[ccp4bb] ideal bond length and bong angel

[yang li]

Dear All,
 I've wonder for a simple problem for a long time, that is: What is the
ideal bond length and angel?
Every lecture or book says this is a criteria from small organic molecules,
but I still donnot know
exactly. Like is bond length point to the peptide bond length? Or many other
bonds?
Does anyone has a simple and graphic explanation for them?

Thanks in advance!

Re: [ccp4bb] how to model glycosylated residues?

[Jiamu Du]

Dear All,
Thank you for your previous response. I have built a 3-mer oligosaccharides
in the electron density by using coot. I prefer to refine my structure in
CNS due the resolution is only 2.6 Ang. I found there are only topology and
parameter files for carbohydrate in CNS but no linkage file for
carbohydrate. So CNS could recognize the sugar molecules individually, but
can not recognize the linkage between them. When I refine it in CNS, a
oxygen will be added beyond C1 of NAG.
Is there anyone who has the linkage file for carbohydrate of CNS? Or is
there any other methods to deal with this situation?

Thanks.

Re: [ccp4bb] How to refine large moleculars?

[Eleanor Dodson]

With such good data you would expect lower R factors I agree.
I use all the COOT validation tools - Ramachandran, diff map peaks etc 
to try to pinpoint errors.


Also anomalous difference maps hoping to verify S positions and check 
the sequence fitting.


You could let Arp/Warp rebuild it from the existing model and check it 
gives the same interpretation..


Can you get higher resolution data? It might be worth pushing the data 
integration a bit further since I think Arp/Warp works better the higher 
the resolution.


Eleanor



Juergen Bosch wrote:

How does the Molprobity report look like ?

How many Rama outlieres, bad Cbeta, rotamers ?
What's your percentile ?
Look at the multicriterion chart to fix your problems :-)

http://molprobity.biochem.duke.edu/

Juergen

Yongchao Li wrote:


Dear all,
Thanks for all replies.
After water addition, R work is 0.27 and R free 0.33.
TLS and NCS results no significant approve.
Space group seem right, other space group like P21212 is worse.
From truncate result, it is not twinning.

More detail is below:
space group P212121 a=150.099  b=148.581 c=153.429
resolution: 2.0 A
completeness: 92.3 % (58%), near complete to 2.15 A.(last shell 90.7%)
Rsym: 0.076 (34.0)
I/sigma = 20 (2.5)



*/Chavas Leo <[EMAIL PROTECTED]>/* wrote:

Dear Li,

I don't know how to reduce them. 



I second Tim in the fact that you should give more details on what
you tried to do as well as your statistics (resolution, data
quality etc.). For instance, did you had water molecules? Did you
try TLS refinement? Do you have a wrong symmetry?

HTH.

Kind regards.

Leo

Chavas Leonard, Ph.D.
Research Associate

Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT

Tel: +44(0)161-275-1586
e-mail: [EMAIL PROTECTED]





Be a better friend, newshound, and know-it-all with Yahoo! Mobile. 
Try it now. 
 

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

[Liz Potterton]

James,

CCP4mg will allow you select a set of atoms and draw a surface over them 
in whatever colour scheme that you choose.


The tutorial explaining this is at

http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/surfaces.html

Cheers

Liz


James Thompson wrote:


Dear CCP4'ers,

Any Windows/Linux/OS X programs have a surface scribing function 
similar to that found in GRASP, to quickly draw the border of a 
surface selection (or subset) and calculate or display local features 
of the molecular surface?  I have no access to SGIs now.  I have a 
memory of similar function elsewhere but am not finding the ability 
within GRASP2, DINO, CHIMERA, etc.  Perhaps I'm thinking of Setor 
which was also IRIX, and perhaps this memory is suspect...   Other 
selection methods for a molecular surface require more of my time to 
define the subset.


Many thanks,

Jim

James R. Thompson

Assistant Professor of Biophysics

Mayo Clinic College of Medicine

Department of Physiology and Biomedical Engineering

Mayo Proteomics Research Center

Office  507-538-3891

Fax 507-538-3954

E-mail  [EMAIL PROTECTED] 

Re: [ccp4bb] ideal bond length and bong angel

[Stuart McNicholas]

On 9 Jan 2008, at 10:34, Eleanor Dodson wrote:


Bong angels are probably ideal already!
There is really no such animal as an ideal bondlength or angle -  
they depend to some extent on the atomic environment.


Not to a complete extent?

Stuart

Re: [ccp4bb] ideal bond length and bong angel

[Eleanor Dodson]

Bong angels are probably ideal already!
There is really no such animal as an ideal bondlength or angle - they 
depend to some extent on the atomic environment.


There are papers by Engh and Huber who looked at small molecule highly 
refined structures to get AVERAGE bond lengths and standard deviations - 
and their targets are the basis for most MX refibnement targets.
And there are many other publications trying to extract predictions from 
quantum chemistry.

Eleanor

yang li wrote:

Dear All,
 I've wonder for a simple problem for a long time, that is: What is the
ideal bond length and angel?
Every lecture or book says this is a criteria from small organic molecules,
but I still donnot know
exactly. Like is bond length point to the peptide bond length? Or many other
bonds?
Does anyone has a simple and graphic explanation for them?

Thanks in advance!

  

Re: [ccp4bb] ideal bond length and bong angel

[Gerard DVD Kleywegt]

   Can you explain the define of the bond length and bond angel--especially
bond angel--here?


i leave the definition of angels (be they ideal or not) to clerics, but if you 
want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE 
OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS TO YOU, why not use google 
(www.google.com), wikipedia (www.wikipedia.org), etc. (and perhaps consider 
getting a better supervisor)? e.g. 
http://en.wikipedia.org/wiki/Molecular_geometry and 
http://en.wikipedia.org/wiki/Dihedral_angle


for more links to basic info, see 
http://xray.bmc.uu.se/gerard/embo2001/modval/03.html under "Refresher"


reading books or reviews (e.g. 
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=56) and using 
those to retrieve original references (such as engh & huber) also helps


(rhetorical question of the day: just like teaching a person how to fish is 
better than to give them a fish, isn't providing the url to google or 
wikipedia better than providing an answer to a basic question?)


--dvd

**
Gerard J.  Kleywegt
[Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
Biomedical Centre  Box 596
SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] ideal bond length and bong angel

[yang li]

By the way, I think my bad english embarrassed my meaning. What I want
to say
is  which bond length is used as the standard? the C=N or Ca-N or even the
side chains?
Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or
others.
At first I suppose the bond length only calculate the C=N bond, and
donnot know which one
is used as the aggel. It should be a quite stupid question for whom knows
it. Just forget it.

Re: [ccp4bb] ideal bond length and bong angel

[yang li]

 Dear Prof Gerard:
 In fact I have read your Model Validation on-line, and I have to say it
is youe lecture
that made me to think about this problem, though I have used it as a common
stand for
the quality of the model without understand it for a long time.
 And the http://en.wikipedia.org/wiki/Molecular_geometry and
http://en.wikipedia.org/wiki/Dihedral_angle, I think both from your
lecture, I have checked
them today before I post my mail, but unable to access them. For some
reason, wiki is
forbiddon here. I really coouldnot find the best answer and have discussed
with others
before, so I just want to make it clear, though maybe nothing to do with
practicals.
Thanks for your reply again.

Best Regards!

Re: [ccp4bb] ideal bond length and bong angel

[Gerard DVD Kleywegt]

them today before I post my mail, but unable to access them. For some 
reason, wiki is forbiddon here. I really coouldnot find the best answer and 
have discussed


i am shocked. i just checked with one of my 25 chinese students here and 
indeed even universities in china do not have access to a basic site such as 
wikipedia. the "some reason" of course being that china is still a 
totalitarian communist state where the government deems it necessary to 
control what information its citizens can and cannot access. in this year of 
the olympics shouldn't the scientific community put some pressure on the 
chinese government, e.g. through an appeal in nature or science? ccp4 care to 
take the initiative?


i'm supposed to teach in a course in beijing this spring but if my innocent 
web-based practicals cannot be used to their full extent i'm not so sure 
anymore


--gerard

(note to self: don't pack the 'free tibet' t-shirt for the beijing trip!)

**
Gerard J.  Kleywegt
[Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
Biomedical Centre  Box 596
SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] ideal bond length and bong angel

[Andreas Förster]

Hey Gerard,

wikipedia might tell you how to angle for fishes, but I fear it falls 
short of teaching you how to fish for angels.



Andreas



Imperial College of Aquatic and Fisheries Sciences London




Gerard DVD Kleywegt wrote:
   Can you explain the define of the bond length and bond 
angel--especially

bond angel--here?


i leave the definition of angels (be they ideal or not) to clerics, but 
if you want to find out about bonds and angles, AND YOUR SUPERVISOR IS 
REALLY UNABLE OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS TO YOU, why 
not use google (www.google.com), wikipedia (www.wikipedia.org), etc. 
(and perhaps consider getting a better supervisor)? e.g. 
http://en.wikipedia.org/wiki/Molecular_geometry and 
http://en.wikipedia.org/wiki/Dihedral_angle


for more links to basic info, see 
http://xray.bmc.uu.se/gerard/embo2001/modval/03.html under "Refresher"


reading books or reviews (e.g. 
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=56) and 
using those to retrieve original references (such as engh & huber) also 
helps


(rhetorical question of the day: just like teaching a person how to fish 
is better than to give them a fish, isn't providing the url to google or 
wikipedia better than providing an answer to a basic question?)


--dvd

**
Gerard J.  Kleywegt
[Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
Biomedical Centre  Box 596
SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] ideal bond length and bong angel

[David J. Schuller]

On Wed, 2008-01-09 at 12:47 +0100, Gerard DVD Kleywegt wrote:

> (rhetorical question of the day: just like teaching a person how to fish is 
> better than to give them a fish, isn't providing the url to google or 
> wikipedia better than providing an answer to a basic question?)

You can read a few paragraphs about "The spirit of helpfulness" here:

http://en.wikipedia.org/wiki/Wikipedia:Help_desk/How_to_answer

-  
===
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome guest - R.G. Ingersoll
===
  David J. Schuller
  modern man in a post-modern world
  MacCHESS, Cornell University
  [EMAIL PROTECTED]

Re: [ccp4bb] ideal bond length and bong angel

[Mischa Machius]

Simply use a bong for a while, and you will hear the angels sing :)

It's amazing to see how this thread devolved, within two or three  
posts, into a discussion about drug abuse and totalitarian political  
regimes...


Good way to start the day :)



On Jan 9, 2008, at 8:35 AM, Jim Pflugrath wrote:


Bong angels are probably ideal already!


Please explain, so that I can teach this to my students.  :)  Jim



 


Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353

Re: [ccp4bb] ideal bond length and bong angel

[Jim Pflugrath]

Bong angels are probably ideal already!


Please explain, so that I can teach this to my students.  :)  Jim

[ccp4bb] crystallization robot

[Nalam, Madhavi]

Hi,
Sorry for the non-ccp4 related question.
We are planning to buy a crystallization robot. We looked at the
'Mosquito'. We felt it is good for setting 96 well plates (for screening
the conditions). Though they say that we can use it for 24 well plates
(hanging drop) it didn't seem to be ideal because all it does is set the
drops and everything else has to be done manually. 
Can anyone suggest us other crystallization robots out in the market
that are good?
Thanks in advance,
Regards,
Madhavi

Re: [ccp4bb] how to model glycosylated residues?

[Craig McElroy]

In your generate.inp file that generates the input pdb and mtf files for 
cns there is a section called carbohydrate links which you can use to 
define the links... see below for an example of a beta link between the 
C1 and Asn N and a beta link between O4 and C1 of the next sugar. Then 
just make sure in your refine.inp file you read in the 
carbohydrate.param and carbohydrate.top files. Hope that helps.

Cheers
Craig

{=== carbohydrate links  
===}


{* Select pairs of residues that are linked *}
{* First entry is the name of the patch residue. *}
{* Second and third entries are the resid and segid for the atoms
  referenced by "-" in the patch. *}
{* Fourth and fifth entries are the resid and segid for the atoms
  referenced by "+" in the patch *}
{+ table: rows=6 numbered
 cols=6 "use" "patch name" "segid -" "resid -" "segid +" "resid 
+" +}


{+ choice: true false +}
{===>} carbo_use_1=true;
{===>} carbo_patch_1="B1N";
{===>} carbo_i_segid_1="B"; carbo_i_resid_1=901;
{===>} carbo_j_segid_1="B"; carbo_j_resid_1=131;

{+ choice: true false +}
{===>} carbo_use_2=true;
{===>} carbo_patch_2="B14";
{===>} carbo_i_segid_2="B"; carbo_i_resid_2=902;
{===>} carbo_j_segid_2="B"; carbo_j_resid_2=901;

Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630



Jiamu Du wrote:

Dear All,
Thank you for your previous response. I have built a 3-mer 
oligosaccharides in the electron density by using coot. I prefer to 
refine my structure in CNS due the resolution is only 2.6 Ang. I found 
there are only topology and parameter files for carbohydrate in CNS 
but no linkage file for carbohydrate. So CNS could recognize the sugar 
molecules individually, but can not recognize the linkage between 
them. When I refine it in CNS, a oxygen will be added beyond C1 of NAG.
Is there anyone who has the linkage file for carbohydrate of CNS? Or 
is there any other methods to deal with this situation?


Thanks.

Re: [ccp4bb] ideal bond length and bong angel

[William Scott]

Hi Yang Li:

Macromolecular crystal refinement programs use ideal bond lengths and angles.

The simplest ones just assume any carbon-carbon single bond (C-C) is the
same as any other, and use one average value, and any carbon-carbon double
bond (C=C) is the same as any other, and use another average value, and so
on for all possible linkages.

Better ones treat individual cases differently, so that the Calpha-Cbeta
bond in amino acids is compared only to other Calpha-Cbeta bond lengths,
for example.

The best ones will have a specific average value for each Calpha-Cbeta
bond length for each amino acid that has this bond.

Similarly for angles.

The standard value is usually established from very high resolution
crystal structures of (for example) individual amino acids, and/or quantum
chemistry calculations.

Various different methods are employed to penalize deviation from ideality
in a refinement.  It is common to use a simple quadratic penalty, which
can be characterized by a Hook's Law spring constant, and this is
justified where the harmonic approximation for bond potentials is valid
(and it should be in crystal structures).

Each refinement program has its own way of implementing the above, so the
best thing to do is to look at the bond parameter dictionaries that your
program uses.

I hope that comes closer to answering your question.

All the best,

Bill Scott




yang li wrote:
> By the way, I think my bad english embarrassed my meaning. What I want
> to say
> is  which bond length is used as the standard? the C=N or Ca-N or even the
> side chains?
> Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or
> others.
> At first I suppose the bond length only calculate the C=N bond, and
> donnot know which one
> is used as the aggel. It should be a quite stupid question for whom knows
> it. Just forget it.
>

Re: [ccp4bb] crystallization robot

[junfeng liu]

Douglas Oryx6 or 8. It works well on sitting drop and microbatch in our 
division.

Nalam, Madhavi wrote:

Hi,
Sorry for the non-ccp4 related question.
We are planning to buy a crystallization robot. We looked at the
'Mosquito'. We felt it is good for setting 96 well plates (for screening
the conditions). Though they say that we can use it for 24 well plates
(hanging drop) it didn't seem to be ideal because all it does is set the
drops and everything else has to be done manually. 
Can anyone suggest us other crystallization robots out in the market

that are good?
Thanks in advance,
Regards,
Madhavi

  

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

We chose the Phoenix crystallization robot because:

It has no expensive consumables (tips) intrinsic to the machine. This
was also a big item for us because we worry about being able to run the
machine for more than 3 years. Would the tips for our 2008 machine be
available in 2014? 

It is easy to program (BIG ITEM) for different tray configurations, and
various dispensing methods- even on the same tray. Right now you may not
think you'll have to vary drop sizes or add additional components
(ligand? detergent?) to your drops, but you probably will.

It can draw from 2ml block plates. Reformatting from block plates to
your trays is a pain.

The nitinol tips won't break (Compared to ~$700 apiece for the
incredibly breakable ceramic tips on some other machines).

It has cooling blocks for your samples. This is more important than you
think.

It's fast.

It is easily integrated into a fully automated lab system. Right now,
though, our humans (including me) are cheaper than rails and robots.

It's incredibly accurate, even with 30% PEG 4000 (we tested this
ourselves). 

You can use it for other low volume dispensing applications.


--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED]  

Re: [ccp4bb] crystallization robot

[Van Den Berg, Bert]

Hi Lisa,
 
is the Phoenix capable of setting up hanging drops? For me that is one of the 
big plusses of the Mosquito. Are there any other robots out there capable of 
doing hanging drops?
 
Cheers, Bert
 
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot



We chose the Phoenix crystallization robot because:

It has no expensive consumables (tips) intrinsic to the machine. This
was also a big item for us because we worry about being able to run the
machine for more than 3 years. Would the tips for our 2008 machine be
available in 2014?

It is easy to program (BIG ITEM) for different tray configurations, and
various dispensing methods- even on the same tray. Right now you may not
think you'll have to vary drop sizes or add additional components
(ligand? detergent?) to your drops, but you probably will.

It can draw from 2ml block plates. Reformatting from block plates to
your trays is a pain.

The nitinol tips won't break (Compared to ~$700 apiece for the
incredibly breakable ceramic tips on some other machines).

It has cooling blocks for your samples. This is more important than you
think.

It's fast.

It is easily integrated into a fully automated lab system. Right now,
though, our humans (including me) are cheaper than rails and robots.

It's incredibly accurate, even with 30% PEG 4000 (we tested this
ourselves).

You can use it for other low volume dispensing applications.


--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

[ccp4bb] apologize

[yang li]

Dear All,
  I am very sorry to involve you into such insignificance discussion, I
have reached agreement
with Prof Gerard, please stop talking about things beyond science, thanks!
  I read a book today, which said "A refined model should exhibit rms
deviations of no more
than 0.02A for bond length and 4 for bond angels", I just wonder about the
standard of the
bond length and the bond angel. I think most of you have read similar words!
But maybe I
didnot express clearly and made some phrasal mistakes.
  At last, happy new year to you all--though very late!


Sincerely!
Yang Li

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

It doesn't have a cover slip flipper. 

We only do sitting drops with our robot- even large volumes (2 ul
drops).

We don't have the space to store the volume of linbro plates that would
be  generated by a robot.

Also, 24 well linbro plates use a lot of well solution- making them very
expensive for initial screening if you use commercial screens.

But you could easily set up your drops  (in reverse) on a glass plate or
framed mylar, and flip it onto a greased tray, or set up on sealing
tape, if that's important to you. 

We have not found that it is important to us. We only move to hanging
drops after optimization, so it is a small number of linbro plates that
are easily be set up by hand.

 


--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

Looking at the mosquito, it doesn't have any cover-slip handling
robotics, either. So it's the same thing- rearrange the dispense
location and flip the cover- which is either a glass plate or mylar or
a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

Re: [ccp4bb] apologize

[William Scott]

Dear Yang Li:


Happy New Year to you, too, (ahead of Feb. 7th).

You certainly owe us no apology; the reverse may not be true.

Your question is an important one, as is what you have written below.

I'm not certain I have a completely satisfactory answer.

The reason is that ideal bond lengths may or may not be "true" in the
sense that the value is established by social consensus, and is thus
guaranteed to be perfectly accurate, even though it may be quite precise.

Because of this, and because of natural deviations from ideality (which
really only become trustworthy observations at extremely high resolution),
a certain amount of "wiggle room" is typically allowed in terms of rmsd.

The more conservative the refinement, the smaller the rmsd from ideality
will be.

Some people believe 0.02 Å deviation from ideality is reasonable, based on
the accuracy of the dictionary values of bond lengths and angles; others
consider that to be "too sloppy" and a way to artificially deflate
Rfactors.

I seem to have detected a tendency in the literature to aim for about 0.01
Å deviation.  The new refinement program phenix.refine, which is supposed
to optimize weighting between X-ray terms and stereochemical constraints
automatically, seems to settle in at quite conservative values, such as
0.005 Å, whereas with refmac, I can't seem to get the geometry any more
ideal than 0.005 Å even if I try to idealize a structure in the absence of
X-ray data.

So, like you, I am a bit confused, and wouldn't mind hearing more from the
experts.

All the best,

Bill






yang li wrote:
> Dear All,
>   I am very sorry to involve you into such insignificance discussion,
> I
> have reached agreement
> with Prof Gerard, please stop talking about things beyond science, thanks!
>   I read a book today, which said "A refined model should exhibit rms
> deviations of no more
> than 0.02A for bond length and 4 for bond angels", I just wonder about the
> standard of the
> bond length and the bond angel. I think most of you have read similar
> words!
> But maybe I
> didnot express clearly and made some phrasal mistakes.
>   At last, happy new year to you all--though very late!
>
>
> Sincerely!
> Yang Li
>

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[William Scott]

Sorry, that should have read

"because the value is established by social consensus, it is thus NOT
guaranteed to be perfectly accurate, ..."

In other words, one can imagine some source of systematic error in
establishing an ideal bond length.  For example, the crystal packing
environment of small molecules might tend to distort a bond by a couple
hundredths of an Ångstrom.


William Scott wrote:
> Dear Yang Li:
>
>
> Happy New Year to you, too, (ahead of Feb. 7th).
>
> You certainly owe us no apology; the reverse may not be true.
>
> Your question is an important one, as is what you have written below.
>
> I'm not certain I have a completely satisfactory answer.
>
> The reason is that ideal bond lengths may or may not be "true" in the
> sense that the value is established by social consensus, and is thus
> guaranteed to be perfectly accurate, even though it may be quite precise.
>
> Because of this, and because of natural deviations from ideality (which
> really only become trustworthy observations at extremely high resolution),
> a certain amount of "wiggle room" is typically allowed in terms of rmsd.
>
> The more conservative the refinement, the smaller the rmsd from ideality
> will be.
>
> Some people believe 0.02 Å deviation from ideality is reasonable, based on
> the accuracy of the dictionary values of bond lengths and angles; others
> consider that to be "too sloppy" and a way to artificially deflate
> Rfactors.
>
> I seem to have detected a tendency in the literature to aim for about 0.01
> Å deviation.  The new refinement program phenix.refine, which is supposed
> to optimize weighting between X-ray terms and stereochemical constraints
> automatically, seems to settle in at quite conservative values, such as
> 0.005 Å, whereas with refmac, I can't seem to get the geometry any more
> ideal than 0.005 Å even if I try to idealize a structure in the absence of
> X-ray data.
>
> So, like you, I am a bit confused, and wouldn't mind hearing more from the
> experts.
>
> All the best,
>
> Bill
>
>
>
>
>
>
> yang li wrote:
>> Dear All,
>>   I am very sorry to involve you into such insignificance
>> discussion,
>> I
>> have reached agreement
>> with Prof Gerard, please stop talking about things beyond science,
>> thanks!
>>   I read a book today, which said "A refined model should exhibit
>> rms
>> deviations of no more
>> than 0.02A for bond length and 4 for bond angels", I just wonder about
>> the
>> standard of the
>> bond length and the bond angel. I think most of you have read similar
>> words!
>> But maybe I
>> didnot express clearly and made some phrasal mistakes.
>>   At last, happy new year to you all--though very late!
>>
>>
>> Sincerely!
>> Yang Li
>>
>

Re: [ccp4bb] crystallization robot

[Van Den Berg, Bert]

The mosquito has special (albeit fairly pricey at $13 each) plastic sheets that 
allow setup of hanging drops in a 96-well format. It can also do multiple drops 
per well. As far as I know this is a capability unique to the Mosquito but I 
may be wrong.
 
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot



Looking at the mosquito, it doesn't have any cover-slip handling robotics, 
either. So it's the same thing- rearrange the dispense location and flip the 
cover- which is either a glass plate or mylar or  a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Nave, C (Colin)]

 
The latest Acta D shows the "social consensus" is sometimes lacking even (or 
especially) among very experienced and able crystallographers.

Experimental determination of optimal root-mean-square deviations of 
macromolecular bond lengths and angles from their restrained ideal values 
Ian J. Tickle 
pages 1274-1281

Numerology versus reality: a voice in a recent dispute 
Mariusz Jaskolski , Miroslaw Gilski , Zbigniew Dauter and Alexander Wlodawer 
pages 1282-1283

Interesting debate

   Colin

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of William Scott
Sent: 09 January 2008 17:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] bond lengths, angles, ideality and refinements

Sorry, that should have read

"because the value is established by social consensus, it is thus NOT 
guaranteed to be perfectly accurate, ..."

In other words, one can imagine some source of systematic error in establishing 
an ideal bond length.  For example, the crystal packing environment of small 
molecules might tend to distort a bond by a couple hundredths of an Ångstrom.


William Scott wrote:
> Dear Yang Li:
>
>
> Happy New Year to you, too, (ahead of Feb. 7th).
>
> You certainly owe us no apology; the reverse may not be true.
>
> Your question is an important one, as is what you have written below.
>
> I'm not certain I have a completely satisfactory answer.
>
> The reason is that ideal bond lengths may or may not be "true" in the 
> sense that the value is established by social consensus, and is thus 
> guaranteed to be perfectly accurate, even though it may be quite precise.
>
> Because of this, and because of natural deviations from ideality 
> (which really only become trustworthy observations at extremely high 
> resolution), a certain amount of "wiggle room" is typically allowed in terms 
> of rmsd.
>
> The more conservative the refinement, the smaller the rmsd from 
> ideality will be.
>
> Some people believe 0.02 Å deviation from ideality is reasonable, 
> based on the accuracy of the dictionary values of bond lengths and 
> angles; others consider that to be "too sloppy" and a way to 
> artificially deflate Rfactors.
>
> I seem to have detected a tendency in the literature to aim for about 
> 0.01 Å deviation.  The new refinement program phenix.refine, which is 
> supposed to optimize weighting between X-ray terms and stereochemical 
> constraints automatically, seems to settle in at quite conservative 
> values, such as
> 0.005 Å, whereas with refmac, I can't seem to get the geometry any 
> more ideal than 0.005 Å even if I try to idealize a structure in the 
> absence of X-ray data.
>
> So, like you, I am a bit confused, and wouldn't mind hearing more from 
> the experts.
>
> All the best,
>
> Bill
>
>
>
>
>
>
> yang li wrote:
>> Dear All,
>>   I am very sorry to involve you into such insignificance 
>> discussion, I have reached agreement with Prof Gerard, please stop 
>> talking about things beyond science, thanks!
>>   I read a book today, which said "A refined model should exhibit 
>> rms deviations of no more than 0.02A for bond length and 4 for bond 
>> angels", I just wonder about the standard of the bond length and the 
>> bond angel. I think most of you have read similar words!
>> But maybe I
>> didnot express clearly and made some phrasal mistakes.
>>   At last, happy new year to you all--though very late!
>>
>>
>> Sincerely!
>> Yang Li
>>
>
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Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Gerard DVD Kleywegt]

For some current thoughts on bond length and bond angle deviations you may
want to look at the following paper:


... but that would be rather a waste of your time (sorry!). if you're only 
going to read one paper about this subject this year, make it iain tickle's!


http://journals.iucr.org/d/issues/2007/12/00/gx5119/gx5119.pdf

and start quoting RMS-Z-scores (from whatcheck or, soon, from refmac) in your 
tables 1 ("table 1s"? what *is* the plural of "table 1"?). i should have 
mentioned this in my talk at the ccp4 study weekend last saturday


--dvd

(if sweden is invaded tomorrow by china and poland, you'll know whom to 
blame!)


**
Gerard J.  Kleywegt
[Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
Biomedical Centre  Box 596
SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

The phoenix can dispense multiple drops per well. You can easily
program dispensing on the deck wherever, whatever and whenever, as long
as it fits in the plate holder . It can handle at least the 1536 pitch
(4 x 384), so if you specify the quadrant of the 384 well cell it will
dispense there. Your drops may merge, though. It has a separate
dispensing head for proteins or additives. You can dispense from up to
16 "protein" tubes (chilled) and 2 ambient tubes, plus whatever is on
the deck, in whatever order you want. Since the setup programming is an
easy gui, it's not a big deal.

 

I am certain that the mosquito sheets would work on any robot. 

 

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Van Den Berg, Bert
Sent: Wednesday, January 09, 2008 11:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

 

The mosquito has special (albeit fairly pricey at $13 each) plastic
sheets that allow setup of hanging drops in a 96-well format. It can
also do multiple drops per well. As far as I know this is a capability
unique to the Mosquito but I may be wrong.

 

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

 



From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

Looking at the mosquito, it doesn't have any cover-slip handling
robotics, either. So it's the same thing- rearrange the dispense
location and flip the cover- which is either a glass plate or mylar or
a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

Re: [ccp4bb] apologize

[Patrick Loll]

Check out the letters in the Dec 2007 edition of Acta D.  There is  
lively discussion even among the experts (and while I recall no  
mention of angels in this discussion, there IS a reference to Winnie  
the Pooh).


Acta Cryst. (2007). D63, 1274-1281
Acta Cryst. (2007). D63, 1282-1283



Some people believe 0.02 Å deviation from ideality is reasonable,  
based on
the accuracy of the dictionary values of bond lengths and angles;  
others

consider that to be "too sloppy" and a way to artificially deflate
Rfactors.

I seem to have detected a tendency in the literature to aim for  
about 0.01
Å deviation.  The new refinement program phenix.refine, which is  
supposed
to optimize weighting between X-ray terms and stereochemical  
constraints
automatically, seems to settle in at quite conservative values,  
such as
0.005 Å, whereas with refmac, I can't seem to get the geometry any  
more
ideal than 0.005 Å even if I try to idealize a structure in the  
absence of

X-ray data.

So, like you, I am a bit confused, and wouldn't mind hearing more  
from the

experts.

All the best,

Bill






yang li wrote:

Dear All,
  I am very sorry to involve you into such insignificance  
discussion,

I
have reached agreement
with Prof Gerard, please stop talking about things beyond science,  
thanks!
  I read a book today, which said "A refined model should  
exhibit rms

deviations of no more
than 0.02A for bond length and 4 for bond angels", I just wonder  
about the

standard of the
bond length and the bond angel. I think most of you have read similar
words!
But maybe I
didnot express clearly and made some phrasal mistakes.
  At last, happy new year to you all--though very late!


Sincerely!
Yang Li



 
---

Patrick J. Loll, Ph. D. (215) 762-7706
Associate Professor FAX: (215) 762-4452
Department of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

[EMAIL PROTECTED]

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Herbert J. Bernstein]

"tables 1" is formally correct but awkward.  "table 1s" is confusing. I 
would suggest that we treat "table 1" like sheep and make the plural the 
same as the singular.  If you don't approve of revising the English 
language, then a valid way to avoid the need for a plural is to say "each 
table 1".


  --  Herbert

=
 Herbert J. Bernstein, Professor of Computer Science
   Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769

 +1-631-244-3035
 [EMAIL PROTECTED]
=

On Wed, 9 Jan 2008, Gerard DVD Kleywegt wrote:

...>
and start quoting RMS-Z-scores (from whatcheck or, soon, from refmac) in your 
tables 1 ("table 1s"? what *is* the plural of "table 1"?).

...

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Todd Holyoak]

For some current thoughts on bond length and bond angle deviations you may want 
to look at the following paper:

Acta Cryst. (2007). D63, 611-620   
Stereochemical restraints revisited: how accurate are refinement targets and 
how much should protein structures be allowed to deviate from them?
M. Jaskolski, M. Gilski, Z. Dauter and A. Wlodawer


Todd Holyoak

Todd Holyoak, Assistant Professor
Dept. of Biochemistry and Molecular Biology
The University of Kansas Medical Center
3901 Rainbow Blvd.
4013A WHW, MS 3030
Kansas City, KS 66160
913-588-0795 (office)
913-588-0796 (lab)
913-588-7440 (fax)
>>> William Scott <[EMAIL PROTECTED]> 01/09/08 11:31 AM >>>
Sorry, that should have read

"because the value is established by social consensus, it is thus NOT
guaranteed to be perfectly accurate, ..."

In other words, one can imagine some source of systematic error in
establishing an ideal bond length.  For example, the crystal packing
environment of small molecules might tend to distort a bond by a couple
hundredths of an Ångstrom.


William Scott wrote:
> Dear Yang Li:
>
>
> Happy New Year to you, too, (ahead of Feb. 7th).
>
> You certainly owe us no apology; the reverse may not be true.
>
> Your question is an important one, as is what you have written below.
>
> I'm not certain I have a completely satisfactory answer.
>
> The reason is that ideal bond lengths may or may not be "true" in the
> sense that the value is established by social consensus, and is thus
> guaranteed to be perfectly accurate, even though it may be quite precise.
>
> Because of this, and because of natural deviations from ideality (which
> really only become trustworthy observations at extremely high resolution),
> a certain amount of "wiggle room" is typically allowed in terms of rmsd.
>
> The more conservative the refinement, the smaller the rmsd from ideality
> will be.
>
> Some people believe 0.02 Å deviation from ideality is reasonable, based on
> the accuracy of the dictionary values of bond lengths and angles; others
> consider that to be "too sloppy" and a way to artificially deflate
> Rfactors.
>
> I seem to have detected a tendency in the literature to aim for about 0.01
> Å deviation.  The new refinement program phenix.refine, which is supposed
> to optimize weighting between X-ray terms and stereochemical constraints
> automatically, seems to settle in at quite conservative values, such as
> 0.005 Å, whereas with refmac, I can't seem to get the geometry any more
> ideal than 0.005 Å even if I try to idealize a structure in the absence of
> X-ray data.
>
> So, like you, I am a bit confused, and wouldn't mind hearing more from the
> experts.
>
> All the best,
>
> Bill
>
>
>
>
>
>
> yang li wrote:
>> Dear All,
>>   I am very sorry to involve you into such insignificance
>> discussion,
>> I
>> have reached agreement
>> with Prof Gerard, please stop talking about things beyond science,
>> thanks!
>>   I read a book today, which said "A refined model should exhibit
>> rms
>> deviations of no more
>> than 0.02A for bond length and 4 for bond angels", I just wonder about
>> the
>> standard of the
>> bond length and the bond angel. I think most of you have read similar
>> words!
>> But maybe I
>> didnot express clearly and made some phrasal mistakes.
>>   At last, happy new year to you all--though very late!
>>
>>
>> Sincerely!
>> Yang Li
>>
>

Re: [ccp4bb] crystallization robot

[Tom Walter]

Hi Madhavi

In conjunction with a 96-syringe hydra for filling reservoirs, we have been 
using two Genomic Solutions 8-tip "Cartesian" systems (Called HoneybeeX8 now I 
believe) for the past 6 years and have been generally very happy with them. 
They require a bit of looking after in terms of cleaning, degassing and general 
maintenance (like most sensitive machines: have a responsible person), but have 
set up about 3 plates by now with 100nl + 100nl drops. We use it routinely 
for optimisation experiments and additive/detergent screens as well as initial 
screening. Consumable costs are pretty low (a few valves, tips and wash pumps 
over the years, along with a supply of isopropanol and water). The Innovadyne 
system is apparently quite similar but I have no experience of this. 
A few points to bear in mind though:
1) Evaporation of drops with small drop sizes - 100nl drops take only a few 
minutes to dry out completely, so you should either use a close-fitting cover 
over the plate, some kind of humidity chamber (each of the wells will be 
different though), have very fast plate setup time or chill the plate (which 
may affect protein solubility). We use a close fitting cover since each plate 
of 96 takes 10 minutes.
2) Contact and non-contact dispensing. Non-contact dispensing seems to be more 
accurate in terms of drop positioning in the well: important for images from 
automated imaging systems, image analysis software, and for fishing crystals 
out to test.
Non-contact dispensing won't give you so many problems with low surface tension 
solutions such as detergents, and is compatible with hydrophobic plates 
(important for membrane proteins).

I dont think there is a perfect robot out there - all the robots I have seen 
have both advantages and disadvantages so it just depends what you will be 
using them for, what disadvantages you are willing to put up with, and of 
course your budget.

Happy shopping!
Tom


**  Tom Walter B.Sc. M.Res.   **
** Oxford Protein Production FacilityTel: +44 (0)1865 287747  **
** Wellcome Trust Centre for Human Genetics  Fax: +44 (0)1865 287547  **
** Roosevelt Drive   [EMAIL PROTECTED]   **
** Headington, Oxford OX3 7BNhttp://www.oppf.ox.ac.uk **


 Original message 
>Date: Wed, 9 Jan 2008 09:56:34 -0500
>From: "Nalam, Madhavi" <[EMAIL PROTECTED]>  
>Subject: [ccp4bb] crystallization robot  
>To: CCP4BB@JISCMAIL.AC.UK
>
>Hi,
>Sorry for the non-ccp4 related question.
>We are planning to buy a crystallization robot. We looked at the
>'Mosquito'. We felt it is good for setting 96 well plates (for screening
>the conditions). Though they say that we can use it for 24 well plates
>(hanging drop) it didn't seem to be ideal because all it does is set the
>drops and everything else has to be done manually. 
>Can anyone suggest us other crystallization robots out in the market
>that are good?
>Thanks in advance,
>Regards,
>Madhavi

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Ian Tickle]

Hi William & others,

Indeed, phenix.refine uses cross-validation to optimise the scaling of the 
X-ray & B-factor weights.  All I did was demonstrate that you can do 
essentially the same thing as phenix.refine but using Refmac instead.  I don't 
claim to have done anything new, except I modified Refmac to print out the free 
likelihood and used that as a target function instead of Rfree, as suggested by 
Gerard Bricogne in Meth. Enzymol. (1997) 276, 361-423.  Whatever value of the 
RMSD (or better the RMS Z-score) comes out of that, you can be sure that it's 
based purely objectively on the experimental data, not on completely arbitrary 
and unjustifiable subjective choices, which is what Jaskolski et al. appear to 
be suggesting.  Cross-validation is a well-established methodology in 
statistics, it's certainly not 'numerology'!

Of course then you have to come up with some theory to explain the experimental 
results, i.e. why the RMSD that comes out must always be <= the RMS standard 
uncertainty, but actually that's not difficult since the RMSD is related to the 
accuracy and the SU is related to the precision, and on the face of it there's 
no reason why these should be related at all (as Gerard nicely demonstrated 
with his dartboard analogy in Leeds!).  Jaskolski et al.'s theory that always 
RMSD =  regardless of resolution just doesn't fit the experimental results, 
and as every good scientist knows, it only takes one ugly fact to destroy a 
beautiful theory.

As you point out, setting a target value of 0.02 Ang or higher for the RMSD 
bonds and similarly for the angles, unless you have very high resolution data, 
will inevitably result in take-up of some fraction of the random experimental 
errors into the refined parameters, in order to inflate the RMSD/RMSZ's to 
their target values and reduce Rwork at the expense of Rfree - otherwise known 
as overfitting!  It's not recommended practice to deliberately cause random 
errors (however small) to be added to your co-ordinates!  This is obvious if 
you think about what happens at low resolution: there's no justification for 
refining individual xyz & B's, so the optimal procedure is to use constrained 
refinement with the torsion angles as parameters, or restrained refinement with 
*very* tight restraints (if that's feasible).  Whether you use constrained 
refinement or its restrained equivalent, it will keep the bond lengths & angles 
fixed at the initial dictionary values so the RMSD's will be identically zero, 
or very nearly so, throughout the refinement.

Someone mentioned 'experienced crystallographers': actually since the 
distinction between RMSD & SU is purely a question of statistics not of 
crystallography, any crystallographic experience is unlikely to be relevant!

The other question you raised is why Refmac doesn't refine the RMSD's much 
nearer to zero - this is something I also commented on; also why the Rfree & 
LLfree plots are so noisy compared with those from CNS & phenix.refine.  I 
think it's to do with rounding errors in the gradient calculation and/or 
optimisation code.  Refmac may be using single precision, whereas phenix.refine 
may be using double - I'm just guessing, maybe the programmers could comment?  
This is something I would like to see improved, in order to make 
cross-validation with Refmac more reliable & useful.

Cheers

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of William Scott
> Sent: 09 January 2008 17:32
> To: William Scott
> Cc: ccp4bb@jiscmail.ac.uk
> Subject: Re: [ccp4bb] bond lengths, angles, ideality and refinements
> 
> Sorry, that should have read
> 
> "because the value is established by social consensus, it is thus NOT
> guaranteed to be perfectly accurate, ..."
> 
> In other words, one can imagine some source of systematic error in
> establishing an ideal bond length.  For example, the crystal packing
> environment of small molecules might tend to distort a bond 
> by a couple
> hundredths of an Ångstrom.
> 
> 
> William Scott wrote:
> > Dear Yang Li:
> >
> >
> > Happy New Year to you, too, (ahead of Feb. 7th).
> >
> > You certainly owe us no apology; the reverse may not be true.
> >
> > Your question is an important one, as is what you have 
> written below.
> >
> > I'm not certain I have a completely satisfactory answer.
> >
> > The reason is that ideal bond lengths may or may not be 
> "true" in the
> > sense that the value is established by social consensus, and is thus
> > guaranteed to be perfectly accurate, even though it may be 
> quite precise.
> >
> > Because of this, and because of natural deviations from 
> ideality (which
> > really only become trustworthy observations at extremely 
> high resolution),
> > a certain amount of "wiggle room" is typically allowed in 
> terms of rmsd.
> >
> > The more conservative the refinement, the smaller the rmsd 
> from ideality
> > will be.
> >
> > Some people believe 0.02 Å deviation from 

Re: [ccp4bb] bond lengths, angles, ideality and refinements

[Anastassis Perrakis]

I would only like to iterate a small comment I posted before:

Should the cell parameters be inaccurate, optimization of weights by  
cross-validation (getting the best Rfree) will result in 'higher' RMSD.
It is easy to think about it: if in a cell is measured to be 1%  
larger than in reality, all bonds would 'prefer' to be 1% larger than  
the 'correct'
dictionary values, resulting in a higher RMSD to satisfy that and  
that structure would have the lowest Rfree because the X-ray data

would be fitted better.

I actually think that inaccurate cells are a big source of misery in  
many refinements. I have found the idea
of WhatCheck to actually check your cell by looking at the projection  
of bond lengths of certain types along the cell axes most useful.
I would hardly advocate to measure your cell that way, but going back  
to you data and looking at the cell again would be worth it.


To make it more fun, cells change during radiation damage, so ...

best regards, Tassos

On 9 Jan 2008, at 20:15, Ian Tickle wrote:


Hi William & others,

Indeed, phenix.refine uses cross-validation to optimise the scaling  
of the X-ray & B-factor weights.  All I did was demonstrate that  
you can do essentially the same thing as phenix.refine but using  
Refmac instead.  I don't claim to have done anything new, except I  
modified Refmac to print out the free likelihood and used that as a  
target function instead of Rfree, as suggested by Gerard Bricogne  
in Meth. Enzymol. (1997) 276, 361-423.  Whatever value of the RMSD  
(or better the RMS Z-score) comes out of that, you can be sure that  
it's based purely objectively on the experimental data, not on  
completely arbitrary and unjustifiable subjective choices, which is  
what Jaskolski et al. appear to be suggesting.  Cross-validation is  
a well-established methodology in statistics, it's certainly not  
'numerology'!


Of course then you have to come up with some theory to explain the  
experimental results, i.e. why the RMSD that comes out must always  
be <= the RMS standard uncertainty, but actually that's not  
difficult since the RMSD is related to the accuracy and the SU is  
related to the precision, and on the face of it there's no reason  
why these should be related at all (as Gerard nicely demonstrated  
with his dartboard analogy in Leeds!).  Jaskolski et al.'s theory  
that always RMSD =  regardless of resolution just doesn't fit  
the experimental results, and as every good scientist knows, it  
only takes one ugly fact to destroy a beautiful theory.


As you point out, setting a target value of 0.02 Ang or higher for  
the RMSD bonds and similarly for the angles, unless you have very  
high resolution data, will inevitably result in take-up of some  
fraction of the random experimental errors into the refined  
parameters, in order to inflate the RMSD/RMSZ's to their target  
values and reduce Rwork at the expense of Rfree - otherwise known  
as overfitting!  It's not recommended practice to deliberately  
cause random errors (however small) to be added to your co- 
ordinates!  This is obvious if you think about what happens at low  
resolution: there's no justification for refining individual xyz &  
B's, so the optimal procedure is to use constrained refinement with  
the torsion angles as parameters, or restrained refinement with  
*very* tight restraints (if that's feasible).  Whether you use  
constrained refinement or its restrained equivalent, it will keep  
the bond lengths & angles fixed at the initial dictionary values so  
the RMSD's will be identically zero, or very nearly so, throughout  
the refinement.


Someone mentioned 'experienced crystallographers': actually since  
the distinction between RMSD & SU is purely a question of  
statistics not of crystallography, any crystallographic experience  
is unlikely to be relevant!


The other question you raised is why Refmac doesn't refine the  
RMSD's much nearer to zero - this is something I also commented on;  
also why the Rfree & LLfree plots are so noisy compared with those  
from CNS & phenix.refine.  I think it's to do with rounding errors  
in the gradient calculation and/or optimisation code.  Refmac may  
be using single precision, whereas phenix.refine may be using  
double - I'm just guessing, maybe the programmers could comment?   
This is something I would like to see improved, in order to make  
cross-validation with Refmac more reliable & useful.


Cheers

-- Ian


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of William Scott
Sent: 09 January 2008 17:32
To: William Scott
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] bond lengths, angles, ideality and refinements

Sorry, that should have read

"because the value is established by social consensus, it is thus NOT
guaranteed to be perfectly accurate, ..."

In other words, one can imagine some source of systematic error in
establishing an ideal bond length.  For example, the cryst

Re: [ccp4bb] crystallization robot

[Balaji Bhyravbhatla]

All,
Just a quick correction on the latest price of the plastic sheets. The  
new ones cost $5.00, so the overall cost will be much cheaper.


Thanks

Balaji

On Jan 9, 2008, at 11:59 AM, Van Den Berg, Bert wrote:

The mosquito has special (albeit fairly pricey at $13 each) plastic  
sheets that allow setup of hanging drops in a 96-well format. It can  
also do multiple drops per well. As far as I know this is a  
capability unique to the Mosquito but I may be wrong.


Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

Looking at the mosquito, it doesn’t have any cover-slip handling  
robotics, either. So it’s the same thing- rearrange the dispense  
location and flip the cover- which is either a glass plate or mylar  
or  a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED]

[ccp4bb] Principal axes and moment of inertia matrix

[Buz Barstow]

Dear All,

Does anyone have a python routine that can be used to calculate the  
moment of inertia matrix and principal axes of a selection of atoms?


Thanks! and all the best,

--Buz

Re: [ccp4bb] ideal bond length and bong angel

[James Stroud]

On Jan 9, 2008, at 5:30 AM, Gerard DVD Kleywegt wrote:
them today before I post my mail, but unable to access them. For  
some reason, wiki is forbiddon here. I really coouldnot find the  
best answer and have discussed


i am shocked. i just checked with one of my 25 chinese students here  
and indeed even universities in china do not have access to a basic  
site such as wikipedia. the "some reason" of course being that china  
is still a totalitarian communist state where the government deems  
it necessary to control what information its citizens can and cannot  
access. in this year of the olympics shouldn't the scientific  
community put some pressure on the chinese government, e.g. through  
an appeal in nature or science? ccp4 care to take the initiative?


i'm supposed to teach in a course in beijing this spring but if my  
innocent web-based practicals cannot be used to their full extent  
i'm not so sure anymore


Be care, you insolence might get someone sent disappear.

--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA  90095

http://www.jamesstroud.com

Re: [ccp4bb] ideal bond length and bong angel

[Gerard DVD Kleywegt]

Be care, you insolence might get someone sent disappear.


is the chinese secret service editing my incoming mail already, or are you 
merely using a microsoft grammar checker?


--dvd

**
Gerard J.  Kleywegt
[Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
Biomedical Centre  Box 596
SE-751 24 Uppsala  SWEDEN

http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

[ccp4bb] Sulfate ion on 2-fold axis

[Jie Liu]

Dear all

I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file
one S atom with occu=0.5 and two O atoms with occu=1, or should
I put one S and four O atoms all with occu=0.5?

Thanks for your inputs.

Jie

Re: [ccp4bb] crystallization robot

[Janet Newman]

The Gilson crystallisation robots (horrible machines: no longer
available) were specific for hanging drops - other robots can set them
up (using the Mosquito sheets or equivalent), but the flipping will have
to be done by hand.  The Douglas Instrument machines can basically
pipette onto anything you want, as it is a one-by-one dispense.  You
still have to flip by hand.  The Mosquito has the ability to do a
'mirror' transfer - which makes the setup of hanging drops easy, as it
compensates for the inversion that you necessarily get when you flip the
piece of plastic (it's a good idea to flip the plastic around the same
axis as the mirror function, BTW).

 

If you want to use this arrangement on the phoenix then you will need to
make up a plate or block with the crystallisation solutions mirrored,
and set up a protocol where the normal array is transferred from the
storage block into the experimental plate reservoirs, and then the
mirrored array of crystallisation solutions is used to make up the
crystallisation droplets.  Certainly do-able, but it means that you need
TWO source blocks for each screen that you want to set up this way.
Best of luck keeping that working in a multi-user lab!

 

We have both a Mosquito and a Phoenix (and an older Cartesian 16+1), and
I could not recommend one over the other of the first two machines -
they are both easy to use, but they do different things well.  The
Mosquito can deal with difficult samples (protein which is crashing out
of solution, for example).  We have been able to set up protein which
gelled to the consistency of hair-gel with our gnat.  The Phoenix does
not dispense viscous samples well from the nano-tip (anything over 10%
glycerol is really iffy, for example), but doesn't require the protein
to be aliquoted out into 8 separate puddles.  The Cartesian was always a
bitch to get running, so given the other two machines, it sits and
collects dust.  Anybody want to start negotiating for a (slightly) used
Cartesian?

 

Janet

 

Janet Newman

CSIRO Molecular and Health Technologies

343 Royal Parade

Parkville  VIC  3052

Australia

tel:  +61 (0)3 9662 7326

fax: +61 (0)3 9662 7101

email: [EMAIL PROTECTED]

 

 

  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Lisa A Nagy
Sent: Thursday, 10 January 2008 4:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

 

The phoenix can dispense multiple drops per well. You can easily
program dispensing on the deck wherever, whatever and whenever, as long
as it fits in the plate holder . It can handle at least the 1536 pitch
(4 x 384), so if you specify the quadrant of the 384 well cell it will
dispense there. Your drops may merge, though. It has a separate
dispensing head for proteins or additives. You can dispense from up to
16 "protein" tubes (chilled) and 2 ambient tubes, plus whatever is on
the deck, in whatever order you want. Since the setup programming is an
easy gui, it's not a big deal.

 

I am certain that the mosquito sheets would work on any robot. 

 

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Van Den Berg, Bert
Sent: Wednesday, January 09, 2008 11:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

 

The mosquito has special (albeit fairly pricey at $13 each) plastic
sheets that allow setup of hanging drops in a 96-well format. It can
also do multiple drops per well. As far as I know this is a capability
unique to the Mosquito but I may be wrong.

 

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

 

  _  

From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

Looking at the mosquito, it doesn't have any cover-slip handling
robotics, either. So it's the same thing- rearrange the dispense
location and flip the cover- which is either a glass plate or mylar or
a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

[ccp4bb] Malic Acid interferes heavy metal binding?

[JINJIN ZHANG]

Dear All,
I have got large and nice crystals in a condition that contains 40% glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No buffer?! I'm so comfused. As far as from the product website, the Malic Acid has no buffering function. I don't know whether it's a precipitant. The protein itself was stored in a buffer contains 20mM Tris pH7.5, 150mM NaCl and 10% glycerol. I'm having difficulties in getting heavy metal bound derivatives. I was wondering whether the Malic Acid interferes heavy metal binding? Does anyone has any success with crystals grow with similar conditions? Any comment and suggestion is highly appreciated.
Regards,
Jinjin Zhang

Re: [ccp4bb] Malic Acid interferes heavy metal binding?

[William Scott]

Dear Jinjin:

Malic acid, a diprotic acid, has a pKa of about 3.4 for the first dissociation 
and a second at about 5.1. So it is best as a buffer within a pH range of about 
2.4 to 6.1, and it at its best around best in the range of 3.4 to 5.1.  If the 
pH of your solution is indeed 7, then it is doing little to buffer it (but the 
small amount of tris might).

Many diprotic and polyprotic organic acids chelate metal ions.

If you could substitute a different dianionic salt in the mother liquor, like a 
sulphate, it might help.

Bill



On Wed, 9 Jan 2008 18:42:06 -0500
JINJIN ZHANG <[EMAIL PROTECTED]> wrote:

 Dear All,
 
 I have got large and nice crystals in a condition that contains 40% 
glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No 
buffer?! I'm so comfused. As far as from the product website, the Malic Acid 
has no buffering function. I don't know whether it's a precipitant. The protein 
itself was stored in a buffer contains 20mM Tris pH7.5, 150mM NaCl and 10% 
glycerol. I'm having difficulties in getting heavy metal bound derivatives. I 
was wondering whether the Malic Acid interferes heavy metal binding? Does 
anyone has any success with crystals grow with similar conditions? Any comment 
and suggestion is highly appreciated.
 
 Regards,
 
 Jinjin Zhang

Re: [ccp4bb] Sulfate ion on 2-fold axis

[Charlie Bond]

Hi Jie,
Depending on your resolution, you may be forced use to use S(0.5) and
4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement.
Cheers,
Charlie


Jie Liu wrote:
> Dear all
> 
> I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file
> one S atom with occu=0.5 and two O atoms with occu=1, or should
> I put one S and four O atoms all with occu=0.5?
> 
> Thanks for your inputs.
> 
> Jie
> 
> .
> 

-- 
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406

[ccp4bb] unbiased electron density map

[michael nelson]

In my understanding, unbiased electron density map usually refers to the Fo-Fc 
map.But I have seen in some papers sentences like that "The initial, unbiased 
2FoFc map is contoured at".I was a bit confused since I was told by my 
instructor that the 2Fo-Fc was usually biased.

Can anyone clear up this concept for me?
Mike

   
-
Looking for last minute shopping deals?  Find them fast with Yahoo! Search.

Re: [ccp4bb] Sulfate ion on 2-fold axis

[Dale Tronrud]

Dear Jie,

   It also depends on whether you believe the SO4 sits
with its internal two-fold along the crystal's two-fold
axis.  If it does you should probably have a 0.5 occ
sulfur and two 1.0 occ oxygen atoms.  If the symmetry
is not obeyed you will have to have four 0.5 occ oxygen
atoms.

   Be careful, some refinement programs will not be able
to handle the bond length and angle restraints if you
only supply two oxygen atoms.  They will not allow
bonds between atoms and symmetry images of atoms.  If
you are using such a program you will have to supply
four oxygen atoms even if this is not what you would
otherwise do.

Dale Tronrud


Charlie Bond wrote:
> Hi Jie,
> Depending on your resolution, you may be forced use to use S(0.5) and
> 4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement.
> Cheers,
> Charlie
> 
> 
> Jie Liu wrote:
>> Dear all
>>
>> I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file
>> one S atom with occu=0.5 and two O atoms with occu=1, or should
>> I put one S and four O atoms all with occu=0.5?
>>
>> Thanks for your inputs.
>>
>> Jie
>>
>> .
>>
> 

Re: [ccp4bb] unbiased electron density map

[William Scott]

The map will be biased by whatever model is used to generate the phases. 
If a heavy atom phasing method was used (MIR, MAD, etc) then at least you
do not have model bias.

A sigma-A weighted 2Fo-Fc map strives to have minimal bias, as does an
EDEN map with phase perturbation.  However, minimally biased doesn't imply
negligible bias. A composite-omit 2Fo-Fc map made with simulated annealing
possibly comes the closest (apart from a heavy atom phased map).

HTH,

Bill

michael nelson wrote:
> In my understanding, unbiased electron density map usually refers to the
> Fo-Fc map.But I have seen in some papers sentences like that "The initial,
> unbiased 2FoFc map is contoured at".I was a bit confused since I was told
> by my instructor that the 2Fo-Fc was usually biased.
>
> Can anyone clear up this concept for me?
> Mike
>
>
> -
> Looking for last minute shopping deals?  Find them fast with Yahoo!
> Search.

Re: [ccp4bb] Principal axes and moment of inertia matrix

[James Stroud]

On Jan 9, 2008, at 11:56 AM, Buz Barstow wrote:
Does anyone have a python routine that can be used to calculate the  
moment

of inertia matrix and principal axes of a selection of atoms?



I compulsively write python code sometimes--its that fun of a  
language...


If you can get the x, y, z, and mass of your atoms, then you can use  
the little module below (moi.py). It approximates atomic nuclei as  
dimensionless ;-). An example usage is at the bottom. "JTools" is my  
own PDB library, but it gives an idea of use. Once you have the moi  
tensor, I think Eigenvalue decomposition gets the principle axes, so  
this becomes a 1-op with numpy. Please let me know if you find errors.


James




#! /usr/bin/env python

"""
moi.py

(c) 2008, James Stroud
This module is released under the GNU Public License 3.0.
See .

A module to find the moment of inertia of some atoms.

See  for
a mathematical discussion.

Anywhere "ref" is optional defaults to the center of mass
except where indicated.
The "sel" argument is always a list of Atoms.
"""
import math

class Atom(object):
  def __init__(self, x, y, z, mass):
self.x = float(x)
self.y = float(y)
self.z = float(z)
self.mass = float(mass)
  def __str__(self):
return "%s @ (%s, %s, %s)" % (self.x, self.y, self.z, self.mass)

class Point(object):
  def __init__(self, x, y, z):
self.x = x
self.y = y
self.z = z
  def __str__(self):
return "(%s, %s, %s)" % (self.x, self.y, self.z)

def dist(atom, ref=None):
  """
  Calculates distance between an atom and a ref.
  If ref is not given, then the origin is assumed.
  """
  if ref is None:
d = math.sqrt(atom.x**2 + atom.y**2 + atom.z**2)
  else:
x = atom.x - ref.x
y = atom.y - ref.y
z = atom.z - ref.z
d = math.sqrt(x**2 + y**2 + z**2)
  return d

def com(sel):
  """
  Calculates the center of mass of a list of atoms.
  """
  m = sum([atom.mass for atom in sel])
  c = []
  for i in 'xyz':
mr = []
for atom in sel:
  mr.append(atom.mass * getattr(atom, i))
c.append(sum(mr)/m)
  return Point(*c)

def kd(i, j):
  """
  The Kronaker delta.
  """
  return int(i==j)

def moi_element(i, j, sel, ref):
  """
  Generalized moment of inertia element--both diagonal and off
  diagonal. Coordinate axes i and j should be 'x', 'y', or 'z'.
  The sel argument is a list of Atoms.
  The ref arguemnt is a Point.
  """
  delta = kd(i, j)
  refi = getattr(ref, i)
  refj = getattr(ref, j)
  el = []
  for atom in sel:
r2d = (dist(atom, ref)**2) * delta
ri = getattr(atom, i) - refi
rj = getattr(atom, j) - refj
el.append(atom.mass*(r2d - ri*rj))
  return sum(el)

def tensor_moi(sel, ref=None):
  """
  Calculates the moment of inertia tensor.
  """
  if ref is None:
ref = com(sel)
  indices = [(i,j) for i in 'xyz' for j in 'xyz']
  tensor = [moi_element(i, j, sel, ref) for (i,j) in indices]
  return [tensor[0:3], tensor[3:6], tensor[6:9]]

def scalar_moi(sel, ref=None):
  """
  Calculates the scalar moment of inertia.
  """
  if ref is None:
ref = com(sel)
  i = []
  for atom in sel:
i.append(atom.mass * dist(atom, ref)**2)
  return sum(i)

def test():
  """
  You will want to construct your own test.
  """
  import JTools
  import numpy

  s = JTools.build_pdb('1ass.pdb')
  sel = []
  for p in s[0]:
for a in p:
  sel.append(Atom(a.x, a.y, a.z, a.get_weight()))

  print "Center of mass of chain 0:"
  print com(sel)

  print
  print "The moi as tensor:"
  tensor = numpy.array(tensor_moi(sel))
  print tensor
  print

  print "The eigenvalue decomposition:"
  decomp = numpy.linalg.eig(tensor)
  print "The eigenvalues:"
  print decomp[0]
  print "The eigenvectors:"
  print decomp[1]
  print

  print "The moi as scalar:"
  print scalar_moi(sel)
  print

  print "The moi as scalar around ori:"
  print scalar_moi(sel, Point(0, 0, 0))
  print

if __name__ == "__main__":
  test()







Thanks! and all the best,

--Buz


--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA  90095

http://www.jamesstroud.com

Re: [ccp4bb] unbiased electron density map

[Dale Tronrud]

   A 2Fo-Fc map is simply an Fc map with two times the Fo-Fc map added
to it.  ( Fc + 2(Fo-Fc) = Fc + 2Fo - 2Fc = 2Fo - Fc )  The phase comes
from the Fc's.  The basic formulation is biased toward the model used
to calculate the Fc's.  You did, after all, start with a pure Fc map!

   Various techniques are used to reduce bias in these maps.  Usually
a technique that reduces bias in one kind of map reduces the bias in
the other, since they are so closely related.  The procedures I know
of work by changing the calculation of Fc (and the weights on the
individual reflections, which aren't mentioned when using the simple
name Fo-Fc but are there none-the-less) and since the Fc is in both
maps both maps are "debiased".

   These methods reduce bias.  "Unbiased" is a stronger claim and if
you use that word you should state clearly how you know the bias is
gone.

   Your quote bring up another matter.  An "initial" map, i.e. before
refinement, is unbiased if it is an omit map.  If you have done no
refinement and you leave the interesting part out of the calculation
of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map.
This is why an initial map is more reliable for proving binding of
a compound, for example, than a bias reduced map after refinement.

Dale Tronrud

michael nelson wrote:
In my understanding, unbiased electron density map usually refers to the 
Fo-Fc map.But I have seen in some papers sentences like that "The 
initial, unbiased 2F_o -F_c map is contoured at".I was a bit confused 
since I was told by my instructor that the 2Fo-Fc was usually biased.


Can anyone clear up this concept for me?
Mike


Looking for last minute shopping deals? Find them fast with Yahoo! 
Search. 
 

[ccp4bb] Crystal imaging system

[Alexander Aleshin]

Could anybody also advise about an imaging system for automatic
inspection of crystallization plates? 

Is there a newsgroup dedicated to crystallization robotics? 

> Hi,
> Sorry for the non-ccp4 related question.
> We are planning to buy a crystallization robot. We looked at the 
> 'Mosquito'. We felt it is good for setting 96 well plates (for 
> screening the conditions). Though they say that we can use it for 24 
> well plates (hanging drop) it didn't seem to be ideal because all it 
> does is set the drops and everything else has to be done manually. Can

> anyone suggest us other crystallization robots out in the market that 
> are good? Thanks in advance,
> Regards,
> Madhavi
>

Alexander Aleshin, PhD
The Burnham Institute
San Diego, CA 
 

Re: [ccp4bb] Malic Acid interferes heavy metal binding?

[Artem Evdokimov]

Hi,

 

Heavy atoms can be unpredictable. There are rules of thumb regarding their
use but these rules are frequently bent and broken.

 

Which heavy atom derivatives have you tried, and at what (approximately)
concentrations and exposure times? Does your protein have residues that
*can* react with HA compounds? What do you mean when you say 'no success' -
do the crystals survive unperturbed, or do they always die?

 

There almost always is a derivative for you out there, but sometimes you
have to spend time looking. If you have tyrosine residues in relative
abundance you can always try iodination (let me know if you want a good
working protocol), etc.

 

More details would let us help you better!

 

Artem

 

  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of JINJIN
ZHANG
Sent: Wednesday, January 09, 2008 6:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Malic Acid interferes heavy metal binding?

 

Dear All,

I have got large and nice crystals in a condition that contains 40%
glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No
buffer?! I'm so comfused. As far as from the product website, the Malic Acid
has no buffering function. I don't know whether it's a precipitant. The
protein itself was stored in a buffer contains 20mM Tris pH7.5, 150mM NaCl
and 10% glycerol. I'm having difficulties in getting heavy metal bound
derivatives. I was wondering whether the Malic Acid interferes heavy metal
binding? Does anyone has any success with crystals grow with similar
conditions? Any comment and suggestion is highly appreciated.

Regards,

Jinjin Zhang

Re: [ccp4bb] Crystal imaging system

[Bernhard Rupp]

The CrysCam manufactured by Art Robbins is quite versatile at 
a very competitive price-performance ratio. They also do quick
custom mods if you have special tasks, and they always provide
a demo. 

http://www.artrobbinsinstruments.com/cryscam.html
  
Best regards, BR


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Alexander Aleshin
Sent: Wednesday, January 09, 2008 7:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystal imaging system

Could anybody also advise about an imaging system for automatic inspection
of crystallization plates? 

Is there a newsgroup dedicated to crystallization robotics? 

> Hi,
> Sorry for the non-ccp4 related question.
> We are planning to buy a crystallization robot. We looked at the 
> 'Mosquito'. We felt it is good for setting 96 well plates (for 
> screening the conditions). Though they say that we can use it for 24 
> well plates (hanging drop) it didn't seem to be ideal because all it 
> does is set the drops and everything else has to be done manually. Can

> anyone suggest us other crystallization robots out in the market that 
> are good? Thanks in advance, Regards, Madhavi
>

Alexander Aleshin, PhD
The Burnham Institute
San Diego, CA 
 

Re: [ccp4bb] how to model glycosylated residues?

[Jiamu Du]

Thank you for your help. I have make my CNS work on the structure refine
successfully.

Best Regards.

On Jan 10, 2008 4:51 AM, Li Zhijie <[EMAIL PROTECTED]> wrote:

>  Hi Jiamu,
>
> I think the glycoside linkages are specified in the generate.inp file.
> The text I list in the end of this email is taken from my generate.inp for
> a structure with (man)3Gn (the tri-mannose core plus a 1.3 arm GlcNAc, not
> the two core GlcNAc):
> (GlcNAc)-b12-(Man)-a13-(Man)-a16-(Man). The numbering is 4-3-2-1 in the
> same order.
>
> The "C" in segid means they are 4 residues in the "C" chain. And the sugar
> giving reducing end is the "-", or, the "carbo_i".
>
>
> I think the N-linkage between a GlcNAc and an Asn is the same thing - but
> I've never really tried. However the default generate.inp seems to already
> have two N-linked entrys (the "B1N"), you just need to specify the residues
> and change the "false" to "true".
>
> I did mine some time ago. Not sure if that is all you need to do. Please
> let know if it works.
>
>
> {=== carbohydrate links
> ===}
>
> {* Select pairs of residues that are linked *}
> {* First entry is the name of the patch residue. *}
> {* Second and third entries are the resid and segid for the atoms
>referenced by "-" in the patch. *}
> {* Fourth and fifth entries are the resid and segid for the atoms
>referenced by "+" in the patch *}
> {+ table: rows=6 numbered
>   cols=6 "use" "patch name" "segid -" "resid -" "segid +" "resid
> +" +}
>
> {+ choice: true false +}
> {===>} carbo_use_1=true;
> {===>} carbo_patch_1="A16";
> {===>} carbo_i_segid_1="C"; carbo_i_resid_1=1;
> {===>} carbo_j_segid_1="C"; carbo_j_resid_1=2;
>
> {+ choice: true false +}
> {===>} carbo_use_2=true;
> {===>} carbo_patch_2="A13";
> {===>} carbo_i_segid_2="C"; carbo_i_resid_2=3;
> {===>} carbo_j_segid_2="C"; carbo_j_resid_2=2;
>
> {+ choice: true false +}
> {===>} carbo_use_3=true;
> {===>} carbo_patch_3="B12";
> {===>} carbo_i_segid_3="C"; carbo_i_resid_3=4;
> {===>} carbo_j_segid_3="C"; carbo_j_resid_3=3;
>
>
>
> {= generate parameters
> =}
>
> - Original Message -
> *From:* Jiamu Du <[EMAIL PROTECTED]>
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Sent:* Wednesday, January 09, 2008 4:14 AM
> *Subject:* Re: [ccp4bb] how to model glycosylated residues?
>
> Dear All,
> Thank you for your previous response. I have built a 3-mer oligosaccharides
> in the electron density by using coot. I prefer to refine my structure in
> CNS due the resolution is only 2.6 Ang. I found there are only topology
> and parameter files for carbohydrate in CNS but no linkage file for
> carbohydrate. So CNS could recognize the sugar molecules individually, but
> can not recognize the linkage between them. When I refine it in CNS, a
> oxygen will be added beyond C1 of NAG.
> Is there anyone who has the linkage file for carbohydrate of CNS? Or is
> there any other methods to deal with this situation?
>
> Thanks.
>
> --
>
> No virus found in this incoming message.
> Checked by AVG Free Edition.
> Version: 7.5.516 / Virus Database: 269.19.0/1216 - Release Date: 1/9/2008
> 10:16 AM
>
>


-- 
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)