You can calculate volumes and much more, here:
http://www.molinspiration.com/cgi-bin/properties
Javier
On Wed, Aug 13, 2014 at 12:06 AM, sreetama das
wrote:
> Dear all,
> Is there any software or web server available to calculate the volume of a
> ligand if the ligand coordinates are provided
Hey,
in my old lab we developed a system to express two proteins from one
plasmid using the before mentioned GAL1-10 Promoter. Giving the use of
different plasmids with different selection markers, coexpression of
multiple proteins is possible in yeast. The system was used in a study
publishe
On 8/13/14 2:29 PM, Theresa Hsu wrote:
Dear all
One of my human membrane proteins have been described to interact with
additional subunits for its activity. To obtain functional form in yeast
(Saccharomyces), I can think of two approach of either cloning all the subunits
under one promoter or
Hello All-
I am interested in monomer/dimer contamination when building a crystal lattice,
ie. if you are building a crystal lattice with a monomeric species of protein,
incorporation of dimers may yield lattice or surface defects. This species may
be considered a macromolecular contaminant. I
Dear all
One of my human membrane proteins have been described to interact with
additional subunits for its activity. To obtain functional form in yeast
(Saccharomyces), I can think of two approach of either cloning all the subunits
under one promoter or reconstitute in vitro.
For the first op
I am pleased to announce the publication of the latest issue of the
Computational Crystallography Newsletter:
http://www.phenix-online.org/newsletter/
A listing of the articles and short communications is given below.
Please note that the newsletter accepts articles of a general nature
of
Hi Remie,
You can add harmonic restraints for parts you do not want to move too much.
Instructions could be found here:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Harmonic
Regards
Garib
On 13 Aug 2014, at 15:44, Remie Fawaz-Touma wrote:
> Hi everyone,
Hi everyone,
Does anyone know of a way to refine with CCP4 - Refmac5 (restrained refinement
is what I do) fixing a part of the the ligand?
Thank you very much for your input,
Remie
It depends to a large extent on the orientation of the Ncs operator.
If that aligns with a crystal axis then there can be bias in the Rfree
selection but if it doesn't NCS does not affect the Free R much ( in my
opinion..)
Eleanor
On 13 August 2014 09:14, Ed Pozharski wrote:
> By all means, tr
On Tue, Aug 12, 2014 at 10:28 PM, Keller, Jacob
wrote:
> A somewhat similar question, with a quick answer I hope: when programs
> output CC's of 1/2 datasets, are several random halvings compared/averaged,
> and if not, does this make a difference, or are the scores so similar
> there's no point?
Dear Kristof,
Have you tried to solve it with the new SHELXT? You can force it to
consider only chiral (Sohnke) space groups by putting -c on the command
line.
Best wishes, George
On 13.08.2014 11:00, Kristof Van Hecke wrote:
Dear,
I’m struggling with the following (small molecule) prob
Dear Careina,
even in vivo, the pka depends on the local environment, so the question boils
down to: is the local environment in vivo different from in vitro? E.g. is your
protein embedded or in contact with a membrane, is it part of a large
multiprotein complex etc? Does your crystallization s
By all means, try it both ways and see whether the R-Rfree gap narrows with
random vs thin shell selection. Depending on resolution and data quality, you
may also consider imposing NCS restraints.
Sent on a Sprint Samsung Galaxy S® III
Original message From: Xianchi Dong
Dat
Hi Careina,
Regardless of what I think of this reviewer's comment, the only technique of which I'm aware that can measure in vivo (and in vitro of course) the pKa's of amino-acids is NMR. Perhaps you can find some NMR literature where in-vivo and in-vitro pKa's have been
compared? Just a tho
[image: Inline image 1]
*PROTEIN STRUCTURE DETERMINATION IN INDUSTRY 2014*
The 22nd PSDI will take place at the Hotel Miragem in Cascais, Portugal, a
coastal town located 30 kilometers west of Lisbon, Portugal.
The meeting will start with registration and an opening reception on
Sunday, 2nd
Thanks to the mailing list I came across this:
http://www.ncbi.nlm.nih.gov/pubmed/24167157
The C code to compute is available on the link mentioned in the paper.
Best wishes,
George
On Wed, Aug 13, 2014 at 8:01 AM, Eugene Krissinel <
eugene.krissi...@stfc.ac.uk> wrote:
> It is probably Gesamt/
thank you, yes I am aware of propka and I know very well that the local
environment of the amino acid is what contributes to its pka based on things
like whether it is buried or exposed or involved in H-bonding. I am in the
process of responding to a reviewer who suggests but does not give refe
Dear Careina,
Following on from what Herman said, if you have a structure you can use the
propKa server
http://propka.ki.ku.dk/
to predict pKas for amino acids in the local environment as found in your
structure.
Perhaps some of the propKa literature might also be helpful?
HTH,
Dave
[image:
Dear Careina,
The pka of amino acids is not dependent on in vivo/in vitro, but on the local
environment, e.g. free in solution vs. part of a folded protein. As part of a
folded protein the shifts will be specific for the particular protein and I am
not aware of any general rules.
Best,
Herman
V
VOIDOO will do this
On 13 Aug 2014, at 2:06 AM, sreetama das wrote:
> Dear all,
> Is there any software or web server available to calculate the volume of a
> ligand if the ligand coordinates are provided?
> Google seems to come up only with options to calculate protein cavity volume.
>
> Than
how many (quasi) equivalent positions do you think the chiral compound can
adopt in the organo-metal framework?
Or the organo-metal framework in the crystal?
If it's two, you can probably do alternate conformations - if there are more,
it could become impossible, even in P1.
Mark J van Raaij
Lab
Dear,
Indeed,. Pc is not compatible with chiral molecules,. my mistake.
I’m trying to process/solve the structure in P1 now and see how far I get.
Thank you very much for pointing things out.
Regards
Kristof
On 13 Aug 2014, at 13:58, herman.schreu...@sanofi.com wrote:
> Dear Kristof,
>
It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather than
PISA -- Eugene
On 13 Aug 2014, at 12:33, Eleanor Dodson wrote:
I think PISA does this for you - it overlaps structural features and gives an
RMSD on those parts that fit and a useful list of matching residues.
You can
Dear Kristof,
Lijun is right, space group Pc is not compatible with chiral molecules. Maybe
diffraction of your non-chiral metal structure overwhelmed the chiral
contribution of your organic framework. Why not use a trick from protein
crystallography: process and solve your structure in P1? Acc
Hi folks
Pc *must* have both enantiomers, since it's got a glide plane ( =
mirror + translation parallel to mirror).
So the sample *cannot* be enantiopure if the space group is Pc (or P2/
c)...
BTW, Pc isn't a centrosymmetric space group.
Unless I'm wrong...
On 13 Aug 2014, at Wed13 Aug
Sorry for off topic question, just wondering if anyone has come across a study
that shows the residue pka of certain amino acids is different in vitro
compared to in vivo?
Best
Careina
Twin laws are possible if there are 2 ways to index your cell, and
non-merefedral twinning is possible in any system depending on the cell.
I am not sure of the small molecule tools to check twinning though.
Eleanor Dodson
On 13 August 2014 05:58, Lijun Liu wrote:
> Hi, Pc may not be the spac
I think PISA does this for you - it overlaps structural features and gives
an RMSD on those parts that fit and a useful list of matching residues.
You can run it from CCP4I or at PDBe.
If you ant more than CA RMSD then you will need to select out the spans to
fit and use the LSQKAB overlap procedu
Hi, Pc may not be the space group for your crystal, if the molecule is
chiral. Seems like the data were forced to be reduced to a mirror_related
SG. Lijun
On Aug 13, 2014 2:00 AM, "Kristof Van Hecke"
wrote:
> Dear,
>
> I’m struggling with the following (small molecule) problem:
>
> We are tryin
Dear,
I’m struggling with the following (small molecule) problem:
We are trying to solve the structure of a metal-organic framework containing a
chiral compound.
The space group is most probably Pc, but when refining, SHELX gives the error
“Possible racemic twin or wrong absolute structure -
Hi
A rough calculation is 18Å^3 per non-hydrogen atom in the ligand - I
use a pencil and a bit of paper for the mechanics of this!
On 13 Aug 2014, at Wed13 Aug 07:06, sreetama das wrote:
Dear all,
Is there any software or web server available to calculate the
volume of a ligand if the lig
Dear Monica,
here are some comments from my side:
-one can ask the bulletin board, or just decrease the occupancy during
refinement and see what happens. If the statistics get better: keep it, if they
get worse: reject the result.
-I think it is not a question of correct or incorrect structures.
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