[ccp4bb] postdoctoral position on radical-SAM Fe-S protein
Dear All, A postdoctoral position is available in my laboratory (University of Bristol, Medical Sciences Building) to continue our characterisation of the radical SAM enzyme Cfr, an Fe-S-containing rRNA methyltransferase that confers resistance to multiple classes of ribosome-acting antibiotics, including linezolid. Full details and directions on how to apply are available at: http://www.bris.ac.uk/boris/jobs/feeds/ads?ID=93491 Progress in this area is described in a recent publication: Protein Expr Purif. 2010 Dec;74(2):204-10. The post is funded by the Leverhulme Trust, for one year in the first instance. Feel free to contact me directly if you need further information, but to apply please follow the instructions on the link above. The closing date is 28th February. Best wishes Jim Spencer -- Dr. James Spencer, Lecturer in Microbiology School of Cellular and Molecular Medicine Medical Sciences Building University of Bristol University Walk Bristol BS8 1TD jim.spen...@bristol.ac.uk http://www.bristol.ac.uk/cellmolmed/staff/spencer.html -- Tel: (44) (0) 117 331 2084 Fax: (44) (0) 117 331 2091
[ccp4bb] PDB deposition ADIT without frames?
Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump between the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] PDB deposition ADIT without frames?
Thanks a lot for your suggestions! Meanwhile, my colleague entered the desired sequence information into the first website without frames, and after that, the usual frame layout re-appeared! I don't know whether this is a bug or intended ... Best regards, Dirk. Am 15.02.11 17:00, schrieb Dirk Kostrewa: Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump between the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] help in CONTACT
Dear CCP4ers, Is there any specific way that can help me locate the interactions between ligand (GTP) to any other residue in the protein(GTPase) using CONTACT. And how do I run CONTACT for a number of .pdb files(around 650) in one single step and separate them based on their interactions without running it individually for each of the .pdb file. The latter method is too time consuming so I need something quicker. Also, I am unable to get access to the script file for contact. Can someone please help me in this regard. Regards, Vineet Joshi
Re: [ccp4bb] help in CONTACT
On 02/15/2011 04:36 PM, vineet joshi wrote: Dear CCP4ers, Is there any specific way that can help me locate the interactions between ligand (GTP) to any other residue in the protein(GTPase) using CONTACT. And how do I run CONTACT for a number of .pdb files(around 650) in one single step and separate them based on their interactions without running it individually for each of the .pdb file. The latter method is too time consuming so I need something quicker. Also, I am unable to get access to the script file for contact. Can someone please help me in this regard. Regards, Vineet Joshi Have you looked at the PISA files held at the EBI for every structure. These should include the ligand-protein interfaces already calculated. Or if you look at the GUI and call up contact for one pdb You will get a script like this: ncont XYZIN /y/people/ccp4/projects/sinRbit/SinR-C_rem-inf-pk-shel-nat_buccaneer3-sym1-coot-3_lsq2.pdb source A/* target B/* mindist 0.0 maxdist 5.0 cells OFF END That would give contacts between chains A B I can see no automatic way of identifying how ligand and protein are labelled in your 600 GTPases though.. Eleanor
Re: [ccp4bb] Model Building: continuous update of distances as fragment moved
On Feb 14, 2011, at 4:01 PM, Paul McLaughlin wrote:
In doing some model building I want to move a domain of a protein
manually, as a rigid body, and see in real time continuous updates of
some distances from points on the domain to the rest of the protein
(we
have cross linking data).
I dimly remember being able to do with this O,at least a decade ago
(probably more), but it doesn't seem to work in current versions (I
have even dimmer recollections that this might have been a special
feature of a particular graphics card in an SGI)
In any event, does anyone know of anything that might allow us to do
this? { I am not asking about computational ways of exploring
alternate
packing of the domain to satisfy distances ( I know about these) -
rather we want to get a feel for what is possible by seeing it for
ourselves).
DIstance monitors in Chimera (www.cgl.ucsf.edu/chimera) automatically
update as structures are moved. Possibly also of interest, Chimera
can monitor steric clashes/contacts as structures are moved:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
Re: [ccp4bb] Model Building: continuous update of distances as fragment moved
Hi Eric -
I remember that the neighbor atom distances would dynamically update, and
even appear and disappear as your moving atom crosses the 3.2 A distance
threshold to another atom. I don't remember if the regular distance
define distances would do the same; I think not. I'm fairly sure that this
still works - the last time I used O was about six months ago, and the O
package I was using was from c. 2005.
More on-topic, Coot seems to have a dynamic distance command (look under
the Measure menu) which will do what you want.
Hope that helps,
Matt
--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric
Pettersen
Sent: Tuesday, February 15, 2011 4:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Model Building: continuous update of distances as
fragment moved
On Feb 14, 2011, at 4:01 PM, Paul McLaughlin wrote:
In doing some model building I want to move a domain of a protein
manually, as a rigid body, and see in real time continuous updates of
some distances from points on the domain to the rest of the protein (we
have cross linking data).
I dimly remember being able to do with this O,at least a decade ago
(probably more), but it doesn't seem to work in current versions (I
have even dimmer recollections that this might have been a special
feature of a particular graphics card in an SGI)
In any event, does anyone know of anything that might allow us to do
this? { I am not asking about computational ways of exploring alternate
packing of the domain to satisfy distances ( I know about these) -
rather we want to get a feel for what is possible by seeing it for
ourselves).
DIstance monitors in Chimera (www.cgl.ucsf.edu/chimera) automatically update
as structures are moved. Possibly also of interest, Chimera can monitor
steric clashes/contacts as structures are moved:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash
.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
