[ccp4bb]
Xie Jiabao schrieb: Hi, Can anyone direct me to a program that calculates a protein cavity's dimensions (average) and not just its volume? Thanks in advance, Xie http://loschmidt.chemi.muni.cz/caver/ The program is called caver. -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] dry shipper on airplaine
Here I must disagree slightly with Preben. I once mentioned 'Twelve Monkeys' to the personnel at the check-in counter to lighten the mood (They didn't like the fumes coming out from the dewar). I really believe it helped them understand what was NOT in the dewar. And we were allowed to board the plane with only the slightest delay. -Bjørn, Ph.D Student Jens Preben Morth wrote: Hi Clemens We normally check in the dewar as normal luggage after we have removed all liquids, we have never had any problems travelling from Aarhus to SLS. just remind the students coming along not to mention movies like Twelve monkeys or outbreak when checking it in. best Preben Dear all, I wonder if it would be still/again possible to check in a dry shipper for a flight inside Europe. What is your experience? Cheers, Clemens
[ccp4bb] Postdoctoral position in Brighton, UK
UNIVERSITY OF SUSSEX School of Life Sciences Department of Chemistry and Biochemistry Postdoctoral Research Assistant in Protein Crystallography Applications are invited for a three year Postdoctoral position, funded by the MRC, in the laboratory of Dr. Darren Thompson. The successful candidate will work on the complement protein, C1. This will involve the use of X-ray crystallography and other biophysical techniques to investigate the structure and stability of this complex. The laboratory is situated on the Falmer campus, Brighton, set on the edge of the Sussex Downs, and just a few minutes away is the lively, friendly seaside town of Brighton with its great leisure facilities and its rich, eclectic cultural life. The Chemistry and Biochemistry department is well equipped for protein biophysics including: Circular dichroism (Jasco CD), and state of the art UV/Vis rapid scan and fluorescence /anisotropy /CD stopped-flow (Applied Photophysics p* and SX18MV stopped flow) and equilibrium fluorescence. Protein crystallography facilities include a RU-H3RHB rotating anode X-ray generator with Osmic max-Flux optics and RAXIS-IV image plate area detector and MSC cryo system facilities. Additional biophysics facilities including ITC and atomic force microscopy. There are also state of the art facilities for microarrays and the newly-created Sussex Centre for Advanced Microscopy provides state of the art facilities for confocal, 2-photon, and CCD microscopy, with fluorescence correlation and lifetime capabilities, a Hitachi7100 transmission electron microscope and cryo- and scanning electron microscopy. Applicants should have appropriate degrees and experience in protein biochemistry or protein crystallography and will hold a PhD, or have submitted their PhD thesis prior to taking up the appointment. The post is available immediately, for a period of three years, Please direct informal enquiries and CVs to Dr. Darren Thompson: [EMAIL PROTECTED]
[ccp4bb] Making a Poly ala model
Dear All, Can anyone recommend a windows/PC-friendly program (website?) to convert a PDB file into a poly-Ala model? Thanks a lot! Matt Matthew J. Bottomley, Ph.D. Senior Research Biochemist IRBM / MRL-Rome Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] FW: Making a Poly ala model
OK - found it, thanks! Matt Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Siemens Multiwire Area Detector X-1000 available
To All at CCP4BB: We have a Siemens X-1000 Multiwire Area Detector to give away. It has been manufactured by Siemens Analytical X-ray Instruments Inc. in Madison, Wisconsin, USA. Equipment available includes multiwire area detector X-1000 itself, its Position Decoding Circuit, the 4-circle goniostat with the remote control and the set of collimators. This equipment is available free of charge except for the shipping costs. We are at University of Glasgow, Glasgow, Scotland, UK. If you are interested in this equipment (in the described set or in any parts of it) please contact me directly using email address [EMAIL PROTECTED] Please do not respond to ccp4bb address. Aleks -- Aleksander W. Roszak, PhD E-mail: [EMAIL PROTECTED] Protein Crystallography Web: www.chem.gla.ac.uk/~aleks University of Glasgow Fax: +44-(0)141-330 3779 Level 3 Room B 317 Tel (office): +44-(0)141-330 4476 Glasgow Biomedical Research Centre Tel (X-ray lab): +44-(0)141-330 3589 120 University PlaceMobile: +44-(0)780 9559996 Glasgow G12 8TA Scotland, UK
Re: [ccp4bb] Making a Poly ala model
If you have perl installed, just use this script to convert as many
files as you want once by typing : perl mutala.pl myfile.pdb myfile2.pdb etc
Bottomley, Matthew wrote:
Dear All,
Can anyone recommend a windows/PC-friendly program (website?) to
convert a PDB file into a poly-Ala model?
Thanks a lot!
Matt
Matthew J. Bottomley, Ph.D.
Senior Research Biochemist
IRBM / MRL-Rome
Notice: This e-mail message, together with any attachments, contains information of
Merck& Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889),
and/or its affiliates (which may be known outside the United States as Merck Frosst,
Merck Sharp& Dohme or MSD and in Japan, as Banyu - direct contact information for
affiliates is available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are not the
intended recipient, and have received this message in error, please notify us
immediately by reply e-mail and then delete it from your system.
--
Nicolas Soler
Institut de Chimie des Substances Naturelles
91190 Gif-sur-Yvette
tel 33-1-69823764
fax 33-1-69823784
http://perso.nicodam.org/
#!/usr/bin/perl -w
# Mutala: script mutate each residue in alanine in a pdb
file#
# Written by Nicolas
Soler
#
FONCTIONS###
foreach $fichier (@ARGV) {
open (ENTREE,$fichier);
if (glob "polyala$fichier"){unlink "polyala$fichier"};
open SORTIE, ">>polyala$fichier";
select SORTIE;
while (){if (/^ATOM.{9}(N |C |O
|CA|CB)..(\w{3})/){s/$2/ALA/;print $_}};
print "END";
close ENTREE;
close SORTIE;}
Re: [ccp4bb] Making a Poly ala model
Within PyMOL: remove polymer and not name N+CA+C+O+CB alter polymer, resn="ALA" save polyALA.pdb Cheers, Warren -- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bottomley, Matthew Sent: Thursday, May 29, 2008 5:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Making a Poly ala model Dear All, Can anyone recommend a windows/PC-friendly program (website?) to convert a PDB file into a poly-Ala model? Thanks a lot! Matt Matthew J. Bottomley, Ph.D. Senior Research Biochemist IRBM / MRL-Rome Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] mutation to cysteines
Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing? Thanks in advance, Amit
Re: [ccp4bb] mutation to cysteines
Hi Amit You can try MODIP http://caps.ncbs.res.in/dsdbase//dsdbase.html, which give you the stereochemical possibility of disulphide linkage between the residues. Not sure about the success rate based on the result from this database. hope this helps VK Kabaleeswaran Venkataraman Arise, Awake and stop not until goal is Reached - Swami Vivekanand - Original Message From: amit sharma <[EMAIL PROTECTED]> To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, May 29, 2008 11:03:48 AM Subject: [ccp4bb] mutation to cysteines Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing? Thanks in advance, Amit
[ccp4bb] Well-paid crystallography postdoc position in Oslo
I have a 2-year postdoctoral research fellowship available in my group (financed by the Norwegian Research Council, project title "Postgenome glycomics: The structures, interactions, and functions of complex sugars attached to proteins and lipids"). The position is available immediately, but the starting date can be agreed on (latest January 1st 2009). In special circumstances, the candidate may be employed as a researcher. The project will be in the field of protein crystallography, with a focus on protein-carbohydrate interactions of medically relevant systems. Experience with membrane proteins can be an advantage. The candidate is further expected to actively take part in the maintenance of the X-ray equipment and crystallographic software. Pay Grade: 54 58 (NOK 394.700 423.800 depending on qualifications and seniority) Application details can be found at: http://www.admin.uio.no/opa/ledige-stillinger/2008/vit/PostdocChemistry-2008--9152.html Deadline: June 17th Cheers, Ute -- Ute Krengel, PhD Chalmers University of Technology Center for Structural Biology Department of Chemistry and Bioscience P.O.Box 462 SE-405 30 Göteborg, Sweden Tel : +46 31 773 3237 Fax : +46 31 773 3910 e-mail : [EMAIL PROTECTED] URL: http://www.csb.gu.se/ute --
Re: [ccp4bb] mutation to cysteines
Try the program disulfide by design: http://www.ehscenter.org/dbd/ Its easy to install (at least on windows) and to run. You put in a PDB file and the program will look in the structure where disulphide bonds are possible. It also ranks the candidates in energies. Finally, it can generate a PDB file with a particular disulphide. Quite a nice program. Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -Original Message- From: CCP4 bulletin board on behalf of amit sharma Sent: Thu 5/29/2008 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mutation to cysteines Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing? Thanks in advance, Amit
[ccp4bb] thermofluor - Thermal Shifts - Tm and Delta Tm
Hello, we want to use the thermofluor thermal shift assay to screen for buffers that our proteins are happy in. Reading around the subject, I am a bit unclear as to what to be looking for with regard to a stabilizing affect. Initially, we thought, the higher the Tm, then the more stabilizing the buffer is, but reading further we have observed several examples where, the Tm is raised, but yet the Delta-Tm indicates a destabilizing affect. How can this be so? Any references regarding a good explanation of Delta-Tm would be great. thanking you Andy Dodds
Re: [ccp4bb] mutation to cysteines
amit sharma wrote: Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing? Thanks in advance, Amit One more option is to use my first ever fortran program SSBOND. You can use it via a web interface at http://eagle.mmid.med.ualberta.ca/forms/ssbond.html It has been cited 57 times, I didn't check them all, but from what I've heard it works well. Bart == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
[ccp4bb] waaay off topic...
...but I know you'll come through. I'm looking for recommendations for a good textbook covering fluorescence spectroscopy. Thanks in advance. Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED]
Re: [ccp4bb] waaay off topic...
A good book is: Principles of Fluorescence Spectroscopy Joeseph R Lakowicz Roopa Thapar On Thu, May 29, 2008 1:16 pm, Patrick Loll wrote: > ...but I know you'll come through. > > I'm looking for recommendations for a good textbook covering > fluorescence spectroscopy. > > Thanks in advance. > > Pat > > > --- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > [EMAIL PROTECTED] > > -- Roopa Thapar Assistant Professor, University of North Carolina Visiting Scientist, Hauptman-Woodward Institute 700 Ellicott Street, Buffalo, NY 14203
Re: [ccp4bb] insect expression system
Thanks to all that replied. You might find this useful. The question was: How to select an insect expression system for mammalian/viral glycoproteins? The following is a summary of the replies. *1. Baculovirus system* 1) For most proteins, the level of expression is far greater with bacuovirus. (Dima Klenchin) 2) An interesting system: BacMam. BacMam recombinant baculovirus in transporter expression: a study of BCRP and OATP1B1. Protein Expr Purif. 2006 Jun;47(2):591-8. Epub 2006 Jan 30. (Pius Stephen Padayatti) *2. Drosophila system* 1) With S2 you can get away without figuring out if the virus works, then again you probably need a stable cell line... (so which ever works...?) (OBS! cant do SeMet labelling with S2!! or if someone can please tell me) (Tommi Kajander) 2) We use S2 (drosophila cells) for generating our protein. Baculovirus is much more complicated to get running whereas S2 may generate slightly lower amounts of protein, but you will be able to get a system up and running quite quickly. In my experience I've had cases where I was only able to get very low virus titres for use, whereas the drosophila cells were able to go rapidly to expression for the same protein. The S2 cells are also a non-lytic system, so your protein will not get degraded so easily as they might in a lytic virus system. In my case I've tried them side-by-side and found S2 cells to be best (but that's obviously just in one case). (Paul A. McEwan) *3. Just use mammalian system!* 1) Why would you worry about insect expression systems if you already can secrete your constructs in mammalian cells? For such proteins, transient expression in HEK cells for example gives higher yields than baculo, is faster, cheaper, you can nicely control glycosylation, easily do Se-Met labelling and so on. Here are some references (PMID): 17355862, 17001101, 16823037, 11788735, 16082028. (Radu Aricescu) 2) I couldn't agree more with Radu. We had great success in expressing mg amounts of a secreted protein in HEK293 cells (with Radu's help :-) . The same protein was initially expressed in Sf9 cells but with much lower yields. Furthermore, we could very easily generate a stable HEK293 cell line expressing the same protein (at similar levels with transient transfections) with the Flp-In system in just a couple of weeks. We also have a LIC vector which is compatible with the Flp-In system. (Vangelis Christodoulou)
[ccp4bb] hkl to mtz with anomalous data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello everyone, we have been trying to convert an unmerged hkl-file to mtz such that the labels F+/F- or F/DANO (or I+/- etc respectively) are calculated, and failed so far. We would appreciate a hint towards the correct program/ options to use. Cheers, Tim - -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFIPwTtUxlJ7aRr7hoRArlLAJ4lTJrPhXjK/vRMf/kjOF0eKseOWACg0fAo iVQ+htqUa6tbyo4PXYMPEYg= =CKRB -END PGP SIGNATURE-
