Re: [ccp4bb] ccp4 6.0.99e test release

[hari jayaram]

Hello ccp4-ers
I have been happily running ccp4-6.0.99e,  which I self compiled on an
Ubuntu 64bit ( Version 8.04) box

Things have been going smoothly till I noticed a segmentation fault when I
tried to get a postscript file using xplot84driver .
The binary run from  a shell and the ccp4i gui give the following error

FROM SHELL
[EMAIL PROTECTED]:~/ccp4-6.0.99e/x-windows/XCCPJIFFY$ ./xplot84driver
~/yjchotmp/yjchotmp_2_1.plt
Warning: Representation size 1 must match superclass's to override
useStringInPlace
Segmentation fault

FROM CCP4 GUI
[EMAIL PROTECTED]:~$ Warning: Representation size 1 must match superclass's to
override useStringInPlace

Any ideas on how to overcome this

I am attaching the Makefile I used to compile this xplot84driver binary on
my system
Thank you for your help
Hari


On Fri, Jul 25, 2008 at 11:54 AM, Martyn Winn <[EMAIL PROTECTED]> wrote:

> Dear All
>
> the latest test version is on the ccp4 ftp server.
>
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-core-src.tar.gz<- core
> ccp4, rapper, clipper
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-phaser-src.tar.gz  <- cctbx and
> phaser
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-balbes_db.tar.gz   <- balbes
> database only
>
> There is also the dependency of PyXML if you want to run balbes
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-PyXML.tar.gz
>
> for the first 3 tarballs unpack into the same directory, then
> configure...make...make install.
> For the PyXML, follow the instructions in the PyXML-0.8.4 directory.
>
> Major changes:
> refmac5.5 built by default.  This gives twinning and sad refinement.
> dbhandler. Many optimisations, so this should be much more responsive.
>
> For other updates see the CHANGES file.
>
> Still to come:
> downloads pages (under internal testing).
> documentation updates (lots of)
>
> Feedback to the usual locale ([EMAIL PROTECTED])
>
> Thanks
>
> Charles and the rest of us here at DL.
>
>
> --
> ***
> * *
> *   Dr. Martyn Winn   *
> * *
> *   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
> *   Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] *
> *   Fax: +44 1925 603825Skype name: martyn.winn   *
> * URL: http://www.ccp4.ac.uk/martyn/  *
> ***
>


Makefile
Description: Binary data

Re: [ccp4bb] pymol cartoon problem

[Warren DeLano]

Pramod,

 

PyMOL is sensitive to residue numbering...

 

set retain_order

 

rebuild

 

may help.

 

Cheers,

Warren

 

P.S. The PyMOL mailing list can be found at:

 

http://sourceforge.net/mail/?group_id=4546

 

 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
pramod madoori
Sent: Tuesday, November 04, 2008 5:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pymol cartoon problem

 

Dear All,

I have a simple but unresolved problem when representing one of my
structure in cartoon mode using Pymol. One of the bond between Trp and
Gly in loop region is represented well in coot as well as other
molecular viewing softwares (Rasmol and Molscript). When I tried to
represent the same in pymol it shows a break at the same position during
cartoon representation and wire representation and not when in lines
representation. For your observation I am forwarding the images of those
regions from coot (with ED map) and pymol. Does any body had this
problem before and any solutions to circumvent this? 

Thanking you 
Pramod Kumar 

Re: [ccp4bb] Crystals grown from high ammonium sulphate

[Mark J. van Raaij]

also, don't forget to measure at least one crystal at RT, probably  
most easily done in a Mitegen loop-and-sleeve - to have an idea of the  
intrinsic diffraction quality of the crystals without freezing.

Mark
Quoting Savvas Savvides <[EMAIL PROTECTED]>:


Dear Sabine,
I recently dealt with a very similar situation as follows:

-I ended up growing the crystals in 4+4 uL drops. Skin formation tends to be
less of a problem in larger drops. This kind of experimentation is of course
only possible if protein production is not a limiting factor.
-For crystal manipulation, I used to add 10-20 uL of the reservoir solution
directly to the drop. In this way I could easily manipulate the 5-6 crystals
that grew per drop within 5 minutes without any noticeable effects on the
crystals.
-I found out that cryo-cooling the crystals by plunging them into liquid
nitrogen straight out the drop was the only way to effectively cryo-cool
such crystals. In fact the crystal condition was very similar to yours (3.2
M AS, 20 mM potassium phosphate pH 6.0).

I cite the most relevant paragraph from our paper (Kyndt et al.
Biochemistry. 2007 46(1):95-105.):

"To prepare crystals for data collection under cryogenic
conditions (100 K), crystals were flash-cooled by plunging
them directly from their native drops into liquid nitrogen. A
series of cryocooling conditions using a variety of cryoprotecting
reagents such as glycerol, sucrose, PEG 400, and
paratone indicated that only crystals flash-cooled by plunging
them directly from their native drops into liquid nitrogen
produced diffraction of acceptable quality."

Best wishes
Savvas



Savvas Savvides
L-ProBE, Unit for Structural Biology
Ghent University
K.L. Ledeganckstraat 35
9000 Ghent, BELGIUM
office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19
Email: [EMAIL PROTECTED]
http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabine
Schneider
Sent: Tuesday, November 04, 2008 7:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystals grown from high ammonium sulphate

Hi everyone,

We got crystals that grew in ~3.2M ammonium sulphate and some
tris-buffer at 18dgC. Unfortunately the crystals take a while to grow
(~4-5 weeks) and so far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin
of the drop the ammonium sulphate started to crystallise. I got the
crystals out, froze them using sort of an artifical mother liquor with
sodium malonate as cryo and tested the diffraction. The freezing seems
to be OK and it is definitely a protein crystal. The crystal suffered
when the ammonium sulphate in the drop started to crystallise, but
didn't seem to deteriorate anymore in the cryo. Well the corners had
already more or less disappeared by the time I got them out of the drop...
Since we only have a few xtals at the moment and I can't try out a lot
of things, I was wondering if anyone has experienced and solved a
similar problem? My freezing attempt so far was in an airconditioned
room with 18dgC. I thought about higher humidity and temperature in the
room, and/or adding the cryo directly to the drop
Any ideas are very much appreciated!

Sabine

--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/





E-mail message checked by Spyware Doctor (6.0.0.386)
Database version: 5.11050
http://www.pctools.com/en/spyware-doctor-antivirus/

Re: [ccp4bb] tricoordinated ion?

[Roger Rowlett]

Before jumping to any conclusions, you should definitely see what this
density looks like without the water molecules in this portion of the
model. I think it would be difficult to decide on what the actual "bond
lengths" are without removing model bias. If you model with waters, of
course the electron density will conform to some degree to what is
modeled there. You may find that without the waters, the electron
density shrinks up a bit, or can be adequately modeled with a trigonal
planar anion. On the other hand, maybe it is just a cluster of water
molecules, or an anion at less than 100% occupancy. From your water
model, however, it looks like you may have enough density for a full
occupancy anion. FYI, the surrounding ligands, Arg + Glu + another
H-bonding donor are certainly compatible with the few known bicarbonate
binding sites in proteins.

Roger Rowlett


Klaus Piontek wrote:

  Hi Sebastiano,

I had similar experiences with various crystal structures. After a lot
of modeling (albeit at about 1 A resolution) I came to the conclusion
that these atoms correspond to disordered solvent molecules, e.g. water
and/or Zn. In other words the atoms have occupancies of < 1, but in the
sum it should be 1.

For CO2 or similar molecules the bond length are far too long (C-O is
about 1.4 A or so).

Good luck.

Klaus Piontek

Sebastiano Pasqualato wrote:
  
  
Hi all,
I wanted to ask you what would you model in the density in which I
have at the moment modelled 4 water molecules, which are however too
close to be waters, I guess (see attached image).
My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP,
glycerol.
I can't think at a tricoordinated ion like that...
thanks in advance for the hints,
ciao
S



  
  

--
Dr. Klaus Piontek
Albert-Ludwigs-University Freiburg
Institute of Organic Chemistry and Biochemistry, Room 401 H
Albertstrasse 21
D-79104 Freiburg
Germany
Phone: ++49-761-203-6036
Fax: ++49-761-203-8714
Email: [EMAIL PROTECTED]
Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/
  

Re: [ccp4bb] tricoordinated ion?

[Klaus Piontek]

Hi Sebastiano,

I had similar experiences with various crystal structures. After a lot 
of modeling (albeit at about 1 A resolution) I came to the conclusion 
that these atoms correspond to disordered solvent molecules, e.g. water 
and/or Zn. In other words the atoms have occupancies of < 1, but in the 
sum it should be 1.


For CO2 or similar molecules the bond length are far too long (C-O is 
about 1.4 A or so).


Good luck.

Klaus Piontek

Sebastiano Pasqualato wrote:

Hi all,
I wanted to ask you what would you model in the density in which I
have at the moment modelled 4 water molecules, which are however too
close to be waters, I guess (see attached image).
My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP,
glycerol.
I can't think at a tricoordinated ion like that...
thanks in advance for the hints,
ciao
S

  



--
Dr. Klaus Piontek
Albert-Ludwigs-University Freiburg
Institute of Organic Chemistry and Biochemistry, Room 401 H 
Albertstrasse 21
D-79104 Freiburg 
Germany

Phone: ++49-761-203-6036
Fax: ++49-761-203-8714
Email: [EMAIL PROTECTED]
Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/

Re: [ccp4bb] Crystals grown from high ammonium sulphate

[Savvas Savvides]

Dear Sabine,
I recently dealt with a very similar situation as follows:

-I ended up growing the crystals in 4+4 uL drops. Skin formation tends to be
less of a problem in larger drops. This kind of experimentation is of course
only possible if protein production is not a limiting factor.
-For crystal manipulation, I used to add 10-20 uL of the reservoir solution
directly to the drop. In this way I could easily manipulate the 5-6 crystals
that grew per drop within 5 minutes without any noticeable effects on the
crystals.
-I found out that cryo-cooling the crystals by plunging them into liquid
nitrogen straight out the drop was the only way to effectively cryo-cool
such crystals. In fact the crystal condition was very similar to yours (3.2
M AS, 20 mM potassium phosphate pH 6.0).

I cite the most relevant paragraph from our paper (Kyndt et al.
Biochemistry. 2007 46(1):95-105.):

"To prepare crystals for data collection under cryogenic
conditions (100 K), crystals were flash-cooled by plunging
them directly from their native drops into liquid nitrogen. A
series of cryocooling conditions using a variety of cryoprotecting
reagents such as glycerol, sucrose, PEG 400, and
paratone indicated that only crystals flash-cooled by plunging
them directly from their native drops into liquid nitrogen
produced diffraction of acceptable quality."

Best wishes
Savvas


 
Savvas Savvides 
L-ProBE, Unit for Structural Biology 
Ghent University 
K.L. Ledeganckstraat 35 
9000 Ghent, BELGIUM 
office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 
Email: [EMAIL PROTECTED] 
http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabine
Schneider
Sent: Tuesday, November 04, 2008 7:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystals grown from high ammonium sulphate

Hi everyone,

We got crystals that grew in ~3.2M ammonium sulphate and some 
tris-buffer at 18dgC. Unfortunately the crystals take a while to grow 
(~4-5 weeks) and so far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin 
of the drop the ammonium sulphate started to crystallise. I got the 
crystals out, froze them using sort of an artifical mother liquor with 
sodium malonate as cryo and tested the diffraction. The freezing seems 
to be OK and it is definitely a protein crystal. The crystal suffered 
when the ammonium sulphate in the drop started to crystallise, but 
didn't seem to deteriorate anymore in the cryo. Well the corners had 
already more or less disappeared by the time I got them out of the drop...
Since we only have a few xtals at the moment and I can't try out a lot 
of things, I was wondering if anyone has experienced and solved a 
similar problem? My freezing attempt so far was in an airconditioned 
room with 18dgC. I thought about higher humidity and temperature in the 
room, and/or adding the cryo directly to the drop 
Any ideas are very much appreciated!

Sabine

--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/





E-mail message checked by Spyware Doctor (6.0.0.386)
Database version: 5.11050
http://www.pctools.com/en/spyware-doctor-antivirus/

Re: [ccp4bb] Crystals grown from high ammonium sulphate

[shiliang]

You can try microseeding. It is really suitable for crystallization in high
ammonium sulphate. I got a similar problem as well, before. Microseeding can
supply nucleus. You can get more crystals and spend less time. 

And for the salt crystallization, I think if you transfer quickly it can be
fine. Or a high humidity might be useful. 

Liang

On Tue, 4 Nov 2008 19:34:20 +0100, Sabine Schneider wrote
> Hi everyone,
> 
> We got crystals that grew in ~3.2M ammonium sulphate and some 
> tris-buffer at 18dgC. Unfortunately the crystals take a while to grow 
> (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze 
> the crystals, but as soon as I broke though the skin of the drop the 
> ammonium sulphate started to crystallise. I got the crystals out,
>  froze them using sort of an artifical mother liquor with sodium 
> malonate as cryo and tested the diffraction. The freezing seems to 
> be OK and it is definitely a protein crystal. The crystal suffered 
> when the ammonium sulphate in the drop started to crystallise, but 
> didn't seem to deteriorate anymore in the cryo. Well the corners had 
> already more or less disappeared by the time I got them out of the drop...
> Since we only have a few xtals at the moment and I can't try out a 
> lot of things, I was wondering if anyone has experienced and solved 
> a similar problem? My freezing attempt so far was in an 
> airconditioned room with 18dgC. I thought about higher humidity and 
> temperature in the room, and/or adding the cryo directly to the 
> drop Any ideas are very much appreciated!
> 
> Sabine
> 
> --
> Dr. Sabine Schneider
> Ludwig-Maximilians-University
> Department of Chemistry and Pharmacy
> Butenandtstrasse 5-13, Building F
> 81377 Munich
> Germany
> Phone: +49 (0)89 2180 77846
> Fax: +49 (0)89 2180 77756
> http://www.carellgroup.de/


--
Open WebMail Project (http://openwebmail.org)

Re: [ccp4bb] tricoordinated ion?

[Borhani, David]

Sebastiano, it might be a trigonal planar anion, as Roger and others
suggest, but the density doesn't look very symmetrical to me; also, the
bond lengths look too long (e.g., bicarbonate should be ~1.4 Angs., I
believe).
 
Try taking the waters out (zero occ.), and see what the maps tell you at
that point after a bit of refinement (you also seem to have a fair
amount of +ve & -ve diff. density peaks around that region already).
 
It could be a planar ion (maybe the bond lengths appear too long, due to
water/water van der Waals repulsions of your refinement program), or
several mutually-exclusive waters (will need alt. conf. flags), or maybe
(hard to tell from a 2D picture) a hydrated Mg2+ ion (bond lengths look
correct; you would expect hexacoordination, pretty close to octahedral
geometry.
 
Hope this helps,
Dave
David Borhani, Ph.D. 
D. E. Shaw Research, LLC 
120 West Forty-Fifth Street, 39th Floor 
New York, NY 10036 
[EMAIL PROTECTED] 
212-478-0698 
http://www.deshawresearch.com   




From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Roger Rowlett
Sent: Tuesday, November 04, 2008 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] tricoordinated ion?


Sebastiano,

The density is possibly consistent with a trigonal planar anion
such as bicarbonate or nitrate. Bicarbonate can enter the solution from
CO2 in the atmosphere.

Cheers,

-- 



Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]

Sebastiano Pasqualato wrote: 

Hi all,
I wanted to ask you what would you model in the density
in which I
have at the moment modelled 4 water molecules, which are
however too
close to be waters, I guess (see attached image).
My crystallisation conditions contain NaCl, MgCl2,
Peg400, TrisHCl, TCEP,
glycerol.
I can't think at a tricoordinated ion like that...
thanks in advance for the hints,
ciao
S

--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 574 303 310
  

Re: [ccp4bb] Crystals grown from high ammonium sulphate

[Tim Gruene]

Generally crystals require a much higher precipitant concentration for 
nucleation than for growth and maybe even less for maintenance of their 
crystalline state.


Therefore I would
a) try micro seeding into less Ammonium Sulpahte 
b) reduce the ammonium sulfate concentration in the drop by adding 
ammonium sulphate free mother liquor to the reservoir (not the drop 
itself!) This would re-equilibrate the drop to lower a AS
concentration. You could remove one crytal and try to find the lowest 
possible AS concentration with it separately.


Tim

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

GPG Key ID = A46BEE1A


On Tue, 4 Nov 2008, Sabine Schneider wrote:


Hi everyone,

We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 
18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so 
far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin of the 
drop the ammonium sulphate started to crystallise. I got the crystals out, 
froze them using sort of an artifical mother liquor with sodium malonate as 
cryo and tested the diffraction. The freezing seems to be OK and it is 
definitely a protein crystal. The crystal suffered when the ammonium sulphate 
in the drop started to crystallise, but didn't seem to deteriorate anymore in 
the cryo. Well the corners had already more or less disappeared by the time I 
got them out of the drop...
Since we only have a few xtals at the moment and I can't try out a lot of 
things, I was wondering if anyone has experienced and solved a similar 
problem? My freezing attempt so far was in an airconditioned room with 18dgC. 
I thought about higher humidity and temperature in the room, and/or adding 
the cryo directly to the drop Any ideas are very much appreciated!


Sabine

--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/

Re: [ccp4bb] Crystals grown from high ammonium sulphate

[Iain Kerr]

Hi Sabine,

I had a similar problem years ago. Have you tried oils ? (mineral oil, 
paraffin oil, 50:50 mixtures of either with N-paratone)


You can either 1. add a small amount (1ul or less) to the drop 
containing the crystals and mount from there or 2. if you are quick 
enough, transfer the crystal to a small drop of oil and mount it in the 
cryostream straight from the oil.


HTH,
Iain

Sabine Schneider wrote:

Hi everyone,

We got crystals that grew in ~3.2M ammonium sulphate and some 
tris-buffer at 18dgC. Unfortunately the crystals take a while to grow 
(~4-5 weeks) and so far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin 
of the drop the ammonium sulphate started to crystallise. I got the 
crystals out, froze them using sort of an artifical mother liquor with 
sodium malonate as cryo and tested the diffraction. The freezing seems 
to be OK and it is definitely a protein crystal. The crystal suffered 
when the ammonium sulphate in the drop started to crystallise, but 
didn't seem to deteriorate anymore in the cryo. Well the corners had 
already more or less disappeared by the time I got them out of the 
drop...
Since we only have a few xtals at the moment and I can't try out a lot 
of things, I was wondering if anyone has experienced and solved a 
similar problem? My freezing attempt so far was in an airconditioned 
room with 18dgC. I thought about higher humidity and temperature in 
the room, and/or adding the cryo directly to the drop Any ideas 
are very much appreciated!


Sabine

--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/

[ccp4bb] Crystals grown from high ammonium sulphate

[Sabine Schneider]

Hi everyone,

We got crystals that grew in ~3.2M ammonium sulphate and some 
tris-buffer at 18dgC. Unfortunately the crystals take a while to grow 
(~4-5 weeks) and so far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin 
of the drop the ammonium sulphate started to crystallise. I got the 
crystals out, froze them using sort of an artifical mother liquor with 
sodium malonate as cryo and tested the diffraction. The freezing seems 
to be OK and it is definitely a protein crystal. The crystal suffered 
when the ammonium sulphate in the drop started to crystallise, but 
didn't seem to deteriorate anymore in the cryo. Well the corners had 
already more or less disappeared by the time I got them out of the drop...
Since we only have a few xtals at the moment and I can't try out a lot 
of things, I was wondering if anyone has experienced and solved a 
similar problem? My freezing attempt so far was in an airconditioned 
room with 18dgC. I thought about higher humidity and temperature in the 
room, and/or adding the cryo directly to the drop 
Any ideas are very much appreciated!


Sabine

--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/

Re: [ccp4bb] tricoordinated ion?

[artem]

May be something that tagged along from purification or one of the
impurities in the chemicals... nitrate, carbonate, etc.

Incidentally, a 3.9 M BMP file was a nasty surprise for my mail box. A
JPEG or PNG file of similar quality would have taken less than 100K...

Artem

>
> Hi all,
> I wanted to ask you what would you model in the density in which I
> have at the moment modelled 4 water molecules, which are however too
> close to be waters, I guess (see attached image).
> My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP,
> glycerol.
> I can't think at a tricoordinated ion like that...
> thanks in advance for the hints,
> ciao
> S
>
> --
> Sebastiano Pasqualato, PhD
> IFOM-IEO Campus
> Dipartimento di Oncologia Sperimentale
> Istituto Europeo di Oncologia
> via Adamello, 16
> 20139 - Milano
> Italy
>
> tel +39 02 9437 5094
> fax +39 02 574 303 310

Re: [ccp4bb] tricoordinated ion?

[Roger Rowlett]

Sebastiano,

The density is possibly consistent with a trigonal planar anion such as
bicarbonate or nitrate. Bicarbonate can enter the solution from CO2 in
the atmosphere.

Cheers,

-- 

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]

Sebastiano Pasqualato wrote:

  Hi all,
I wanted to ask you what would you model in the density in which I
have at the moment modelled 4 water molecules, which are however too
close to be waters, I guess (see attached image).
My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP,
glycerol.
I can't think at a tricoordinated ion like that...
thanks in advance for the hints,
ciao
S

--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 574 303 310
  
  
  
  
  

Re: [ccp4bb] phased MR

[Eleanor Dodson]

You can read phases into both MOLREP and Amore and search for the 
translation against the phased map.. It often gives good results.


Eleanor

Pietro Roversi wrote:

Dear Ed,
   in the past we have successfully searched in an
electron density map (computed in the whole cell) with Molrep.

If you have a second crystal form and you can cut the density of the
monomer off, Phaser also gives very good results when
searching with that electron density - after that your maps can be
improved with dmmulti cross-crystal averaging.

Good luck!

Pietro

  

Re: [ccp4bb] m-3m vs. m-3

[Eleanor Dodson]

In the $CHTML/twinning.html it tries to explain:
From the table:

# All *P2i3* and related *2i3* space groups:
(h,k,l) already equivalent to (-h,-k,l) so we only need to check:
real axes:  (a,b,c) and (b,a,-c)
reciprocal axes:(a*,b*,c*)  and (b*,a*,-c*)

/i.e./ reindex (h,k,l) to (k,h,-l).
# Twinning possible with this operator - apparent symmetry for two fold 
perfect twin would be P43 (operator k,h,-l)

space group number  space group point group possible twinning 
operator
195 P23 PG23k,h,-l
196 F23 PG23k,h,-l
197 I23 PG23k,h,-l
198 P213PG23k,h,-l
199 I213PG23k,h,-l



See  if it all makes sense..
Eleanor

yanming Zhang wrote:

Dear 'old' crystallographers,

During one case of structure solution, the data processing programs output 
incorrect space group-primitive cubic P4132, which later found out that the 
correct one should be face centerd cubic f23. This problem was caused by 
perfect twinning.

Now I'd like to invite you to help me understand, and explain in details, 
WHY, IN CASE OF PERFECT TWINNING, THE LAUE GROUP m-3 WILL BE MIS-INDEXED TO m-3m by some data processing programs? I, sort of, understand the reason behind this is caused by the perfect twin operator which will emulate an additional 2-fold axis. But not fully understand the symmetry in details in this case. Your help and teaching are highly appreciated. 

Yanming Zhang 



  



  

[ccp4bb] Group Leader Position in Structural Biology at EMBL Heidelberg

[Christoph Mueller]

EMBL Heidelberg, Germany

Group Leader in Structural Biology: X-ray Crystallography / Electron 
Microscopy


The Structural and Computational Biology Unit at EMBL Heidelberg seeks 
to recruit an outstanding group leader in structural biology with a 
research focus directed towards the structure-function analysis of 
macromolecular complexes and protein-protein interaction networks.The 
vision of the unit is to provide a detailed spatial and temporal 
description of various biological systems across different scales of 
resolution (from molecules to cells) by combining different structure 
determination techniques (X-ray, NMR, single particle EM, EM tomography, 
single molecule light microscopy) with computational, chemical and 
systems biology.


The advertised position is suitable for candidates using X-ray 
crystallography or cryo-electron microscopy (single-particle analysis 
and/or cryo-electron tomography) as principal techniques combined with 
other biophysical techniques, molecular biology, biochemistry and cell 
biology. The successful candidate should demonstrate a strong motivation 
to work in the multidisciplinary and collaborative environment of EMBL.


An initial contract of 5 years will be offered to the successful 
candidate. This can be renewed, depending on circumstances at the time 
of review.


Closing date: 30 November 2008

Web page: http://www.embl.de

Further information about research in the Structural and Computational 
Biology Unit and the position can be obtained from Joint Unit 
Coordinators Peer Bork [EMAIL PROTECTED] and Christoph Müller 
[EMAIL PROTECTED]


To apply, please email a CV, three references and a concise description 
of research interests and future plans quoting ref. no. W/08/086 in the 
subject line, to: [EMAIL PROTECTED]

Personnel, EMBL, Postfach 10.2209, 69012 Heidelberg, Germany.
Fax: +49 6221 387555   E-mail:  [EMAIL PROTECTED]

-
Dr. Christoph W. Muller
Joint Coordinator
Structural and Computational Biology Unit

EMBL
Meyerhofstrasse 1
69012 Heidelberg, Germany

email: [EMAIL PROTECTED]
phone: 0049-6221-387-8320
fax: 0049-6221-387-519
http://www.embl.de
-

Re: [ccp4bb] phased MR

[Pete Meyer]

For what it's worth, I'd try to get as much as possible out of the
experimental phases before going on to phased MR.

> I have SeMet MAD data to 3.6A that gives decent looking anomalous
> difference peaks, looks stable in mlphare, and produces solvent
> flattened maps to 2.8A in DM that look like the density might be a
> sensible shape - wrt solvent gaps etc - but not interpretable so far (I
> will be trying phasing in SHARP, CNS etc).

One thing to try would be  the bp3/pirate combination for
phasing/density modification.  With some datasets, this works very well
(in my hands, not with all datasets).

Another (which you've probably already tried) would be to check the MAD
maps after solvent flattening, but before phase extension, as well as
comparing the MAD maps to SAS maps.

It's probably also worth checking the dispersive difference peaks, and
cross checking them with the anomalous difference peaks.  You should get
the same peaks out, but it'll let you guess as the relative phasing
signal for dispersive vs anomalous (but so will comparing MAD vs SAS).

> Any advice gratefully received.

Hopefully I'm not giving you too many suggestions you've already tried.

Pete

Re: [ccp4bb] phased MR

[Gerard Bricogne]

Dear Tassos,

 I suppose that the "eternal pdb file" you refer to conforms to the
finally agreed standard for the pdb, expected to be valid for the rest of
time ... .

 This clearly shows that SHARP does keep up with the latest and most
forward-looking advances in the field.


 With best wishes,
 
  Gerard.

--
On Tue, Nov 04, 2008 at 01:38:25PM +0100, Anastassis Perrakis wrote:
> Hi -
>
> I would not use mlphare for anything marginal (to be honest not at all).
>
> Both SHARP (use eternal pdb file in top page of the gui) and the new Phaser 
> (look at the doc for scripts for this case) can do what you want.
>
> Tassos
>
>
> On Nov 4, 2008, at 11:55, Thomas Edwards wrote:
>
>> Dear BB,
>>
>> I would like to ask for some advice on phased molecular replacement if 
>> possible.
>>
>> I have a MR model that has so far not proved successful with Phaser, 
>> Molrep, Amore, Beast etc.
>>
>> I have SeMet MAD data to 3.6A that gives decent looking anomalous 
>> difference peaks, looks stable in mlphare, and produces solvent flattened 
>> maps to 2.8A in DM that look like the density might be a sensible shape - 
>> wrt solvent gaps etc - but not interpretable so far (I will be trying 
>> phasing in SHARP, CNS etc).
>> In the mean time, is there a good way to combine phases that may be 
>> slightly sensible with molecular replacement? Things may also be 
>> complicated by the possibility of NCS translations…
>>
>> Any advice gratefully received.
>>
>> Many thanks to all those who continue to provide excellent suggestions,
>> Cheers
>> Ed
>>
>> __
>> T.Edwards Ph.D.
>> Garstang 8.53d
>> Astbury Centre for Structural Molecular Biology
>> University of Leeds, Leeds, LS2 9JT
>> Telephone: 0113 343 3031
>> http://www.bmb.leeds.ac.uk/staff/tae/
>> If you're not part of the solution, you're part of the precipitate. ~Henry 
>> J. Tillman
>>
>>
>

-- 

 ===
 * *
 * Gerard Bricogne [EMAIL PROTECTED]  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

[ccp4bb] is it possible or is it existing ?

[Jayashankar]

Dear ccp4bb caretakers,
I am very young for the ccp4bb thread(2007 jan-my thread date of birth).

Is is possible to compile very important issues in a hyperlinked style
of the important  problems,discussions  and queries with in ccp4 threads.
for example when am reading a query of 2006 regarding software
compatability, i may have very apt answer which is posted on
2005 or any other time. Or regarding MAD phasing in 2008, might have answer
in 2007..like that.

or, is there something already like this.


S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.

Re: [ccp4bb] phased MR

[Anastassis Perrakis]

Hi -

I would not use mlphare for anything marginal (to be honest not at all).

Both SHARP (use eternal pdb file in top page of the gui) and the new  
Phaser (look at the doc for scripts for this case) can do what you want.


Tassos


On Nov 4, 2008, at 11:55, Thomas Edwards wrote:


Dear BB,

I would like to ask for some advice on phased molecular replacement  
if possible.


I have a MR model that has so far not proved successful with Phaser,  
Molrep, Amore, Beast etc.


I have SeMet MAD data to 3.6A that gives decent looking anomalous  
difference peaks, looks stable in mlphare, and produces solvent  
flattened maps to 2.8A in DM that look like the density might be a  
sensible shape - wrt solvent gaps etc - but not interpretable so far  
(I will be trying phasing in SHARP, CNS etc).
In the mean time, is there a good way to combine phases that may be  
slightly sensible with molecular replacement? Things may also be  
complicated by the possibility of NCS translations…


Any advice gratefully received.

Many thanks to all those who continue to provide excellent  
suggestions,

Cheers
Ed

__
T.Edwards Ph.D.
Garstang 8.53d
Astbury Centre for Structural Molecular Biology
University of Leeds, Leeds, LS2 9JT
Telephone: 0113 343 3031
http://www.bmb.leeds.ac.uk/staff/tae/
If you're not part of the solution, you're part of the precipitate.  
~Henry J. Tillman

[ccp4bb] Postdoc position

[Lucy Malinina]

*Postdoctoral Positions in Macromolecular Crystallography* are immediately
available in the Lucy Malinina laboratory at the Structural Biology
Department of CICbioGUNE (Bilbao, Spain). We use the X-ray crystallographic
approaches to elucidate structural principles of a biological intermolecular
recognition for developing the means to effectively use and
pharmacologically modulate protein specificity of a diverse nature. We focus
our efforts on human neurodegenerative diseases, and currently study
complexes with RNA in Project_1 "Structural Basis for Suppression of Human
Trinucleotide Repeat Expansion Diseases  (TREDs)" and glycolipids in
Project_2 "Molecular Basis for Manipulating the Selectivity of Glycolipid
Transfer". Other projects are under development.



*The crystallographic platform* includes a Bruker Microstar-H rotating anode
generator, MAR345-DTB image plate, Bruker-135 mm CCD detector system, Helios
confocal optics, two Oxford Cryosystem Series 700, TECAN-EVO100 liquid
handling robot, Mosquito nanodispenser, a Bruker Crystal Farm, and
supporting computers/software.

*The biochemical laboratory *is supported by all necessary equipment for
protein expression/isolation/purification, and oligonucleotide
synthesis/purification as well.



*Key Qualifications:*

- PhD in physics, chemistry, biochemistry, biophysics or related field

- Experience working in the area of macromolecular crystallography,
including

o the X-ray data collection for biological crystallography,

o the use of computer programs required for biological crystallography,

o crystallization with use of robotics hardware and control systems.



To apply please submit before December 20, 2008 a cover letter, CV, and
three references addressed to [EMAIL PROTECTED] with ref.  "postdoc
application" in the subject line.

Re: [ccp4bb] phased MR

[Pietro Roversi]

Dear Ed,
   in the past we have successfully searched in an
electron density map (computed in the whole cell) with Molrep.

If you have a second crystal form and you can cut the density of the
monomer off, Phaser also gives very good results when
searching with that electron density - after that your maps can be
improved with dmmulti cross-crystal averaging.

Good luck!

Pietro

-- 
Pietro Roversi
EP Abraham Fellow in Biochemistry - Lincoln College - Oxford
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3RE, England UK
Tel. 0044-1865-275385

[ccp4bb] phased MR

[Thomas Edwards]

Dear BB,

 

I would like to ask for some advice on phased molecular replacement if
possible.

 

I have a MR model that has so far not proved successful with Phaser,
Molrep, Amore, Beast etc.

 

I have SeMet MAD data to 3.6A that gives decent looking anomalous
difference peaks, looks stable in mlphare, and produces solvent
flattened maps to 2.8A in DM that look like the density might be a
sensible shape - wrt solvent gaps etc - but not interpretable so far (I
will be trying phasing in SHARP, CNS etc).

In the mean time, is there a good way to combine phases that may be
slightly sensible with molecular replacement? Things may also be
complicated by the possibility of NCS translations...

 

Any advice gratefully received.

 

Many thanks to all those who continue to provide excellent suggestions,

Cheers

Ed

 

__
T.Edwards Ph.D.
Garstang 8.53d
Astbury Centre for Structural Molecular Biology 
University of Leeds, Leeds, LS2 9JT 
Telephone: 0113 343 3031


http://www.bmb.leeds.ac.uk/staff/tae/
If you're not part of the solution, you're part of the precipitate.
~Henry J. Tillman

 

[ccp4bb] ESRF School - 2nd - 5th February 2009

[nurizzo]

Dear all,

We are pleased to announce the ESRF School titled

*"Getting the most from the ESRF MX beamlines"*
ESRF, Grenoble, France, 2nd - 5th February 2009

As part of its 2009 Users Meeting, the ESRF will host a short school 
*"Getting the most from the ESRF MX beamlines"* from 2nd to 5th February 
2009. The School will be held on 3 days either side of the Users Meeting 
and is aimed at younger, relatively inexperienced users of the ESRF's MX 
beam-lines. The school is designed to (a) introduce the art of 
collecting good diffraction data at synchrotron-based MX facilities, (b) 
familiarize the participants with the tools available at the beam-line 
to allow correct pre- and post-data collection decisions to be taken and 
(c) present the various ancillary techniques and equipment accessible at 
the ESRF’s MX beam-lines.


The number of participants will be limited to 20 with all _local costs_ 
(i.e. registration fees, accommodation, subsistence) being met by the 
ESRF. The deadline for applications is 15th December 2008. More detailed 
information, a preliminary programme and instructions as to how to apply 
to attend the school can be found at: 
http://www.esrf.fr/events/conferences/usersmeeting2009/mx-school


The organising Committee