Hi,
If you have the latest version of pymol and ANISOU in your pdb file, you
just have to type:
show ellipsoids,
http://www.pymolwiki.org/index.php/Ellipsoids
Mathieu
These kind of problems with r3d can usually be traced back to the
header. In fact, the rastep page has the following snippet:
Interestingly, in the interactive 3D applet view of the ligand from the PDB
the two are perfectly in plane, whereas in the protein viewer the two groups
are clearly out of plane. I assume that this means that the coordinates for
the 3D ligand view are re-computed internally and are not representati
RE: Ian's and Eckhard's wise suggestion to deposit non-standard
parameters used to refine ligands:
I have had some ligands where the 1 & 8 peri-substituents (amino &
methyl groups) on a 6/6 fused aromatic ring (deazapteridine derivatives)
were very clearly out of the plane. It took extensive fiddl
These kind of problems with r3d can usually be traced back to the
header. In fact, the rastep page has the following snippet:
Describe the same ellipsoids colored by Biso, and create an input
module with no header records for inclusion in a composite image:
rastep -h -Bcolor 10. 30. < in
Hello,
I would like to display thermal ellipsoids in pymol. What I did was using
rastep to make a r3d file and open it in pymol.
If I generate the r3d file with no extra options: rastep < infile.pdb >
outfile.r3d, pymol can open it.
But if I generate the file with rastep -auto -fancy1 < infil
On Tue, 2008-12-09 at 09:31 +0100, Tim Gruene wrote:
> ...you must set the occupancy of those residues to
> zero...
I think this approach (which Tim is not supporting) makes no sense.
When I place an ATOM record into a pdb-file, what I am really saying is
"based on the data, this atom's posit
Yes of course; but the photons don't care what axis is being rotated
about, they kill just as rapidly.
phx.
George M. Sheldrick wrote:
When discussing this issue, perhaps we should not lose sight of
the fact that the statistics behind Rp.i.m. assume 'independent
observations'. Surely doing m
On Tuesday 09 December 2008 11:22:04 Joseph Ho wrote:
> Hello,
>
> I have a refined 1.8A structure that I wonder if I could squeeze out some
> anisotropy information. I did TLS refinement on the protein, and it helped my
> Rfree. But I would like to ask a biological question based on the thermal
When discussing this issue, perhaps we should not lose sight of
the fact that the statistics behind Rp.i.m. assume 'independent
observations'. Surely doing more than one rotation about the
same axis is likely to repeat the same systematic errors?
George
Prof. George M. Sheldrick FRS
Dept. Stru
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy
Hello,
Thank you for the reply about the refmac 5.5.0066 error. I downloaded refmac
5.5.0068 but there appears to be a problem for ARPwARP to recognise the
version. I reinstalled ARPwARP and the install shell script freezes when it
looks for the refmac file.
On behalf of the scientific organizers, I would like to invite you to
participate at the:
Winter School on Soft X-rays in Macromolecular Crystallography, February
18-20th, 2009
at BESSY-II, Helmholtz-Zentrum Berlin für Materialien und Energie.
The third Winter School on Soft X-rays in Macromo
I think if you cant see it dont build it, but deposit the data..
There are many (most?) structures with missing loops
Eleanor
Pavel Afonine wrote:
This might help:
Acta Cryst. (1997). D53, 540-543 Local Improvement of
Electron-Density Maps
Pavel.
PS> It will be implemented in PHENIX som
I am aware of to opposing schools of thought about modelling residues
without density:
- You can argue that since you know those residues are present in the
sequence, you can model them, even though there is no or hardly any
density. If you do so, you must set the occupancy of those resid
Hi Frank,
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy if o
Dear developers,
I wonder if the restrictions for MBATCH=1000 in CCP4-v6.0.2 and for scala
(maxbat=1000,maxpmr=2000,maxmat=1000, maxrun=3) hold also in V6.1?
Otherwise I cannot use the precompiled versions and have to recompile!?
Thank you,
Jürgen
Hello,
I have a refined 1.8A structure that I wonder if I could squeeze out some
anisotropy information. I did TLS refinement on the protein, and it helped my
Rfree. But I would like to ask a biological question based on the thermal
movement of only a few waters (7 total). In theory, that is no
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