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Dear Peng,
The choice of asymmetric unit is somewhat arbitrary. Please forgive me and
ignore this if I am saying something obvious and you already know this does not
apply in your case, but I see most of your previous posts concern EM
structures, so perhaps you are relatively new to solving
Dear Nicolas,
Thank you for your help.
Our DNA is not a palindromic sequence, and I think it should not be degraded
easily.
The data can be processed in the space groups C2221, P41212 or lower, with
12bp, 6bp ,24bp or longer in one NCS. I can see the connection between two
symmetric DNA
Hello community.
HarkerBIO is structural biology-focused biotechnology company based in
Buffalo, NY with a close relationship to the renowned Hauptman-Woodward
Medical Research Institute. We are rapidly growing and are seeking to
quickly fill a few open crystallography/structural biology
Hi Claudia,
another program that I used with success is Hollow (
https://www.ncbi.nlm.nih.gov/pubmed/19014592).
It is really easy to use. You can get is here http://hollow.sourceforge.net/
It finds pockets in a defined area, fills them with water molecules and
generates a pdb with those waters.
Hi Claudia,
For the identification of cavities and residues linning them, metapocket is
one of the preferred choice as it uses prediction from various program.
Output of the server is pdb file.
I found caver program represent cavities in a best manner. There is caver
plugin available for pymol.
Hi Claudia,
Another possibility is CastP: http://sts.bioe.uic.edu/castp/index.html
They also have a Pymol plugin. I have not used this plugin since I'm displaying the CastP o/p files in UCSF-chimera which handles them nicely.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Hi Claudia
Two options I've used recently, liked and displayed without fuss in
PyMOL are ProFunc
(https://www.ebi.ac.uk/thornton-srv/databases/profunc/) and Ghecom
(http://strcomp.protein.osaka-u.ac.jp/ghecom/). Ghecom gives you PDB
files directly. ProFunc gives you rasmol scripts but they
Hi
XCHEMBB, cc'd should be able to help. Please join the mailing list @
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=XCHEMBB=1
Are the refinement problems are occuirng during the export step, not
aftwerwards?
The logs are typically located in
Hi everyone,
I need suggestions to calculate and represent cavities of protein
structures. For years I have been using Voidoo that produces maps in ezd
format which could be converted in map format (ccp4) using the online
server http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl. However, this
I am trying to convince XChemExplorer to refine my PANDDA models – i.e. those
which have had ligands saved / placed into promising density. However, the
large majority of refinement jobs (started by exporting all PANDDA models)
simply fail.
Is there a log file or something I can look at to see
Dear Peng,
to me your problem sound a bit strange, except if it's a palindromic
sequence. I don't understand how you can have one part of the DNA in one
asymmetric unit and one in another one. My question are : maybe you
considering a NCS as a true symmetry and underestimate the unit-cell
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