry axes, but I'm not sure what the
 notation convention is. For example, I'd like to say something about
 a 2(1) along the x-axis, but the phrase the 2(1) symmetry axis
 along x is a bit cumbersome to repeat many times or to put in a
 table. So I'd like a shorthand, maybe something like x(2_1) (where
 the preceding _ means that the 1 is subscript. Another way I
 like is x_{2(1)} (where the curly braces mean that all of 2(1)
 is subscript).
 
 Does anyone know what the convention is or if there is one?

 One would think that this document would have the answer:

 
 http://www.iucr.org/resources/commissions/crystallographic-nomenclature/symel

 But it's too cryptic for me.

 I'd go with the full expression in the text. 
 For table entries, I'd want something shorter.
 International Tables for Crystallography, Vol A defines the glyph used to 
 indicate
 2_1 screws in the space group diagrams (a solid oval with two flagella).  
 But finding a font to print it in your table could be challenging. 
 There is a cryst.mf font for TeX if that helps.
   http://www.tex.ac.uk/CTAN/fonts/cryst/

This font (by Ulrich Müller) is available in many formats on the IUCr
web site:

http://www.iucr.org/resources/symmetry-font


 I can't find these symbols in the Unicode character tables.
 Perhaps the IUCr should propose to have Unicode code points assigned for
 the standard set of crystallographic symmetry elements.

That has occurred to me too! As far as I know, no proposal has yet been
made.

-- 
Ian ◎

Re: [ccp4bb] problem in mtz2various

[Ian Clifton]

Sita Ram Meena sitaramme...@gmail.com writes:

Hello everyone
 I Was trying to convert my mtz output of the SCALA to CNS format in
mtz2various but its gives some error
please look at log file 

[...]

 Data line--- OUTPUT CNS
 Data line--- labin  FP=F_New SIGFP=SIGF_New FPH=F_New SIGFPH=SIGF_New
DP=DANO_New SIGDP=SIGDANO_New FREE=FreeR_flag F(+)=F_New(+)
SIGF(+)=SIGF_New(+) F(-)=F_New(+) SIGF(-)=SIGF_New(+)

[...]

/home/ajay/programs/ccp4/ccp4-6.2.0/lib/data/syminfo.lib
 MTZ2VARIOUS:   *** You are inputting F(+) AND  FP  - incompatible ***

[...]

This just means you have to choose one of the sets {FP, SIGFP, DP,
SIGDP} or {F(+), F(-) SIGF(+), SIGF(-)} — you can’t have both.
-- 
Ian Clifton ⚗ Phone: +44 1865 275677
Chemistry Research Laboratory Fax:   +44 1865 285002
Oxford University ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK

Re: [ccp4bb] How to build N-terminal PCA?

[Ian Clifton]

Huayue Li lihua...@naver.com writes:

I have got a problem on building the N-terminal pyroglutamic acid
(PCA).


I'm afraid I have successfully defined *.top, *.param and *.link files
of PCA; and also successfully output *.mtf and *.pdb files.

Everything seems right! I can not find any problem within these files.

However, when the annealing.inp executed,  it did not output *.pdb
files.

What is the problem? I will attach corresponding files together.


It just seems to fail mid‐job! Are you sure it’s nothing trivial, like
disk space?
-- 
Ian ◎

[ccp4bb] Plain‐text posting (was: Re: [ccp4bb] APBS)

[Ian Clifton]

Tim Gruene t...@shelx.uni-ac.gwdg.de writes:

 [summer break flame]
 I'm sure there are a lot more computer admins than crystallographers who
 prefer high-tech over fancyness - aka outlook usually marking my signed(!)
 emails as spam ;-)

 And, yes, I know that both thunderbird/enigmail and kmail combine both very
 elegantly, but with mutt I can simply use an ssh-client to read my email from
 anywhere in the world without having to worry too much about security whereas
 I shall not configure some internet-cafe's email client with my credentials to
 read my mail in the absence of a private internet connection..
 [/summer break flame]

 Cheers, Tim


 On Wed, Jul 06, 2011 at 11:09:46AM +0200, Flip Hoedemaeker wrote:
 Leave it to the crystallographers to be the last on the Planet with
 text-only email readers Just before the ccp4bb will migrate to
 google+ :)
 
 Flip

[...]

Well, I’d like to plonk my support behind good old plain text. I think
there are valid reasons for it which are nothing to do with Luddism. The
more formatting you put into your emails (unnecessarily, I would say),
the more you’re constraining how your emails should be read. Some people
might want or need to read your email in a much larger font than you
would use. There is a legitimate use for HTML email, in science you
might well want to illustrate your thoughts with graphs and chemical
diagrams, but HTML for everything as a default, I don’t like! Remember
Homer Simpson’s web page?

Of course purists would say the most universal email format is US-ASCII,
format=flowed…

-- 
Ian Clifton ⚗ Phone: +44 1865 275677
Chemistry Research Laboratory Fax:   +44 1865 285002
Oxford University ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK

Re: [ccp4bb] Generating a PDB file for a known ligand

[Ian Clifton]

On 15/03/11 12:57, A Leslie wrote:
…
 
 I then try using LIBCHECK standalone to get the PDB file. I get the  
 same error if I use the FILE_CIF input keyword and give it the  
 filename for ADN.cif, no surprise, as this is (I assume) what COOT does.
 
 I then copy over ADN.cif to my local directory, run LIBCHECK again and  
 use the FILE_L keyword to specify the (local) ADN.cif file. I then get  
 the error:
 
ERR: item _chem_comp_tree.atom_id :O2'  not found in the atom list
MON,BLOCK :ADN data_comp_ADN
 
 suggesting that there is an error in ADN.cif !
 

I can’t reproduce this (CCP4-6.1.13), but I’m immediately suspicious of
the apostrophe (U+0027) character in the error message. I’m not a DNA
dabbler, so I can’t help much, but I bet the problem is due to “primed”
atom names being replaced by stars, or something else. In my CCP4
distribution, the atom names are starred in the dictionary file for ADN.
In official PDB files, they’re primed I think.
-- 
Best wishes,
Ian.

Re: [ccp4bb] adding gaussian noise to an mtz data column

[Ian Clifton]

On 04/02/11 12:40, Vellieux Frederic wrote:
 Before re-inventing the wheel...
 
 Is there anywhere some software (freely available software, I mean) that 
 can add some Gaussian noise to data. The data is currently stored in a 
 data column in an mtz (not phase data, but amplitudes, sigma 
 values...) but can be exported to another format if required.
 
 Before writing a computer program to do this, does anyone know if this 
 can be done without writing any code. If it can then obviously I won't 
 write new code.
 

There's also the RAN_G function in SFTOOLS's CALC command (works on your
MTZ directly, of course).