[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb]
hmmm... is this the beginning of a potential endless loop of emails? P David W Borhani wrote: Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
Re: [ccp4bb] dmmulti NCS mask
On Feb 23, 2007, at 23:19, Peter Adrian Meyer wrote: I would be very much afraid that the only way to get the masks properly would be to edit them interactively. I used to do that in the PHASES package by Bill Furey and MapViewX which is still alive and kicking under the BnP flagship. I am pretty sure though that Dr. DVD will be online soon and will point out the correct succession of MAMA/RAVE/O commands ;-) As far as I know, mapview does section by section 2d editing. Indeed. Unless mapview_x has been updated recently, O is probably less painful for interactively editing masks (although my prefered set of mask editing commands in O have been declared obsolete). I agree - but somehow I personally preferred 2d-sections for editing. I guess its just a habit. Tassos Pete A. On Feb 22, 2007, at 1:08, Jianghai Zhu wrote: Forgot to mention that the NCSs are improper. On Feb 21, 2007, at 6:22 PM, Jianghai Zhu wrote: Dear all, I have two low resolution (3.8 A) MAD data sets from two different space groups. There are 4 copies of my molecule in one space group and 2 copies in the other. The density-modified maps from these data sets are poor, but still allow me to build a crude model on them. All the domains should be at the right or close to right orientations and positions. I would like to try multi- crystal averaging to improve my maps. Since I already have the model, I used NCSMASK to make 6 masks for the 6 copies of my model. Then I used DMMULTI to perform the multi-crystal averaging. The maps came out of DMMULTI showed great improvement. Some densities were not seen before showed up nicely. However, after I read the manual carefully, I realize that DMMULTI would not take care of the mask overlap. So some regions in my density map between the NCS-related and symmetry- related molecules must be messed up. Could any expert out there give me some suggestions about how to make proper NCS masks for DMMULTI? Thanks at advance. Jianghai Pete Meyer Fu Lab BMCB grad student Cornell University
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
Re: [ccp4bb] Problems with CNS
Make sure there is an END statement at the end of your coordinate file.
Axel Brunger
C. Ainsley Davis wrote:
Hello all,
I have been having major issues with CNS that I havent been able to figure out.
My protein has 2 molecules in the asu, ds DNA, ions, and a ligand. I have been
using refmac for refinement but need to make a composite omit map so that I can
check things out in CNS.
here is the problem
every time I run generate.inp I get errors like this in the logfile
COOR>HETATM 3389 NA NA E 1 -4.719 7.010 17.729 1.00 33.51
NA
SEGMNT: 3 residues were inserted into segment ""
CHAIN> end
SEGMENT> if ( &ion_rename_$counter = true ) then
%SEGMENT-ERR: unrecognized command:
if
^^
%SEGMENT-ERR: unrecognized command:
if (
^
%SEGMENT-ERR: unrecognized command:
if ( false
^
%SEGMENT-ERR: unrecognized command:
if ( false =
^
%SEGMENT-ERR: unrecognized command:
if ( false = true
%SEGMENT-ERR: unrecognized command:
if ( false = true )
^
%SEGMENT-ERR: unrecognized command:
if ( false = true ) then
SEGMENT> do (refy=$counter) (attr refx=)
%SEGMENT-ERR: unrecognized command:
do
^^
%SEGMENT-ERR: unrecognized command:
do (r
^
%SEGMENT-ERR: unrecognized command:
do (refy=
%SEGMENT-ERR: unrecognized command:
do (refy=$
^
%SEGMENT-ERR: unrecognized command:
do (refy=$counter)
%PARSER error encountered: Encountered too many parsing errors.
(CNS is in mode: SET ABORT=NORMal END)
I have changed all of my files so that CNS will like them. (outputs from coot
are not liked by cns) I changed the dna using fix_dna_rna indna > outdna. and
manually changed the c5m for thymine to c5a for cns. Also made sure the sugar
ring atoms had (') and not (*). I also changed the CD1 ILE to CD ILE because
CNS hates CD1 ILE for some reason. One of my ligands is funny so I downloaded
the topology and parameter files from HIcCup and put them in the necessary
sections in generate.inp. I have run this before when refining a similar data
set with not as many issues, but I really would like to know what this means.
thanks all
Ainsley
C. Ainsley Davis, Ph.D.
Post-Doctoral Fellow
Massachusetts Institute of Technology
Department of Chemistry 56-546
32 Vassar Street
Cambridge, MA 02142
Phone Number:(617) 258-7021
Fax Number: (617) 258-7847
E-mail: [EMAIL PROTECTED]
--
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web:http://atb.slac.stanford.edu
Email: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax:+1 650-745-1463
[ccp4bb]
Hi, David Borhani is no longer with Abbott. Please resend your email to: [EMAIL PROTECTED]
[ccp4bb] Problems with CNS
Hello all,
I have been having major issues with CNS that I havent been able to figure out.
My protein has 2 molecules in the asu, ds DNA, ions, and a ligand. I have been
using refmac for refinement but need to make a composite omit map so that I can
check things out in CNS.
here is the problem
every time I run generate.inp I get errors like this in the logfile
COOR>HETATM 3389 NA NA E 1 -4.719 7.010 17.729 1.00 33.51
NA
SEGMNT: 3 residues were inserted into segment ""
CHAIN> end
SEGMENT> if ( &ion_rename_$counter = true ) then
%SEGMENT-ERR: unrecognized command:
if
^^
%SEGMENT-ERR: unrecognized command:
if (
^
%SEGMENT-ERR: unrecognized command:
if ( false
^
%SEGMENT-ERR: unrecognized command:
if ( false =
^
%SEGMENT-ERR: unrecognized command:
if ( false = true
%SEGMENT-ERR: unrecognized command:
if ( false = true )
^
%SEGMENT-ERR: unrecognized command:
if ( false = true ) then
SEGMENT> do (refy=$counter) (attr refx=)
%SEGMENT-ERR: unrecognized command:
do
^^
%SEGMENT-ERR: unrecognized command:
do (r
^
%SEGMENT-ERR: unrecognized command:
do (refy=
%SEGMENT-ERR: unrecognized command:
do (refy=$
^
%SEGMENT-ERR: unrecognized command:
do (refy=$counter)
%PARSER error encountered: Encountered too many parsing errors.
(CNS is in mode: SET ABORT=NORMal END)
I have changed all of my files so that CNS will like them. (outputs from coot
are not liked by cns) I changed the dna using fix_dna_rna indna > outdna. and
manually changed the c5m for thymine to c5a for cns. Also made sure the sugar
ring atoms had (') and not (*). I also changed the CD1 ILE to CD ILE because
CNS hates CD1 ILE for some reason. One of my ligands is funny so I downloaded
the topology and parameter files from HIcCup and put them in the necessary
sections in generate.inp. I have run this before when refining a similar data
set with not as many issues, but I really would like to know what this means.
thanks all
Ainsley
C. Ainsley Davis, Ph.D.
Post-Doctoral Fellow
Massachusetts Institute of Technology
Department of Chemistry 56-546
32 Vassar Street
Cambridge, MA 02142
Phone Number:(617) 258-7021
Fax Number: (617) 258-7847
E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] dmmulti NCS mask
> I would be very much afraid that the only way to get the masks > properly would be to edit them interactively. > I used to do that in the PHASES package by Bill Furey and MapViewX > which is still alive and kicking under the BnP flagship. > > I am pretty sure though that Dr. DVD will be online soon and will > point out the correct succession of MAMA/RAVE/O commands ;-) > As far as I know, mapview does section by section 2d editing. Unless mapview_x has been updated recently, O is probably less painful for interactively editing masks (although my prefered set of mask editing commands in O have been declared obsolete). Pete > > A. > > On Feb 22, 2007, at 1:08, Jianghai Zhu wrote: > >> Forgot to mention that the NCSs are improper. >> >> >> >> On Feb 21, 2007, at 6:22 PM, Jianghai Zhu wrote: >> >>> Dear all, >>> >>> I have two low resolution (3.8 A) MAD data sets from two different >>> space groups. There are 4 copies of my molecule in one space >>> group and 2 copies in the other. The density-modified maps from >>> these data sets are poor, but still allow me to build a crude >>> model on them. All the domains should be at the right or close to >>> right orientations and positions. I would like to try multi- >>> crystal averaging to improve my maps. Since I already have the >>> model, I used NCSMASK to make 6 masks for the 6 copies of my >>> model. Then I used DMMULTI to perform the multi-crystal >>> averaging. The maps came out of DMMULTI showed great >>> improvement. Some densities were not seen before showed up >>> nicely. However, after I read the manual carefully, I realize >>> that DMMULTI would not take care of the mask overlap. So some >>> regions in my density map between the NCS-related and symmetry- >>> related molecules must be messed up. Could any expert out there >>> give me some suggestions about how to make proper NCS masks for >>> DMMULTI? Thanks at advance. >>> >>> Jianghai >> > > Pete Meyer Fu Lab BMCB grad student Cornell University
[ccp4bb] Toyopearl GF column vs. Superdex
Dear folks, I have a question related to protein purification: We are thinking to buy a new GF column. We already have the HiLoad-superdex-75; we want to get the superdex-200 pg. However, some colleague mentioned the Toyopearl-HW as another alternative for Gel filteration. I wonder if people could share their experience with Toyopearl vs. Superdex GF columns. regards, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. 201 Althouse Lab. University Park, PA16802 Tel (814) 863 8703 Fax (814) 865 7927
Re: [ccp4bb] Main topic of the day: Protein crystallization
We have one protein (bacterial antitoxin HigA, 2ICT) that crystallizes in many conditions (30-40) at 0.3-0.6 mg/ml; the crystals diffract to 1.63 A. -- Mark Arbing, PhD Email: [EMAIL PROTECTED] Tel: (212) 854-5236 Fax: (212) 865-8246 Dept. of Biological Sciences Columbia University 702 Fairchild Center, MC2437 1212 Amsterdam Ave., NY, NY, 10027 Quoting Tassos Papageorgiou <[EMAIL PROTECTED]>: > Just to add that in one case we were able to get suitable > crystals after using a > protein concentration of as low as 1.5 mg/ml (kapetaniou et al. > Acta Cryst. > 2005, F61, 479-481) and microdialysis to slowly remove the excess > of salt. > Lower concentrations (0.50-0.75 mg/ml) could also produce > crystals but they > were too small. > > Tassos Papageorgiou > > > > Quoting Patrick Shaw Stewart <[EMAIL PROTECTED]>: > > > Ronaldo > > > > I have a database of crystallization conditions extracted from > the > > PDB. I was able to parse the data to extract the concentration > of > > protein in around 900 cases. > > > > The lowest 9 protein concentrations were as follows: > > > > PDB ID TYPEDATEProtein conc, mg/ml > > 1EYMISOMERASE. 07/05/2000 0.75 > > 1ADQCOMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN)18/02/1997 1 > > 1W5GFOUR HELIX BUNDLE. 06/08/2004 1 > > 1UU4HYDROLASE. 15/12/2003 1 > > 1W2UHYDROLASE. 08/07/2004 1 > > 1DXPSERINE PROTEASE.13/01/2000 1 > > 1DY8SERINE PROTEASE.18/01/2000 1 > > 1DY9SERINE PROTEASE.31/01/2000 1 > > 1DG6APOPTOSIS. 23/11/1999 1.2 > > > > The maximum protein conc was 200 mg/ml (1BLF) > > > > My database goes up to October 2004. Janet Newman and Tom Peat > have > > done this job far more conscientiously and could probably give > you > > better and more up-to-date data. > > > > Patrick > > > > > > On 2/23/07, Ronaldo Alves Pinto Nagem <[EMAIL PROTECTED]> > wrote: > > > > > > > > > Dear all, > > > > > > As protein crystallization is the main topic of the day may I > include > > > another question? > > > > > > What was the minimun protein concentration reported with > success in > > > crystallization trials? > > > > > > I ask that because the protein I am trying to crystallize is > much less > > > soluble than the one mentioned in the lasts emails. > > > > > > Thanks > > > > > > Ronaldo. > > > > > > > > -- > A.C.(Tassos) Papageorgiou, PhD phone: +358 2 333 8012 > (office) > Senior Scientist, Group leader fax: +358 2 333 8000 > Turku Centre for Biotechnology E-mail: > [EMAIL PROTECTED] > BioCity, Turku URL: > http://www.btk.utu.fi/~apapageo > FIN-20521, Finland >
Re: [ccp4bb] previous message monomer library
Hi, create the SMILES string using http://www.molinspiration.com/cgi-bin/properties (you can get the SMILES editor from the author- Peter Ertl, Novartis) use it as a input to build the 3D coordinates using http://www.molecular-networks.com/online_demos/corina_demo.html or elbow.builder in phenix. use the structure in refmac which will create the library file with all the restraints. Raj "Nalam, Madhavi" <[EMAIL PROTECTED]> wrote: Hi Arti, Another way of generating coordinates for your molecule of interest is by Chemdraw and Chem3d if you have the program. I find it easier compared to sketcher since the chirality of an atom can be defined while drawing the molecule in Chemdraw. Once I get the 3D coordinates from Chem3D, I follow the procedure which Matt described below. Madhavi -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, February 23, 2007 12:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] previous message monomer library CCP4 bulletin board wrote on 02/23/2007 11:22:04 AM: > Hello all, > Kindly disregard my message about monomer libraries. The problem ( atoms > blowing apart) seems to be due to something (yet undetermined) else. Thank > you for clearing up ones about COM_COM. > However, I still wonder if I can add my own ligand libraries to the > default one, like you can do for ONO. > Arti Pandey > > Hi Arti - You absolutely can. I used to do this all the time when I was working on small-molecule drug complexes. If all you want to do is take an existing library file (e.g. from HIC-UP) and use it, skip to the last paragraph of this email. If you want to make a library file, read on. The simplest way to do this is to create a pdb file containing the idealized, energy-minimized coordinates of your molecule of interest. How you make this file is a little more complicated - I used InsightII from Accelrys, but that's a very expensive program that you probably don't have access to. Sketcher, in CCP4, will also do this but I never got it to work for me. Even PyMOL will build molecules for you but it won't energy-minimize them so bond lengths and angles can be distorted. The CCP4 site suggests these programs (I've never used them): http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html Make sure that your new molecule has a unique 3-letter residue code so that Refmac won't be confused and think it's one of the entries in its monomer library. There is a file called 'mon_lib.list' in $CCP4_HOME/lib/data/monomers that gives the codes of everything in the monomer library. If you have a number in your residue code you'll probably avoid conflicts. The next step is to run a short Refmac job on this coordinate file, using a simple script like the one here: http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html Refmac will generate a library file for your new molecule, then stop. You can then open up the new library file (which will have 'lib' in the filename) and check through it with a text editor. You'll see a long list of topology, bond lengths, angles, etc. I find that the auto-generation over-constrains torsion angles, so I delete the ones that aren't fixed at 0 or 180 degrees. Also watch out for incorrect planarity restraints - you get this a lot with linked aromatic ring systems. Then take your new library file and feed it to Refmac (using the LIBIN keyword for a script file or the "Library" line in ccp4i. Your new definitions will supplement the default library. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. S.Shanmuga Sundara Raj http://www.geocities.com/raj_sss Email: [EMAIL PROTECTED],[EMAIL PROTECTED] - Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out.
Re: [ccp4bb] previous message monomer library
Hi Arti, Another way of generating coordinates for your molecule of interest is by Chemdraw and Chem3d if you have the program. I find it easier compared to sketcher since the chirality of an atom can be defined while drawing the molecule in Chemdraw. Once I get the 3D coordinates from Chem3D, I follow the procedure which Matt described below. Madhavi -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, February 23, 2007 12:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] previous message monomer library CCP4 bulletin board wrote on 02/23/2007 11:22:04 AM: > Hello all, > Kindly disregard my message about monomer libraries. The problem ( atoms > blowing apart) seems to be due to something (yet undetermined) else. Thank > you for clearing up ones about COM_COM. > However, I still wonder if I can add my own ligand libraries to the > default one, like you can do for ONO. > Arti Pandey > > Hi Arti - You absolutely can. I used to do this all the time when I was working on small-molecule drug complexes. If all you want to do is take an existing library file (e.g. from HIC-UP) and use it, skip to the last paragraph of this email. If you want to make a library file, read on. The simplest way to do this is to create a pdb file containing the idealized, energy-minimized coordinates of your molecule of interest. How you make this file is a little more complicated - I used InsightII from Accelrys, but that's a very expensive program that you probably don't have access to. Sketcher, in CCP4, will also do this but I never got it to work for me. Even PyMOL will build molecules for you but it won't energy-minimize them so bond lengths and angles can be distorted. The CCP4 site suggests these programs (I've never used them): http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html Make sure that your new molecule has a unique 3-letter residue code so that Refmac won't be confused and think it's one of the entries in its monomer library. There is a file called 'mon_lib.list' in $CCP4_HOME/lib/data/monomers that gives the codes of everything in the monomer library. If you have a number in your residue code you'll probably avoid conflicts. The next step is to run a short Refmac job on this coordinate file, using a simple script like the one here: http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html Refmac will generate a library file for your new molecule, then stop. You can then open up the new library file (which will have 'lib' in the filename) and check through it with a text editor. You'll see a long list of topology, bond lengths, angles, etc. I find that the auto-generation over-constrains torsion angles, so I delete the ones that aren't fixed at 0 or 180 degrees. Also watch out for incorrect planarity restraints - you get this a lot with linked aromatic ring systems. Then take your new library file and feed it to Refmac (using the LIBIN keyword for a script file or the "Library" line in ccp4i. Your new definitions will supplement the default library. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] previous message monomer library [VASCL:A10EE53AD1F]
> Hello Matt, Thank you for the suggestion. Yes, I have been doing just that, meaning making a lib file using sketcher and then using the file that it creates in refmac. I work with a lot of ligands and mostly on my own computer, so thought maybe I could just add these to the monomer lib. that refmac uses, without having to enter them separately in the library input in ccp4i. I have combined the lib. created into one file and use that every time I run refmac, but still wondered if there was a way that all these monomers could be added to the list of monomers in /ccp4/lib/monomers/full list. I played with that too, I manually entered my own molecule to the list and put its lib in the "c" directory of the monomeres directory, but it doesnt work, even though the atom names were the same as a similar molecule in the library.So I am probably missing something. Of course I can dismiss this as being not important, as things still do work. But its just curiosity that hasnt killed anybody yet. Thanks again, Matt. Arti Pandey > > CCP4 bulletin board wrote on 02/23/2007 11:22:04 > AM: > >> Hello all, >> Kindly disregard my message about monomer libraries. The problem ( atoms >> blowing apart) seems to be due to something (yet undetermined) else. > Thank >> you for clearing up ones about COM_COM. >> However, I still wonder if I can add my own ligand libraries to the >> default one, like you can do for ONO. >> Arti Pandey >> >> > > Hi Arti - > > You absolutely can. I used to do this all the time when I was working on > small-molecule drug complexes. > > If all you want to do is take an existing library file (e.g. from HIC-UP) > and use it, skip to the last paragraph of this email. If you want to make > a library file, read on. > > The simplest way to do this is to create a pdb file containing the > idealized, energy-minimized coordinates of your molecule of interest. How > you make this file is a little more complicated - I used InsightII from > Accelrys, but that's a very expensive program that you probably don't have > access to. Sketcher, in CCP4, will also do this but I never got it to > work > for me. Even PyMOL will build molecules for you but it won't > energy-minimize them so bond lengths and angles can be distorted. > > The CCP4 site suggests these programs (I've never used them): > http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html > > Make sure that your new molecule has a unique 3-letter residue code so > that > Refmac won't be confused and think it's one of the entries in its monomer > library. There is a file called 'mon_lib.list' in > $CCP4_HOME/lib/data/monomers that gives the codes of everything in the > monomer library. If you have a number in your residue code you'll > probably > avoid conflicts. > > The next step is to run a short Refmac job on this coordinate file, using > a > simple script like the one here: > http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html > > Refmac will generate a library file for your new molecule, then stop. You > can then open up the new library file (which will have 'lib' in the > filename) and check through it with a text editor. You'll see a long list > of topology, bond lengths, angles, etc. I find that the auto-generation > over-constrains torsion angles, so I delete the ones that aren't fixed at > 0 > or 180 degrees. Also watch out for incorrect planarity restraints - you > get this a lot with linked aromatic ring systems. > > Then take your new library file and feed it to Refmac (using the LIBIN > keyword for a script file or the "Library" line in ccp4i. Your new > definitions will supplement the default library. > > Hope that helps, > > Matt > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > Confidentiality Note: This e-mail, and any attachment to it, contains > privileged and confidential information intended only for the use of the > individual(s) or entity named on the e-mail. If the reader of this e-mail > is not the intended recipient, or the employee or agent responsible for > delivering it to the intended recipient, you are hereby notified that > reading it is strictly prohibited. If you have received this e-mail in > error, please immediately return it to the sender and delete it from your > system. Thank you. > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] previous message monomer library
CCP4 bulletin board wrote on 02/23/2007 11:22:04 AM: > Hello all, > Kindly disregard my message about monomer libraries. The problem ( atoms > blowing apart) seems to be due to something (yet undetermined) else. Thank > you for clearing up ones about COM_COM. > However, I still wonder if I can add my own ligand libraries to the > default one, like you can do for ONO. > Arti Pandey > > Hi Arti - You absolutely can. I used to do this all the time when I was working on small-molecule drug complexes. If all you want to do is take an existing library file (e.g. from HIC-UP) and use it, skip to the last paragraph of this email. If you want to make a library file, read on. The simplest way to do this is to create a pdb file containing the idealized, energy-minimized coordinates of your molecule of interest. How you make this file is a little more complicated - I used InsightII from Accelrys, but that's a very expensive program that you probably don't have access to. Sketcher, in CCP4, will also do this but I never got it to work for me. Even PyMOL will build molecules for you but it won't energy-minimize them so bond lengths and angles can be distorted. The CCP4 site suggests these programs (I've never used them): http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html Make sure that your new molecule has a unique 3-letter residue code so that Refmac won't be confused and think it's one of the entries in its monomer library. There is a file called 'mon_lib.list' in $CCP4_HOME/lib/data/monomers that gives the codes of everything in the monomer library. If you have a number in your residue code you'll probably avoid conflicts. The next step is to run a short Refmac job on this coordinate file, using a simple script like the one here: http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html Refmac will generate a library file for your new molecule, then stop. You can then open up the new library file (which will have 'lib' in the filename) and check through it with a text editor. You'll see a long list of topology, bond lengths, angles, etc. I find that the auto-generation over-constrains torsion angles, so I delete the ones that aren't fixed at 0 or 180 degrees. Also watch out for incorrect planarity restraints - you get this a lot with linked aromatic ring systems. Then take your new library file and feed it to Refmac (using the LIBIN keyword for a script file or the "Library" line in ccp4i. Your new definitions will supplement the default library. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] TLSView under Mac OS X
On Friday 23 February 2007 09:05, Richard Gillilan wrote: > Thanks to all for suggesting a number of solutions! Although TLSView > is now working for Mac, I have found that it is also possible to > import principle axes of the thermal ellipsoids into PyMol without > too much trouble. The program TLSANL will add full ANISO records to > the pdb file based on the TLS groups. Rastep (Rasmol package) will > produce a .r3d file which can be parsed by a few lines of C code to > create a cgo (compiled graphics object) file for PyMol. Axes are > represented by thin CYLINDER primitives. With a bit more work one > could probably also generate ellipsoids. If anyone is interested, I > would be happy to supply the code and notes, such as they are. Small correction: rastep is part of Raster3D (not Rasmol). rastep will itself generate ellipsoids; indeed that is its primary purpose. -- Ethan A Merritt
Re: [ccp4bb] TLSView under Mac OS X
Thanks to all for suggesting a number of solutions! Although TLSView is now working for Mac, I have found that it is also possible to import principle axes of the thermal ellipsoids into PyMol without too much trouble. The program TLSANL will add full ANISO records to the pdb file based on the TLS groups. Rastep (Rasmol package) will produce a .r3d file which can be parsed by a few lines of C code to create a cgo (compiled graphics object) file for PyMol. Axes are represented by thin CYLINDER primitives. With a bit more work one could probably also generate ellipsoids. If anyone is interested, I would be happy to supply the code and notes, such as they are. Richard Gillilan MacCHESS
[ccp4bb] previous message monomer library
Hello all, Kindly disregard my message about monomer libraries. The problem ( atoms blowing apart) seems to be due to something (yet undetermined) else. Thank you for clearing up ones about COM_COM. However, I still wonder if I can add my own ligand libraries to the default one, like you can do for ONO. Arti Pandey Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
[ccp4bb] Beam time available at X6A
Beam time available @ X6A http://protein.nsls.bnl.gov NEXT BEAM TIME MARCH 4 The NIGMS beam line X6A at the National Synchrotron Light Source provides FAST access to beam time through out the year. To apply submit a short proposal to http://protein.nsls.bnl.gov at any time. Proposals are continuously reviewed and beam time can be scheduled within a week. For comments or further questions please contact the scientific staff at: [EMAIL PROTECTED] or call: +1 (631) 344 8375 Vivian Stojanoff National Synchrotron light Source Brookhaven National Laboratory Bldg 725D Upton, NY 11973 USA Email: [EMAIL PROTECTED]; [EMAIL PROTECTED] phone: +1 631 344 8375 fax: +1 631 344 3238
Re: [ccp4bb] Main topic of the day: Protein crystallization
Just to add that in one case we were able to get suitable crystals after using a protein concentration of as low as 1.5 mg/ml (kapetaniou et al. Acta Cryst. 2005, F61, 479-481) and microdialysis to slowly remove the excess of salt. Lower concentrations (0.50-0.75 mg/ml) could also produce crystals but they were too small. Tassos Papageorgiou Quoting Patrick Shaw Stewart <[EMAIL PROTECTED]>: > Ronaldo > > I have a database of crystallization conditions extracted from the > PDB. I was able to parse the data to extract the concentration of > protein in around 900 cases. > > The lowest 9 protein concentrations were as follows: > > PDB IDTYPEDATEProtein conc, mg/ml > 1EYM ISOMERASE. 07/05/2000 0.75 > 1ADQ COMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN)18/02/1997 1 > 1W5G FOUR HELIX BUNDLE. 06/08/2004 1 > 1UU4 HYDROLASE. 15/12/2003 1 > 1W2U HYDROLASE. 08/07/2004 1 > 1DXP SERINE PROTEASE.13/01/2000 1 > 1DY8 SERINE PROTEASE.18/01/2000 1 > 1DY9 SERINE PROTEASE.31/01/2000 1 > 1DG6 APOPTOSIS. 23/11/1999 1.2 > > The maximum protein conc was 200 mg/ml (1BLF) > > My database goes up to October 2004. Janet Newman and Tom Peat have > done this job far more conscientiously and could probably give you > better and more up-to-date data. > > Patrick > > > On 2/23/07, Ronaldo Alves Pinto Nagem <[EMAIL PROTECTED]> wrote: > > > > > > Dear all, > > > > As protein crystallization is the main topic of the day may I include > > another question? > > > > What was the minimun protein concentration reported with success in > > crystallization trials? > > > > I ask that because the protein I am trying to crystallize is much less > > soluble than the one mentioned in the lasts emails. > > > > Thanks > > > > Ronaldo. > > > -- A.C.(Tassos) Papageorgiou, PhD phone: +358 2 333 8012 (office) Senior Scientist, Group leader fax: +358 2 333 8000 Turku Centre for Biotechnology E-mail: [EMAIL PROTECTED] BioCity, Turku URL: http://www.btk.utu.fi/~apapageo FIN-20521, Finland
[ccp4bb] summary: stuck datasets
Hello Everyone Thanks for all the responses. Many were about twinning detection. IMO, the best tip was toward the cctbx utilities (I think these come from the phenix developers??) for twinning detection and detwinning. The output from mmtbx.xtriage and mmtbx.twin_map_utils is particularly clear. (Thanks to Peter Zwart and Bill Scott) In the particular case of the (not so) hypothetical dataset I was concerned about - that dataset is not twinned, rather the struck refinement was due to severe data anisotropy [not noticed during late night synchrotron data reduction but detected with sfcheck - we hadn't yet figured that out when I posted the message.] A run through the anisotropy server at UCLA http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ has unstuck the refinement and made the maps much more pleasing. Sue Sue Roberts Biochemistry & Biopphysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] Postdoctoral Position Opening
A post-doctoral position is immediately available in the group of JP Samama, in the Department of structural biology and genomics at IGBMC, for structural characterization a novel protein implicated in cancers of the head and neck and prostate. The project involves five laboratories in a consortium that evaluate the therapeutic, prognostic and diagnostic potential of this protein implicated in cell division and cell migration. The Department of structural biology and genomics comprises state-of-the-art equipment for protein expression, purification, characterization, nanoscale crystallization facility and inhouse-diffractometers. IGBMC is located in a green field area near Strasbourg, with over 600 research personnel and comprehensive facilities and platforms. The successful candidate should have expertise in protein expression and purification, and PhD in crystallography, or a related research area such as biophysics or biochemistry. Interested applicants please send a CV with the names of two references to: Dr. Jean-Pierre Samama [EMAIL PROTECTED] Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS ULP - U 596 INSERM , 1 Rue Laurent Fries, BP 10142, 67404 Illkirch cedex, France. Tel. 33 (0) 3 88 65 57 70 NOTE THE NEW PHONE NUMBER Dr. Jean-Pierre Samama Directeur de recherche CNRS Département de Biologie et Génomique Structurales IGBMC, 1 rue Laurent Fries, BP10142 67404 ILLKIRCH- France tel: 03 88 65 57 70 (33 3 88 65 57 70) Fax: 03 88 65 32 76 (33 3 88 65 32 76) email: [EMAIL PROTECTED]
Re: [ccp4bb] Easy proteins to crystallize & Main topic of the day: Protein crystallization
Douglas and Ronaldo, I wanted to put in my two cents worth on both of your queries at the same time. You should look up glycerol dehydrogenase from the yeast S. pombe. Sp-GlyDH was solved accidently a few years ago by Anne Mulichak in our group (PDB 1TA9). We were trying to crystallize another enzyme that was expressed in S. pombe, but Sp-GlyDH also co- purifed on a Co-Talon column. A common cleavage product of the target protein (mammalian hexokinase III) would produce the very minor band at 45 KDa, which was almost exactly the same size as Sp- GlyDH. The minor band represented much less than 5% of the total protein. We easily got crystals which turned out to be Sp-GlyDH. Thus, Sp-GlyDH at less than 0.5 mg/mL will crystallize in the presence of ~9-10 mg/mL of another "contaminating" protein. Never did get crystals of mammalian hexokinase III. Michael R. Michael Garavito, Ph.D. Email: [EMAIL PROTECTED] Biochemistry & Molecular BiologyOffice: (517) 355-9724 Michigan State University Lab: (517) 353-9125 East Lansing, MI 48824-1319FAX: (517) 353-9334 On Feb 22, 2007, at 3:53 PM, Douglas L. Theobald wrote: On Feb 22, 2007, at 2:35 PM, Nat Echols wrote: I take it you're only interested in well-characterized and well- known proteins? Actually no -- well-characterized is good, but well-known is unnecessary. I have a receiver domain that expresses at >100mg/L and forms crystals right out of most screens that diffract to atomic/ subatomic resolution, but it's still being functionally characterized and the system it's a part of is of limited interest outside of a specific field of microbiology. Experimentally, though, I can't imagine an easier protein to work with. On Thu, 22 Feb 2007, Douglas L. Theobald wrote: Hi all, I'd like to pick the collective brain of crystallographers on this list -- what are some of the most easily crystallizable proteins? I'm especially interested in those that over-express and diffract well, and in ones that might be less well-known than, say, lysozyme (but nearly as nice). Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: [ccp4bb] Summary crystallisation of an extremely soluble protein
The term T{delta}S is not proportional to temperature however since
entropy is itself a function of T. Thus (for example) the hydrophobic
effect
reaches a maximum at around 25 deg C rather than being a monotonic
function of temperature.
Incidentally human adult Hb (HbA) has a concentration of about 340
mg/ml in
your red cells as you read this email, so 190 mg/ml is really quite
dilute
in comparison.
On Feb 23, 2007, at 8:50 PM, Andy Purkiss-Trew wrote:
On Thu, 2007-02-22 at 16:32 -0600, Carlos Huerta wrote:
This may sound like hocus-pocus but it worked for me and may work in
other conditions. Try chilling your solution in ice, or prepare your
plate with reservoir solution and chill the plate in a tub of ice
(surround the plate with ice, do not place the plate on top of the
ice). Finishing setting the plate in the ice and place you plate at
cooler temperatures such as 4-16 degrees Celcius after set-up.
My progress was substantially improved with this method. I previously
had crystals that were small and diffracted anisotropically. I tried
other screens to improve crystal size such as additive screen, slowing
vapor diffusion using oils and incubating at different temperatures
after setting up at room temperature. The crystal grew at a lower
concentration of PEG that originally gave precipitation setting up at
RT and placing at different incubation temperatures. The end result
the crystal increased in size by 5x and gave isotropic diffraction to
high-resolution.
Well, this isn't really hocus-pocus. Remember that the entropy term when
calculating a free energy change is -T{delta}S
So, if altering the sidechains of a protein to reduce entropy works in
some cases, so will reducing the temperature!! Of course, you might have
to go to very low temperatures (where the solution will be frozen) to
get the same effect as a good mutation :)
Hope this helps
Andy
-
Cat, n.: Lapwarmer with built-in buzzer.
+--+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
| E-mail [EMAIL PROTECTED]|
+--+
Re: [ccp4bb] Summary crystallisation of an extremely soluble protein
On Thu, 2007-02-22 at 16:32 -0600, Carlos Huerta wrote:
> This may sound like hocus-pocus but it worked for me and may work in other
> conditions. Try chilling your solution in ice, or prepare your plate with
> reservoir solution and chill the plate in a tub of ice (surround the plate
> with ice, do not place the plate on top of the ice). Finishing setting the
> plate in the ice and place you plate at cooler temperatures such as 4-16
> degrees Celcius after set-up.
>
> My progress was substantially improved with this method. I previously had
> crystals that were small and diffracted anisotropically. I tried other
> screens to improve crystal size such as additive screen, slowing vapor
> diffusion using oils and incubating at different temperatures after setting
> up at room temperature. The crystal grew at a lower concentration of PEG
> that originally gave precipitation setting up at RT and placing at different
> incubation temperatures. The end result the crystal increased in size by 5x
> and gave isotropic diffraction to high-resolution.
Well, this isn't really hocus-pocus. Remember that the entropy term when
calculating a free energy change is -T{delta}S
So, if altering the sidechains of a protein to reduce entropy works in
some cases, so will reducing the temperature!! Of course, you might have
to go to very low temperatures (where the solution will be frozen) to
get the same effect as a good mutation :)
Hope this helps
Andy
-
Cat, n.: Lapwarmer with built-in buzzer.
+--+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
| E-mail [EMAIL PROTECTED]|
+--+
Re: [ccp4bb] monomer library in Refmac
On Fri, 2007-02-23 at 11:08 +, Roberto Steiner wrote: > There is something wrong with COM (actually I do not understand why > it is COM_COM rather than COM? > Alexei? Garib?) Basically because Windows platforms get confused with things called COM. PRN_PRN.cif is another one. Martyn
Re: [ccp4bb] monomer library in Refmac
Hi Arti, Hi all, I am having problems understanding how to add my own monomer to the ccp4 monomer library. 1. Can it be done. Yes it can be done. 2. How can I convert minimum description of a monomer to a complete one ( libcheck fails when it tries to create the cartesian coordinates for this monomer (COM_COM)) from the library. There is something wrong with COM (actually I do not understand why it is COM_COM rather than COM? Alexei? Garib?) Anyway, I have created you ligand COM (1-THIOETHANESULFONIC ACID) interactively using Sketcher and generated a complete ligand description for you (exactly as described in Paragraph 5.1 of the paper you mention). PDB (COM_libcheck.pdb) and Library (COM_mon_lib.cif) files attached. Now, it should work. Best regards, Roberto 3.If I ask Refmac to use the lib that I created for this monomer, it runs but the atoms in the pdb are either ripped apart or have links where they shouldnt be, this is when viewed in Coot. Refmac run without restrains doesnt show this, so the file is OK. 4. An excerpt "The dictionary can be extended easily by users. Users can create and organize personal monomer entries as well as modifications and links. In case of conflict, a user's definitions always override those stored within the distributed dictionary." from REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Acta Cryst. (2004). D60, 2184-2195 Can a user use the default lib as well as the new ones. I am using ccp4-6.0.2. I would appreciate any help. Thank you. Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717 COM_libcheck.pdb Description: Binary data COM_mon_lib.cif Description: Binary data --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]
Re: [ccp4bb] Question about glove boxes for protein crystallization
Dear Mathews, we were successful in crystallizing two ferredoxins under strict anaerobic conditions using the much cheaper solution of a glove bag and filling it with argon. I guess that in both cases (box and bag) the thickness of the gloves is a problem especially if you are dealing with cover slides. The glove bag occupies also much less space however its major problem was the very bad visualization of the inner space and finally we added a plexiglas window on the bag. Needless to say how essential is not to forget anything outside the bag/box before starting the crystallization set up. Finally you can also consider the possibility to use a crystallization robot. In some of them it is possible to create anaerobic conditions using argon. good luck Nikos * Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] * - Original Message - From: "Mathews, Irimpan" <[EMAIL PROTECTED]> To: Sent: Friday, 23 February, 2007 3:03 AM Subject: [ccp4bb] Question about glove boxes for protein crystallization Dear Friends, Sorry for the non CCP4 question. We are planning to purchase a small glove box to setup crystallization trays under anaerobic conditions. If you have used glove boxes for crystallization, would you please give me some idea? We are thinking of getting the 815 series from Plas-labs (link below). http://www.plas-labs.com/ Thank you very much, Mathews Ps: If others are interested, I will post a summary.
Re: [ccp4bb] Question about glove boxes for protein crystallization
Hi Mathews, An anaerobic chamber from Belle Technology (http://www.belle- technology.com/) served me well in the past. Belle's glove boxes are made of acrylic material. That offers relatively low-cost and all-round visibility. Cheers, Roberto On 23 Feb 2007, at 02:03, Mathews, Irimpan wrote: Dear Friends, Sorry for the non CCP4 question. We are planning to purchase a small glove box to setup crystallization trays under anaerobic conditions. If you have used glove boxes for crystallization, would you please give me some idea? We are thinking of getting the 815 series from Plas-labs (link below). http://www.plas-labs.com/ Thank you very much, Mathews Ps: If others are interested, I will post a summary. --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]
[ccp4bb] AW: [ccp4bb] Question about glove boxes for protein crystallization
Dear Patrick, as a (probably more general) follow up-question: Does anyone have experience with batch crystallization under oil for membrane proteins (in detergent) ? alex > Dr. Alexander Pautsch > Protein Crystallography /Structural Research > Boehringer Ingelheim Pharma GmbH & Co. KG Deutschland > Birkendorferstrasse 65 > 88400 BIBERACH, Germany > tel. +49 - (0)7351 - 54 4683 > fax. +49 - (0)7351 - 83 4683 > email [EMAIL PROTECTED] > > -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Patrick Shaw Stewart Gesendet: Freitag, 23. Februar 2007 10:02 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Question about glove boxes for protein crystallization Hi Mathews One of our customers, Bret Dillard at the University of Georgia, has had great success with one of our robots in a Bactron X anaerobic chamber. In this case, Bret mainly used the microbatch-under-oil method, which works very well for anaerobic work: (1) the oil protects the sample and reduces exposure to oxygen, (2) the amount of work is far less because you can keep several degassed screens in the chamber to use many times with different protein samples. With vapor diffusion you will have to degass the solutions every for every few samples (if not every sample). Bret won our competition for this work last year. You can find his report at http://www.douglas.co.uk/news.htm, plus more info below Patrick _ Douglas Instruments has announced the winner of the second round of its competition for the best new crystallization technique. Congratulations to Bret Dillard from the University of Georgia, for his winning entry, "Automatic Protein Crystallization in an Anaerobic Environment." Bret placed an Oryx1-6 robot in a Bactron X anaerobic chamber, and used mainly microbatch-under-oil crystallization to crystallize four proteins that are not stable in an environment with oxygen. He found that microbatch avoided the need for frequent degassing of solutions which reduced the work-load enormously. The oil also provided extra protection from oxidation. One of the proteins crystallized is rubrerythrin from the hyperthermophilic archaeon, Pyrococcus furiosus. The native protein contains iron, but is unstable in oxygen. A previously-reported structure was determined in the presence of oxygen, but the iron had been replaced by zinc. Using the anaerobic system, Bret has now obtained the native form containing iron. _ On 2/23/07, Mathews, Irimpan <[EMAIL PROTECTED]> wrote: > > > Dear Friends, > > Sorry for the non CCP4 question. We are planning to purchase a small glove > box to setup crystallization trays under anaerobic conditions. If you have > used glove boxes for crystallization, would you please give me some idea? > > We are thinking of getting the 815 series from Plas-labs (link below). > > http://www.plas-labs.com/ > > Thank you very much, > Mathews > > Ps: If others are interested, I will post a summary. >
Re: [ccp4bb] Main topic of the day: Protein crystallization
Ronaldo I have a database of crystallization conditions extracted from the PDB. I was able to parse the data to extract the concentration of protein in around 900 cases. The lowest 9 protein concentrations were as follows: PDB ID TYPEDATEProtein conc, mg/ml 1EYMISOMERASE. 07/05/2000 0.75 1ADQCOMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN)18/02/1997 1 1W5GFOUR HELIX BUNDLE. 06/08/2004 1 1UU4HYDROLASE. 15/12/2003 1 1W2UHYDROLASE. 08/07/2004 1 1DXPSERINE PROTEASE.13/01/2000 1 1DY8SERINE PROTEASE.18/01/2000 1 1DY9SERINE PROTEASE.31/01/2000 1 1DG6APOPTOSIS. 23/11/1999 1.2 The maximum protein conc was 200 mg/ml (1BLF) My database goes up to October 2004. Janet Newman and Tom Peat have done this job far more conscientiously and could probably give you better and more up-to-date data. Patrick On 2/23/07, Ronaldo Alves Pinto Nagem <[EMAIL PROTECTED]> wrote: Dear all, As protein crystallization is the main topic of the day may I include another question? What was the minimun protein concentration reported with success in crystallization trials? I ask that because the protein I am trying to crystallize is much less soluble than the one mentioned in the lasts emails. Thanks Ronaldo.
Re: [ccp4bb] Question about glove boxes for protein crystallization
Hi Mathews One of our customers, Bret Dillard at the University of Georgia, has had great success with one of our robots in a Bactron X anaerobic chamber. In this case, Bret mainly used the microbatch-under-oil method, which works very well for anaerobic work: (1) the oil protects the sample and reduces exposure to oxygen, (2) the amount of work is far less because you can keep several degassed screens in the chamber to use many times with different protein samples. With vapor diffusion you will have to degass the solutions every for every few samples (if not every sample). Bret won our competition for this work last year. You can find his report at http://www.douglas.co.uk/news.htm, plus more info below Patrick _ Douglas Instruments has announced the winner of the second round of its competition for the best new crystallization technique. Congratulations to Bret Dillard from the University of Georgia, for his winning entry, "Automatic Protein Crystallization in an Anaerobic Environment." Bret placed an Oryx1-6 robot in a Bactron X anaerobic chamber, and used mainly microbatch-under-oil crystallization to crystallize four proteins that are not stable in an environment with oxygen. He found that microbatch avoided the need for frequent degassing of solutions which reduced the work-load enormously. The oil also provided extra protection from oxidation. One of the proteins crystallized is rubrerythrin from the hyperthermophilic archaeon, Pyrococcus furiosus. The native protein contains iron, but is unstable in oxygen. A previously-reported structure was determined in the presence of oxygen, but the iron had been replaced by zinc. Using the anaerobic system, Bret has now obtained the native form containing iron. _ On 2/23/07, Mathews, Irimpan <[EMAIL PROTECTED]> wrote: Dear Friends, Sorry for the non CCP4 question. We are planning to purchase a small glove box to setup crystallization trays under anaerobic conditions. If you have used glove boxes for crystallization, would you please give me some idea? We are thinking of getting the 815 series from Plas-labs (link below). http://www.plas-labs.com/ Thank you very much, Mathews Ps: If others are interested, I will post a summary.
