mas Huxley
+
Dr. Paul Smith
Assistant Professor
Department of Chemistry
Fordham University
441 E. Fordham Road
Bronx, NY 10458
phone: 718-817-4461
fax: 718-817-4432
email: psmit...@fordham.edu
office: JMH 638
http://www.fordham.edu/academics/programs_at_fordham_/chemistry/inde
Hello CCP4bb,
Firstly, thanks to all for your comments. However, I'm still unsure how to
sort all of this riding hydrogen business out.
Robbie's comments seem particularly apt:
"Because there were some reporting errors in the past
(http://proteincrystallography.org/ccp4bb/message18808.html) i
Hello CCP4 community,
I'm posting at large regarding a previously raised issue for REFMAC for which I
cannot find the conclusion in the old threads.
Specifically, does REFMAC add riding hydrogens during default refinement?
Though I've not requested that any hydrogens be added, only used if in t
Michael,
Unfortunately, I actually don't know who serves these machines apart from GE.
Because you brought up the subject of GE equipment and service, I thought I
would ask the community about the best options for routine crystallographic
scale FPLC.
In my opinion, following the takeover of Ph
ight to get all of modern crystallographic software
to run under windows. Even better, the other way around -- run linux native
and windows in a VM.
For the record:
Shelx is awesome
Fortran is a perfectly good programming language
I keep a slide rule in my desk.
--Paul
Paul Smith, Ph.D. -- p...@smit
Hello Evette,
I've encountered the same problem.
I have a perl utility that does much of what you would like.
It will run scalepack for you iteratively until the number of rejections
converges, or it will parse scalepack output. The output has by shell
gleaned from the scale log with the sam
Stefano,
I second the previous posts. Essential is a solid NVIDIA graphics card -
quadro or geforce and not something low end. Vendors don't matter so much, we
use both Dell and Hp and both are fine (essentially the same hardware inside).
Also, linux version doesn't matter. We use both Suse
Hi Seema,
In theory, Ammonium Sulfate contains some small fraction of neutral ammonia
which can act as a strong nucleophile and react with many heavy metal compounds.
That being said, I recently phased two structures with mercury soaks, both of
which contained ammonium sulfate. The first was a
I'm interested in opinions/advice on home source systems.
As synchrotron beamlines are more powerful and more accessible than ever, a
home source is really only needed for crystal screening, if at all.
With that idea in mind, what are options out there for buying and running a
home source in th
Hi Ed,
Yes, the entire core line is great for crystallography setups. As has been
mentioned, there are often issues with AMD processors as the occasional binary
that is distributed has been compiled with intel CPU optimizations.
I'm particularly fond of Dell's entry level servers with Quad-cor
Hi Hailiang,
Be sure to include "PARTIAL WCMB" in your sigmaa script. This option outputs
something more like a conventional FOM for use in DM.
Also, I would allow DM to run more cycles and suggest starting with default
parameters for solvent masking and density levels and then looking at the
Hi Jacob,
I see you're still in the crystallography business.
While you have an interesting idea, I doubt refining structures against entire
images would be of any use in obtaining higher quality macromolecular
structures. Much of what you see on the screen is a function of parameters
complet
Hello,
I'm not entirely sure I know what you mean, but what came to my mind was malic
enzyme. Check out Liang Tong's summary of structural data:
http://como.bio.columbia.edu/tong/Research/me.html
This protein has 2 nucleotide binding sites, one in a canonical Rossman fold
and another on the s
Also,
TLS parameters can be converted to conventional B-factors with both an
isotropic and an anisotropic component which can then represented in
conventional PDB format. PHENIX does this automatically, but I'm sure other
software can perform the conversion as well.
--Paul
Does anyone know of a source of AMP-N-PP?
Thanks,
--Paul
a wide range of different protein and solvent
density levels along with a custom mask and look at the resulting maps
(including NCS averaging) to see what's best.
Good Luck!
Paul Smith, Ph.D.
--- On Wed, 7/22/09, Jerry McCully wrote:
> From: Jerry McCully
> Subject: [ccp4bb] model co
Matthew,
Here's my $0.02:
Try more sophisticated twin tests such as xtriage from phenix or Ctruncate from
the latest CCP4 distro. Both programs include multiple twining tests. Second,
your R-factors seem very reasonable for a well refined structure missing 20% of
a not-so-well ordered domain
Jacob,
In CNS/XPLOR all topology files are created equal. You are free to combine all
topology into a single file and read that into CNS. Do you have two copies of
the same ligand or two different ligands? If you have two different ligands,
you can use prodrg or xplo2d/hic-up to generate uni
Mariah,
Try ChemDraw-3D, you can draw any chemical structure conceivable and write it
out as a pdb. It can also do a wide variety of energy minimizations for you.
Best,
--Paul
--- On Tue, 7/21/09, protein.chemist protein.chemist wrote:
> From: protein.chemist protein.chemist
> Subject: [cc
to STDOUT in ascii using automatically determining
ranges and binning values. These two programs work well like so:
"./titrate.pl FASTA.seq | ./plot.pl"
to produce a nice ascii plot of charge vs. pH.
I hope these are helpful to someone.
Best,
Paul Smith
Paladin
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