Hi Charlie,
From molscript 2.1.2 you can directly create png, jpeg or gif also,
default being postscript file. At least it is working in linux. I am not
sure in iMac. Just type molscript -h. It should give the options...
HTH
-Karthik
On 5/6/2014 10:45 PM, Carter, Charlie wrote:
I need help
It can be done with pymol:
In the box in the lower left corner is an item selecting residues. By
clicking on residues you can change it to atoms or C-alphas
When you now click on the appropriate active site atoms, you can select the
alpha carbons and a (sele) item appears.
In the (sele) item
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes
* refmac5: 5.8.0071, fix for peptide planarity
* buccaneer: version 1.6 with new MR modes and user interface
* pointless: version 1.9.8, fixes for multilattice and output in qtrview
*
the negative difference density surrounding your metal ion shows that the
lower occupancy could not be fudged by a higher B-factor
Because there is a clear difference between high B-factor and low occupancy:
High B factor attenuates high resolution scattering most, while lower occupancy
just
Many thanks to Tim and Nat for, respectively, answering both questions fully,
and to Ethan Merritt for subsequent help!!
Charlie
On May 6, 2014, at 1:24 PM, Tim Gruene wrote:
Dear Charlie,
I still use molscript quite a bit, it is not so old fashioned as you
might think. Raster3D is even
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P.S.: For clarity, I meant to say 'calculate' (with full-matrix
refinement) instead of 'collect'.
Tim
On 05/07/2014 04:52 PM, Tim Gruene wrote:
Dear Bernhard,
I just happen to collect the correlation between ADP and occupancy
for a publication
We're in the final stages of planning for our June Computing School
and *registration
will close on Friday. *Join us in June for our data processing workshop
followed by Phenix and Schrodinger/BioLuminate workshops.
*Register Here
Hi Amit
Most likely nothing is going wrong. Your final Rfree looks quite
respectable for 2.8 Ang. data. It's meaningless to compare the Rfree at
the beginning of a refinement with that at the end. Rfree is only
meaningful if the refinement has converged. So it is valid to compare the
Rfree at
Hello,
I have a 2.8 angstrom structure of a protein ligand complex. The R/R free
before adding the ligand was 0.21614/0.27760 and after adding the ligand,
the R/Rfree is 0.2030/0.2691.
.
However while refining the structure by Refmac 5, I see a decrease in R
factor but an increase in R free as
On 05/07/2014 10:52 AM, Tim Gruene wrote:
At 2.5A resolution (the resolution this thread is about)
But maps ae not made at 2.5 A but from say 30A to 2.5 A.
In principle (i.e. if the 0,0,0 reflection were used), the effect
of diminishing the amplitude of high resolution terms is not to
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Hi Ed,
I guess it depends on what 'successfully' means. The large correlation
implies quite an error margin, and I find an occupancy range of +/-
0.2 - 0.3 quite a lot, although this impression may vary depending on
what you are discussing w.r.t. the
Hi all,
I have a 360 degree data set collect on home beam.
I used XDS to integrate the frames in P1.
I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the
log below.
The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are
much higher than normal at
additional info:
If I let xds go through, it will choose P6. actually pointless suggest P62/P64.
The thing is the Rmeas and Rmerge are significantly higher for P2/P3/P6 than
P1, especially the highest shell.
That indicates those higher symmetry ones are not the choice, it that right?
(Actually,
I thought there was a theoretical Rmeas number for I/sigma=2 that is around
50%? In my case, the Rmeas is much higher.
Before, we reported P62(4) and got rejected.
I'll just change a journal. Hopefully reviewer will not be too picky about
that.
Thanks to everyone!
It is definitely P6something or P3something with a twinning about the
unique axis. The differences in merging statistics between P2 P3 and P6 are
not very significant in my opinion.
On May 7, 2014, at 1:16 PM, Rain Field rainfiel...@163.com wrote:
additional info:
If I let xds go through,
Hello Rain Field,
I third Felix and Craig, there is nothing unusual about the statistics
table you present. The data look pretty good and I would assume
P6_something and integrate further than 3.1A.
Regards,
Tim
On 05/07/2014 08:16 PM, Rain Field wrote:
additional info:
If I let xds go
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