LIGPLOT will show this graphically, if the correct parameters are set in
ligplot.prm, but not state the interactions explicitly:
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
The relevant lines in ligplot.prm:
PLOT PARAMETERS
---
Y<- Include: Hydrophobic interactions - (Y/N)?
Hi Ed,
Bruker used to supply a utility called FRM2FRM that would "unwarp" their
images so that they were readable by Mosflm. You may want to consult
them directly; Matt Benning (I believe he's still there) was most
helpful when I was having problems with Bruker images a few years ago.
HTH,
I
l (and, by extension, HBPLUS).
best,
Iain
Iain Kerr
Senior Scientist
Dept. of Cellular & Molecular Pharmacology and
The Sandler Center for Drug Discovery
Phone: 415-502-8219 Fax: 415-502-8193
E-mail: ik...@cmp.ucsf.edu
QB3/Byers Hall Rm. 509
1700 4th Street
University of California
San Franc
Hi Raji,
Yeah, this can be frustrating. I had a related problem a few years ago.
The following thread may be informative:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=COOT&P=R2679&1=COOT&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
As Antony points out, it's a problem with X11 as imp
Hi Rex,
This can also be done in COOT, via the scripting interface:
(print-sequence imol)
best,
Iain
On 4/4/2010 6:55 AM, Rex Palmer wrote:
Is there software that will extract a protein sequence in either 3
letter or single letter code from a given pdb file?
Rex Palmer
Birkbeck College
No
I have a GRASP session saved which I startup by reading in "grasp.state". I
have changed some colours in "defcol.dat" and I would like these changes to
take effect in my saved session, but everytime I read in "grasp.state" it
changes the colour palette back to the default set again.
Does anyone kn
I'm trying to colour a molecular surface by sequence conservation...(sorry,
I think I incorrectly posted this to COOTBB the other day)
I've figured out how to do it in GRASP - modify the B-factor column in the
PDB file to represent the percentage conservation and then colour the
surface by B-facto
u not just mutate the
offending residue in your PDB file to get protskin to run (eg in coot
or pdb-mode). Then afterwards you can manually alter the B-factor for
that residue to what it should actually be and then run grasp etc.
Cheers,
Charlie
Iain Kerr wrote:
I tried that. My protein has a m
form.
Please give it a try and let us know.
Christophe Deprez
Iain Kerr wrote:
Of course, should have tried that BUT, it appears PROTSKIN has
problems everytime it encounters a gap. It now complains about res.
296 in the same fashion (287-295 are missing from the coordinates)
There must
Mark,
I had a very similar problem. Varying twin fraction in identical drops -
no logical pattern. I eventually solved the structure as you seem to
have, screening dozens of crystals to find an untwinned crystal or at
least one with very low or statistically insignificant twin fraction
(which
Dear all,
I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds 0.008A/1.1deg
angles.
In COOT (0.31) many of the residues whose side chains are (fully or
partially) set to 0.00 occupancy have really bad geometry...for w
"correct" the geometry of all atoms though so you
can make a prettier picture - but with no more information content re
the model if the occupancies stay 0.00
..
Eleanor
Iain Kerr wrote:
Dear all,
I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
Rfree ~
Dear all,
I find myself posed with a rather interesting if somewhat confusing problem.
Two crystals grown from the same conditions, let's call them A and B..
A:
Resolution 2.1A
SpacegroupP4?
Rmerge0.137 (0.324)
Mean((I)/sd(I)) 41.0 (17.8)
Completeness
Apologies, I think I neglected to attach the wilson plots...I'll do so
on Friday.
best,
Iain
Iain Kerr wrote:
Dear all,
I find myself posed with a rather interesting if somewhat confusing
problem.
Two crystals grown from the same conditions, let's call them A and B..
A:
Thanks very much for all the suggestions so far.
While I am pursuing all the checks and balances for twinning here are
the Wilson plots I forgot to attach before..I am not sure what is going
on, especially in B !
best,
Iain
On Oct 25 2007, Iain Kerr wrote:
Dear all,
I find myself
Does anyone know where I can find a copy of "libccp4map.so" for
Mapslicer please ?
Thanks,
Iain
Sorry, to clarify the library is missing from my system (wasn't compiled
during CCP4 installation)..I need a copy to add to $CLIB.
Thanks,
Iain
Iain Kerr wrote:
Does anyone know where I can find a copy of "libccp4map.so" for
Mapslicer please ?
Thanks,
Iain
Deena,
A lot of this comes down to personal preference at the end of the
day..you just have to find what works for you.
I primarily use MacOSX and Linux. I also have a Vista partition on my
laptop to share Microsoft office files with others in the department
that use Windows or Macs..no comm
Patrick,
I've not used fink to install ccp4 so can't comment on that, but if you
want a quickie working suite:
I downloaded the pre-compiled binaries from the CCP4 ftp site and they
work fine.
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/
Use the Tcl/tk and Blt distributions on the CCP4 websit
Oh, you tried the binaries..sorry..
Hmmm..I don't recall having the same problem..I'll have a look at what
I've got here. You could always compile it from source code..
Iain
Iain Kerr wrote:
Patrick,
I've not used fink to install ccp4 so can't comment on that, b
Hi Sabine,
I had a similar problem years ago. Have you tried oils ? (mineral oil,
paraffin oil, 50:50 mixtures of either with N-paratone)
You can either 1. add a small amount (1ul or less) to the drop
containing the crystals and mount from there or 2. if you are quick
enough, transfer the cr
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