**PhD student position at the Institute of Protein Biochemistry, Ulm
University (Germany),
Group Prof. Dr. M. Fändrich
The Institute of Protein Biochemistry
(_https://www.uni-ulm.de/nawi/nawi-pbc.html_) investigates the molecular
basis of amyloid diseases, such as Alzheimer's disease and syste
Dear Marina,
Just an observation from my side: if you are able to process your data in P622,
there must be some 2-fold perpendicular to l, which would most likely be a
non-crystallographic or a twinning axis. Is there a NCS 2-fold in the P321 data
set you solved? If so, is it perpendicular to l
Dear Helen and Andrew,
Thank you very much for your suggestions and help. It is working now and
able to run the aimless successfully.
Your help is much appreciated
Mike
On Thu, Jul 11, 2019 at 7:53 PM Helen Ginn wrote:
> Dear Mike and Andrew,
>
> I've since updated to a later version of cc
Dear Mike and Andrew,
I've since updated to a later version of ccp4 (7.0.076) and now have the XMLOUT
tags specified automatically. Woops!
Thanks for that error log Andrew - I had a look at the aimless.script file to
see how that filename was generated, and looked up the command on the CCP4
de
Hello Marina,
In short: at first I'd build the model and refine it with the untwinned P3(2)21
data set until convergence. Then, I'd process all other data sets (including
the twinned ones) in that space group as well. If using XDS, I'd use the
XDS_ASCII.HKL of the untwinned data set as REFEREN
Dear Mike and Helen,
As I understand it, the XML is only written when POINTLESS/AIMLESS are run
through the CCP4 GUI and the command comes from the GUI script, so there is no
way you can turn this off from POINTLESS itself.
However, if you use the “Run&View com file” option from CCP4i GUI, you
Dear Mike,
No problem! Happy to provide suggestions, though I'd prefer to be addressed
directly on here.
Here's another suggestion, no promises. If you can provide more detail on the
GUI input and the output log files, it would be easier to know why this is
happening in the first place. Howeve
Are all the trigonal cells related?
Eleanor
If so, you can use your untwinned data set as a guide to pointless to make
sure all others are in the same indexing system, assign all the spacegroups
to P3221
Then just start refinement with the key word twin from your good model.
Eleanor
On Thu, 11 J
Hello everyone,
I have the following problem:
I have some really good data sets of about 1.6 A which could be
processed in P 6 2 2 as well as in P 3 2 1.
Intensity statistics tests indicate twinning (merohedral, twinning
law: -h, -k, l, in P 3 2 1).
But I did not find a good MR solution (R v
Dear Andrew,
Thanks for your suggestion. Yes, you are right that the error is because
.xml file is not being written. but not able to find the reasons...I
checked...Disk space is free and have permission to write also. I could
able to run Pointless, but not Aimless.
Any other reason??
Thanks
Mi
Read the log file?
Do you mean MOLREP self-rotation?
Eleanor
On Thu, 11 Jul 2019 at 08:28, Madhurima Roy wrote:
> Dear All,
>
> How do we find the contour levels, peak heights and angles in self
> rotation function ?
>
>
>
> Madhurima
>
>
> --
>
> To unsubscribe from
I think this is very wise. It can be better to say that you don't know then to
guess if people will take your answer for granted.
Cheers,
Robbie
On 11 Jul 2019 11:09, Raz Zarivach
<33371661b7b1-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi All
With so many alternative suggestions, wouldn't be b
Hi
This is a linear-algebra question (with structural biology hidden
behind...).
I came across the following matrix equation :
A = S X
where :
* A, S and X are real square matrices
* A is a known (constant) matrix
* S and X are unknown
* S must be symmet
Hi All
With so many alternative suggestions, wouldn't be better to leave it
without guessing the wrong molecule?
Raz
On 11/07/2019 10:55, Anthony Addlagatta wrote:
For some reason if your sulfur on cysteine becomes sulfide anion, you can model
sodium/potassium. Distance seems to be optimum
For some reason if your sulfur on cysteine becomes sulfide anion, you can model
sodium/potassium. Distance seems to be optimum for S...Na contact. Since you do
not see any anomalous signal, this is one possibility. I also see small blobs
around which may resolve to be water molecules.
Anthony
Dear Shengyuang,
Some further suggestions. To create a model towards MR searches, you could try
our server for modelling coiled coils:
https://pharm.kuleuven.be/apps/biocryst/ccfold.php
It takes a few seconds to run.
The reference is here: https://www.ncbi.nlm.nih.gov/pubmed/28968723
I reco
Dear All,
How do we find the contour levels, peak heights and angles in self rotation
function ?
Madhurima
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