Thank you Ethan.
Supposing I want to compare with the experimental map, a small fragment of
the model (let's say residues 15-30 in a protein of 100 residues).
Supposing I start with one model but now extract from that model residues
15-30 (let's call it model 1) , modify it and now want to check
On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote:
> Thank you Ian.
> To clarify, I actually want to compare the new PDB file to the old MTZ
> file to see how well the residues fit. This is why I mentioned that I have
> the old MTZ file I generated from SF's which I got from the PDB.
>
Thank you all for your reply! Here I summarize what I got from the answers:
1. Seems single channel pipette is a better choice than multi-channel with
small volumn.
2. Positive displacement pipette is more advantageous than regular air
displacement pipette.
3. Tips with repellent surface is also h
Thank you Ian.
To clarify, I actually want to compare the new PDB file to the old MTZ
file to see how well the residues fit. This is why I mentioned that I have
the old MTZ file I generated from SF's which I got from the PDB.
I am not trying to improve the deposited structure, I am trying to get
Dear Structural Biology community,
I would be grateful if you could please bring the following postdoctoral
position to the attention of talented graduate students.
Many thanks,
Antonina Roll-Mecak
*Postdoctoral Fellowship at the NIH *
*Cell Biology and Biophysics Unit, National Institutes
Hi, sorry small clarification.
The "complete PDB file that you used to run the refinement job" (i.e. the
input PDB file) will obviously only be suitable in the case that you did 0
cycles of refinement. If you did some refinement of the model then the
co-ordinates will have changed, and then you n
Hi, I'm puzzled by what you are trying to do. You say you have the
original MTZ/MAP files. What have the original files got to do with it?
EDSTATS requires the MTZ/MAP file calculated for the supplied model. The
documentation states: "... the PDB file and the maps should all be from the
same ref
HI,
I want to calculate real-space R factor/RSCC and such parameters using
EDSTATS in CCP4 but only for a selected fragment that has been
extracted and then modified (changed the Phi and Psi) from the native.
I have the original MTZ and MAP.
Is it even possible to calculate these values witho
Hi Nick,
Is this conformation refineable in refmac5 or phenix if the occupancy is
> set to zero?
>
> Should I allow clashes to push both copies either side of the density as
> is currently happening?
>
> Any tips on dealing with this?
>
if occupancy is to 0 then it is not refined in phenix.refine
On 10/06/2014 18:48, Nicholas Keep wrote:
is set to zero
Sorry in my last email this should read "is set to a fraction eg 0.5"
Nick
Am refining a structure in P3(1)21 with three copies in the ASU. It is
pretty close to completion R/Rfree 18/21 with 2A data.
However in one copy a section that
You may want to drop the symmetry to see what is happening with the loop.
James
On Jun 10, 2014, at 11:48 AM, Nicholas Keep wrote:
> Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty
> close to completion R/Rfree 18/21 with 2A data.
> However in one copy a section t
Am refining a structure in P3(1)21 with three copies in the ASU. It is
pretty close to completion R/Rfree 18/21 with 2A data.
However in one copy a section that is clear in the other two is poor as
it meets itself on a two fold.
My interpretation is that one copy of the loop is in a visible
co
Phil, absolutely. I have routinely use AIMLESS on XDS and sometimes on
SCALEPACK output.
I should clarify that in the scenario I described earlier, complete XDS or
SCALEPACK output would *not* be available, but only Is and SIGIs. What
would be the best strategy to 'trick' POINTLESS/AIMLESS into acc
XDS_ASCII.HKL or scalepack format ('no merge original index') can be read
directly by Pointless which should (I hope) do a better job than COMBAT.
Aimless (& Pointless) assume two reflections are part of the same one if they
have the same "true" hkl (same ISYM) and adjacent batch numbers (and a
Hello all,
suppose I extracted
H K L Intensity sigma[Intensity]
from a file of unmerged intensities, such XDS_ASCII.HKL or scalepack format
('no merge original index'). Batch or rotation angle information would have
been omitted, due to a limitation of the output file's format.
Should I not sti
Dear all,
We would be very interested to characterize some cellulosic materials by
X-ray diffraction (type, apparent crystallinity,...).
We have no experience in this domain and any advice on how to deal with
this (mount sample, analyze data, software to use, ...) will be greatly
appreciated.
Th
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Hash: SHA1
I hope that the contents of this section is obvious to most readers of
the ccp4 bulletin board.
Cheer,
Tim
On 06/10/2014 03:40 PM, Jeffrey Bell wrote:
> An editorial comment about protein crystallography appeared under
> that title. It's short and wo
An editorial comment about protein crystallography appeared under that title.
It's short and worth considering.
http://pipeline.corante.com/
Hi Nadir,
Which "One" do you use? I may have missed it in the thread.
Thanks,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer
Hi Jacob,
Hbo energy is an empirical function for most biological molecules.
The one I use takes into account Coulomb's law for charges and van der Waals
(both attractive and repulsive) interactions.
The equation's parameters are adjusted to implicitly take into account
contributions from "c
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