Re: [ccp4bb] validating a homlology model

2018-03-03 Thread Ed Pozharski


Assuming that your homology model is that of a dimer, you could put it in a 
large unit cell (just add CRYST1 record).  The only interface you will get from 
pisa will be your dimer interface.
If your homology model is a monomer, then pisa will not help, of course, and 
you would need to predict dimerization mode first. 


Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5

 Original message 
From: Careina Edgooms <02531c126adf-dmarc-requ...@jiscmail.ac.uk> 
Date: 3/2/18  6:44 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] validating a homlology model 

Dear all
What programs are best used for validate homology models? I know of molprobity 
but if there are no coordinates I cannot use it. Is there a way to use such 
programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface but again for 
homology model this cannot be done as there is no PDB model. Does anybody know 
way to use PISA software on my own model that is not deposited in PDB?
Thank you in advanceCareina

Re: [ccp4bb] question related to MTZ file

2015-01-03 Thread Ed Pozharski
I suspect the question might be about converting intensities to anplitudes.  If 
so ctruncate is your friend.


Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5


 Original message 
From: Eleanor Dodson eleanor.dod...@york.ac.uk 
Date:01/03/2015  3:42 PM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] question related to MTZ file 

I don't really understand your question. 
An mtz file is simply a format to hold at least a  list of 
h k l Observations Sigma_observations 

It is a binary file format which makes it very suitable to store information 
with a large range of value - viz, observations.. 


Then other information pertinent to reflection indices can be added to the file

e.g. IF you have a model you could calculate Fcalc and PHIcalc. and append then

IF you had some experimental information to help you determine phases such as 
anomalous measurements you may want to store these, plus the derived phases and 
Figs_of_Merit.

Is this any help?  Phases have to be based on extra information..

Eleanor



On 3 January 2015 at 04:00, luzuok luzuo...@126.com wrote:
How initial this MTZ file? 
Does this mtz file contain phase information? 

Lu Zuokun




--
卢作焜
南开大学新生物站A202

在 2015-01-02 00:52:53,Jurgen Bosch jbos...@jhu.edu 写道:

I assume you mean with initial mtz file the one derived from Mosflm after 
processing your images. If so, then how about running that file through scala 
http://www.ccp4.ac.uk/html/scala.html  ?
I bet there are some tutorials on the CCP4 webpage on that topic.

Jürgen

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

On Dec 31, 2014, at 9:19 PM, Dialing Pretty 
03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote:

Dear All,

After I got the initial MTZ file without the structure factors, will you please 
tell me by which CCP4 program I can get the MTZ file with the structure factors?

I am looking forward to getting your reply.

Dialing






Re: [ccp4bb] water at the same exactly position

2014-10-29 Thread Ed Pozharski
Why? Merging waters like that in coot is a user error, and it does not happen 
too often.  I realize you are talking about changeable settings, but it would 
be really annoying if a refinement program kept removing water molecules that 
were placed manually because it does not fit some internal standard. Adding 
waters by default may obscure density that is due to other components.

I just feel one should be careful when changing chemical compositon of a model. 
That is something algorithms do not (yet) do well. 


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Pavel Afonine 
pafon...@gmail.com /divdivDate:10/30/2014  12:27 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] water at 
the same exactly position /divdiv
/divThis conversation makes me more and more certain that water update 
(add/remove/refine water) done as part of (a default) refinement run is a good 
idea -:)

Pavel

On Wed, Oct 29, 2014 at 5:08 AM, luzuok luzuo...@126.com wrote:
Dear all,
I found that there are some water molecules in my pdb that share the same 
position. This maybe cause by merging molecules in coot. It seems that I have 
mereged water molecules into my protein for more than one time. 
Does anyone tell me how to fix this problem?

Best regards!
Lu Zuokun




--
卢作焜
南开大学新生物站A202





Re: [ccp4bb] Merge PDB chains

2014-10-23 Thread Ed Pozharski
Edit the ATOM records?


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: luzuok 
luzuo...@126.com /divdivDate:10/23/2014  6:51 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] Merge PDB 
chains /divdiv
/divDear all,
   Sorry to ask a simple question. There are many SO4 in my PDB file, one 
belongs to a different chain. I want to merge them into one chain, can anyone 
tell me how to do this?

Best regards!

Lu Zuokun




--
卢作焜
南开大学新生物站A202




Re: [ccp4bb] I222 - P22121 space-group ambiguity

2014-10-13 Thread Ed Pozharski
Yes, having different crystal forms in the same crystallization conditions is, 
while clearly uncommon, not unheard of. I had a case once where at least four 
different crystal forms were observed in crystals harvested from identically 
prepared drops.  It may be that there is some major set of contacts that 
promote certain arrangement of protein molecules (fiber-like), and these can 
then be packed in multiple ways as controlled by another ser of weaker 
interactions. 


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Florian Schmitzberger 
schmitzber...@crystal.harvard.edu /divdivDate:10/13/2014  4:47 AM  
(GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] 
I222 - P22121 space-group ambiguity /divdiv
/divHi everybody,

I collected a number of X-ray data sets from crystals originating from the same 
cryst. drop. I solved the initial structure in P22121 space group by MR with 
Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 
0.213/0.244.

Processing of some of the other data sets with XDS/Aimless is consistent with 
I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The 
unit-cell dimensions for I222 and the initial P22121 space groups for two of 
the data sets are:
I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98;

I superposed the molecule in I222 onto one of the two located for the initially 
solved P22121; the orientation of the NCS-related molecule in P22121 differs 
from the crystallographic-symmetry related one in I222. Trying to solve this 
P22121 data set in I222 with MR, does not result in high Z scores, and maps do 
not look good.

Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in 
P22121, locating two molecules (differences may not be that clear in this case, 
since the resolution is lower).

Some other data sets process in P22121 with Aimless; with a substantial 
off-origin Patterson peak, indicating translational NCS. For these, Phaser 
positions two molecules that are related by crystallographic translational NCS. 
These two molecules are crystallographic-symmetry related in the original 
P22121 data set. I can also solve these data sets in I222 space group, with the 
overall Z score higher than for the P22121 data. 

I am uncertain, what the ‘true’ space group for some of my data sets is. Could 
it be that for data that process in P22121, but can be solved in I222, 
reflections that would indicate I222 space group were not collected? 
Alternatively, perhaps what I am seeing is that there is a (gradual) transition 
of the crystal lattice (between P22121 and I222 or vice versa), caused by 
variation in crystal handling/cooling or exposure to X-rays.

It’s relevant to me, because in P22121 space group, a region of the molecule 
that is of biological interest makes NCS-related crystal contacts that are 
crystallographic-symmetry related in I222.

Has anybody observed similar cases? I would appreciate comments.

Cheers,

Florian




[ccp4bb]

2014-08-19 Thread Ed Pozharski
Try refining your model both ways (with and without covalent link) and see if 
electron density maps give you an indication.  At this resolution there will be 
some model bias, so be critical. 


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: rohit kumar 
rohit...@gmail.com /divdivDate:08/19/2014  2:56 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] /divdiv
/divDear All,
i have solved a structure of 3.2 A. That is a PLP depended enzyme. 
In their resting state, PLP-dependent enzymes are usually joined by a covalent 
aldimine linkage to an essential lysine residue with a C=N bond. This generates 
the so-called internal aldimine moiety.
Could anybody tell me how we can say that this  PLP is covalently attached to 
the Lys or its making Schiff base or not. 

-- 
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067


Re: [ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Ed Pozharski
Probably the only way is to take unmerged scalepack output to aimless.


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Faisal Tarique 
faisaltari...@gmail.com /divdivDate:08/15/2014  9:40 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] cc1/2 value 
in hkl2000 /divdiv
/divHello everyone

Can anybody please tell me where to locate the Corelation value between half 
sets (CC1/2) of a data processed through HKL2000 ?? 

-- 
Regards

Faisal
School of Life Sciences
JNU



Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Ed Pozharski
Same here.  Ultimately, the KD test must be used in the end to finalize the 
resolution (keeping in mind recently discussed issues of effective resolution 
given data completeness).  I just want to add that at least some versions of 
aimless report overestimated resolution based on CC1/2 cutoff when outliers are 
present (e.g. due to ice rings or salt diffraction). It seems that aimless just 
picks the highest resolution bin where cc1/2 0.5 even if some lower resolution 
bins are below 0.5 as well. I have written a script for more robust automated 
evaluation of these curves.  In a nutshell, it fits CC1/2 (d) curve to 1/(1+exp 
(-x)) and returns the resolution at midpoint.  I'm pretty sure that theoretical 
CC1/2 (d) dependence is different from this, but it seems good enough for a 
rough estimate. 


Sent on a Sprint Samsung Galaxy S® III







div Original message /divdivFrom: Roger Rowlett 
rrowl...@colgate.edu /divdivDate:08/14/2014  5:44 PM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] CC-half 
value ?? /divdiv
/divExactly. Aimless will give you suggested resolution cutoffs based on CC 
1/2 in the log file.

Roger Rowlett

On Aug 14, 2014 5:04 PM, conan仙人指路 conan_...@hotmail.com wrote:
Hi Faisal,

  CC-half standard is valuable in evaluating the cut-off of highest resolution. 
Sometimes even if I/sigI is close to 1 and completeness is not as high, if 
CC-half is still significant, it may be worth incorporate the extra high-res 
shell data and extend the resolution. Again, if only the reliability and unbias 
are carefully confirmed, and the apparent significant CC-half is not due to an 
artifact of some other factors like ice ring etc.
(Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 
https://www.pubmed.com/pubmed/22628654)

  It has yet to be appreciated by most population of the crystallography 
society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has 
gradually less a direct measurement of the data quality and or determinant of 
resolution cut-off. 

Best,
Conan

Hongnan Cao, Ph.D.
Department of Biochemistry
Rice University

Date: Fri, 15 Aug 2014 01:39:48 +0530
From: faisaltari...@gmail.com
Subject: [ccp4bb] CC-half value ??
To: CCP4BB@JISCMAIL.AC.UK

Dear all

How CC-half value of a data set determines the maximum resolution limit during 
data processing ?? Although much we know about the Rsym and I/Isig values of 
the highest resolution shell while processing the data, what are the parameters 
we need to check related to CC-half values ?? 

-- 
Regards

Faisal
School of Life Sciences
JNU



Re: [ccp4bb] thin shell Rfree set selection

2014-08-13 Thread Ed Pozharski
By all means, try it both ways and see whether the R-Rfree gap narrows with 
random vs thin shell selection. Depending on resolution and data quality, you 
may also consider imposing NCS restraints.


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Xianchi Dong 
dongxian...@gmail.com /divdivDate:08/12/2014  4:45 PM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] thin shell 
Rfree set selection /divdiv
/divDear all,
I have a dataset of C2 symmetry and 2 molecules in the ASU. I am wondering if I 
have to use thin shell Rfree set selection to avoid Rfree bias by NCS. And 
which Rfree selection method is better?

Thanks in advance.

Xianchi

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

2014-07-15 Thread Ed Pozharski
You may need to

1) modify _chem_comp.group to be DNA in the cif-file
2) import the resulting cif-file in coot

Cheers


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Wang, Wei 
wew...@ucsd.edu /divdivDate:07/15/2014  5:14 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] The modified 
DNA could not be linked to the downstream DNA in the COOT? /divdiv
/divHi,

There is a problem about modified DNA refinement.

I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. 
However I found the modified DNA could not be linked to the downstream DNA when 
I refined it in the COOT. Then I generated another CIF file using sketcher of 
CCP4, but the problem still existed.

Is there any expert to help me?

Thanks!!
Best

Wei

Re: [ccp4bb] emergency substitute for RT loop cover?

2014-07-07 Thread Ed Pozharski
Try to put your crystal into oil drop? 


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Frank von Delft 
frank.vonde...@sgc.ox.ac.uk /divdivDate:07/07/2014  12:32 PM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] emergency 
substitute for RT loop cover? /divdiv
/divHi all

Pretend you were stuck having to do RT data collection but without 
access to either Mitegen MicroRT Capillaries or the more old-fashioned 
quartz capillaries, to pop over the loop.

Anybody have suggestions of alternative ways of doing this?  I do want 
to use loops (I never learnt how to suck up crystals in capillaries).

I have access to a passably stocked biochemistry teaching lab, and could 
at a pinch go rifle some more advanced research labs.  (No, I'm not at 
home ;)

Thanks!
phx


Re: [ccp4bb] Kabat, insertion codes refinement

2014-06-16 Thread Ed Pozharski
There is no actual requirement to use Kabat numbering, you can avoid it 
alrogether.  Some argue that L27A is actually 28th amino acid in the protein 
sequence, and labeling it as L27A is simply incorrect.  I would suggest doing 
refinement with plain numbering (no insertion codes) and changing it only for 
the final model if needed for comparative analysis. 

Ed


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Hargreaves, David 
david.hargrea...@astrazeneca.com /divdivDate:06/16/2014  6:07 AM  
(GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] 
Kabat, insertion codes  refinement /divdiv
/divDear CCP4bb,
 
I’m refining an antibody structure which requires Kabat residue numbering with 
insertion codes. My setup of Refmac5 and Buster both break peptide bonds 
between some (not all) of the residues with insertion codes. I was wondering 
whether there is a special way of handling these residues in refinement?
 
Thanks,
 
David
 
David Hargreaves
Associate Principal Scientist
_
AstraZeneca
Discovery Sciences, Structure  Biophysics
Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF
Tel +44 (0)01625 518521  Fax +44 (0) 1625 232693
David.Hargreaves @astrazeneca.com
 
Please consider the environment before printing this e-mail
 
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Re: [ccp4bb] metal ion dominating density!

2014-06-05 Thread Ed Pozharski
Or, if for whatever reason sphere refine isn't an option, fix the metal and all 
of its ligands


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Paul Emsley 
pems...@mrc-lmb.cam.ac.uk /divdivDate:06/05/2014  3:51 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] metal ion 
dominating density! /divdiv
/divOn 05/06/14 08:27, Dean Derbyshire wrote:

 Hi all, I recall there was a post a while back, but silly me can’t 
 remember the details –

 How does one stop metal ions dominating real space refinement in COOT?



sphere refine?

Paul.


Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Ed Pozharski
This may not work if a program implements its own algorithm for parsing command 
line parameters


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Tim Gruene 
t...@shelx.uni-ac.gwdg.de /divdivDate:06/03/2014  8:27 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage: 
no tables were found in this file /divdiv
/div-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Eleanor,

yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing
# mkdir dir with spaces
# cd dir\ with\ spaces/
# touch file with spaces
# echo Some text  file\ with\ spaces
causes no problems at all. Changing code reliably to include accents,
though, might be much more work than enclosing words with double quotes.

Best,
Tim

On 06/03/2014 02:23 PM, Eleanor Dodson wrote:
 I thought the addition of  ... around file names got round this
 problem
 
 eg This_is_Mine.pdb and That is Yours.pdb
 
 Eleanor
 
 
 
 
 On 3 June 2014 13:15, Eugene Krissinel
 eugene.krissi...@stfc.ac.uk wrote:
 
 I am afraid that it is us who will need to conform eventually :),
 same to say about Program Files (x86) and the overall culture
 in Windows, the system where some 40% () of CCP4 users have
 chosen to work.
 
 Eugene
 
 
 On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:
 
 completely agree with avoiding spaces in paths and file names,
 but
 Google Drive is very handy for sharing files, so every once in a
 while I forget to move a file someone shares with me before
 running Unix programs on it and get strange errors. Depending on
 how awake one is at the time finding out the source can be
 time-consuming...Google should really remove the space!
 
 Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas 
 Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049
 Madrid, Spain tel. (+34) 91 585 4616 
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
 
 I take this chance to to confirm once more, as publicly as
 possible,
 that file paths with spaces are discouraged in today's CCP4.
 This inconvenience originates from ancient times in computing
 when good half of CCP4 was written and when spaces were
 disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives
 (albeit
 infrequent) bug reports, where surprising behaviour is due to
 using file paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because
 of
 technical choices made quite a number of years ago. But good news
 are that this limitation will be removed in new CCP4 Gui under
 development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
 This also occurred to me once where the file path had a
 space,(/Google
 Drive/), when I moved the file somewhere else it worked. I was
 using baverage from the CCP4i GUI.
 
 Mark J van Raaij Lab 20B Dpto de Estructura de
 Macromoleculas Centro Nacional de Biotecnologia - CSIC 
 c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 09:20, Tim Gruene wrote:
 
 Dear Bing,
 
 can you post the exact command you were using, please?
 Also please
 check
 with a different PDB file. In case you are using baverage
 from the command line, can you make sure you are actually
 using the program
 from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards. Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage
 in the ccp4
 suit to check the temperature factor, it always tell me No
 tables were fund in this file. Could you tell me how to fix this
 problem? Or is there another software instead of baverage I could
 use to check the temperature factor?
 
 Thanks!
 
 Bing
 
 
 -- Dr Tim Gruene Institut fuer anorganische Chemie 
 Tammannstr. 4 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 
 
 -- Scanned by iCritical.
 
 
 
 
 -- Scanned by iCritical.
 
 
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFTjb8eUxlJ7aRr7hoRApyPAKCGq/1XweO13d57W9vaho+DoXLHSgCeJXYW
7mc+g+F1Win65zZc8+nLN6I=
=U7dS
-END PGP SIGNATURE-


Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Ed Pozharski
Would a no-space symlink resolve this?


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Mark J van Raaij 
mjvanra...@cnb.csic.es /divdivDate:06/03/2014  8:03 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage: 
no tables were found in this file /divdiv
/divcompletely agree with avoiding spaces in paths and file names, but Google 
Drive is very handy for sharing files, so every once in a while I forget to 
move a file someone shares with me before running Unix programs on it and get 
strange errors. Depending on how awake one is at the time finding out the 
source can be time-consuming...Google should really remove the space!

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:

 I take this chance to to confirm once more, as publicly as possible, that 
 file paths with spaces are discouraged in today's CCP4. This inconvenience 
 originates from ancient times in computing when good half of CCP4 was written 
 and when spaces were disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives (albeit 
 infrequent) bug reports, where surprising behaviour is due to using file 
 paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because of technical 
 choices made quite a number of years ago. But good news are that this 
 limitation will be removed in new CCP4 Gui under development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
 This also occurred to me once where the file path had a space,(/Google 
 Drive/), when I moved the file somewhere else it worked. I was using 
 baverage from the CCP4i GUI.
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 09:20, Tim Gruene wrote:
 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me No tables were fund in 
 this file. Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?
 
 Thanks!
 
 Bing
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 
 
 -- 
 Scanned by iCritical.
 


Re: [ccp4bb] negative density around disulfide bond

2014-06-02 Thread Ed Pozharski
Try refining without disulfide bond - from the way density looks it might work. 
 Whether this is what happens in vivo is a different question entirely. 


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: Eze Chivi 
ezech...@outlook.com.ar /divdivDate:06/02/2014  1:08 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] negative 
density around disulfide bond /divdiv
/divHello, when I refine my structure, I see negative density around the 
disulfide bond. I have 7 copies per ASU, and I can see this density in many of 
them. In some cases, I see positive density also (negative in the center of the 
straight line linking S atoms, and positive in both sides). What can I try to 
solve it? Is it due to radiation damage? Alternative conformation (partial 
oxidation)? Incorrect disulfide geometry parameters? My resolution is 2.1 A, 
R/Rfree are around 0.220/0.243, and similar results with refmac5, phenix and 
PDBREDO. Please find two example pictures in attachment.
Thanks for your help!


Ezequiel


Re: [ccp4bb] (high) values of R-factors in outermost resolution shell

2014-06-02 Thread Ed Pozharski
My suggestion is to ignore Rmerge when making decisions about resolution 
cutoff.  While cc1/2 may still perhaps qualify for the recent discussion tag 
(is two years recent?), deeply flawed nature of the Rmerge concept is over a 
decade old.


Sent on a Sprint Samsung Galaxy S® III

div Original message /divdivFrom: sreetama das 
somon_...@yahoo.co.in /divdivDate:06/02/2014  4:27 AM  (GMT-05:00) 
/divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] (high) values 
of R-factors in outermost resolution shell /divdiv
/divDear All,
  What are reasonable values of Rmerge in the outermost resolution 
shell? 

Some of the recent discussions suggest going to those sheels where I/sig(I) 
~2 and CC1/2 = 0.5. But I am getting Rmerge  Rmeas  1 in the outermost shell 
for those values of I/sig(I) and CC1/2, and I don't think that makes any 
sense. Reducing the resolution cut-off while data reduction  scaling (aimless) 
reduces the R-values, but I am not sure how much I should reduce the resolution 
(if at all). 

Following are the results from the aimless log file:
At a resolution cut-off of 1.62A:
   Overall  InnerShell  OuterShell
Low resolution limit   42.12 42.12  1.65
High resolution limit   1.62  8.87  1.62

Rmerge  (within I+/I-) 0.071 0.019 1.325
Rmerge  (all I+ and I-)0.074 0.020 1.381
Rmeas (within I+/I-)   0.078 0.021 1.446
Rmeas (all I+  I-)0.077 0.022 1.441
Rpim (within I+/I-)0.031 0.009 0.575
Rpim (all I+  I-) 0.022 0.007 0.410
Rmerge in top intensity bin0.031- - 
Total number of observations  311022  1839 14876
Total number unique25311   184  1212
Mean((I)/sd(I)) 19.2  52.7   2.0
Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.740
Completeness   100.0  99.4 100.0
Multiplicity12.3  10.0  12.3

At 1.6A, the I/sig(I) and CC1/2 in the outermost shell are lower, and the 
R-merge,meas,pim are higher.

looking forward to your suggestions,
thanking you,
sreetama


Re: [ccp4bb] distinguish ligand binding sites within a protein

2013-11-20 Thread Ed Pozharski
Baerbel,

Certainly, constraints of the crystal lattice affect everything.  The
magnitude of the influence is what is in question here. Let's do the
numbers (this is admittedly simplistic but reflect general trends well).

Let's say you observe difference in occupancies for two identical sites
that is 50%/75%.  This means that difference in binding affinities is
due to change in free energy of binding at DDG=RTlog(K1/K2).  If ligand
is in excess with respect to the protein, K~(1-occ)*L/occ.  Thus the
estimate of DDG is ~0.6kcal/mol.  Point is that it does not take much
free energy to result in difference in occupancy.  Yet anyone who ever
done ITC would tell you that such small difference would be hard to
detect with the technique.  So the prior is that Wei sees significant
DDG.  

Determining affinities from crystal soaks is, of course, overkill.
There are other easier methods that do not pose the problem you mention.
However, the original post was not about determining affinities, but
rather which of the two sites has the higher affinity.   Is it possible
that lattice constraints invert the affinity ratio? Sure.  But given
that the prior of the lattice DDG=0, it is more likely that the sign
of the affinity ratio in crystal is the same as in solution.  The
likelihood of this, of course, depends on the value of solution DDG
with respect to lattice DDG.

Again, mutagenesis works too, but if crystals and beamtime are
available, such experiment makes sense, at least in my opinion.

Cheers,

Ed.

On Wed, 2013-11-20 at 08:20 +0100, Bärbel Blaum wrote:
 Hi Ed,
 
 you are right about the original question, but what I mean is this: if  
 the occupancies (and B-factors) differ so much in crystals with  
 IDENTICAL binding sites, i.e. identical affinities, does this not show  
 that occupancies (and B-factors) do not reflect affinities alone, but  
 equally local packing? There might be individual cases in which such  
 effects can be neglected, but generally I think trying to determine  
 affinities from crystal soaks is, hmm, not very good pratice, simply  
 because there are other dedicated methods to do it that suffer less  
 from side effects. Including the docking approach.
 
 Kind regards, Baerbel
 
 
 Quoting Ed Pozharski epozh...@umaryland.edu:
 
  If I understand the original post correctly, the binding sites in
  question are not chemically identical.  While it's possible that lattice
  may invert the order in which sites are occupied, it is not very likely
  given that affinity gap is sufficient to be observable by ITC.
 
  Mutagenesis is a good option too.
 
  On Tue, 2013-11-19 at 17:12 +0100, Bärbel Blaum wrote:
  Hello,
 
  we work with proteins that have typically several chemically identical
  binding sites (viral capsid proteins fully assembled or as multimeric
  assembly-intermediates). Depending on how long at which concentrations
  they are soaked the chemically identical ligand pockets within one
  asymmetric unit are typically occupied to different levels purely
  because of individual crystal contacts and accessibility. I therefore
  think that neither soaking with different concentrations nor B-factor
  analysis are solid methods to determine some sort of relative
  affinities. I'd suggest to design mutants for either binding site and
  ITC measurements with the mutant proteins. This might also tell you if
  some sort of co-op exists between both sites.
 
  Baerbel
 
  Quoting Ed Pozharski epozh...@umaryland.edu:
 
   IMHO, while explaining binding affinity from a structure is fun, it does
   not prove anything.  Assuming that I understand your situation
   correctly, you can (relatively) easily find out from experiment which
   pocket has higher affinity.  Just do soaks with different ligand
   concentrations - the expectation is that the weaker binding site will
   become partially occupied first.
  
   On Tue, 2013-11-19 at 04:58 +, Xiaodi Yu wrote:
   Hi Wei:
  
   Based on the structure, you can calculate the binding surface between
   the protein and the ligand. Maybe the two binding pockets will give
   you two different numbers. And the larger one usually can have the
   higher binding affinity.  You also can analyse how the ligand
   interacts with the protein though hydrophobic or electrostatic
   interaction , etc?  the last, you may also compare the b factors of
   the ligand or the protein binding pocket regions after you refining
   the structure. These things may give you some hints about which
   binding site is more strong.
  
   Dee
  
  
   __
   Date: Mon, 18 Nov 2013 22:45:58 -0500
   From: wei.shi...@gmail.com
   Subject: Re: [ccp4bb] distinguish ligand binding sites within a
   protein
   To: CCP4BB@JISCMAIL.AC.UK
  
   Thank you so much for the suggestions, Tomas! Yes, my ligand is a
   small molecule. I have the crystal structure of the ligands bound to
   the protein, do I still need

Re: [ccp4bb] distinguish ligand binding sites within a protein

2013-11-19 Thread Ed Pozharski
If I understand the original post correctly, the binding sites in
question are not chemically identical.  While it's possible that lattice
may invert the order in which sites are occupied, it is not very likely
given that affinity gap is sufficient to be observable by ITC.

Mutagenesis is a good option too.

On Tue, 2013-11-19 at 17:12 +0100, Bärbel Blaum wrote:
 Hello,
 
 we work with proteins that have typically several chemically identical  
 binding sites (viral capsid proteins fully assembled or as multimeric  
 assembly-intermediates). Depending on how long at which concentrations  
 they are soaked the chemically identical ligand pockets within one  
 asymmetric unit are typically occupied to different levels purely  
 because of individual crystal contacts and accessibility. I therefore  
 think that neither soaking with different concentrations nor B-factor  
 analysis are solid methods to determine some sort of relative  
 affinities. I'd suggest to design mutants for either binding site and  
 ITC measurements with the mutant proteins. This might also tell you if  
 some sort of co-op exists between both sites.
 
 Baerbel
 
 Quoting Ed Pozharski epozh...@umaryland.edu:
 
  IMHO, while explaining binding affinity from a structure is fun, it does
  not prove anything.  Assuming that I understand your situation
  correctly, you can (relatively) easily find out from experiment which
  pocket has higher affinity.  Just do soaks with different ligand
  concentrations - the expectation is that the weaker binding site will
  become partially occupied first.
 
  On Tue, 2013-11-19 at 04:58 +, Xiaodi Yu wrote:
  Hi Wei:
 
  Based on the structure, you can calculate the binding surface between
  the protein and the ligand. Maybe the two binding pockets will give
  you two different numbers. And the larger one usually can have the
  higher binding affinity.  You also can analyse how the ligand
  interacts with the protein though hydrophobic or electrostatic
  interaction , etc?  the last, you may also compare the b factors of
  the ligand or the protein binding pocket regions after you refining
  the structure. These things may give you some hints about which
  binding site is more strong.
 
  Dee
 
 
  __
  Date: Mon, 18 Nov 2013 22:45:58 -0500
  From: wei.shi...@gmail.com
  Subject: Re: [ccp4bb] distinguish ligand binding sites within a
  protein
  To: CCP4BB@JISCMAIL.AC.UK
 
  Thank you so much for the suggestions, Tomas! Yes, my ligand is a
  small molecule. I have the crystal structure of the ligands bound to
  the protein, do I still need to computationally dock the ligand to the
  two pockets, can I calculate the parameters of binding directly using
  the crystal structure?
 
  Best,
  Wei
 
 
 
  On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas
  tomas.malinaus...@gmail.com wrote:
  Dear Wei Shi,
  is your ligand a small molecule? If it is a small molecule, I
  would
  try to computationally dock the small molecule to two pockets
  separately using AutoDock, and look at the estimated free
  energies of
  binding.
  Best wishes,
  Tomas
 
  On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi
  wei.shi...@gmail.com wrote:
   Hi all,
   I got the crystal structure of a transcription factor, and
  every monomer
   binds two molecules of the same ligand in different binding
  pockets. And I
   also did the ITC experiment, titrating the ligand into the
  protein, and got
   a U-shaped curve. The binding affinity for the first binding
  site is higher
   than the second binding site.
   I am wondering whether I could computationally determine
  from the
   protein-ligand complex structure that which binding site has
  higher affinity
   for the ligand and correlate the binding sites with the
  parameters I got
   from ITC experiment.
   Thank you so much!
  
   Best,
   Wei
 
 
 
 
  --
  Edwin Pozharski, PhD, Assistant Professor
  University of Maryland, Baltimore
  --
  When the Way is forgotten duty and justice appear;
  Then knowledge and wisdom are born along with hypocrisy.
  When harmonious relationships dissolve then respect and devotion arise;
  When a nation falls to chaos then loyalty and patriotism are born.
  --   / Lao Tse /
 
 
 
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born

Re: [ccp4bb] Comparison of Water Positions across PDBs

2013-10-29 Thread Ed Pozharski

http://www.ccp4.ac.uk/html/watertidy.html


On 10/29/2013 04:43 PM, Elise B wrote:

Hello,

I am working on a project with several (separate) structures of the 
same protein. I would like to be able to compare the solvent molecules 
between the structures, and it would be best if the waters that exist 
in roughly the same position in each PDB share the same residue 
number. Basically, I want to compare solvent molecule coordinates and 
assign similar locations the same name in each structure.


 What would be the best strategy for re-numbering the water molecules 
such that those with similar coordinates in all the structures receive 
the same residue number? I'd appreciate any suggestions.


Elise Blankenship




--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Is there someone work with Lipids?

2013-09-30 Thread Ed Pozharski
 May I ask a question?
 

This is a catch-22 situation.  If you ask permission to ask a question,
you are already asking a question.  Answering this with no would
probably create a wormhole.  I'd also like to see a bulletin board where
asking questions requires separate permission.

 When we prepare lipids, we always used chloroform to dissolve lipids,
 then resuspended in buffer. But sometime we can dissolve lipids with
 detergent, for example E.coli total lipids. Why we still need to use
 chloroform to dissolve it firstly based on standard method?

Chloroform is a good way to store lipids (keep it in -80 to minimize
evaporation, use teflon cap liners, warm up prior to use to avoid water
absorption and top off with argon after each withdrawal).  Chloroform
can be easily removed (bulk with gentle stream of argon under the hood
and residual by 1-2 hour dessication under oil pump) and you can then
have a very good control over buffer content (charged lipids will come
with counterions, of course).  Thus, it's a very robust general
procedure.

Using detergents to dissolve lipids is much messier, I presume.  Of
course, this depends on what you are trying to accomplish.

Cheers,

Ed.

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 10:07 -0400, Bosch, Juergen wrote:
 Yes, I'm also surprised why people run gradients for the capturing
 step ? 

Because we can.  Joking aside, I've seen some examples where protein
eluted at relatively low imidazole and upon running the gradient there
remains some (minimal) overlap with non-specific binders.  Mainly I just
never seen consensus on what is the right imidazole concentration for
the wash buffer (10mM? 50mM? may even depend on expession
circumstances), running the gradient takes that uncertainty away.  Also,
batch method probably leaves more contamination behind.

One can run imidazole gradient in 1-2 hours, batch is not really much
faster, if at all.  So if one has FPLC access, doing imidazole gradient
seems like a good standard policy.  Benefits might be minor and rare,
but it is not much more work and certainly not worse than batch in any
respect.

My two cents (which in Russia turns into three rusty kopecks),

Ed.

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 13:58 -0400, Bosch, Juergen wrote:
 well if we hit the timer after lysis, say via cell disruptor then I
 have my eluted protein in less than 1 hour, including 40 minutes batch
 binding.

then proceeds to wait six weeks for crystals to appear... :)

Cheers,

Ed.

PS.  There are many ways to skin a kangaroo and ultimately indeed all
things serve the Beam.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs


Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 14:22 -0400, Bosch, Juergen wrote:
 But when it sits and crystallizes it is cleaner - unless some
 opportunistic fungal contamination helps you trim off those nasty
 loops that you would have omitted anyhow from your model.


Jurgen,

Good point and admittedly I never considered that.  On the other hand,
when supernatant is injected in the column on FPLC, other components
that may harm the protein are either rapidly removed from the
environment or immobilized on the resin and can do no further damage.
Does this mean that the batch method exposes protein for longer time as
you incubate it with the resin?

Of course, we are splitting hairs (at least I am) - both methods work
just fine most of the time and one can find problematic examples with
both.

Cheers,

Ed.

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-21 Thread Ed Pozharski
According to Qiagen


 Since imidazole absorbs UV radiation at 280 nm, an elution profile
 measured at 280 nm while purifying a 6xHis tagged protein by FPLC will
 show an increase in absorbance above the background signal allowing
 quantitation of your protein. The absorbance of imidazole can vary
 depending on its source and purity, but elution buffer containing 250
 mM imidazole usually has an A280 of 0.2–0.4.

Cheers,
Ed.


On Wed, 2013-08-21 at 11:25 -0400, Edward A. Berry wrote:
 Would you happen to know what the A280 of a 1M (or .1 M) solution is?
 I wonder if this absorbance is really due to impurities or is the tail of a 
 weak absorbance band of imidazole itself. I 
 notice A280 is not one of the properties sigma lists for its imidazole.
 
 Jan wrote:
  Hi Bernhard,
  this one works for us:
  Sigma BioUltra imidazole, 99.5% by GC, 56749
 
  Cheers,
  Jan
  --
  Jan Abendroth
  Emerald BioStructures
  Seattle / Bainbridge Island WA, USA
  home: Jan.Abendroth_at_gmail.com
  work: JAbendroth_at_embios.com
  http://www.emeraldbiostructures.com
 
  On Aug 21, 2013, at 7:33 AM, Bernhard Rupp hofkristall...@gmail.com 
  mailto:hofkristall...@gmail.com wrote:
 
  Hi Fellows,
  could someone please point me towards the source of a known high purity 
  imidazole
  with low absorbance at 280 nm? I am facing the problem of detecting a low 
  absorption protein
  in high imidazole background after IMAC gradient elution. In the UV 
  spectra of the
  2 imidazoles I checked there is some contaminant that absorbs at 280…
  Thx, BR
  
  Bernhard Rupp
  Marie Curie Incoming International Fellow
  Innsbruck Medical University
  Schöpfstrasse 41
  A 6020 Innsbruck – Austria
  +43 (676) 571-0536
  bernhard.r...@i-med.ac.at mailto:bernhard.r...@i-med.ac.at
  
  Dept. of Forensic Crystallography
  k.-k. Hofkristallamt
  Vista, CA 92084
  001 (925) 209-7429
  b...@ruppweb.org mailto:b...@ruppweb.org
  b...@hofkristallamt.org mailto:b...@hofkristallamt.org
  http://www.ruppweb.org/
  ---
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] Problems with SANS data analysis

2013-08-07 Thread Ed Pozharski
This question may be better suited for more small-angle-oriented forum, 
e.g.

http://www.saxier.org/forum/


On 08/07/2013 11:22 AM, Remec, Mark wrote:


Dear CCP4bb,

I have a few questions concerning SANS data recently collected that 
I'm having trouble analyzing. The data was collected at 2 different 
detector distances (4m, 2.5m) to achieve higher q-range, but I worry 
that the curves don't overlap enough at intermediate q, which might 
indicate a problem with the data. The links below are pictures of the 
corresponding datasets, before truncating the 4m high-q data and 
merging them into one. Is there a problem evident with the data, or am 
I imagining a problem?


http://postimg.org/image/qb00y20qr/

http://postimg.org/image/8trbp7akj/

http://postimg.org/image/hni86axj7/

http://postimg.org/image/3sjxnu343/

http://postimg.org/image/4ysj0dgsj/

http://postimg.org/image/9ypz8bmf7/

http://postimg.org/image/m358pazb7/

http://postimg.org/image/jzuthmzib/

My second question concerns the values obtained in the analysis of the 
final scattering curves. The second sample in my experiment shows 
serious deviation in the values obtained for I(0) and Rg by Guinier 
analysis compared to the values obtained by the P(r) analysis. In 
other words, either the P(r) values match the Guinier and the P(r) fit 
is terrible, or else the P(r) fit is good but doesn't match the 
Guinier at all (5-10 difference in Rg, 2x difference in I(0)). I've 
checked to make sure the buffer subtraction algorithm was OK, and I'm 
pretty certain that the buffers were exact matches, so I don't know 
how to explain this variation. There's no evidence of aggregation or 
polydispersity to throw off the values, either. Does anyone know how 
this can happen?






--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs



Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski

On 08/07/2013 01:51 PM, James Stroud wrote:

In the long term, the MM structure community should perhaps get its inspiration 
from SQL
For this to work, a particular interface must monopolize access to 
structural data.  Then maintainers of that victorious interface could 
change the underlying format whichever way they want while supplying the 
never ending stream of useful features.  And all other programs would be 
just frontends to the interface.  As long as data format remains easily 
readable and there is more than one person willing to fiddle with code, 
persistence or at the very least backward compatibility of the data 
format will remain a (minor to me) issue.  It is also important that it 
is much easier to write a pdb parser in your favourite language than to 
implement general purpose relational database management system.


For full disclosure, I personally do not share the apocalyptic feeling 
about transition to mmCIF.


Cheers,

Ed.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski

On 08/07/2013 03:54 PM, James Stroud wrote:

On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:

On 08/07/2013 01:51 PM, James Stroud wrote:

In the long term, the MM structure community should perhaps get its inspiration 
from SQL

For this to work, a particular interface must monopolize access to structural 
data.

Not necessarily, although the alternative pathway might be more idealistic and 
hence unrealistic.

All that needs to happen is that the community agree on

1. What is the finite set of essential/useful attributes of macromolecular 
structural data.
2. What is the syntax of (a) accessing and (b) modifying those attributes.
3. What is the syntax of selecting subsets of structural data based on those 
attributes.

The resulting syntax (i.e. language) itself should be terse, easy to learn, 
easy to use, and preferably easy to implement.

If such a standard is created, then I believe awk-ing/grep-ing/sed-ing/etc PDBs 
and mmCIFs would quickly become historical.

James

James,

frankly, I am not sure which part of your description is not equivalent 
to monopolistic interface.


If I understand your proposal and reference to SQL correctly, you want 
some scripting language that sounds like simple English.  Is the 
advantage over existing APIs here that one does not need to learn 
Python, C++, (or, heaven forbid, FORTRAN)?  I.e. programs would look 
like this


---
GRAB protein FROM FILE best_model_ever.cif;
SELECT CHAIN A FROM protein AS chA;
SET chA BFACTORS TO 30.0;
GRAB data FROM FILE best_data_ever.cif;
BIND protein TO data;
REFINE protein USING BUSTER WITH TLS+ANISO;
DROP protein INTO FILE better_model_yet.cif;
---

Not necessarily a bad idea but now through the fog of time I remember 
something oddly reminiscent... ah, CNS! (for those googling for it it's 
not the central nervous system :).


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski

James,

On 08/07/2013 05:36 PM, James Stroud wrote:
Anyone can learn Python in an hour and a half. 


Isn't this a bit of an exaggeration?  Python is designed to be easy to 
learn, but we probably talking about different definitions of learning 
and anyone.



I.e. programs would look like this

---
GRAB protein FROM FILE best_model_ever.cif;
SELECT CHAIN A FROM protein AS chA;
SET chA BFACTORS TO 30.0;
GRAB data FROM FILE best_data_ever.cif;
BIND protein TO data;
REFINE protein USING BUSTER WITH TLS+ANISO;
DROP protein INTO FILE better_model_yet.cif;
---

Not necessarily a bad idea but now through the fog of time I remember something oddly 
reminiscent... ah, CNS! (for those googling for it it's not the central nervous 
system :).
Although a little too much like natural language, it is not a bad idea. But, 
where is the link describing the layer of CNS that looks like that?


I should probably use tongue-in-cheek/tongue-in-check markup next 
time to prevent my poor attempt at humorous tribute to CNS from being 
understood so literally.  At the very least you might agree that CNS is 
the closest thing we ever had to MX-oriented general purpose 
interpreter.  Your quote is also from 
below-the-magic-line-do-not-change area of a CNS script.


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski

On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset 
or many other tools.  Writing code for this should only be necessary 
if you're processing large numbers of models, or have a spectacularly 
misformatted PDB file.  Again, I'll repeat what I said before: if it's 
truly necessary to view or edit a model by hand or with custom shell 
scripts, this often means that the available software is deficient.  
PLEASE tell the developers what you need to get your job done; we 
can't read minds.


Nat,

I don't think anyone here really means that the only way to change a 
chain ID is to write, say, a perl script.  But an interpreter of the 
kind advocated by James (as much as I have hijacked/misinterpreted his 
vision) could indeed be very useful for people pursuing simple 
bioinformatics projects and new ways to analyse structural models. While 
I understand your view that everyone should seek assistance from 
developers with every problem encountered, I also recall some 
reasonable idea about self-sufficiency that should cover scientific 
research (something like give man a fish and you feed him for a day, 
teach him to fish and he starts paying taxes... something along these 
lines ;).  There is a difference betweens tools that allow to easily 
perform useful non-standard analysis and highly specialized tools that 
strive to cover every situation imaginable.


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] ctruncate bug?

2013-06-21 Thread Ed Pozharski

On 06/21/2013 10:19 AM, Ian Tickle wrote:
If you observe the symptoms of translational NCS in the diffraction 
pattern (i.e. systematically weak zones of reflections) you must take 
it into account when calculating the averages, i.e. if you do it 
properly parity groups should be normalised separately (though I 
concede there may be a practical issue in that I'm not aware of any 
software that currently has this feature). 


Ian,

I think this is exactly what I was trying to emphasize, that applying 
some conversion to raw intensities may have negative impact when 
conversion is based on incorrect or incomplete assumptions.


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] ctruncate bug?

2013-06-19 Thread Ed Pozharski
Dear Kay and Jeff,

frankly, I do not see much justification for any rejection based on
h-cutoff.  

FrenchWilson only talk about I/sigI cutoff, which also warrants further
scrutiny.  It probably could be argued that reflections with I/sigI-4
are still more likely to be weak than strong so F~0 seems to make more
sense than rejection.  The nature of these outliers should probably be
resolved at the integration stage, but these really aren't that
numerous.

As for h-4 requirement, I don't see FrenchWilson even arguing for that
anywhere in the paper.  h variable does not reflect any physical
quantity that would come with prior expectation of being non-negative
and while the posterior of the true intensity (for acentric reflections)
is distributed according to the truncated normal distribution N(sigma*h,
sigma^2), I don't really see why h-4 is bad.

From what I understand, Kay has removed h-cutoff from XDSCONV (or never
included it in the first place).  Perhaps ctruncate/phenix should change
too?  Or am I misunderstanding something and there is some rationale for
h-4 cutoff?

Cheers,

Ed.


On Wed, 2013-06-19 at 06:47 +0100, Kay Diederichs wrote:
 Hi Jeff,
 
 what I did in XDSCONV is to mitigate the numerical difficulties associated 
 with low h (called Score in XDSCONV output) values, and I removed the h  
 -4 cutoff. The more negative h becomes, the closer to zero is the resulting 
 amplitude, so not applying a h cutoff makes sense (to me, anyway).
 XDSCONV still applies the I  -3*sigma cutoff, by default.
 
 thanks,
 
 Kay

-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


Re: [ccp4bb] sigma value in structure file

2013-06-17 Thread Ed Pozharski
The only thing that seems to make sense is bonds rmsd - but you should
ask the annotator for specifics directly.  If it is bonds rmsd, this has
been discussed many times - just google rmsd bonds ccp4bb and look for
most recent entries.

On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote:
 Dear all
 
 
 During PDB deposition the annotator me to verify and review the sigma
 value in the structure file which in my case was -0.03. I have some
 basic queries and request you all to please answer them. My first
 question is, what actually is a sigma value of a structure file.
 2nd) where the value is mentioned?. 3rd) and What is the optimum sigma
 value range ?
 
 
 -- 
 Regards
 
 Faisal
 School of Life Sciences
 JNU

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


[ccp4bb] ctruncate bug?

2013-06-17 Thread Ed Pozharski
I noticed something strange when processing a dataset with imosflm.  The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to FrenchWilson.  Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97% complete)!

About half of the reflections that go missing are negative, but half are
positive.  About 5x more negative intensities are successfully
converted.  Most impacted are high resolution shells with weak signal,
so I am sure impact on normal refinement would be minimal.

However, I am just puzzled why would ctruncate reject positive
intensities (or negative for that matter - I don't see any cutoff
described in the manual and the lowest I/sigI for successfully converted
reflection is -18).

Is this a bug or feature?

Cheers,

Ed.

-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


Re: [ccp4bb] ctruncate bug?

2013-06-17 Thread Ed Pozharski

Jeff,

thanks - I can see the same equation and cutoff applied in ctruncate 
source.Here is the relevant part of the code


// Bayesian statistics tells us to modify I/sigma by 
subtracting off sigma/S

// where S is the mean intensity in the resolution shell
h = I/sigma - sigma/S;
// reject as unphysical reflections for which I  -3.7 sigma, 
or h  -4.0

if (I/sigma  -3.7 || h  -4.0 ) {
nrej++;
if (debug) printf(unphys: %f %f %f %f\n,I,sigma,S,h);
return(0);
}


This seems to be arbitrary cutoff choice, given that they are 
hard-coded.  At the very least, cutoffs should depend on the total 
number of reflections to represent famyliwise error rates.


It is however the h-based rejection that seems most problematic to me.  
In the dataset in question, up to 20% reflections are rejected in the 
highest resolution shell (granted, I/sigI there is 0.33).  I would 
expect that reflections are rejected when they are deemed to be outliers 
due to reasons other than statistical errors (e.g. streaks, secondary 
lattice spots in the background, etc).  I must say that this was done 
with extremely good quality data, so I doubt that 1 out of 5 reflections 
returns some physically impossible measurement.


What is happening is that sigma=3S in the highest resolution shell, 
and for many reflection h-4.0.  This does not mean that reflections are 
unphysical though, just that shell as a whole has mostly weak data (in 
this case 89% with I/sigI2 and 73% with I/sigI1).


What is counterintuitive is why do I have to discard reflections that 
are just plain weak, and not really outliers?


Cheers,

Ed.



On 06/17/2013 10:29 PM, Jeff Headd wrote:

Hi Ed,

I'm not directly familiar with the ctruncate implementation of French 
and Wilson, but from the implementation that I put into Phenix (based 
on the original FW paper) I can tell you that any reflection where 
(I/sigI) - (sigI/mean_intensity) is less than a defined cutoff (in our 
case -4.0), then it is rejected. Depending on sigI and the mean 
intensity for a given shell, this can result in positive intensities 
that are also rejected. Typically this will effect very small positive 
intensities as you've observed.


I don't recall the mathematical justification for this and don't have 
a copy of FW here at home, but I can have a look in the morning when 
I get into the lab and let you know.


Jeff


On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski epozh...@umaryland.edu 
mailto:epozh...@umaryland.edu wrote:


I noticed something strange when processing a dataset with
imosflm.  The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to FrenchWilson.  Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97% complete)!

About half of the reflections that go missing are negative, but
half are
positive.  About 5x more negative intensities are successfully
converted.  Most impacted are high resolution shells with weak signal,
so I am sure impact on normal refinement would be minimal.

However, I am just puzzled why would ctruncate reject positive
intensities (or negative for that matter - I don't see any cutoff
described in the manual and the lowest I/sigI for successfully
converted
reflection is -18).

Is this a bug or feature?

Cheers,

Ed.

--
I don't know why the sacrifice thing didn't work.
Science behind it seemed so solid.
Julian, King of Lemurs





--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs



Re: [ccp4bb] Concerns about statistics

2013-06-15 Thread Ed Pozharski

On 06/14/2013 07:00 AM, John R Helliwell wrote:
Alternatively, at poorer resolutions than that, you can monitor if the 
Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as 
more data are steadily added to your model refinements.

Dear John,

unfortunately the behavior of DPIfree is less than satisfactory here - 
in a couple of cases I looked at it just steadily improves with 
resolution.  Example I have in front of me right now takes resolution 
down from 2.0A to 1.55A, and DPIfree goes down from ~0.17A to 0.09A at 
almost constant pace (slows down from 0.021 A/0.1A to 0.017 A/0.1A 
around 1.75A).


Notice that in this specific case I/sigI at 1.55A is ~0.4 and 
CC(1/2)~0.012 (even this non-repentant big-endian couldn't argue there 
is good signal there).


DPIfree is essentially proportional to Rfree * d^(2.5)  (this is 
assuming that No~1/d^3, Na and completeness do not change).  To keep up 
with resolution changes, Rfree would have to go up ~1.9 times, and 
obviously that is not going to happen no matter how much weak data I 
throw in.


The maximum-likelihood e.s.u. reported by Refmac makes more sense in 
this particular case as it clearly slows down big time around 1.77A (see 
https://plus.google.com/photos/113111298819619451614/albums/5889708830403779217). 
Coincidentally, Rfree also starts going up rapidly around the same 
resolution.  If anyone is curious what's I/sigI is at the breaking 
point it's ~1.5 and CC(1/2)~0.6.  And to bash Rmerge a little more, 
it's 112%.


So there are two questions I am very much interested in here.

a) Why is DPIfree so bad at this?  Can we even believe it given it's 
erratic behavior in this scenario?


b) I would normally set up a simple data mining project to see how 
common this ML_esu behavior is, but there is no easily accessible source 
of data processed to beyond I/sigI=2, let alone I/sigI=1 (are structural 
genomics folks reading this and do they maybe have such data to mine?).  
I can look into all of my own datasets, but that would be a biased 
selection of several crystal forms.  Perhaps others have looked into 
this too, and what are your observations? Or maybe you have a dataset 
processed way beyond I/sigI=1 and are willing to either share it with me 
together with a final model or run refinement at a bunch of different 
resolutions and report the result (I can provide bash scripts as needed).


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Ed Pozharski
On Thu, 2013-06-13 at 08:44 -0700, Andrea Edwards wrote:
 In this case, the author should report a correlation coefficient along
 with the other standard statistics (I/sigI, Rmerg, Completeness,
 redundancy, ect.)? 

Won't hurt.  

 What about Rpim instead of Rmerg? and if Rpim is reported, what should
 be the criteria for resolution cutoff?

Rmerge is known to be deeply flawed for ~15 years.  IMHO, it shall not
be reported at all.  While Rpim is better, the whole point of
KarplusDiederichs is that R-type measures are not very useful in
deciding resolution cutoff.

 Also, if this paper is the new standard how should we regard
 statistic reported in the literature? 

We should keep in mind that conservative resolution cutoff criteria has
been used in the field for decades. 

 Or.. more importantly, how do we go about reviewing current literature
 that does not report this statistic?

Structures refined up to I/sigma=2 should be considered likely to have
been refined to resolution that was cut off too low.

With that said, I am pretty sure that in vast majority of cases
structural conclusions derived with I/s=2 vs CC1/2=0.5 vs DR=0 cutoff
will be essentially the same.
 

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs


Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Ed Pozharski
Tim,

my personal preference always was I/sigI=1.  In my Scalepack days, I
always noticed that ~30% of the reflections in the I/sigI=1 shells had
I/sigI2, and formed an unverified belief that there should be some
information there.

In my experience, CC1/2=0.5 would normally yield I/sigI~1, not 2.  This
is based predominantly on Scala/Aimless.

Cheers,

Ed.

On Thu, 2013-06-13 at 18:20 +0200, Tim Gruene wrote:
 
 On 06/13/2013 06:16 PM, Ed Pozharski wrote:
  [...] With that said, I am pretty sure that in vast majority of
  cases structural conclusions derived with I/s=2 vs CC1/2=0.5 vs
  DR=0 cutoff will be essentially the same.
 
 Hi Ed,
 in my experience, CC(1/2)  0.7 corresponds quite well to I/sigI  2.0
 rather than CC(1/2)  0.5 (again, with the default resolution shells
 from xprep that also plots CC(1/2) vs. resolution. Are above numbers
 based on experience, too? If so, which program do you usually use to
 look at these statistics?
 
 Tim
 
 

-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread Ed Pozharski
ATOM records have fixed format so you can (and should) use string
slicing instead, like so (one-liner)

serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = line[6:11], line[12:16], line[16], line[17:20], line[21],
line[22:26], line[26], line[30:38], line[38:46], line[46:54],
line[54:60], line[60:66], line[76:78], line[78:80]

or with more explicit typing

serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = int(line[6:11]), line[12:16].strip(), line[16].strip(),
line[17:20].strip(), line[21], int(line[22:26]), line[26],
float(line[30:38]), float(line[38:46]), float(line[46:54]),
float(line[54:60]), float(line[60:66]), line[76:78].strip(), line[78:80]

Cheers,

Ed.



On Thu, 2013-06-06 at 04:37 +, GRANT MILLS wrote:
 Dear CCP4BB,
 
 I'm trying to write a simple python script to retrieve and manipulate
 PDB data using the following code:
 
 #for line in open(PDBfile.pdb):
 #if ATOM in line:
 #column=line.split()
 #c4=column[4]
 
 and then writing to a new document with:
 
 #with open(selection.pdb, a) as myfile:
 #myfile.write(c4+\n)
 
 Except for if the PDB contains columns which run together such as the
 occupancy and B-factor in the following:
 
 ATOM608  SG  CYS A  47  12.866 -28.741  -1.611  1.00201.10
 S  
 ATOM609  OXT CYS A  47  14.622 -24.151  -1.842  1.00100.24
 O 
 
 My script seems to miscount the columns and read the two as one
 column, does anyone know how to avoid this? (PS, I've googled this
 like crazy but I either don't understand or the link is irrelevant)
 
 Any advice would help.
 Thanks for your time,
 Grant
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread Ed Pozharski
On Thu, 2013-06-06 at 14:41 +1000, Nat Echols wrote:
 You should resist the temptation to write your own PDB parser; that
 way lies pain and suffering.  There are multiple free libraries for
 Python that can be used for this task - I recommend either CCTBX or
 BioPython (probably the latter if you don't need to do very much with
 the models).

Well, that depends on what one is trying to accomplish.  Say, I just
want to count how many atoms I have that are partially occupied in an
average PDB file.  All I need to know is that occupancy is stored in
columns 55:60 as Real(6.2), and that atom record lines begin with ATOM
|HETATM.  With basic python/c/perl/whatever knowledge I can write my
own occupancy parser faster than this post.  Getting BioPython or
CCTBX to work will definitely take longer.

By writing primitive parsers one also gains speed and portability, as
well as extends programming skills.  Basically this choice depends on
the complexity of the task and long/short-term goals.

Cheers,

Ed.

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] use only companies that you know to purchase chemicals

2013-05-29 Thread Ed Pozharski
On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote:
 In this particular case you can see the website was registered in
 September of 2012, which is a good indication that it was set up just
 to scam people.

Just curious - why registration date indicates unsavory nature of
Jieke?

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

2013-05-29 Thread Ed Pozharski
 I am wondering whether there is a function I could use to build the
 missing bases in one strand of the DNA to base pair with the other
 strand of DNA which is complete...

Calculate-Other modeling tools- Base pair...

-- 
Coot verendus est


Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
It is probably a wrong question to ask here.  Pretty much everything is 
tolerated by PDB during deposition, the report you get is an advice, 
not instruction.  I wonder whether anyone has an example of the 
RCSB/PDBe/PDBj ever turning down submitted structure.


The right question is whether the short contact you mention is tolerated 
by laws of nature.  It's fairly common to have, say, a water molecule 
split in two positions near symmetry axis - as long as you have it at 
occupancy1.0, it's ok.


On 05/27/2013 05:21 AM, Kavyashree Manjunath wrote:

Dear users,

  Is short contact (1.83Ang) between an atom and symmetry
equivalent of itself tolerated during deposition? I am not
able to get rid of this short contact appearing after refinement.

Thank you
Regards
Kavya





--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski

On 05/27/2013 11:27 AM, ka...@ssl.serc.iisc.in wrote:

Sir,

Ok. It is an acetate ion which interacts with its symmetry
equivalent ion only one of its oxygen atoms is closer to
its symmetry equivalent and not the entire ion. So do I
need to give lower occupancy for this ion?

Thank you
Regards
Kavya




It does not interact - you cannot have 1.8A distance between atoms. 
Assuming that it is indeed acetate it must be partially occupied, 0.5 or 
less.  Keep in mind that when you lower occupancy you may see additional 
density for whatever occupies the space on the other side of the 
symmetry element (e.g. water) which you may need to model.




--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski

On 05/27/2013 12:14 PM, Kavyashree Manjunath wrote:

Later I tried with 0.8, 0.99 for which the map was normal
and also validation did not report it as short contact.
Is it ok if I give 0.99 occupancy?
Validation most likely will not report any short contacts if occupancy 
is 1.  If the distance between atoms is still ~1.8A, you have a 
problem.  Perhaps it is not an acetate.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] cryo condition

2013-05-23 Thread Ed Pozharski
Matt,

with this technique, how do you prevent crystal from drying up (other
than doing it fast)?  I know Thorne's group does this trick under oil.
If you take no extra precautions, do you have an estimate of how often
diffraction is destroyed by this?  

On the other hand, it's quite possible that what destroys resolution
when crystals dry up is increase in concentration of non-volatile mother
liquor components, which shouldn't be happening here to the same degree.

Cheers,

Ed.

On Thu, 2013-05-23 at 14:38 +0200, Matthew BOWLER wrote:
 Hi Faisal,
 if your solvent channels are smaller than 40A in the largest dimension 
 (most are) you can use a mesh loop to pick up the crystal and then wick 
 away all of the mother liquor. You can then flash cool your crystal 
 without having to transfer the crystal to another solution. Good luck, 
 Matt

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
Tim,

naturally, the issue is specific to a particular pdb file (it would be
indeed strange if the conversion tool from a major software package
would fail in general sense).

Ed.

On Wed, 2013-05-22 at 08:12 +0200, Tim Gruene wrote:
 Hi Ed,
 
 
 # pdbvconv -p udo.pdb -o udov.pdb
 # pdbvconv -p udov.pdb -o udovv.pdb
 # diff -q udo.pdb udov.pdb
 Files udo.pdb and udov.pdb differ
 # diff -q udov.pdb udovv.pdb
 Files udov.pdb and udovv.pdb differ
 # diff -q udo.pdb udovv.pdb
 #
 
 it works for me, Version: 1.0 (11 June 2008) from buster 2.10. Which
 version of pdbvconv are you using?
 Best,
 Tim
 
 
 On 05/21/2013 10:40 PM, Ed Pozharski wrote:
  On 05/21/2013 04:35 PM, Francis Reyes wrote:
  Since you're using buster, have you tried global phasing's own 
  pdbvconv tool?
  Naturally, but it leaves file unchanged.
  
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
 the answers you received were correct with respect to the question you
 asked. If they are not satisfactory, you have not given sufficient
 information.
 
Tim,

Not sure when I expressed any dissatisfaction with replies I received.
I asked whether someone had a simple tool to turn v3 DNA records back to
v2.  I got an excellent off-list suggestion to use Remediator tool from
kinemage/molprobity (writen by Jeff Headd and Robert Immormino).  

It was probably easy to guess that I tried pdbvconv and ran into
problems (in fact, buster takes care of conversion internally unless it
fails).  I appreciate your initial comment that pdbvconv works for you
and was simply pointing out that my observations are not of general
nature and obviously specific to a particular file I was trying to
convert.  It appears that you were offended by that and if so, it was
not my intent.  In my defense, I only asked for available conversion
tools and did not ask specifically for help with pdbvconv. With this in
mind, I hope I can be forgiven for not posting unpublished structural
model on a bulletin board in order to provide sufficient information for
answering a question I did not ask.

If you are interested in specifics, the problem was that some other
program made residue names left-justified.

Cheers,

Ed.


-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs


Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
Dear Tim,

I am sorry that you feel offended.  It is rather unfortunate that you
got an impression from my secondary comment that I am asking for help
with pdbvconv when I wasn't.  It is also rather unfortunate that I have
figured out what the problem was myself and therefore did not have an
opportunity to ask for and fully utilize your help and that of other
ccp4bb members.  In general, it is rather unfortunate that helping
others often feels and occasionally is a waste of time.  Hopefully this
unfortunate experience will not dissuade you from positively
contributing to the ccp4bb to the same extent to which it dissuades me
from ever again soliciting any advice through this venue.

Cheers,

Ed.

PS.  Naturally, at the time of the original post and the subsequent one
you responded to I did not yet know what was wrong with the specific pdb
file.  To have such knowledge and yet ask why pdbvconv fails (which I
did not ask) would be both stupid and evil.  Then again, I may be both
of these things.

On Wed, 2013-05-22 at 21:55 +0200, Tim Gruene wrote:
 Dear Ed,
 
 I do feel offended because I follow the ccp4bb with the intention of
 helping people with my answers, which does take time. If it turns out
 the I wasted my time because of the lack of information I consider the
 question asked not follow what I consider netiquette. I doubt that one
 line from a PDB file or the point that you have used pbdvconv before
 (especially in case you were aware of the problem being due to a
 simple shift - of course I do not know whether you were aware of it
 when opening the thread) and it failed would have revealed any
 information that would give your competitors any advantage, but it
 would have narrowed down the problem and probably the number of people
 spending time trying to find and give a helpful answer.
 
 Regards,
 Tim
 
 On 05/22/2013 07:55 PM, Ed Pozharski wrote:
  On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
  the answers you received were correct with respect to the 
  question you asked. If they are not satisfactory, you have not 
  given sufficient information.
  
  Tim,
  
  Not sure when I expressed any dissatisfaction with replies I 
  received. I asked whether someone had a simple tool to turn v3 DNA 
  records back to v2.  I got an excellent off-list suggestion to use 
  Remediator tool from kinemage/molprobity (writen by Jeff Headd and 
  Robert Immormino).
  
  It was probably easy to guess that I tried pdbvconv and ran into 
  problems (in fact, buster takes care of conversion internally 
  unless it fails).  I appreciate your initial comment that pdbvconv 
  works for you and was simply pointing out that my observations are 
  not of general nature and obviously specific to a particular file
  I was trying to convert.  It appears that you were offended by
  that and if so, it was not my intent.  In my defense, I only asked
  for available conversion tools and did not ask specifically for
  help with pdbvconv. With this in mind, I hope I can be forgiven for
  not posting unpublished structural model on a bulletin board in
  order to provide sufficient information for answering a question I
  did not ask.
  
  If you are interested in specifics, the problem was that some other
  program made residue names left-justified.
  
  Cheers,
  
  Ed.
  
  
 

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


[ccp4bb] DNA version converter

2013-05-21 Thread Ed Pozharski
Does anyone have a script to convert pdb file with DNA atom records from 
v3 back to v2?  I can certainly right my own and asking only if you 
already have it written.  Strictly speaking, this is not ccp4-related - 
apparently, buster expects the old format.


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] DNA version converter

2013-05-21 Thread Ed Pozharski

On 05/21/2013 04:35 PM, Francis Reyes wrote:

Since you're using buster, have you tried global phasing's own pdbvconv tool?

Naturally, but it leaves file unchanged.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] question about CCP4 scripts

2013-05-09 Thread Ed Pozharski
At this point you do have the scalepack2mtz output file (BTW,
imosflm/aimless is wholeheartedly recommended by this convert), and you
can easily extract all the info from there.  There is mtzdmp, of course,
but it's easier to parse the actual mtz file (hey, the records are
actually text).  Like so:

egrep -oa SYMINF.{74} foo.mtz | awk '{print symm $5}'

Gives you the space group *number*, most ccp4 programs I know accept
that in addition to string symbol.  But if you really need the latter, 

echo symm $(egrep -oa SYMINF.{74} foo.mtz | cut -d' -f 2 | sed
s///g) 

will do.

As for unit cell parameters, this should work

egrep -oa CELL.{76} foo.mtz | sed -n 1p

Keep in mind that this extracts the global cell and will be
problematic if you have multi-dataset file (which I presume you don't).
If you need Nth dataset grab DCELL record, e.g. for the dataset #1

egrep -oa DCELL.{75} foo.mtz | sed -n 2p

Cheers and 

https://xkcd.com/208/


Ed

On Wed, 2013-05-08 at 23:37 -0400, Joe Chen wrote:

 Hi All,
 
 
 
 
 
 I am trying to write a shell script to streamline a few steps, one of
 which is Unique, see below.  As you can see, this program requires
 symmetry and cell parameters.  In CCP4 GUI Scalepack2mtz, these info
 are automatically extracted from .sca file (first two lines).  But I
 don't know if there is a way to do this in script, so I don't need to
 type these values for each dataset.  Thank you in advance for your
 help.
 
 
 #!/bin/sh
 # unique.exam
 # 
 # runnnable test script for the program unique - this will use this
 # program to generate a reflection list containing null values.
 # 
 
 set -e
 
 unique hklout ${CCP4_SCR}/unique_out.mtz  eof
 labout F=F SIGF=SIGF
 symmetry p43212
 resolution 1.6
 cell 78.1 78.1 55.2 90.0 90.0 90.0
 eof
 
 
 
 
 
 
 -- 
 Best regards,
 
 Joe

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /



Re: [ccp4bb] Program or server to predict Kd from complex structure

2013-04-18 Thread Ed. Pozharski
Don't believe such program/server does exist.   Notice that you are asking for 
something that *can* predict Kd.  One can *try* making such predictions and 
they may even be routinely in the ballpark, assuming that you are satisfied 
with being routinely off by, say, an order of magnitude. 

One can easily predict general trends.  For example, larger buried apolar 
surface will generally result in lower Kd. As for individual Kd prediction 
accuracy,  that's another story. 

It's unknown to me what your goal is, but if you are trying to replace 
experimental Kd determination with a magic program, please don't.

Cheers, 

Ed.

 Original message 
From: Wei Liu we...@me.com 
Date: 04/18/2013  4:39 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Program or server to predict Kd from complex structure 
 
Dear all,

Does anyone know a program or web server that can predict Kd value between two 
proteins from a solved complex structure?

Regards
Wei

Re: [ccp4bb] salt or not?

2013-04-15 Thread Ed. Pozharski
Protein-DNA complex crystal with channels too small for the dye is *extremely* 
unlikely, imho.

 Original message 
From: Ulrike Demmer ulrike.dem...@biophys.mpg.de 
Date: 04/15/2013  8:48 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] salt or not? 
 
Dear Careina,

altough your crystals does't take up the Izit dye it sounds promising. The 
uptake of Izit depends on the solvent channels of the protein molecule - 
sometimes the dye just can't enter the molecule.
Concerning the Calciumchloride - if the concentration is not too high and 
without other ingredients which could cause less solube salt there is the 
possiblity that you have got protein crystals. I once had a condition whith 34 
% MPD + 0.1M buffer + 0.1 M Calciumchloride which produced nicely diffracting  
crystals
To speak from my experience I think 1 month after setting up the trays the 
drops should not be dried out. If the wells are sealed properly new crytals can 
appear even after 1 year.

You should definately check the diffraction then you will know for sure.

Cheers,

Ulrike


Re: [ccp4bb] DNA structures superimpose

2013-04-12 Thread Ed. Pozharski
Doesn't lsqkab work? It just needs proper atom matching. 

Coot definitely does superimpose DNA.  One problem is that simple-lsq works on 
a single chain, but you can trick it by changing chain id and renumbering the 
other strand.

As for helix rotation, you can derive it from rotation reported by lsq.  But it 
is more common to look at DNA geometry directly for changes (3DNA or Curves+).

 Original message 
From: Veerendra Kumar (Dr) veeren...@ntu.edu.sg 
Date: 04/12/2013  2:18 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] DNA structures superimpose 
 
Dear CCP4 members,
Is there any program to superimpose the DNA structures? I also want to measure 
the relative domain rotation angle. I tried using DynDom but it does not work 
for me. 
Can someone suggest a program which can output the rotation angles? 

Thank you 

Best Regards

Veerendra kumar

CONFIDENTIALITY:This email is intended solely for the person(s) named and may 
be confidential and/or privileged.If you are not the intended recipient,please 
delete it,notify us and do not copy,use,or disclose its content.

Towards A Sustainable Earth:Print Only When Necessary.Thank you.


Re: [ccp4bb] CCP4 Update victim of own success

2013-04-12 Thread Ed Pozharski

On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan 
bshaa...@exchange.bgu.ac.il mailto:bshaa...@exchange.bgu.ac.il wrote:


Whichever way the input file for the run is prepared (via GUI or
command line), anybody who doesn't inspect the log file at the end
of the run is doomed and bound to commit senseless errors. I was
taught a long time ago that computers always do what you told them
to do and not what you think you told them, which is why
inspecting the log file helps.


I agree in principle - I would not advocate that anyone (*especially* 
novices) run crystallography software as a black box.  However, 
whether or not a program constitutes a black box has nothing to do 
whether it runs in a GUI or not.  The one advantage a GUI has is the 
ability to convey inherently graphical information (plots, etc.).  
That it is still necessary to inspect the log file(s) carefully 
reflects the design of the underlying programs; ideally any and all 
essential feedback should also be displayed in the GUI (if one 
exists).  Obviously there is still much work to be done here.


-Nat


It is hard to blame novices for running crystallography software as a 
black box when the websites from which they download the said software 
use the word automated to describe it.  Because, at least according to 
wikipedia (another great resource that should be used with care), 
automation is the operation of machinery without human supervision.  
Checking the log-files or messages supplied by GUI seems to fall under 
human supervision, which automated programmes should not really 
require.  I am not advocating return to the stone age when naming a 
tutorial for a widely used model building software ... for morons was 
probably considered a joke (not a good one too).  I am just saying that 
it is perhaps quite predictable that with promise of automation comes 
the expectation of, well, automation.  Whether the true automation of 
crystallographic structure determination may become available in the 
future is perhaps debatable.  Whether it is already available probably 
isn't.


On a broader question of GUI versus command line, both obviously have 
their uses.  Mastering command line gives one flexibility and perhaps 
greater insight into what programmes actually do.  Do I prefer a little 
button that opens a file chooser dialog over sam-atom-in?  Absolutely.  
But I am glad that --pdb and --auto command line options are supplied, 
because I can then write a little bash pipeline to pass 50 expected 
protein-ligand complex datasets through simple refmac-coot cycle to 
quickly see which ones are interesting.  In that regard, both ccp4 and 
phenix are doing it the right way - gui is simply a gateway to the 
command-line controlled code. I can then choose the interface that fits 
particular situation.


As for the relatively new CCP4 update feature, it is absolutely awesome.

Cheers,

Ed.



--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs



Re: [ccp4bb] Building ideal B DNA model in Coot

2013-04-06 Thread Ed Pozharski

On 04/04/2013 04:51 PM, 李翔 wrote:

Hi everyone,

I met a problem when trying to build ideal DNA model in Coot. The 
calculated DNA looks less than 10.5 bp/ turn, probably is about 10 bp/ 
turn. Is there a way for me to change the pitch to make it 10.5 
bp/turn in Coot?


Thanks for your kind help!

Sincerely,
Frank
I do not know the answer to your question (but suspect the answer is 
no).  If you want a better control over DNA conformation, consider 3DNA 
(http://x3dna.org) - it can build the DNA molecule from set of 
parameters you provide.




--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] COOT usage for structure comparison

2013-04-04 Thread Ed Pozharski

On 04/04/2013 04:29 AM, Tim Gruene wrote:

Dear --,
Are we, the ccp4bb community, recently on the hunt to find new and 
exciting ways to make sure people stop asking questions?  Gentleman from 
Moscow has clearly disclosed his full name and affiliation, but perhaps 
I am wrong and subtle criticism of his signature-formatting skills is 
highly relevant.  Feel free to call me Julian from now on :)


Cheers,

Ed.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Rfree reflections

2013-03-26 Thread Ed. Pozharski
As I recall, number of reflections set aside for cross-validation also affects 
stability of sigmaA estimates.  With 500 reflections and 20 resolution shells 
you are down to 25 reflections per shell, which may be a bit too low.

 Original message 
From: Robbie Joosten robbie_joos...@hotmail.com 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Rfree reflections 
 
Hi Tim,

The derivation of sigma(Rw-free) is in this paper: Acta Cryst. (2000). D56,
442-450. Tickle et al.
Note the difference between the sigma of weighted/generalized/Hamilton
R-free and that of the 'regular' R-free (there is a 2 there somewhere). From
my own tests (10 fold cross-validation on 38 small datasets) I also find
sigma(R-free) = R-free/sqrt(Ntest).

For large datasets you really do not need to do k-fold cross validation,
because sigma(R-free) can be predicted quite well. We just need to realize
that it exists,

Cheers,
Robbie

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Tim Gruene
 Sent: Tuesday, March 26, 2013 11:05
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Rfree reflections
 
 Hi Robbie,
 
 thank you for the explanation. Heinz Gut and Michael Hadders pointed me at
 Axel Brunger's publication Methods Enzymol. 1997;277:366-96.,
 http://www.ncbi.nlm.nih.gov/pubmed/18488318, which is where I got the
 notion of
 500-1000 from. In this article a decrease of the error margin of Rfree
with
 n^(1/2) is mentioned (p.384), but only as an observation. Is your
statement
 inverse proportional with the number of reflections based on some
 statistical treatment, or also just on observation?
 
 It is a pity that k-cross validation is not standard routine because it
seems so
 easy and so quickly to do with nowadays computers and a simple script. But
 that's probably like reminding people of not using R_int anymore in favour
of
 R_meas...
 
 Cheers,
 Tim
 
 On Tue, Mar 26, 2013 at 10:24:51AM +0100, Robbie Joosten wrote:
  Hi Tim,
 
  I don't think the 5-10% or 500-1000 reflections are real rules, but
  rather practical choices. The error margin in R-free is inverse
  proportional with the number of reflections in your test set and also
  proportional with R-free itself. So for R-free to be 'significant' you
  need some absolute number of reflections to reach your cut-off of
  significance. This is where the 1000 comes from (500 is really pushing
the
 limit).
  You want to make sure the error margin in R and R-free are not too far
  apart and you probably also want to keep the test set representative
  of the whole data set (this is particularly important because we use
  hold-out validation, you only get one shot at validating). This is where
the
 5%-10% comes from.
  Another consideration for going for the 5%-10% thing is that this
  makes it feasible to do 'full' (i.e. k-fold) cross-validation: you
  only have to do
  20-10 refinements.  If you would go for 1000 reflections you would
  have to do 48 refinements for the average dataset.
 
  Personally, I take 5% and increase this percentage to maximum 10% if
  using 5% gives me a test set smaller than 1000 reflections.
 
  HTH,
  Robbie
 
   -Original Message-
   From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
   Of Tim Gruene
   Sent: Tuesday, March 26, 2013 09:33
   To: CCP4BB@JISCMAIL.AC.UK
   Subject: [ccp4bb] Rfree reflections
  
   Dear all,
  
   I recall that the set of Rfree reflections should be 500-1000,
   rather than
  5-
   10%, but I cannot find the reference for it (maybe Ian Tickle?).
  
   I would therefore like to be confirmed or corrected:
  
   Is there an absolute number required for Rfree to be significant, i.e.
  500-1000
   irrespective of the total number of unique reflections in the data
   set, or
  is it
   5-10% (as a compromise)?
  
   Thanks and regards,
   Tim
  
   --
   --
   Dr Tim Gruene
   Institut fuer anorganische Chemie
   Tammannstr. 4
   D-37077 Goettingen
  
   GPG Key ID = A46BEE1A
 
 
 --
 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A


Re: [ccp4bb] Isothermal titration calorimetry

2013-03-26 Thread Ed. Pozharski
This might have changed, but in the past file formats were different.   
Microcal files are text, while TA's are binary.  I do have the actual 
description of TA's format if anyone is interested, but it must be easier to 
use native text export than write a converter. 

 Original message 
From: Bosch, Juergen jubo...@jhsph.edu 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Isothermal titration calorimetry 
 
Hi George,
this is probably a very stupid suggestion and you likely have tried it, but 
I'll suggest the obvious nevertheless.
What happens to your .nitc file when you rename it to .itc can you read it in 
Origin then ?

Jürgen


On Mar 24, 2013, at 6:39 AM, George Kontopidis wrote:

Chris,  indeed nanoITC  instrument analysis software is very robust and user
friendly (probable more friendly than microcal, GE). 

Although when you need  to subtract  Q (heat)  values (from 2 or 3 blank
experiments) from your experimental data you cannot. NanoITC software  can
subtract  Q values only  from 1 blank experiment.
Also if you want to present  your data in a form of  heat/mol in Y
(vertical) axes  again you cannot. It presents  data in Y axes only in form
of heat/injection. 
If you have found a way to extract 2 or 3 blank experiments from
experimental data or present data in form of heat/mol, please let me know it
will be very useful.

The main problem in the output files from nanoITC come with an extension
.nitc, by default.  Unfortunately Origin (that can do all the above) can
read only,  filenames with an extension .itc

Cheers,

George

-Original Message-
From: Colbert, Christopher [mailto:christopher.colb...@ndsu.edu] 
Sent: Saturday, March 23, 2013 5:56 PM
To: George Kontopidis; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Isothermal titration calorimetry


George, would you please explain your comments?  We've found the TA
Instruments analysis software very robust and user friendly.

We have the low volume nanoITC from TA instruments and get equivalent #'s in
our comparison tests to the Microcal instrument.

Cheers,

Chris


--
Christopher L. Colbert, Ph.D.
Assistant Professor
Department of Chemistry and Biochemistry North Dakota State University P.O.
Box 6050 Dept. 2710 Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324





On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.gr wrote:

Keep in mind that output files from  nanoITC, TA instrument cannot be 
red by Origin. At some point you will need to analyse your data 
further.

George

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Anastassis Perrakis
Sent: Saturday, March 23, 2013 12:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Isothermal titration calorimetry

It might be worth to consider the question more in detail.

Do you want to study thermodynamics of the interaction, or a KD would do?
If
the former, you need ITC. If the latter, and you want to study things
at the level of KD only, maybe investing on a plate reader, 
thermophoresis, or some biosensor technology (spr or interferometry 
based systems) should be considered.

Then, what interactions will you study with the ITC? In general, I 
would agree that the lower sample volume is worth the nano options, but 
depending on the typical systems under study, sometimes the gain on 
sample quantity is not worth the money - while many times its worth it.

John is if course right that for studying specific systems as the one 
he describes the 200 is great.

A. 

Sent from my iPhone

On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote:

I would recommend the Microcal ITC 200, hands down. Not only is it an
amazing instrument with the optional automated sample loader (which is 
worth every penny), but we were able to do experiments (multiple) using 
FULL-LENGTH p53 binding to a weak cognate protein. I believe this was 
the first time ITC was ever used with full length p53, as it is so 
labile and just loves immediately to oligomerize. Sample sizes pay for 
the instrument.
Best,
John

John Fisher, M.D./PhD
St. Jude Children's Research Hospital Department of Oncology
Department of Structural Biology
W: 901-595-6193
C: 901-409-5699

On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com
wrote:

Dear All,


I am sorry for the off topic question. I am going to buy ITC to
study
protein-protein  protein-ligand interactions

I am comparing microcal, GE and nanoITC, TA instrument..
any suggestions, recommendations, good experiences or bad experiences.
is
there a better system.


Thank in advance for the help.


Regards


Sameh

--
Sameh Soror

Postdoc. fellow




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

Re: [ccp4bb] How to convert file format from CNS to CCP4

2013-03-23 Thread Ed Pozharski

On 03/23/2013 09:59 AM, Wei Feng wrote:
Can you help me to check out why these maps can not be converted by 
sftools?
sftools is not for manipulating map files.  Mapman from uppsala software 
factory would be a good choice.  xdlmapman, a gui frontend to it, used 
to be part of ccp4.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Philosophical question

2013-03-19 Thread Ed Pozharski

On 03/19/2013 02:41 PM, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all 
features of the theoretical LUCA 
No it won't.  Different features would have different tolerance levels 
to modifications.


Philosophically, one is wrong to expect that living organisms will 
evolve in a fashion that we find optimal.  Whenever I feel that a 
protein behaves in a way I find stupid, I simply say giraffe laryngeal 
nerve and all comes back to normal.


Re: [ccp4bb] Philosophical question

2013-03-19 Thread Ed Pozharski

Jacob,
So you'd have to explain why the codon convention is so 
intolerant/invariant relative to the other features--it seems to me 
that either it is at an optimum or there is some big barrier holding 
it in place.


Because altering codon convention will result in massive translation errors.

However the original question refers to start codon and its relation to 
methionine.  Notice that AUG is the *only* codon for methionine. If you 
change amino acid specificity of the methionine tRNA synthetase, you'd 
replace every methionine in every protein.  It is very unlikely that an 
organism other than one with a very small genome can survive that.  
Given high fidelity required of tRNA synthetases, changing their 
specificity is also not easy.  Most mutations are likely to incapacitate 
the enzyme rather than switch its specificity, resulting in organism 
that is unable to develop (due to stalled translation), let alone survive.


As for the optimization part - I am also not sure what significant 
benefit you expect from replacing starting methionine with a different 
amino acid.  It is mostly removed anyway.  Why that is? My (uneducated) 
guess is that it is rarely structural and there is benefit in recycling it.


Cheers,

Ed.


Re: [ccp4bb] Strange density in solvent channel and high Rfree

2013-03-15 Thread Ed Pozharski
Check for translational NCS

And you are way too conservative with resolution.  Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff.  If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.

Cheers,

Ed.

On Fri, 2013-03-15 at 15:39 -0300, Andrey Nascimento wrote:
 Dear all,
 
 I have collected a good quality dataset of a protein with 64% of
 solvent in P 2 21 21 space group at 1.7A resolution with good
 statistical parameters (values for last shell: Rmerge=0.202;
 I/Isig.=4.4; Complet.=93% Redun.=2.4, the overall values are better
 than last shell). The structure solution with molecular replacement
 goes well, the map quality at the protein chain is very good, but in
 the final of refinement, after addition of a lot of waters and other
 solvent molecules, TLS refinement, etc. ... the Rfree is a quite high
 yet, considering this resolution (1.77A).(Rfree= 0.29966 and Rfactor=
 0.25534). Moreover, I reprocess the data in a lower symmetry space
 group (P21), but I got the same problem, and I tried all possible
 space groups for P222, but with other screw axis I can not even solve
 the structure.
 
 A strange thing in the structure are the large solvent channels with a
 lot of electron density positive peaks!? I usually did not see too
 many peaks in the solvent channel like this. This peaks are the only
 reason for these high R's in refinement that I can find. But, why are
 there too many peaks in the solvent channel???
 
 I put a .pdf file (ccp4bb_maps.pdf) with some more information and map
 figures in this
 link: https://dl.dropbox.com/u/16221126/ccp4bb_maps.pdf
 
 
 Do someone have an explanation or solution for this?
 
  
 
 Cheers,
 
 Andrey
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Pete,

 Actually, I was trying to say the opposite - that the decision to 
 include something in the model (or not) could change the nature of the 
 error.  

Duly noted

 Pete
 
 PS - IIUC := ?
 

IIUC - If I Understand Correctly

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


Re: [ccp4bb] [ccp4b] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Adam,

OK, seems like you are going with it's always statistical error we just
don't yet know what it is option.

Ed.

On Tue, 2013-03-12 at 16:15 +, Adam Ralph wrote:
 Hi Ed,
 
 
  You can have both types of error in a single experiment, however
 you cannot determine 
 statistical (precision or as Ian says uncontrollable) error with one
 experiment. The manufacturer
 will usually give some specs on the pipette, 6ul +/- 1ul. In order to
 verify the specs
 you would need to perform many pipetting experiments. But even if the
 manufacturer does not give 
 any specs you still know that the pipette is not perfect and there
 will be a statistical error, you
 just do not know what it is.
 
 
 In theory, accuracy or bias could be determined with one
 experiment. Lets say you thought
 you had a 6ul pipette but actually it was a 12ul pipette. If you then
 compare the 'new' pipette
 against a standard you could tell if it was inaccurate. Of course
 normally you would repeat 
 this experiment as well because of statistical error. If detected bias
 can be removed. Systematic 
 error may not be so easily detected. What if the standard is also
 biased.
 
 
 Adam
 
 
 
 
  One can say it's inaccuracy when it is not estimated and imprecision
  when it is.  Or one can accept Ian's suggestion and notice that
 there is
  no fundamental difference between things you can control and things
 you
  can potentially control.

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Kay,

  the latter is _not_ a systematic error; rather, you are sampling (once!) a 
 statistical error component. 

OK.  Other words, what is potentially removable error is always
statistical error, whether it is sampled or not.

So is it fair to say that if there are some factors that I either do not
know about, willfully choose to ignore or just cannot sample, then I am
underestimating precision of the experiment?  

Cheers,

Ed.


-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Ian,

thanks - I think I had it backwards after reading your first post and
thought of controllable errors being those that can be brought under
conrtol by sampling, whereas uncontrollable would be those that cannot
be sampled and therefore their amplitude is unknown.

Yet you also seem to agree that characterization is dependent on
specifics of experimental setup, leaving the door open for the
possibility that noise-vs-bias choice may be driven by experimental
circumstance.  

And in practice, wouldn't it be more consistent to stick with the
definition that statistical error/noise/precision is defined by what is
really sampled?  Because if some factor is not sampled, I have zero
knowledge of the corresponding error magnitude.  I agree with Tim that
not sampling what can be easily sampled is a poorly designed experiment,
but it can also be characterized (which is probably a nicer term) as an
experiment with large systematic error (due to poor design).

Cheers,

Ed.

On Wed, 2013-03-13 at 12:33 +, Ian Tickle wrote:
 Ed, sorry for delay.  I was not trying to make any significant
 distinction between controllable and potentially controllable:
 from a statistical POV they are the same thing.  The distinction is
 purely one of practicality, i.e. within the current experimental
 parameters is it possible to eliminate the systematic error, for
 example is there a calibration step where you determine the systematic
 error by use of a standard of known concentration.  The error is still
 controllable regardless of whether you actually take the trouble to
 control it!  Note that the experimental setup has not changed, you are
 merely using the same apparatus in a different way but any random
 errors associated with the measurements will still be present.
 
 
 Of course if you change the experimental setup (note that this
 potentially includes the experimenter!) then all bets are off!  It's
 very important to describe the experimental setup precisely before you
 attempt to characterise the errors associated with a particular setup.
 
 
 BTW I agree completely with Kay's analysis of the problem: as he said
 you are sampling (once!) a statistical error component.  This is
 what I was trying to say, he just said it in a much more concise way!
 This random (uncontrollable) error then gets propagated through the
 sequence of steps in the experiment along with all the other
 uncontrollable errors.
 
 Cheers
 
 
 -- Ian
 
 
 
 On 11 March 2013 19:04, Ed Pozharski epozh...@umaryland.edu wrote:
 Ian,
 
 thanks for the quick suggestion.
 
 On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote:
  Personally I tend to avoid the systematic vs random error
 distinction
  and think instead in terms of controllable and
 uncontrollable errors:
  systematic errors are potentially under your control (given
 a
  particular experimental setup), whereas random errors
 aren't.
 
 
 Should you make a distinction then between controllable
 (cycling cuvette
 in and out of the holder) and potentially controllable errors
 (dilution)?  And the latter may then become controllable with
 a
 different experimental setup?
 
 Cheers,
 
 Ed.
 
 --
 I don't know why the sacrifice thing didn't work.
 Science behind it seemed so solid.
 Julian, King of Lemurs
 
 
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
 OK.  Other words, what is potentially removable error is always
 statistical error, whether it is sampled or not.

Clarification - what I meant is potentially removable by proper sampling
and reducing standard error to zero with infinite number of
measurements.  Not removable by better calibration or experimental
setup.

-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Ian,

On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote:
 So I don't see there's a question of wilfully choosing to ignore. or
 not sampling certain factors: if the experiment is properly calibrated
 to get the SD estimate you can't ignore it.
 

So perhaps I can explain better by using the same example of protein
concentration measurement.  It is certainly true that only taking one
dilution is poor design. (Although in crystallization practice it may
not matter given that it is not imperative to have a protein exactly at
10 mg/ml, 9.7 will do).  If I don't bother including pipetting precision
in my error estimate either by direct experiment or by using
manufacturer's declaration I am willfully ignoring this source of error.
That would be wrong.

But what if I only have one measurement worth of sample?  And pipetting
precision cannot be calibrated (I know it can be so this is hypothetical
- say pipettor was stolen and company that made it is out of business,
their offices burned down by raging mob).  Is the pipetting error now
systematic because experimental situation (not design) prevents it from
being sampled or estimated?

I actually like the immutable error type better for my own purposes, but
I am trying to see whether some argument might stand that allows some
error that can be sampled to be called inaccuracy nonetheless.  

Cheers and thanks,

Ed.


-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


[ccp4bb] qtrview command line options

2013-03-11 Thread Ed Pozharski
Is there some way of opening a log file (specifically, the
pointandscale.log that imosflm bridge to scala generates) with qtrview
from command line?

I tried, of course, this

qtrview pointandscale.log

but it opens empty, no log-file. I tried qtrview -h and qtrview --help
and man qtrview but there is seemingly no documentation.

I found the source code (yes, I can google) and can deduce that
available options at startup are 

--log-file
--report-xml
--report-xrt
--inp-file

The only thing that works is 

qrtview --log-file pointandscale.log

but that only shows me the log-file itself, i.e. no graphs etc.  I
understand that the program was designed primarily for ccp4 gui and I
know loggraph (and it works).

By the way, checkout instructions for the qtrview repository at

https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/

don't work throwing this error

bzr: ERROR: Connection error: curl connection error (server certificate
verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
none)
on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart 

Cheers,

Ed.

-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs


[ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Salve,

I would like to solicit opinions on a certain question about the
relationship between statistical and systematic error. Please read and
consider the following in its entirety before commenting.

Statistical error (experiment precision) is determined by the degree to
which experimental measurement is reproducible. It is derived from
variance of the data when an experiment is repeated multiple times under
otherwise identical conditions. Statistical error is by its very nature
irremovable and originates from various sources of random noise, which
can be reduced but not entirely eliminated.

Systematic error (experiment accuracy) reflects degree to which precise
average deviates from a true value. Theoretically, corrections can be
introduced to the experimental method that eliminate various sources of
bias. Systematic error refers to some disconnect between the quantities
one tries to determine and what is actually measured.

The issue is whether the classification of various sources of error into
the two types depends on procedure. Let me explain using an example.

To determine the concentration of a protein stock, I derive extinction
coefficient from its sequence, dilute it 20x to and take OD measurement.
The OD value is then divided by extinction coefficient and inflated 20
times to calculate concentration.

So what is the statistical error of this when I am at the
spectrophotometer? I can cycle sample cuvette in and out of the holder
to correct for reproducibility of its position and instrument noise.
This gives me the estimated statistical error of the OD measurement.
Scaled by extinction coefficient and dilution factor, this number
corresponds to the statistical error (precision) of the protein
concentration.

There are two sources of the systematic error originating from the two
factors used to convert OD to concentration. First is irremovable
inaccuracy of the extinction coefficient. 

Second: dilution factor. Here main contribution to the systematic error
is pipetting. Importantly, this includes both systematic (pipettor
calibration) and statistical (pipetting precision) error. Notice that I
only prepared one sample, so if on that particular instance I picked up
4.8ul and not 5.0ul, this will translate into systematically
underestimating protein concentration, even though it could have equally
likely been 5.2ul.

So if pipetting error could have contributed ~4% into the overall
systematic error while the spectrophotometer measures with 0.1%
precision, it makes sense to consider how this systematic error can be
eliminated. The experiment can be modified to include multiple samples
prepared for OD determination from the same protein stock.

An interesting thing happens when I do that. What used to be a
systematic error of pipetting now becomes statistical error, because my
experiment now includes reproducing dilution of the stock. In a
nutshell,

Whether a particular source of error contributes to accuracy or
precision of an experiment depends on how experiment is conducted. 

And one more thing. No need to waste precious protein on evaluating
error of pipetting. I can determine that from a separate calibration
experiment using lysozyme solution of comparable concentration/surface
tension. Technically, a single measurement has accuracy of said 4%
(padded by whatever is error in extinction coefficient). But one can
also project that with actual dilution repeats, the precision would be
this same 4% (assuming that this is a dominant source of error).

So, is there anything wrong with this? Naturally, the question really is
not about extinction coefficients, but rather about semantics of what is
accuracy and what is precision and whether certain source of
experimental error is rigidly assigned to one of the two categories.
There is, of course, the wikipedia article on accuracy vs precision, and
section 3.1 from Ian's paper (ActaD 68:454) can be used as a point of
reference.

Cheers,

Ed.

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the great Tao is abandoned, Ideas of humanitarianism and 
   righteousness appear.
When intellectualism arises It is accompanied by great hypocrisy.
When there is strife within a family Ideas of brotherly love appear.
When nation is plunged into chaos Politicians become patriotic.
--   / Lao Tse /


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Tim,

On Mon, 2013-03-11 at 18:51 +0100, Tim Gruene wrote:
 I don't share your opinion about a single measurement translating into
 a systematic error. I would call it a poorly designed experiment in
 case you were actually iterested in how accurately you determined the
 protein concentration.
 
OK.  As I said, this is not about protein concentration, but let's say I
only have about 6ul of protein sample, so that I can only have *one*
dilution.  Would pipetting uncertainty then be considered systematic
error or statistical error?

I am afraid this is a matter of unsettled definitions.  By the way, it
wasn't an opinion, more of an option in interpretation.  I can say that
whatever is not sampled in a particular experimental setup is systematic
error.  Or I can say that (as you seem to suggest, and I like this
option better) that whenever there is a theoretical possibility of
sampling something, it is statistical error even though the particular
setup does not allow accounting for it.

Ed.

-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Ian,

thanks for the quick suggestion.

On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote:
 Personally I tend to avoid the systematic vs random error distinction
 and think instead in terms of controllable and uncontrollable errors:
 systematic errors are potentially under your control (given a
 particular experimental setup), whereas random errors aren't.
 
Should you make a distinction then between controllable (cycling cuvette
in and out of the holder) and potentially controllable errors
(dilution)?  And the latter may then become controllable with a
different experimental setup?

Cheers,

Ed.

-- 
I don't know why the sacrifice thing didn't work.  
Science behind it seemed so solid.
Julian, King of Lemurs


Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Pete,

On Mon, 2013-03-11 at 13:42 -0500, Pete Meyer wrote:
 My take on it is slightly different - the difference seems to be more
 on 
 how the source of error is modeled (although that may dictate changes
 to 
 the experiment) rather than essentially depending on how the
 experiment 
 was conducted.
 
 Or (possibly) more clearly, systematic error is a result of the model
 of 
 the experiment incorrectly reflecting the actual experiment;
 measurement 
 error is due to living in a non-deterministic universe.

I see your point. 

I want to clarify that reproducing an experiment as far back as possible
is best.  Of course it's possible to design an experiment better and
account for pipetting errors.  The question is not whether it has to be
done (certainly yes) but whether pipetting error should be considered as
inaccuracy or imprecision when the experiment is not repeated.

One can say it's inaccuracy when it is not estimated and imprecision
when it is.  Or one can accept Ian's suggestion and notice that there is
no fundamental difference between things you can control and things you
can potentially control.

IIUC, you are saying that nature of the error should be independent of
my decision to model it or not.  Other words, if I can potentially
sample some additional random variable in my experiment, it contributes
to precision whether I do it or not.  When it's not sampled, the
precision is simply underestimated.  Does that make more sense?

Cheers,

Ed.


-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
By the way, am I the only one who gets this thing with every post?  If
anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his
mailbox or unsubscribe, that would be truly appreciated.  Delete button
is easy and fun to use, but this has been going on for quite some time.



On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote:
 ransmit Report:
 
 liebe...@korea.ac.kr ߼; 5 õ Ͽ4ϴ.
 ( / : 554 Transaction failed. 402 Local User Inbox Full
 (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98))
 
  / 
 User unknown   :; ڰ x =
 Socket connect fail: 
 DATA write fail: ޼ ۽ 
 DATA reponse fail  : κ ޼ 
 

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-06 Thread Ed Pozharski

On 03/04/2013 10:02 AM, Marcin Wojdyr wrote:

It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get after compiling refmac?


My numbers are not as impressive, but I also get quite detectable 
improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This 
is with gcc-4.6 though.  Importantly, both binaries are the *same* 
version of refmac, 5.7.0032.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-06 Thread Ed Pozharski

Thierry,

I ran both versions on the same input file and numerical results are 
essentially the same.  After 10 cycles of refinement the r.m.s.d. 
between two models produced with different versions is 0.0004A.  
Basically, about 5% of coordinates differ in the last digit (i.e. by 
0.001A).  Frankly, I expected results to be exactly identical, but the 
difference is too small to be of concern, imho.


Cheers,

Ed.

On 03/04/2013 10:19 AM, Fischmann, Thierry wrote:

Ed,

Are the numerical results the same ? Not likely that there is a problem. But if 
you haven't done it already it is worth checking by running the tests provided 
with the suite. Aggressive optimization can be a source of bugs.

Best regards
Thierry

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed 
Pozharski
Sent: Monday, March 04, 2013 8:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:

Running times were, correspondingly, 32.2s, 35.1s and 18.7s.


Numbers are almost too impressive to believe :)

How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free) for most DIY
compilation given licensing issues)?




--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
Adam,

On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote:
 One of the first routines called by CCP4
 progs is ccp4fyp. This initialises the CCP4 environment. 

I think you might have missed in my original post that I get an error
when I *do* source ccp4 environment.
 
 Does the error occur with
 refmac alone or with every CCP4 prog? 

I cannot tell because I am compiling only refmac, not all of the ccp4.

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
Indeed, the problem goes away when -static flag is omitted.
Interestingly, the resulting binary dependencies do not include any
ccp4-related libraries.  For those interested, I was able to track the
segfault down to the close() operator - so basically it fails when
closing a file opened with ccpdpn routine.  At that point I had a lucky
guess of removing the flag (somewhat inspired by noticing that refmac5
binary from cc4-6.3.0 is dynamic and after trying to compile separately
a short piece of code that only opened and closed a file), so the issue
is solved as far as my goals are concerned. 

On Mon, 2013-03-04 at 10:04 +, Garib N Murshudov wrote:
 Dear all
 
 
 I think this error has been dealt with (Ed will correct me if I am
 wrong). The problem was -static in compilation. For whatever reason in
 some gcc (gfortran) -static does not work (it compiles but has
 problems in running, what is the reason is not clear to me). Sometimes
 in later gcc -static-libgcc -static-libgfortran works but not always.
 These flags are needed for distribution purposes. If you are compiling
 and using on the same computer then you should not need it.
 
 
 regards
 Garib
 
 
 
 On 4 Mar 2013, at 09:56, Adam Ralph wrote:
 
  Dear Ed,
  
  
 The error does indeed happen in ccp4lib. One of the first
  routines called by CCP4
  progs is ccp4fyp. This initialises the CCP4 environment. See
  lib/cctbx/cctbx_sources/ccp4io/lib/src/ccp4_general.c.
  
  
  If you look at the code you can see that $CINCL is determined at
  run-time. You are 
  right that this environment var is not needed at compile time. Files
  like environ.def and 
  default.def are read at this time. Perhaps there has been a
  corruption of one of these 
  files or you are pointing to an earlier version of $CINCL. Does the
  error occur with
  refmac alone or with every CCP4 prog?
  
  
  Adam
  
  
 
 Dr Garib N Murshudov
 Group Leader, MRC Laboratory of Molecular Biology
 Hills Road 
 Cambridge 
 CB2 0QH UK
 Email: ga...@mrc-lmb.cam.ac.uk 
 Web http://www.mrc-lmb.cam.ac.uk
 
 
 
 
 
 
 
 
 
 
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
 Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
 
Numbers are almost too impressive to believe :)

How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free) for most DIY
compilation given licensing issues)?

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-02-28 Thread Ed Pozharski
Adam,

I am not compiling CCP4, just refmac.  IIUC, all that sourcing
ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c
and libccp4f.  And presumably lapack and libblas, but that's a separate
issue.

On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote:
 Hi Ed,
 
 
It looks as though you have not sourced $CCP4/include/ccp4.setup.
 This needs to be customized and sourced before you configure and make
 CCP4.
 
 
 Adam
  

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


[ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-02-27 Thread Ed Pozharski
I am trying to compile refmac from source on a machine running Ubuntu
12.04.  In a nutshell, after some troubleshooting I end up with
executable that generates a segmentation fault.  Log-file states that

 CCP4 library signal ccp4_parser:Failed to open external command
file (Success)
 raised in ccp4_parser 

(hardly a success).  Potentially relevant details are that I had to
compile libccp4 and libmmdb to get to this point.  If I don't configure
the CCP4, I get this when trying to run refmac

 CCP4 library signal ccp4_general:Cannot open environ.def (Error)
 raised in ccp4fyp 
 refmacgfortran:  Cannot open environ.def
 refmacgfortran:  Cannot open environ.def

So perhaps it's some incompatibility between libccp4/libmmdb that I
compiled and those that came with CCP4 installation (by the way, the new
update feature rocks indeed).  But I tried lifting these libraries from
CCP4 installation when compiling refmac and I get the same segmentation
fault.

Any suggestions for troubleshooting/advice on how to compile refmac from
source are appreciated.  

Refmac version is 5.7.0032.

Cheers,

Ed.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs


Re: [ccp4bb] Link problem with Refmac.

2013-02-21 Thread Ed. Pozharski
We might have just found a new recurring discussion - what to do with insertion 
codes! I am sure the opinion split is close to 50/50.

Personally, I don't think insertion codes make sense in the first place. Are 
catalytic triad residues always the same distance from the N-terminus? No. The 
residue number designates its position in the sequence, not its relationship to 
other like-minded enzymes.  That is a useful (as it defines peptide bonds) and 
consistent definition.  Even with antibodies, where these can be indeed 
interpreted as insertions, the mess is enormous since only half the structures 
conform to WuKabat numbering (and there are two of those).

It is true however that it's just as easy to implement sorting that pays 
attention to insertion codes as it is structural alignment based residue 
matching.

Cheers,

Ed.

 Original message 
From: herman.schreu...@sanofi.com 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Link problem with Refmac. 
 
I fully second this. The treatment of insertion codes of many programs
is a mess, leaving you with the option to renumber (and loose contact
with often a huge body of existing literature), or stuff the pdb with
link and gap records (if recognized at all by the program used).  

It would be a great help if the programmers would use a simple distance
criterion (e.g. N - C distance  2.0 A) to decide whether amino acids
are linked instead of forcing a link between residues which are more
than 10 A apart as in the current case.

Cheers,
Herman


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Robbie Joosten
Sent: Monday, February 18, 2013 10:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Link problem with Refmac.

Hi Ian,

I avoid renumbering whenever I can. If I do have to renumber things
(e.g. to get proper connectivity in PDB entry 2j8g), I do it by hand. So
no help there.

As for dealing with insertion codes in general, why not try to convince
the developers of the 'brain-damaged'  to support insertion codes? I've
asked quite a few for these sort of updates and many were very helpful.
The problem is that most developers discover the existence of insertion
codes after they set up a data structure for the coordinates. Adding
support afterwards can be quite a hassle. The more users ask for such
support, the more likely it will be implemented. 

Cheers,
Robbie 


 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
 Ian Tickle
 Sent: Monday, February 18, 2013 19:40
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Link problem with Refmac.
 
 Hi Robbie
 
 
 OK I just realised what's going on.  In my script I renumber the input

 PDB
file
 (starting at 1 for each chain and incrementing by 1) and keep the 
 mapping
so
 I can renumber it back afterwards for human consumption.  So you're 
 completely correct: there is indeed a residue A59 after renumbering!  
 This
is
 to avoid headaches with brain-damaged programs that can't cope with 
 insertion codes and residue numbers out of sequence.  So I guess I'm 
 going to have to be smarter in my renumbering program and make sure I 
 maintain any increasing gaps in the numbering which indicate real gaps

 in the sequence and only renumber over insertions and decreasing gaps.

 It
doesn't
 actually matter what the new numbers are since the user never sees
them.
 
 
 But this must be a common problem: how do others handle this?  E.g. 
 pdbset blindly renumbers with a increment of 1 (and anyway it doesn't 
 renumber any LINK, SSBOND  CISPEP records as I do) so it would have 
 the same problem.
 
 
 Cheers
 
 
 -- Ian
 
 
 
 On 18 February 2013 17:09, Robbie Joosten robbie_joos...@hotmail.com
 wrote:
 
 
 Hi Ian,
 
 The warning refers to a MET 59 in chain A whereas you only have
MET 
 72. That
 is very suspicious. Non-sequential residues further apart than x

 Angstrom
 automatically get a gap record. Have you tried a newer version
of 
 Refmac,
 because this feature was added quite a while ago?
 What is your setting for 'MAKE CONN' when you run Refmac?
 
 Cheers,
 Robbie
 
 
 
 
  -Original Message-
  From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf 
 Of
  Ian Tickle
  Sent: Monday, February 18, 2013 17:32
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: [ccp4bb] Link problem with Refmac.
 
 
  All, I'm having a problem with Refmac (v. 5.7.0025) that I
don't
 understand.
  It's linking 2 residues that it shouldn't be.  Here's the
relevant 
 message
 in the
  log file:
 
    WARNING : large distance for conn:TRANS    dist =    10.768
  ch:AA   res:  58  THR --  59  MET
 ideal_dist= 1.329
 
  Note that there are no LINK (or LINKR) records in the PDB
header.
 
 
  Here are the input co-ords for the relevant residues (not
linked):
 
  ATOM    887  N   THR A  58  13.587   1.365  19.814  1.00
14.28
A
 N
  ATOM    888  CA  THR A  58  14.743   1.126  

Re: [ccp4bb] Renumbering and retaining state information pdb file

2013-02-14 Thread Ed. Pozharski
There should be many ways to do this.  You can split the file, renumber with 
pdbset, and then reassemble it.  This may be useful
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Useful_scripts_(aka_smart_piece_of_code)
Cheers, 
Ed

 Original message 
From: Amar Joshi aj...@leicester.ac.uk 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Renumbering and retaining state information pdb file 
 
Hi,

I am trying to tidy up an old NMR structure (not mine) and I want to renumber 
the residues in all the states.
When I use pdbset starting at X, the numbers are changed but the state 
information is lost. How can I retain the state in my modified pdb file?

Thanks,
Amar

-
Amar Joshi Ph.D

Bayliss Lab
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road, Leicester
LE1 9HN

Tel: 0116 229 7082
Email: aj...@leicester.ac.uk
--



Re: [ccp4bb] S-nitrosylation protein

2013-02-13 Thread Ed. Pozharski
Maybe you can try different energies hoping that damage is wavelength 
dependent.  It must be dose dependent though, so you may consider merging short 
sweeps from multiple crystals.

 Original message 
From: Uma Ratu rosiso2...@gmail.com 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] S-nitrosylation protein 
 
Dear All:
 
I plan to use X-ray crystallography method to study the S-nitrosylated protein 
structure.
 
The native protein crystals diffracted to 2A with synchrontron. I now have the 
crystals of S-ntrosylated protein.
 
Since S-NO moiety appears to be unstable to synchrotron radiation, could you 
advice /  comments on the stratage on the data collection of S-nitrosylated 
protein crystals?
 
The protein crystals did not diffract well with in house X-ray.
 
Thank you for your comments.
 
Uma



Re: [ccp4bb] refmac5 MMA bug

2013-02-11 Thread Ed Pozharski
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote:
 This is a 'compatability' option in Refmac that internally renames
 atoms. If you comment out 'MMA .C7 CM' in your
 mon_lib_list.cif file, the problem will disappear.
 

Robbie,

thanks a lot - this fixes it.  

Is this still considered a bug?  From what I understand, the
data_comp_synonym_atom_list entry indicates that whenever MMA C7 atom is
encountered, it will be internally renamed to CM.  However, the
$CCP4_LIB/data/monomers/m/MMA.cif should then refer to CM as well. But
that cif-file still uses C7.

Maybe this gets fixed in ccp4 updates, which reminds me to get that set
up at last.

Cheers,

Ed.

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


[ccp4bb] refmac5 MMA bug

2013-02-10 Thread Ed Pozharski
I see a strange issue with a model that includes O1-methyl-mannose 
(three letter code MMA).  Basically, refmac fails and says that C7 is 
missing in the model while CM is absent from the library.  The problem 
is that there is no CM atom in the pdb file, while C7 is right there. 
This happens with Refmac_5.7.0029, and I see no obvious issues with the 
corresponding cif-file in the monomer library.


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed. Pozharski
Patrick,

Something related:

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Conditions_prone_to_salt_crystallization

Truth be told, we recently had a major breakthrough with the peg/fluoride 
condition I came to consider a useless salt crystal generator.  So tables like 
these are undoubtedly useful but do not reduce workload. :)

This is also a rather interesting finding
http://www.google.com/url?sa=tsource=webcd=12ved=0CDEQFjABOAourl=http%3A%2F%2Fwww.aseanbiotechnology.info%2FAbstract%2F21021153.pdfei=N_kUUYfkBafV0gG09ICoAgusg=AFQjCNE7C-m6IkLPUay9gEEM60yJF46ZQg

Basically, presence of protein may induce salt crustallization.  To me, this 
means that diffraction pattern is the best indicator. Frank already said 
exactly that, of course. 

Cheers, 

Ed.



 Original message 
From: Patrick Shaw Stewart patr...@douglas.co.uk 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] protein crystals or salt crystals 
 

Good morning Frank

On a related idea, do you typically use a limited number of buffers (buffer 
plus salt) for the final purification step of your proteins?

If so, do you have a chart of where salt crystals may appear in the screens 
that you use most often?  Could you put that chart on your web site to help the 
community?

People could pick one of your standard buffer mixes to make their lives easier 
later on.

Best wishes

Patrick





On 8 February 2013 07:18, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote:
Test the diffraction - that's the only way.  But given the other junk in the 
drop, chances are they're salt.

(And don't post 5Mb attachments, please.)


On 07/02/2013 22:24, amro selem wrote:




Hallo my colleagues. 
 i hope every one doing ok . i did screening since two 
weeks . i noticed today this crystals. i don`t know either 
it salt or protein crystal . my protein has zero tryptophan so i could 
distinguish by UV camera.
the condition was conditions:  
0.1M SPG buffer pH 8 and 25%PEG 1500. in addition to Nickle chlorid 1mM.
 

best regards
Amr

 








-- 
 patr...@douglas.co.uk    Douglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090    US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36


Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 09:13 -0500, Edward A. Berry wrote:
 I like to take a 5-sec 180* oscillation which gives plenty of
 spots in a nice  pattern for a salt crystal 

Second that

It also confuses bystanders really well - what a strange diffraction
pattern - half salt (small unit cell) / half protein (lots of spots).  
Takes your mind off the gloom of your dashed hopes :)

-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs


Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote:
 Protein crystals behave rather as gelatine and not as solid

I'd have to disagree on that.  Protein crystals are fragile but not
soft.  If your crystals are like gelatine it's unusual.  It has been
demonstrated that elastic properties of protein crystals are similar to
organic solids. 

Cheers,

Ed.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs


Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 09:57 -0500, Jacob Keller wrote:
 do you have a reference quickly on hand 

http://www.ncbi.nlm.nih.gov/pubmed/8129868

and references therein

http://www.sciencedirect.com/science/article/pii/S0022024801010922

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300955/

The last reference is not strictly speaking about protein crystals, but
also emphasizes how protein as elastic material is more of a solid (with
some peculiar properties likely arising from large entropic contribution
to its deformation energy.

-- 
Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.


Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
Michael,

It seems to me we have no disagreement, as we both say that it is
*unusual* for protein crystals to be non-fragile.  Furthermore, my
objection is to gelatin characterization.  I may be, as is my custom,
wrong, but in terms of elasticity gels are purely entropic.  Protein
crystals, even the malleable ones you describe, have both enthalpic and
entropic components to the deformation free energy (admittedly the
entropic component is stronger than in regular materials).

Your comment on the PEG-induced slow cross-linking is very interesting.
What you describe fits perfectly the behavior of long rods of a
deliberately cross-linked crystal - they bend and don't snap.  Protein
crystals (at least some) are also characterized by an unusually broad
range of linear response to mechanical deformation, up to 10%  

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143058/

According to the theory in this paper though, you might be destroying
diffraction by bending the crystal, since in crystal denaturation is
likely irreversible.  From what you are describing (60 degrees,
150x40x40 um), the linear deformation should reach almost 50%,
definitely enough for partial crystal denaturation.

Cheers,

Ed.



On Fri, 2013-02-08 at 11:22 -0500, R. M. Garavito wrote:
 Ed,
 
 
   Protein crystals are fragile but not soft.  
   If your crystals are like gelatine it's unusual.
 
 
 I hate to disagree with the disagreement, but there are many
 exceptions to this rule.  I have seen many protein crystals that are
 quite malleable and bendable.  One protein produced rod-shaped
 crystals  (150x40x40 um) that I could bend by almost 60 degrees and it
 would slowly snap back.  Mounting it old school was a real pain, and
 their diffraction was mediocre.  However, the majority of the crystals
 I have worked with adhere to the general rule you describe.  
 
 
 Where the crystal physical behavior is anomalous, it is often when PEG
 is used and/or there are multiple components that contribute to the
 crystal's integrity (as in the case of membrane protein crystals with
 detergent).  
 
 
 In the former case, crystals that sit in PEG solutions too long tend
 to be cross-linked (most likely due to the aldehydes that can exist in
 some batches of PEG).  One could argue that the crosslinking adds
 long-range elasticity and a resistance to fracturing.
 
 
 In the latter case, I have observed large beautiful crystals of
 membrane proteins that have the consistency and malleability of warm
 butter.  Sometimes optimization improved their integrity, and other
 times a new crystal form is needed.
 
 
 Regards,
 
 
 Michael
 
 
 
 
 
 
 R. Michael Garavito, Ph.D.
 Professor of Biochemistry  Molecular Biology
 603 Wilson Rd., Rm. 513   
 Michigan State University  
 East Lansing, MI 48824-1319
 Office:  (517) 355-9724 Lab:  (517) 353-9125
 FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
 
 
 
 
 
 
 
 On Feb 8, 2013, at 9:23 AM, Ed Pozharski wrote:
 
  On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote:
   Protein crystals behave rather as gelatine and not as solid
  
  I'd have to disagree on that.  Protein crystals are fragile but not
  soft.  If your crystals are like gelatine it's unusual.  It has been
  demonstrated that elastic properties of protein crystals are similar
  to
  organic solids. 
  
  Cheers,
  
  Ed.
  
  -- 
  I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
  
 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /


Re: [ccp4bb] gedit on mac terminal

2013-01-26 Thread Ed. Pozharski
Try this

http://www.mac-forums.com/forums/os-x-apps-games/239657-gedit-command-not-found-terminal.html

 Original message 
From: LISA science...@gmail.com 
Date:  
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] gedit on mac terminal 
 
Hi all,
I installed gedit on my mac applications. But i can not use it by terminal. 
Please help me figure it out. Thanks.

lisa


[ccp4bb] engh huber

2013-01-14 Thread Ed Pozharski
To what extent modern geometric restraints have been upgraded over
original EnghHuber?  And where I can find a consensus set of values
(with variances)?  

For example, Fisher et al., Acta D68:800 discusses how histidine angles
change with protonation, and refers to EnghHuber when it says that
ND1-CE1-NE2 goes from 111.2 to 107.5 when histidine acquires positive
charge (Fig.6).  But angle table (Table 3) in original EnghHuber from
1991 does not have any 107.5 value and seems to suggest that the numbers
should rather be 111.7+-1.3 and 108.4+-1.0, respectively.

I understand that these values are derived from structural databases and
thus can be frequently updated.  Is there some resource where most
current values would be listed?

Cheers,

Ed.

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] engh huber

2013-01-14 Thread Ed Pozharski
Article in the Tables is the answer to my question about the latest
EnghHuber parameters.  These still don't match Fig.6 from Fisher, but I
am OK with using Tables for my internal purposes.

Thanks to Mitchell and Dale for prompt response.

Cheers,

Ed.

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs


Re: [ccp4bb] How to merge data from 2 separate sections of same crystal

2012-12-10 Thread Ed Pozharski

On 12/10/2012 08:45 PM, Yuri Pompeu wrote:

hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are 
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from Mosflm when I scale them?
Attempts to process them in the same session keep maling the program crash!
Thank you very much
Did you try the 85 frames to mosflm in one session (maybe move bad files 
away from the current folder for a clean try).


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
Francois,

I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).

I do concur that insertion code is evil.  I had to re-refine an old
antibody structure recently and it messes up coot sequence window and
breaks refmac bond restraints.  Evil, evil,.evil.

Cheers,

Ed.

On Wed, 2012-12-05 at 16:58 +0900, Francois Berenger wrote:
 Especially the renumber command that changes
 residue insertion codes into an increment of
 the impacted residue numbers.
 
 Regards,
 F.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs


Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
 Does 128A come before or after 128? 

Robbie,

shouldn't it simply depend on which residue record comes first in the
pdb file?

Ed.

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


Re: [ccp4bb] Mg++ interactions

2012-11-30 Thread Ed Pozharski
On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote:
 Are Mg++ ions ever observed to chelate primary amines?

MESPEUS reports, for example, 13 structure where magnesium is
coordinated by a lysine.  7 with arginines and a bunch of asn/gln side
chains as well.  It does not prove, of course, that primary amines
coordinate magnesium ions, only that in a limited number of cases
crystallographers have interpreted their data this way.

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs


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