Re: [ccp4bb] Comparison of Water Positions across PDBs

[Joel Sussman]

For detailed examination of this topic, see:

Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. & Steiner, 
T. (2000).
Active-site gorge and buried water molecules in crystal structures of 
acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 
296, 713-735.

http://www.ncbi.nlm.nih.gov/pubmed/10669619

best regards,
Joel

On 30 Oct 2013, at 01:35, Ed Pozharski 
mailto:epozh...@umaryland.edu>> wrote:

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

[ccp4bb] Add C-terminal amide

[Bernhard Lechtenberg]

Hello experts,

I am currently working on a structure of a protein-peptide complex. The peptide 
was synthesized with a C-terminal amide group. What is the best way to add this 
in Coot and refine in Refmac? I did a search on the web but only found a 
protocol for CNS not for Coot/Refmac.

Thanks for the help.

Bernhard

Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, CA 92037, USA
Phone: 858.646.3100 x 4216
Email: blechtenb...@sanfordburnham.org

Re: [ccp4bb] Comparison of Water Positions across PDBs

[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] Comparison of Water Positions across PDBs

[Miller, Mitchell D.]

Hi Elise,   
Not exactly what you are asking for, but 
lsqman will compare waters between structures with a
cut-off. (However, it will not renumber the
waters as you wanted)
http://xray.bmc.uu.se/usf/lsqman_man.html#S71 

If you want to look at waters related by NCS in a 
single PDB file with multiple macromolecule chains, 
then you can use sortwater which will renumber
NCS related waters with the same residue number but
different chain identifiers. (I think watncs
also does a similar thing, but I have not used it).

Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom 
Bellini
Sent: Tuesday, October 29, 2013 3:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs

Hi Elise,



How about taking the homologue structure with highest number of waters and use 
it to run molecular replacement on all other datasets? Then you could keep only 
the good waters (manually unfortunately) which will ensure they will all have 
the same numbers.



Probably not the fastest way but it should give what I think you were asking 
for?



HTWorks



D






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera 
[swastik.phul...@gmail.com]
Sent: 29 October 2013 21:16
To: ccp4bb
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs


Downloading structures of the same homologous family with blast. Then 
superimpose them on a reference structure. You may then try to look at over 
lapping water molecules

On 30 Oct 2013 02:23, "Elise B" mailto:ek...@case.edu>> 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




-- 

This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.

Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 

Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.

Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

 

[ccp4bb] PhD studentship

[A. Jeyaprakash Arulanandam]

Dear Colleagues,

A three year Wellcome Trust funded PhD studentship has recently become 
available at the Wellcome Trust Centre for Cell Biology (www.wcb.ed.ac.uk). The 
successful candidate will join students in the second year of the Wellcome 
Trust Four Year PhD Programme in Cell Biology.
 Qualifications required:
BSc with first or upper second class honours (or equivalent) in a relevant 
subject
MSc by Research in a cell biology related discipline
A good knowledge of spoken and written English
 This position is only available to UK and EU citizens due to funding 
restrictions.   A generous stipend, research costs and tuition fees (at the 
home/EU rate) are provided. Funds will also be available for travel and 
training. 
Suitably qualified applicants should submit an application form, CV and ask 
referees to send two references to Karen Traill (karen.tra...@ed.ac.uk) by 11 
November.

Applicants are required to nominate a PhD project supervisor.  Suitable 
applicants interested in pursuing PhD towards understanding the molecular 
mechanisms of accurate cell division using structural and cell biological 
methods are welcome to contact me (ajeya...@staffmail.ed.ac.uk, 
http://jeyaprakash.bio.ed.ac.uk) to discuss possible projects. 

With best wishes,
JP Arulanandam

Dr. A. Jeyaprakash Arulanandam
Wellcome Trust Centre for Cell Biology 
University of Edinburgh
Michael Swann Building
King's Buildings
Mayfield Road
Edinburgh EH9 3JR
Tel: +44 131 6507113
Web: http://jeyaprakash.bio.ed.ac.uk/

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Dom Bellini]

Hi Elise,



How about taking the homologue structure with highest number of waters and use 
it to run molecular replacement on all other datasets? Then you could keep only 
the good waters (manually unfortunately) which will ensure they will all have 
the same numbers.



Probably not the fastest way but it should give what I think you were asking 
for?



HTWorks



D






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera 
[swastik.phul...@gmail.com]
Sent: 29 October 2013 21:16
To: ccp4bb
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs


Downloading structures of the same homologous family with blast. Then 
superimpose them on a reference structure. You may then try to look at over 
lapping water molecules

On 30 Oct 2013 02:23, "Elise B" mailto:ek...@case.edu>> 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




-- 

This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.

Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 

Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.

Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

 

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Swastik Phulera]

Downloading structures of the same homologous family with blast. Then
superimpose them on a reference structure. You may then try to look at over
lapping water molecules
On 30 Oct 2013 02:23, "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
>
>

[ccp4bb] Comparison of Water Positions across PDBs

[Elise B]

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

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Arka Chakraborty]

Hi Andre,

Are you sure that the cryoprotectant has been optimized?..I am sure you
must have already done it but just in case..sometimes the cryo protectant
which makes the ice rings disappear is  not the best one and playing around
that concentration as well as different alternatives can have a huge
impact. Another thing, again trivial, is to shoot different parts of the
crystal. For big crystals sometimes the regions near the tips diffract
better than regions in the interior ( plausibly correlated with penetration
of the cryoprotectant during treatment as well as other deformities in the
central portions that might have occurred during crystal growth or
vitrification.)

My humble two cents,

Best,

Arka Chakraborty




On Tue, Oct 29, 2013 at 5:17 PM, Danilo Belviso wrote:

> Dear Andre,
>
> you could try with the protocol described in the following paper
>
> Acta Crystallogr D Biol Crystallogr. 2013 69,920-3.
> Using high-throughput in situ plate screening to evaluate the effect of
> dehydration on protein crystals.
> Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Moraes I,
> Brandao-Neto J.
>
> It gives very good results with membrane proteins where the water content
> is high.
>
> Danilo
>
>
> On Tue, 29 Oct 2013 08:18:21 -0700, Andre Godoy 
> wrote:
>
>> Dear all
>>
>> I'm trying to solve a beautiful large crystal that, unfortunately,
>> doesn't go further than 5 A resolution. I believe that in this case,
>> the lack of resolution is due the high solvent content (about 66%).
>> Therefore, my next strategy should be the dehydratation. Yet, I never
>> (sucessfully) did that. I read different approachs, were people
>> equilibrate crystals in dehydratation solution for days, or do more
>> than 20 steps, or add solvents. Since i never had sucess in my trials,
>> I was thinking that someone can suggest a protocol (should I remove
>> all salt?, should I keep the additive concentration?, how much
>> precipitant should I add? how many steps?).
>>
>> crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3%
>> galactose (orthorhombic crystals, with about 0.6 x 0.6 mm)
>>
>> all the best,
>>
>> Andre Godoy
>>
>


-- 
*Arka Chakraborty*
*ibmb (Institut de Biologia Molecular de Barcelona)**
**BARCELONA, SPAIN**
*

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Leonid Sazanov]

Hi, you could try dehydration in microdialysis buttons - this allows for slow 
gradual increase in PEG over few days and full control of other parameters, 
including lowering salt concentration.
It was the only dehydration method that worked well for our large membrane 
protein:
http://www.ncbi.nlm.nih.gov/pubmed/21822288
Described in more detail here:
http://www.ncbi.nlm.nih.gov/pubmed/24059518

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Robbie Joosten]

Can the fixes in the CCP4 dictionary be rolled out through the update system
of CCP4? That way we can avoid (at least to some extent) that people keep
working with erroneous restraint files. Some of these errors can really mess
up your structure.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Paul Emsley
> Sent: Tuesday, October 29, 2013 17:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4
library to
> contain errors ?
> 
> On 29/10/13 06:54, Jodie Johnston wrote:
> > Thanks Everyone for your input
> > I shall triple check my reasoning tomorrow and email Garib if I do
> > think there is an issue.
> >
> >
> 
> Make suer that you are using the latest dictionary (of course)
> 
> http://www2.mrc-
> lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.ht
> ml
> 
> P.

Re: [ccp4bb] bluetooth monitor

[David Schuller]

The best technology would be "Wigig," but I don't think it's on the 
market yet.


Some wireless monitor connection solutions appear to be available using 
Intel WiDi and Miracast. Check your favourite vendor for availability 
and requirements.



On 10/29/2013 01:05 PM, Brett, Thomas wrote:

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc.
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] bluetooth monitor

[Gianluca Santoni]

The biggest I could find is a 7inches monitor for car media centers.
I'm not sure it will be a great deal for a wall monitor.

Gian

On 10/29/13 6:10 PM, David Schuller wrote:

IMHO Bluetooth is way too slow for a monitor connection.

On 10/29/2013 01:05 PM, Brett, Thomas wrote:

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth 
LED or LCD monitor. I would like to have a wall mounted monitor that 
one could easily connect laptops and imacs to for structure display, 
doing tutorials on building into maps, etc.

thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/






--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1  
France  
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

Re: [ccp4bb] bluetooth monitor

[David Schuller]

IMHO Bluetooth is way too slow for a monitor connection.

On 10/29/2013 01:05 PM, Brett, Thomas wrote:

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc.
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] bluetooth monitor

[Brett, Thomas]

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc. 
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

[ccp4bb] Postdoctoral position in UC Irvine

[Gmail]

UNIVERSITY OF CALIFORNIA, IRVINE

DEPARTMENT OF PHYSIOLOGY & BIOPHYSICS

POSTDOCTORAL SCHOLAR

One postdoctoral position is available immediately in Dr. Rongsheng Jin’s 
laboratory at the Department of Physiology and Biophysics, UC Irvine, and will 
remain open until filled. The new postdoctoral scholar is expected to 
participate in one of two major research projects: the structural and 
functional characterization of ion channels, receptors, and signaling molecules 
at synapses, and the mechanism of action of bacterial virulence factors in 
their cellular context. Our laboratory employs a multidisciplinary approach 
that combines X-ray crystallography, SAXS, electron microscopy with the more 
traditional approaches of biochemistry and biophysics. We also have built 
long-standing collaborative relationships in the areas of cell biology, 
electrophysiology, toxicology, and animal studies. The successful candidates 
should have a Ph.D. degree, high motivation, and strong background in one or 
more of the following research areas: biochemistry, biophysics, molecular 
biology, and structural biology. Experience in insect cell and/or mammalian 
cell culture would be desirable, but is not required. Salary is commensurate 
with qualifications and experience. 

To apply for this position please send cover letter, curriculum vitae, and 
names of three references to Rongsheng Jin (r@uci.edu)

“The University of California, Irvine is an Equal Opportunity Employer 
committed to excellence through diversity.”

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Paul Emsley]

On 29/10/13 06:54, Jodie Johnston wrote:

Thanks Everyone for your input
I shall triple check my reasoning tomorrow and
email Garib if I do think there is an issue.




Make suer that you are using the latest dictionary (of course)

http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html

P.

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Danilo Belviso]

Dear Andre,

you could try with the protocol described in the following paper

Acta Crystallogr D Biol Crystallogr. 2013 69,920-3.
Using high-throughput in situ plate screening to evaluate the effect of 
dehydration on protein crystals.
Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Moraes I, 
Brandao-Neto J.


It gives very good results with membrane proteins where the water 
content is high.


Danilo

On Tue, 29 Oct 2013 08:18:21 -0700, Andre Godoy 
 wrote:

Dear all

I'm trying to solve a beautiful large crystal that, unfortunately,
doesn't go further than 5 A resolution. I believe that in this case,
the lack of resolution is due the high solvent content (about 66%).
Therefore, my next strategy should be the dehydratation. Yet, I never
(sucessfully) did that. I read different approachs, were people
equilibrate crystals in dehydratation solution for days, or do more
than 20 steps, or add solvents. Since i never had sucess in my 
trials,

I was thinking that someone can suggest a protocol (should I remove
all salt?, should I keep the additive concentration?, how much
precipitant should I add? how many steps?).

crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3%
galactose (orthorhombic crystals, with about 0.6 x 0.6 mm)

all the best,

Andre Godoy

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Edward A. Berry]

I wonder if there is a big difference between dehydrating in a drop, where the amount of 
mother liquor is essentially unlimited, and dehydrating a mounted crystal in something 
like the FMS, where there is only a thin film of ML on the surface. In the latter case, 
once the surface fluid is gone, assuming surface tension prevents air from entering the 
channels, the tendency for further evaporation will cause reduced hydrostatic pressure in 
the channels, and the pressure differential will exert a physical force to shrink the 
crystal (and to oppose further evaporation). If soaking in a droplet with salt at high 
osmolarity, salt freely enters the channels, so there is no hydrostatic pressure 
difference betwene inside and outside. With PEG it would depend whether the PEG can enter 
channels, with large PEG and small channels there would be an osmotic pressure gradient to 
shrink the crystal. So it would seem that equilibrating at a certain RH in the FMS vs in a 
droplet could have very different results. is there any data on this?


Matthew Bowler wrote:

Hi Andre,
a very effective method is the use of a humidity control device. It has the 
great
advantage that you can characterize changes that occur and also move straight 
to data
collection. There are several HC1 devices in Europe (developed here at the EMBL 
and
available at Diamond, BESSY and MaxLab) and at least 1 in the USA - there is 
also the FMS.
You can of course also do this in the lab but the disadvantage is that any 
change induced
cannot be observed. The relative humidity (RH) that is in equilibrium with your 
mother
liquor is 99%, you could think about slowly replacing the reservoir solution 
with
increasing salt solutions so as to dehydrate in the drop - this avoids handling 
the
crystal - equations to convert between PEG concentrations and salt 
concentrations for RH
matching can be found here:
http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/forms/equation-4

Below are some links that might help, best wishes, Matt.


Website for HC1 experiments at the ESRF:
http://www.esrf.eu/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b

Calculation website for mother liquor RH equilibria: http://go.esrf.eu/RH




On 29/10/2013 16:18, Andre Godoy wrote:

Dear all

I'm trying to solve a beautiful large crystal that, unfortunately, doesn't go 
further
than 5 A resolution. I believe that in this case, the lack of resolution is due 
the high
solvent content (about 66%). Therefore, my next strategy should be the 
dehydratation.
Yet, I never (sucessfully) did that. I read different approachs, were people 
equilibrate
crystals in dehydratation solution for days, or do more than 20 steps, or add 
solvents.
Since i never had sucess in my trials, I was thinking that someone can suggest a
protocol (should I remove all salt?, should I keep the additive concentration?, 
how much
precipitant should I add? how many steps?).

crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% galactose 
(orthorhombic
crystals, with about  0.6 x 0.6 mm)

all the best,

Andre Godoy


--
Matthew Bowler
Synchrotron Science Group
European Molecular Biology Laboratory
BP 181, 6 rue Jules Horowitz
38042 Grenoble Cedex 9
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.88.29.04

http://www.embl.fr/
===

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Singh, Harkewal]

Dear Andre,

We had a similar case where the crystals were bigger and diffraction was lousy. 
 Our standard dehydration approaches were not very successful.
I suggest reading this -
Post-crystallization treatments for improving diffraction quality of protein 
crystals.
Heras 
B,
 Martin 
JL.Acta
 Crystallogr D Biol Crystallogr. 
2005 Sep;61(Pt 9):1173-80. Epub 2005 Aug 16.

But we were able to get a different crystal form (~2A) with high solvent 
content (75%) by making  a bunch of surface mutants. I am not saying that 
surface mutagenesis is the last resort but something that you might want to 
consider.

See this paper -

http://www.jbc.org/content/early/2012/01/31/jbc.M111.327536

Best Regards

Harkewal

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Andre Godoy 
[andre_go...@yahoo.com.br]
Sent: Tuesday, October 29, 2013 10:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystals with large solvent content -dehydratation

Dear all

I'm trying to solve a beautiful large crystal that, unfortunately, doesn't go 
further than 5 A resolution. I believe that in this case, the lack of 
resolution is due the high solvent content (about 66%). Therefore, my next 
strategy should be the dehydratation. Yet, I never (sucessfully) did that. I 
read different approachs, were people equilibrate crystals in dehydratation 
solution for days, or do more than 20 steps, or add solvents. Since i never had 
sucess in my trials, I was thinking that someone can suggest a protocol (should 
I remove all salt?, should I keep the additive concentration?, how much 
precipitant should I add? how many steps?).

crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% galactose 
(orthorhombic crystals, with about  0.6 x 0.6 mm)

all the best,

Andre Godoy

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Enrico Stura]

Dear Andre,

66% solvent is on the high side but not a good reason for poor resolution.
Other with similaa solvent content have achieved resolutions of 1.5 Ang.  
and even better.
I would screen at a lower protein concentration. It will require more  
precipitant

and you should end up with less water in the cell.

Enrico.


On Tue, 29 Oct 2013 16:18:21 +0100, Andre Godoy   
wrote:



Dear all

I'm trying to solve a beautiful large crystal that, unfortunately,  
doesn't go further than 5 A resolution. I believe that in this case, the  
lack of resolution is due the high solvent content (about 66%).  
Therefore, my next strategy should be the dehydratation. Yet, I never  
(sucessfully) did that. I read different approachs, were people  
equilibrate crystals in dehydratation solution for days, or do more than  
20 steps, or add solvents. Since i never had sucess in my trials, I was  
thinking that someone can suggest a protocol (should I remove all salt?,  
should I keep the additive concentration?, how much precipitant should I  
add? how many steps?).


crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3%  
galactose (orthorhombic crystals, with about  0.6 x 0.6 mm)


all the best,

Andre Godoy



--
Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab
http://www-dsv.cea.fr/ibitecs/simopro/ltmb/cristallogenese
LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette,   FRANCE
http://scholar.google.com/citations?hl=en&user=Kvm06WIoPAsC&pagesize=100&sortby=pubdate
http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html
e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71

Re: [ccp4bb] crystals with large solvent content -dehydratation

[Matthew Bowler]

Hi Andre,
a very effective method is the use of a humidity control device. It has 
the great advantage that you can characterize changes that occur and 
also move straight to data collection. There are several HC1 devices in 
Europe (developed here at the EMBL and available at Diamond, BESSY and 
MaxLab) and at least 1 in the USA - there is also the FMS. You can of 
course also do this in the lab but the disadvantage is that any change 
induced cannot be observed. The relative humidity (RH) that is in 
equilibrium with your mother liquor is 99%, you could think about slowly 
replacing the reservoir solution with increasing salt solutions so as to 
dehydrate in the drop - this avoids handling the crystal - equations to 
convert between PEG concentrations and salt concentrations for RH 
matching can be found here: 
http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/forms/equation-4


Below are some links that might help, best wishes, Matt.


Website for HC1 experiments at the ESRF: 
http://www.esrf.eu/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b 



Calculation website for mother liquor RH equilibria: http://go.esrf.eu/RH




On 29/10/2013 16:18, Andre Godoy wrote:

Dear all

I'm trying to solve a beautiful large crystal that, unfortunately, 
doesn't go further than 5 A resolution. I believe that in this case, 
the lack of resolution is due the high solvent content (about 66%). 
Therefore, my next strategy should be the dehydratation. Yet, I never 
(sucessfully) did that. I read different approachs, were people 
equilibrate crystals in dehydratation solution for days, or do more 
than 20 steps, or add solvents. Since i never had sucess in my trials, 
I was thinking that someone can suggest a protocol (should I remove 
all salt?, should I keep the additive concentration?, how much 
precipitant should I add? how many steps?).


crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% 
galactose (orthorhombic crystals, with about  0.6 x 0.6 mm)


all the best,

Andre Godoy


--
Matthew Bowler
Synchrotron Science Group
European Molecular Biology Laboratory
BP 181, 6 rue Jules Horowitz
38042 Grenoble Cedex 9
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.88.29.04

http://www.embl.fr/
===

[ccp4bb] crystals with large solvent content -dehydratation

[Andre Godoy]

Dear all

I'm trying to solve a beautiful large crystal that, unfortunately, doesn't go 
further than 5 A resolution. I believe that in this case, the lack of 
resolution is due the high solvent content (about 66%). Therefore, my next 
strategy should be the dehydratation. Yet, I never (sucessfully) did that. I 
read different approachs, were people equilibrate crystals in dehydratation 
solution for days, or do more than 20 steps, or add solvents. Since i never had 
sucess in my trials, I was thinking that someone can suggest a protocol (should 
I remove all salt?, should I keep the additive concentration?, how much 
precipitant should I add? how many steps?).

crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% galactose 
(orthorhombic crystals, with about  0.6 x 0.6 mm)

all the best,

Andre Godoy

Re: [ccp4bb] Data mining interactions in the PDB

[Barry Finzel]

If you are interested in finding other interactions that look like one  
particular one,  rather than just classifying things (e.g., "is this  
cyan, sea-foam, turquoise or teal?"), then I'd recommend the  
substructure searching capabilities of the DrugSite server


You can specify any arbitrary segments of an existing structure (by  
residue ranges, small or large)  and find all other structures that  
have the same backbone geometry.
If the target residue segments are from different molecules in a known  
complex,  it will find similar complexes.
The server returns coordinates overlaid using only the residues in  
your defined target.


https://drugsite.msi.umn.edu/

Barry C. Finzel
Medicinal Chemistry Department
University of Minnesota
finze...@umn.edu



On Oct 28, 2013, at 1:23 PM, Katherine Sippel wrote:


Hi all,

I was wondering if anyone knew of a software or server to mine the  
PDB for a specific class of interactions? I've tried PDBeMotif  
without much luck and I thought I'd check to see if there was an  
alternative before I go re-inventing the wheel.


Cheers,
Katherine

--
"Nil illegitimo carborundum" - Didactylos

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Jodie Johnston]

Thanks Everyone for your input
I shall triple check my reasoning tomorrow and
email Garib if I do think there is an issue. 

Thanks

Jodie


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[eleanor.dod...@york.ac.uk]
Sent: Tuesday, 29 October 2013 11:51 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 
library to contain errors ?

There are errors in every branch of human endeavour I am sure!
Please if you find something wrong. send your suggested correction to
Garib & Paul, and once there is a fix notify us all via the BB.

CCP4 has always depended heavily on the users noticing the bugs
Thank you for your observation. Eleanor

On 29 October 2013 10:21, Tim Gruene  wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jodie,
>
> except for the matter if there is 'right' and 'wrong' in science or
> rather 'good' and 'bad' models, Garib Murshudov maintains the
> cif-library and if you send him a compilation of possible fixes he
> would surely appreciate your input.
>
> Best,
> Tim
>
> On 10/29/2013 10:15 AM, Jodie Johnston wrote:
>> Hi
>>
>>
>>
>> I wanted to check is it possible that there could
>>
>> be errors in the library cif files associated with CCP4 and coot ?
>>
>> I have noticed a couple of potential errors in a ligand cif file
>> from the CCP4 library.
>>
>>
>>
>> Perhaps it is my error - I shall need to triple check it again but,
>> if it appears not to be, is it possible
>>
>> to talk to someone about correcting the cif file ?
>>
>>
>>
>>
>>
>> Many Thanks
>>
>>
>>
>> Jodie
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.15 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ
> EfmUgIVb9xKGdzmxSaRsBbw=
> =7+vC
> -END PGP SIGNATURE-

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Eleanor Dodson]

There are errors in every branch of human endeavour I am sure!
Please if you find something wrong. send your suggested correction to
Garib & Paul, and once there is a fix notify us all via the BB.

CCP4 has always depended heavily on the users noticing the bugs
Thank you for your observation. Eleanor

On 29 October 2013 10:21, Tim Gruene  wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jodie,
>
> except for the matter if there is 'right' and 'wrong' in science or
> rather 'good' and 'bad' models, Garib Murshudov maintains the
> cif-library and if you send him a compilation of possible fixes he
> would surely appreciate your input.
>
> Best,
> Tim
>
> On 10/29/2013 10:15 AM, Jodie Johnston wrote:
>> Hi
>>
>>
>>
>> I wanted to check is it possible that there could
>>
>> be errors in the library cif files associated with CCP4 and coot ?
>>
>> I have noticed a couple of potential errors in a ligand cif file
>> from the CCP4 library.
>>
>>
>>
>> Perhaps it is my error - I shall need to triple check it again but,
>> if it appears not to be, is it possible
>>
>> to talk to someone about correcting the cif file ?
>>
>>
>>
>>
>>
>> Many Thanks
>>
>>
>>
>> Jodie
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.15 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ
> EfmUgIVb9xKGdzmxSaRsBbw=
> =7+vC
> -END PGP SIGNATURE-

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jodie,

except for the matter if there is 'right' and 'wrong' in science or
rather 'good' and 'bad' models, Garib Murshudov maintains the
cif-library and if you send him a compilation of possible fixes he
would surely appreciate your input.

Best,
Tim

On 10/29/2013 10:15 AM, Jodie Johnston wrote:
> Hi
> 
> 
> 
> I wanted to check is it possible that there could
> 
> be errors in the library cif files associated with CCP4 and coot ?
> 
> I have noticed a couple of potential errors in a ligand cif file
> from the CCP4 library.
> 
> 
> 
> Perhaps it is my error - I shall need to triple check it again but,
> if it appears not to be, is it possible
> 
> to talk to someone about correcting the cif file ?
> 
> 
> 
> 
> 
> Many Thanks
> 
> 
> 
> Jodie
> 

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.15 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ
EfmUgIVb9xKGdzmxSaRsBbw=
=7+vC
-END PGP SIGNATURE-

[ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

[Jodie Johnston]

Hi



I wanted to check is it possible that there could

be errors in the library cif files associated with CCP4 and coot ?

I have noticed a couple of potential errors in a ligand cif file from the CCP4 
library.



Perhaps it is my error - I shall need to triple check it again but, if it 
appears not to be, is it possible

to talk to someone about correcting the cif file ?





Many Thanks



Jodie