[ccp4bb] Postdoc position in the Fesik Lab at Vanderbilt University

[Phan, Jason]

Please post:

Advertisement for a postdoctoral structural biologist position at Vanderbilt 
University Medical Center, Department of Biochemistry

A postdoc position is available in the laboratory of Dr. Stephen Fesik 
(https://lab.vanderbilt.edu/fesik-lab/)
 for a structural biologist with experience in protein NMR or X-ray 
crystallography.  Responsibilities will include protein 
expression/purification, conducting fragment screens using NMR, and all aspects 
of x-ray crystallography, including preparation of protein-inhibitor complexes, 
crystallization, home/synchrotron data collection, and structure determination. 
Experience in cloning, site-directed mutagenesis, and the use of robots are 
highly preferred.  The ideal candidate should be self-motivated and be able to 
communicate effectively in a highly collaborative environment.




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[ccp4bb] Job post

[Phan, Jason]

Please post an ad for us:

Advertisement for a postdoctoral structural biologist position at Vanderbilt 
University Medical Center, Department of Biochemistry

A postdoc position is available in the laboratory of Dr. Stephen Fesik 
(https://lab.vanderbilt.edu/fesik-lab/) for a structural biologist with 
experience in protein NMR or X-ray crystallography.  Responsibilities will 
include protein expression/purification, conducting fragment screens using NMR, 
and all aspects of x-ray crystallography, including preparation of 
protein-inhibitor complexes, crystallization, home/synchrotron data collection, 
and structure determination. Experience in cloning, site-directed mutagenesis, 
and the use of robots are highly preferred.  The ideal candidate should be 
self-motivated and be able to communicate effectively in a highly collaborative 
environment.




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

Re: [ccp4bb] cif questions

[Phan, Jason]

I’ve just discovered that for Coot 0.8.8, when importing the cif file for the 
ligand, select All under the “Select Mol” pulldown menu to get the restraints 
imported properly, then all the Chi angles become available.

HTH.

Jason

On Mar 8, 2018, at 11:55 AM, Thomas, Leonard M. 
mailto:lmtho...@ou.edu>> wrote:

Hello All,

We have run into a problem recently when working with cif files for ligands 
that have been either soaked or cocrystallized with the proteins we are looking 
at.  Most of the ligands cif files have been used previously and while not in 
the CCP4 library database are available from the pdb ligand database.  Now when 
we go to use them, specifically in coot after refinement in Refmac we get an 
error saying there are no restraints for the ligand.  We have tried reading the 
cif file in before and after reading the pdb file in.

We can put the molecule/ligand and cif file into Phenix and all seems well with 
coot but when moving back to CCP4/coot we still have the problem.Both CCP4 
and Phenix are using the same version of coot so I don’t think it is a version 
problem with coot.

Any insight would be appreciated.

Thanks,

Leonard Thomas, Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://structuralbiology.ou.edu/mcl

Re: [ccp4bb] Ambiguous metal ion at active site.

[Phan, Jason]

Looks like Ni (II) in the 4-coordination tetrahedral config. Could it be loose 
Ni ions from the IMAC column if you’d used one? Ni and Mg have very close 
atomic radii and Ni (II) can form the 6-coordinate complex as well.

> On Jul 9, 2015, at 4:35 AM, Dilip Kumar  wrote:
> 
> Dear All
> 
> I have solved a structure of a metal-ion dependent exonuclease enzyme. In 
> homologous structures, two or three Manganese ions are present at catalytic 
> center. However, I have used 2 mM MgCl2 in protein purification buffer. I 
> tried to fit both of these metal ions at catalytic center but in both cases 
> it still shows green density (Sigma level ~ 7) in difference map and low 
> b-factor (<10) for these metal ions. For better understanding I have attached 
> the screenshot of metal ions with difference map on. Please suggest me the 
> possible reasons or methods to validate the presence of any other metal ions 
> at catalytic center.
> 
> Thanks in advance.
> 
> Regards
> Dilip Kumar
> Research Associate
> Chemical and Systems Biology Unit
> CSIR-Institute of Genomics & Integrative Biology
> Delhi-110025
> 

[ccp4bb] Protein purification and crystallization position available in the Fesik Lab at Vanderbilt University

[Phan, Jason]

An opening is available in the laboratory of Dr. Stephen Fesik 
(http://www.mc.vanderbilt.edu/fesiklab) for the Research Associate position in 
structural biology and drug discovery. The candidate must possess a degree in 
biochemistry or a related field with 1-2 years of experience in protein 
purification. Experience in protein crystallography is a plus but not required. 
The ideal candidate should be courteous, responsible, organized, hard-working, 
and be able to multi-task and communicate efficiently.  The successful 
candidate will be trained initially but will work independently or with limited 
supervision on assigned duties thereafter. Please send CV or resume to 
jason.p...@vanderbilt.edu

Re: [ccp4bb] Problem sourcing resolved

[Phan, Jason]

Thank you, Ian, Ben and Bill. 
My apology for the S in setenv, a typo.
I expanded the variables in $PATH and found the culprit: set PATH =
(/usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64) in my /etc/cshrc
file. I have the line "source /etc/cshrc" at the top of my ~/.cshrc
file. After commenting it out, voila!!! 

Thank you, Gentlemen. It'll be a good weekend. One less thing to think
about.

Jason


-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com] 
Sent: Friday, March 27, 2009 5:38 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: !RE: [ccp4bb] Problem sourcing


Hi Jason

Nothing obviously wrong there (I assume that the capital 'S' in 'Setenv'
is just your mail client being silly?).  Is that the last line printed?
(sorry I got it wrong before, I just checked & the source will stop
*after* the offending line, not before as I said, so it's the last line
you want).  If you paste the bad line at the shell prompt do you get the
same error?  Try 'set echo' & source again (you can turn both verbosity
and echoing on for max info!).  This will expand the variables ($PATH
etc).

Are you actually using C shell (csh) or TC shell (tcsh)?  csh has some
rubbish features & I wouldn't recommend it!  If you have actually
installed csh I would install tcsh instead!  I think the CCP4 shell
script actually assumes you have tcsh not csh.

Hope this helps!

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phan, Jason
> Sent: 27 March 2009 18:52
> To: Ian Tickle
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] Problem sourcing
> 
> Dear Ian,
> 
> I got bumped out at this line:
> 
> Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
> 
> Could you shed some light on this? I'm using C shell. It can't be the
> syntax since I could source as root.
> 
> Thanks,
> Jason
> 
> 
> 
> -Original Message-
> From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
> Sent: Friday, March 27, 2009 12:39 PM
> To: Phan, Jason
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] Problems sourcing
> 
> 
> Hi Jason
> 
> Type 'set verbose' (without the apostrophes) and trying sourcing
again,
> it should stop just before the offending line.
> 
> Cheers
> 
> -- Ian
> 
> > -Original Message-
> > From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk]
> On
> > Behalf Of Phan, Jason
> > Sent: 27 March 2009 16:24
> > To: CCP4BB@jiscmail.ac.uk
> > Subject: RE: [ccp4bb] Problems sourcing
> >
> > Dear List,
> >
> > I am trying to install the latest CCP4 6.1.1 binaries on Linux and
> > running into sourcing problem. I could source the ccp4.setup file as
> > root (c-shell) and ccp4 ran just fine. But as a user, with the same
> > shell, I could not source the setup file. The error is "setenv: Too
> many
> > arguments". There are so many environment variables in that file
it's
> > impossible to find the culprit. Could someone help me out?
> >
> > Thanks,
> > Jason
> >
> >
> > This transmission may be confidential or protected from disclosure
and
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> > only for review and use by the intended recipient. Access by anyone
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> > is unauthorized. Any unauthorized reader is hereby notified that any
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information,
> or
> > any act or omission taken in reliance on it, is prohibited and may
be
> > unlawful. If you received this transmission in error, please notify
> the
> > sender immediately. Thank you.
> 
> 
> 
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Re: [ccp4bb] Problem sourcing

[Phan, Jason]

Dear Ian,

I got bumped out at this line:

Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test

Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.

Thanks,
Jason



-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com] 
Sent: Friday, March 27, 2009 12:39 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing


Hi Jason

Type 'set verbose' (without the apostrophes) and trying sourcing again,
it should stop just before the offending line.

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phan, Jason
> Sent: 27 March 2009 16:24
> To: CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] Problems sourcing
> 
> Dear List,
> 
> I am trying to install the latest CCP4 6.1.1 binaries on Linux and
> running into sourcing problem. I could source the ccp4.setup file as
> root (c-shell) and ccp4 ran just fine. But as a user, with the same
> shell, I could not source the setup file. The error is "setenv: Too
many
> arguments". There are so many environment variables in that file it's
> impossible to find the culprit. Could someone help me out?
> 
> Thanks,
> Jason
> 
> 
> This transmission may be confidential or protected from disclosure and
is
> only for review and use by the intended recipient. Access by anyone
else
> is unauthorized. Any unauthorized reader is hereby notified that any
> review, use, dissemination, disclosure or copying of this information,
or
> any act or omission taken in reliance on it, is prohibited and may be
> unlawful. If you received this transmission in error, please notify
the
> sender immediately. Thank you.



Disclaimer
This communication is confidential and may contain privileged
information intended solely for the named addressee(s). It may not be
used or disclosed except for the purpose for which it has been sent. If
you are not the intended recipient you must not review, use, disclose,
copy, distribute or take any action in reliance upon it. If you have
received this communication in error, please notify Astex Therapeutics
Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies
of the message and any attached documents. 
Astex Therapeutics Ltd monitors, controls and protects all its messaging
traffic in compliance with its corporate email policy. The Company
accepts no liability or responsibility for any onward transmission or
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This transmission may be confidential or protected from disclosure and is only 
for review and use by the intended recipient. Access by anyone else is 
unauthorized. Any unauthorized reader is hereby notified that any review, use, 
dissemination, disclosure or copying of this information, or any act or 
omission taken in reliance on it, is prohibited and may be unlawful. If you 
received this transmission in error, please notify the sender immediately. 
Thank you.

Re: [ccp4bb] Problems sourcing

[Phan, Jason]

Dear List,

I am trying to install the latest CCP4 6.1.1 binaries on Linux and
running into sourcing problem. I could source the ccp4.setup file as
root (c-shell) and ccp4 ran just fine. But as a user, with the same
shell, I could not source the setup file. The error is "setenv: Too many
arguments". There are so many environment variables in that file it's
impossible to find the culprit. Could someone help me out?

Thanks,
Jason


This transmission may be confidential or protected from disclosure and is only 
for review and use by the intended recipient. Access by anyone else is 
unauthorized. Any unauthorized reader is hereby notified that any review, use, 
dissemination, disclosure or copying of this information, or any act or 
omission taken in reliance on it, is prohibited and may be unlawful. If you 
received this transmission in error, please notify the sender immediately. 
Thank you.