[ccp4bb] Postdoctoral Positions available at Scripps Research

[Robyn Stanfield]

Fully funded postdoctoral positions are available in the laboratory of Prof. 
Ian Wilson at Scripps Research  (http://wilson.scripps.edu, email: 
wil...@scripps.edu) for highly motivated candidates who are interested in 
immune recognition and inhibition of microbial pathogens. Specifically, we are 
looking for individuals interested in working on projects focused on 
structure-based design of vaccine candidates, as well as antibody and small 
molecule therapeutics against microbial pathogens. Candidates with prior 
experience in structural biology with interests in virology, immunology, 
infectious disease, antibody and antigen characterization, and 
design/development of vaccines and therapeutics, are encouraged to apply.  For 
more information and the full job posting see:  
https://www.scripps.edu/careers/  under the Department of Integrative 
Structural and Computational Biology, Wilson lab.




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Kabat antibody numbering

[Robyn Stanfield]

Hi Ariel,
   Andrew Martin has a server that does it for the variable domain portion of 
your Ab- it's at:

http://www.bioinf.org.uk/abs/abnum/

Have fun,
Robyn

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ariel 
Talavera
Sent: Tuesday, May 18, 2010 3:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Kabat antibody numbering

Hi there CCP4ers,

I need to number a PDB file following the Kabat numbering. Is there any 
script to do this numbering automatically?

Thanks a lot in advanced.

Best,
Ariel

-- 
*
Ariel Talavera Pérez, PhD
Nanobiology Group
Center of Molecular Immunology
calle 216 esq. A 15, Atabey, Playa
Havana 11600, CUBA
tel: (53-7) 214 3178
fax: (53-7) 272 0644
email: talav...@cim.sld.cu
*

Re: [ccp4bb] X-Ray films

[Robyn Stanfield]

I'm not sure there was actually any science in the movie, but 'The Incredible 
Hulk' had some opening scenes shot at the beautiful ALS synchrotron... and I 
just want to point out that I only saw that movie because my kids made me!  
Took a lot of junk food to make it through that one
-Robyn

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of harry 
powell
Sent: Thursday, April 15, 2010 9:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] X-Ray films

Hi

Not a question about films for recording X-rays on, but a question  
about films about X-rays, Crystallography and related subjects!

I was wondering what ccp4bbers favourite movies involving real  
science, especially crystallography might be? If they're from  
Hollywood, though, I'd guess it should be "favorite"...

I'm a little tired, but the only one I can think of at the moment is  
actually based on results from fibre diffraction - "Life Story", with  
Jeff Goldblum. There must be others, though.

Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH

Re: [ccp4bb] problem in calculation of elbow angle.

[Robyn Stanfield]

Dear Tarique,



   The elbow angle in a Fab is just the angle between two pseudo-twofold axes: 
one relating VL to VH and one relating CL to CH. You can find the 
pseudo-twofold axes using many different least-squares alignment programs, just 
pick your favorite. Then, just take the dot product of the two resulting 
axes/vectors for your elbow angle.  You can do this quite accurately with a 
pencil and paper and maybe a handheld calculator.



The error message you report indicates problems calculating the pseudo-two fold 
axes;  you probably either have (a) an unusual Fab where the axes relating 
light to heavy chains

deviate significantly from 180 degrees (b) a glitch or unusual feature in your  
PDB file that has thrown off the calculation of the pseudo-two folds (thus 
making them appear to deviate from 180).  Bernhard might be able to enlighten 
you more as he wrote the code and error 
messages(b...@ruppweb.org)



Cheers,

Robyn

ro...@scripps.edu


From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of tarique 
khan
Sent: Wednesday, January 13, 2010 4:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] problem in calculation of elbow angle.

Dear all,
I am trying to calculate elbow angle of my fab structure using a online 
software developed by Robyn L. Stanfield et. al. but it is giving a solution 
with the following errors.

WARNING: rotation matrix contains significant additional contributions



WARNING: and deviates significantly from a pseudo-twofold0.721



WARNING: rotation matrix contains significant additional contributions





WARNING: and deviates significantly from a pseudo-twofold :0.726





WARNING: there have been deviations from expected values -

   please read the log above!)

   No guarantee that the calulated elbow angle is meaningful





   The Elbow angle is probably 174.5 deg.



Kindly suggest some other way of accurately, calculating elbow angle.



regards.



Tarique khan