[ccp4bb] Post-doc position - Biophysics and RNA virus proteins
Post-doc in Peersen Laboratory Biochemistry & Molecular Biology Colorado State University Post-doctoral fellow position in structural biology and biophysical studies of RNA virus replication. The projects are focused on the structures of viral RNA-dependent RNA polymerases, functional complexes involved in RNA synthesis, and the assembly of membrane anchored replication centers formed by single stranded RNA viruses. The project will build on recent studies of viral elongation complexes to further our understanding of polymerase function and replication fidelity. Prior studies are described in Gong & Peersen, PNAS 107:22505, Hobdey et al., J. Virology 84:8072, and Nadig et al., PNAS+ (in press). Previous experience in X-ray crystallography, RNA biochemistry, and/or fluorescence methods would be advantageous. Job Requirements: --- The position requires a Ph.D. at time of hire with prior experience in protein biochemistry, molecular biology, and/or biophysical methods. Applications should be received by August 20, 2012 for full consideration. Interested individuals should submit a CV, statement of research and career interests, and contact information for three references at http://www.natsci.colostate.edu/employment/bmbPdoc/ CSU is an EO/EA/AA employer. CSU conducts background checks on all final candidates.
Re: [ccp4bb] Zalman displays and Macs?
Here are the SwitchResX settings for the ZM-M220W that I alluded to in last
night's reply - these get it work via a Thunderbolt port using a DisplayPort to
VGA adapter cable on a new 27" iMac. I'm not sure if all these settings need
to be entered and even after entering the frequency specs the software could
not quite figure out the 1680x1050 resolution right. I thus configured it as a
Custom Resolution and got it to work.
Display Information Panel: (gleaned from manual)
V. freq 56 - 75 Hz
H. freq 31.50 - 80.00 kHz
Pixel Clock 28.32 - 135 MHz
Default Resolution1680 x 1050 @ 60 Hz
Current Resolutions Panel:
Set to 1680 x 1050, 60 Hz (likely only available after setting custom
resolution in next panel)
Custom Resolutions:
Created a new one by clicking "+" button
Check the "Use simplified settings" button and selected CVT-RB from popup
menu
Set Active area as 1680 and 1050
Set Scan rate Vertical to 56.632 Hz
Selected Positive sync for Horizontal only.
Then saved and rebooted. Finally, it looks like you have to set the resolution
in the Displays panel for each use of the system (I use the Displays Menu bar
icon). And SwitchResX will set you back 14 ⬠(~$18) after a ten day demo
period.
Cheers,
Olve
==
Final (auto-calculated) result was the following:
Pixel Clock118.75 MHz
{ParameterHorizVert}
Active 1680 1050
Front Porch483
Sync width 32 6
Back porch 8021
Blanking 160 30 (not editable)
Total 1840 1080 (not editable)
Scan Rate 64.538 kHz 59.757 Hz
Selected Positive sync for Horizontal only
Final config became "1680 x 1050, 56.76 Hz"
Re: [ccp4bb] Zalman displays and Macs?
I've been having the same issues and appreciate the update in this thread about pins 15/16 being swapped - likely explains why the DVI port seems "dead" when connecting to a new Mac but works fine on older systems. On the VGA side, I did get the MZ-M220W to work correctly with a DisplayPort-->VGA adapter, but to get the native 1680 x 1050 resolution needed for the stereo to work I had to patch the system with the utility "SwitchResX" (http://www.madrau.com/indexSRX4.html). It basically lets you supplement the OSX equivalent of modeline and thus define new monitor resolutions. The exact settings I used are in the lab at the moment, but I'll do my best to remember to post them tomorrow. It was not as straightforward as I had thought, but then again I did not bother to read the manual before playing with it and still solved the problem in about ten minutes. Olve
[ccp4bb] Post-doc positions at Colorado State
This is a reposting of Post-doc ad with the full-consideration application deadline next week. Note that there are multiple independent post-docs with projects involving mostly crystallography or mostly biochemistry. === Post-doctoral fellow positions in ubiquitin signaling and RNA virus replication The Peersen and Cohen laboratories at Colorado State University in Fort Collins are recruiting up to three post-doc positions for studies of macromolecular interactions and structure. The positions require a Ph.D. at time of hire with prior experience in protein biochemistry, molecular biology, or biophysical methods. The Peersen lab projects are focused on the structures of viral RNA-dependent RNA polymerases and the assembly of membrane anchored replication centers formed by single stranded RNA viruses. The projects will build on recent studies of viral elongation complexes (Gong & Peersen, PNAS 107:22505, Hobdey et al., J. Virology 84:8072) to further our understanding of polymerase function, replication fidelity, and higher order assemblies. Previous experience in X-ray crystallography, RNA biochemistry, membrane systems, or fluorescence methods would be advantageous. The Cohen laboratory position is to study mechanisms of signaling by polyubiquitin. Recent work defined the linkage-specific avidity mechanism for polyubiquitin binding (Sims & Cohen, Mol Cell 33:775-783; Sims et al., Nat. Struct. Mol. Biol. 16:883-889). Available projects include studies of polyubiquitin receptor proteins, development of linkage-specific polyubiquitin sensors, and investigation of the role of linkage-specificity in signaling by polyubiquitin in vivo. Candidates should have prior experience in protein biochemistry and molecular biology; familiarity with biophysical methods or mammalian cell culture is desirable. Applications should be received by August 5, 2011 for full consideration. Interested individuals should submit a CV, statement of research and career interests, and contact information for three references at http://www.natsci.colostate.edu/employment/bmbPdoc/ CSU is an EO/EA/AA employer. CSU conducts background checks on all final candidates.
[ccp4bb] Multiple post-doc positions at Colorado State University
Post-doctoral Fellows Peersen and Cohen Laboratories Department of Biochemistry & Molecular Biology Colorado State University Post-doctoral fellow positions in ubiquitin signaling and RNA virus replication biochemistry / structural biology The Peersen and Cohen laboratories at Colorado State University in Fort Collins are recruiting up to three post-doc positions for studies of macromolecular interactions and structure. The positions require a Ph.D. at time of hire with prior experience in protein biochemistry, molecular biology, or biophysical methods. The Peersen lab projects are focused on the structures of viral RNA-dependent RNA polymerases and the assembly of membrane anchored replication centers formed by single stranded RNA viruses. The projects will build on recent studies of viral elongation complexes (Gong & Peersen, PNAS 107:22505, Hobdey et al., J. Virology 84:8072) to further our understanding of polymerase function, replication fidelity, and higher order assemblies. Previous experience in X-ray crystallography, RNA biochemistry, membrane systems, or fluorescence methods would be advantageous. The Cohen laboratory position is to study mechanisms of signaling by polyubiquitin. Recent work defined the linkage-specific avidity mechanism for polyubiquitin binding (Sims & Cohen, Mol Cell 33:775-783; Sims et al., Nat. Struct. Mol. Biol. 16:883-889). Available projects include studies of polyubiquitin receptor proteins, development of linkage-specific polyubiquitin sensors, and investigation of the role of linkage-specificity in signaling by polyubiquitin in vivo. Candidates should have prior experience in protein biochemistry and molecular biology; familiarity with biophysical methods or mammalian cell culture is desirable. Applications should be received by August 5, 2011 for full consideration. Interested individuals should submit a CV, statement of research and career interests, and contact information for three references at http://www.natsci.colostate.edu/employment/bmbPdoc/ CSU is an EO/EA/AA employer. CSU conducts background checks on all final candidates.
Re: [ccp4bb] rmsd calculation
I would highly recommend Doug Theobald's program Theseus for this - the pictures at www.theseus3d.org say it all. Theseus does maximum likely hood superimpositions of multiple structures (i.e. NOT pairwise against a "master" copy), and the real beauty of it is that you don't have to pick which residues you want to superimpose. Places where the whole set of structures show divergence are effectively down-weighted and don't contribute much to the final solution vs. least squares where every atom position has equal weight and the "bad" parts screw up the alignment of the "good" parts. For this, I would do a Theseus superposition of all the structures and then analyze the set of superimposed structures by whatever method you want (e.g. rmsd of variances in important sections of the structures). - Olve ------- Olve Peersen Associate Professor Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office (MRB 279) 970.491-0271Lab (MRB 149) 970.491-0494Fax [EMAIL PROTECTED] --- On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote: Eleanor Dodson wrote: It is a bit clunky - you can use siperpose molecules - fit residues to fit a selected range (1-40; 60-100 say) and write out a complete fitted pdb file. Then you could use a VERY old program compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb) and it will match all pairs with the same RESIDUE ID and give the RMSD distance There is documentation for it. There's a nice (non-CCP4) program called ProFit that does a pretty nice job of superimposing with a lot of flexibility. Thanks, Donnie
Re: [ccp4bb] Extraction of test set from CNS reflection file
A few years ago I did this by first using the solved structure to
generate a hypothetical (FCALC) data set to some rather optimistic
resolution limit (2A when I was stuck at 2.7), carrying out a random
Rfree selection on this FCALC set, and then dumping the FCALCs while
retaining the Rfree selections. This then became a "master" Rfree
selection set that I would merge into new data as it became
available, ensuring that all my data retained the same Rfree
selections (and the percentage Rfree generally stayed pretty
constant). For some reason (probably patience), I only figuring out
how to do the merging-in of the Rfree set using XPLOR rather than CNS
- the script is below.
These days we've largely gone to running a simulated annealing job to
uncouple new random Rfree sets, and also using dtcell (from d*TREK)
to rotate new data into the same orientation as the master dataset/
molecular orientation.
- Olve
-------
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO 80523-1870
---
970.491-0433Office (MRB 279)
970.491-0271Lab (MRB 149)
970.491-0494Fax
[EMAIL PROTECTED]
---
{+ file: F432master.inp +}
{+ directory: xtal_util +}
{+ description: Make a master TEST set in F432 for the alpha-8mer
data by
inheriting the old TEST room temparature TEST set
from the
file na03a.cvi and then declaring additional TEST
reflections
by taking a random 10% of the HKLs NOT PRESENT in
na03a.cvi.
Output file CONTAINS ONLY THE TEST
ARRAY +}
{+ authors: Olve Peersen +}
{- begin block parameter definition -} define(
{== files ===}
{* reflection file - which contains a previously used test *}
{===>} reflection_old="na03a.cvi";
{* reflection file - to which test set array will be added *}
{===>} reflection_new="F432master.hkl";
{* percentage of reflections to be used for TEST set - ie. 10% *}
{===>} percentage=10.0;
{* output reflection file *}
{===>} reflection_outfile="F432master.cvt";
{===
}
{things below this line do not normally need to be
changed }
{===
}
) {- end block parameter definition -}
checkversion 0.9
evaluate ($log_level=quiet)
xray
{=== Read old data
Make a copy of the pre-existing TEST set into OLD_TEST
Make an array to keep track of "known" (i.e. TEST = 0/1)
HKLS in OLD_SIGMA
Undeclare all other likely arrays to free up memory ==}
reflection @&reflection_old end
declare name=old_test type=integer domain=reciprocal end
do (old_test=test) (all)
declare name=old_sigma type=real domain=reciprocal end
do (old_sigma=sigma) (all)
undeclare name=fobs domain=reciprocal end
undeclare name=sigma domain=reciprocal end
undeclare name=iobs domain=reciprocal end
undeclare name=sigi domain=reciprocal end
undeclare name=test domain=reciprocal end
{=== Read in the new data file, undeclare then redeclare TEST to
make sure it
exists. Then undeclare all other likely arrays to free up
memory ==}
reflection @&reflection_new end
undeclare name=test domain=reciprocal end
declare name=test type=integer domain=reciprocal end
undeclare name=fobs domain=reciprocal end
undeclare name=sigma domain=reciprocal end
undeclare name=iobs domain=reciprocal end
undeclare name=sigi domain=reciprocal end
{== Set up an array OLD to keep track of previously known
reflections versus
those that have never been considered for inclusion in the
TEST set ==}
declare name=old type=integer domain=reciprocal end
do (old=0) (all)
do (old=1) (old_sigma >= 0.001) { HKL is in old data/TEST set }
{== Set up TEST=1 for percentage of data }
do (test=0) (all){ Reset all to working set }
do (test=1) (old_test=1) { Inherit old TEST values
for knowns }
do (test=1*int(random()+&percentage/100.)){ Randomly assign
TEST = 1 for }
(old=0) { percentage of new
HKLs }
write reflection { Output new file with TEST
flag only }
output=&reflection_outfile
test
end
end
stop
On Mar 1, 2007, at 11:55 AM, Axel Brunger wrote:
Actually, the merge script will create the superset of both reflection
data sets, so it won't delete reflections from one data set that are
not present in the other data s
Re: [ccp4bb] journals with on-hold policy
However, be warned that your structure needs to be very sexy to get into Cosmo, and then there might be better choices. If it is not, but has a few stacked beta sheets, you may be able to color the figures in plaid designs and get into American Rifleman (I assume there is no European Rifleman). On Feb 16, 2007, at 8:17 AM, William Scott wrote: I would like to find out which journals (that publish structural work) are OK with placing structures on hold for the full year permitted by the PDB. American Rifleman, Cosmopolitan, and Dog World
[ccp4bb] REPOST: Post-doc at Colorado State
This is merely a second posting of a message from about 10 days ago - there is no need to reply if you have already expressed interest A post-doctoral position is available in Dr. Olve Peersen’s laboratory at Colorado State University to study protein–protein and protein–nucleic acid interactions in positive strand RNA virus replication proteins. A wide range of projects ranging from X-ray crystallography to dynamics studies to biochemical and biophysical characterization of macromolecular complexes can be pursued, depending on the interests and qualifications of the applicant. Interested individuals should send a CV and contact information for 2-3 references to [EMAIL PROTECTED] Further details about post-doctoral positions in the Department of Biochemistry & Molecular Biology at Colorado State University can be found at http:// www.bmb.colostate.edu/jobs_detailed.cfm?jobs_id=28. Colorado State University is located in Fort Collins, a city just ranked one of the “Best Places to Live” by Money magazine based on numerous (and probably highly correlated) quality of life indicators. The University is an equal opportunity/affirmative action employer and complies with all Federal and Colorado State laws, regulations, and executive orders regarding affirmative action requirements for all programs. The Office of Equal Opportunity (OEO) is located in 101 Student Services Building. In order to assist Colorado State University in meeting its affirmative action responsibilities, ethnic minorities, women, and other protected class members are encouraged to apply and to so identify themselves. --- Olve Peersen Associate Professor Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office (MRB 279) 970.491-0271Lab (MRB 149) 970.491-0494Fax [EMAIL PROTECTED] ---
[ccp4bb] Post-doc at Colorado State studying RNA virus replication complexes
There is a post-doctoral position is available in Dr. Olve Peersen’s laboratory at Colorado State University to study protein–protein and protein–nucleic acid interactions in positive strand RNA virus replication complexes. A wide range of projects ranging from X-ray crystallography to dynamics studies to biochemical and biophysical characterization of macromolecular complexes can be pursued, depending on the interests and qualifications of the applicant. Interested individuals should send a CV and contact information for 2-3 references to [EMAIL PROTECTED] Further details about post-doctoral positions in the Department of Biochemistry & Molecular Biology at Colorado State University can be found at http:// www.bmb.colostate.edu/jobs_detailed.cfm?jobs_id=28. Colorado State University is located in Fort Collins, a city just ranked one of the “Best Places to Live” by Money magazine based on numerous (and probably highly correlated) quality of life indicators. The University is an equal opportunity/affirmative action employer and complies with all Federal and Colorado State laws, regulations, and executive orders regarding affirmative action requirements for all programs. The Office of Equal Opportunity (OEO) is located in 101 Student Services Building. In order to assist Colorado State University in meeting its affirmative action responsibilities, ethnic minorities, women, and other protected class members are encouraged to apply and to so identify themselves. --- Olve Peersen Associate Professor Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office (MRB 279) 970.491-0271Lab (MRB 149) 970.491-0494Fax [EMAIL PROTECTED] ---
