Dear CCP4i citizens,
I have been looking for online servers or programs that identify and
calculate the intermolecular bonding energy, such as cation-pi, H-bond, salt
bridge...etc, which can be used as a guide to prioritise the binding site
residues for mutational studies. I have been using
On Tue, Sep 21, 2010 at 7:10 PM, William G. Scott <
wgsc...@chemistry.ucsc.edu> wrote:
> In fact, the only source-code I can find for pymol is on the fink mirror,
> for the OS X fink package I have been maintaining, i.e.,
>
> http://distfiles.master.finkmirrors.net/pymol-1.3-src.tar.bz2
How abou
On Tuesday 21 September 2010, William G. Scott wrote:
> Hi Citizens:
>
> I have an invoice for a PyMol academic 3 year subscription through March 31,
> 2011, invoice #2794.
>
> When I enter my subscription access credentials into the pymol.org web
> server, nothing happens.
>
> The source co
Dear Colleagues,
There is a nice pymol source code repository on sourceforge at
http://pymol.svn.sourceforge.net/viewvc/pymol/
and you can make perfectly reasonable builds from that source. I
append a copy of the license in that repository below. The terms
are quite simple and reasonable.
Take a look at
http://sourceforge.net/projects/pymol
Under develop - the svn tree is there...
Have not tried to compile it Last change four weeks ago
Ezra
On 9/21/2010 10:10 PM, William G. Scott wrote:
Hi Citizens:
I have an invoice for a PyMol academic 3 year subscription thro
Dear Filip,
Thank you for your advice, in my lab there is a discussion where a senior
investigator who suggested that if you cannot see evidence of an interaction by
coomassie then you have no chance of crystallizing the complex. I disagreed but
I did not have a reference to support my stance.
> (2). Why RMS-Z(bonds) should be lower than that for low resolution data
and higher for high resolution? Or why high-resolution can allows more
outliers?
Imagine torsion angle refinement only, at low resolution: The bond
lengths are fixed to target values, their rmsd will be zero.
Imagine free r
Hi Ian:
Thanks a lot! I have 2 questions:
(1). Can I say the X-ray weighting is optimal when it yields the smallest
Rfree, meanwhile RMS-Z(bonds) is smaller than "0.85 - 0.146*resolution"
(angles also maybe)?
(2). Why RMS-Z(bonds) should be lower than that for low resolution data
and higher for
The automatic weighting feature in the latest
releases of refmac is pretty good. However, if you are setting the
X-ray weighting factor manually, typical targets for rms bond
angles are 1.0-2.0 degrees and rms bond lengths of 0.01-0.02 A.
On 9/21/2010 3:54 PM,
To give credit where it is due I should perhaps have explained that
the formula for RMS-Z(bonds) that I quoted was derived from an
analysis of re-refinements from the PDB-REDO project
(http://www.cmbi.ru.nl/pdb_redo), not from the PDB itself. PDB-REDO
itself uses the LLfree optimisation method tha
Hi Hailiang
The short answer is that the optimal X-ray weighting factor minimises
Rfree, or better -LLfree.
However this is tricky to carry out in practice since it means you
have to run several jobs adjusting the weight manually each time to
find the optimum. Also, ideally the same procedure sh
Hi,
I seem to recall a paper from a few years back that used heterologous
proteins for macro/micro seeding, and of course now I can't find it. Seems
likely that lysozyme would be involved... I've found plenty on using
non-protein compounds as seeds, but nothing for protein. Does anyone know
i
Hi all:
I have a question about deciding an ideal "Weight matrix" value in REFMAC.
When I change it from 0.1 to 0.001, the bond distance rmsd changes from
0.075 to 0.008, while the R changes from 0.26 to 0.33 (resolution 3.2A).
Now I am not sure what is the best balance based on these numbers. Are
Dear All,
Firstly, sorry for the non-crystallography question but I am trying to do a
pulldown assay using Cobalt-NTA resin between two DNA replication proteins one
of which contains a C-terminal 6x his tag. According to previous genetic
studies, these two proteins are involved in replication a
Dear All,
Thank you for all your replies, I think there are some additional
informations about this screening to help judgment:
1. this screening was set in a 0.2+0.2 microliter drop, so the
microcrystals(?) are very small.
2. these things came out in different conditions, after
Dear Ian,
many thanks for your explanations - they've changed my view! I was
always a bit puzzled by the supposedly contradictory transition between
restraints and constraints with increasing weight, which has been
clarified by their effect on the number of parameters, and not on the
number
Dirk,
Apologies, my last e-mail was incomplete, I meant to say that there
was one thing I should have added:
>From Table 2 in the paper the expected Rfree/Rwork ratio comes out as:
< Rfree / Rwork > = sqrt( (f+m') / (f-m') ) = sqrt( (x+1) / (x-1) )
where x = f / m' = no of X-ray data /
Dirk,
One thing I should have added:
The expected Rfree/Rwork ratio comes out as:
wrote:
> Hi Dirk
>
> First, constraints are just a special case of restraints in the limit
> of infinite weights, in fact one way of getting constraints is simply
> to use restraints with very large weights (thoug
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