Thank you Clare for all your contributions to the community throughout
these 25 years, particularly for bringing the technicians' perspective into
focus, and providing helpful feedback. You will be missed.
Best of luck in your next role,
Jon
On Wed, 9 Feb 2022 at 09:58, Clare Stevenson (JIC) <
I have subscribed to the CCP4 bulletin board for over 25 years and attended
many CCP4 meetings. I am changing role shortly and will no longer be a
crystallographer so will unsubscribe from the board. I just wanted to pass on
my thanks to everyone who has written posts, contributed to
A further note on assembly search: since April the RCSB PDB offers
structure search for assemblies. See the "Structure Similarity" section in
https://www.rcsb.org/search/advanced. This works only for PDB-deposited
structures but we are working on making it available for 3D coordinates
submitted by
Dear All
Many thanks to Johann for the suggestion of Topsearch - rather pleasingly our
tetramer is novel in the tetrameric arrangement, but each of the dimers has its
DNA recognition helices in agreement with several hits a win all round
Bringing joy to my lockdown.
Best
Andy
Bill,
I followed Abraham Szöke’s work from a distance, but never met him. I knew he
was imaginative, and that he made original contributions to density
modification.
I was much moved to read your appreciation of him.
Many thanks,
Charlie
Hi Fellows,
thanks again to all who took the time to respond (often very
extensively) to my queries regarding funding experience and resource
distribution. The summary is available now ahead of print:
http://www.ncbi.nlm.nih.gov/pubmed/26051321
Let's hope it has some positive
Your Figure 1 suggest a secret message - or at least I view it that way.
The early steps “basic research” seems to be funded by Euros, while the in
silico part is funded in Dollars.
Or was that unintentional ?
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School
Thank you Francois
for positive feedback.
Eugene
On 15 Feb 2013, at 05:40, Francois Berenger wrote:
It is easy to use and even nice looking.
Regards,
F.
--
Scanned by iCritical.
It is easy to use and even nice looking.
Regards,
F.
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure recently and it messes up coot sequence window and
breaks refmac bond restraints. Evil, evil,.evil.
not god I don't think I wrote that bit!
Phil
On 5 Dec 2012, at 15:06, Ed Pozharski wrote:
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure
The last time I tried the pdbset renumber command because of issues with
insertion codes in certain programs, it failed to also renumber the LINK,
SSBOND CISPEP records. Needless to say, thanking god (or even God) was
not my first thought! (more along the lines of why can't software
developers
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ian Tickle
Sent: Wednesday, December 05, 2012 16:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] thanks god for pdbset
The last time I tried the pdbset renumber command because of issues
.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ian Tickle
Sent: Wednesday, December 05, 2012 16:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] thanks god for pdbset
The last time I tried the pdbset renumber
Hi Robbie,
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Hi Ian,
It's easy to forget about LINK records and such when dealing with the
coordinates (I recently had to fix a bug in my own code for that).
The problem with insertion codes is that they are very poorly defined in the
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Does 128A come before or after 128?
Robbie,
shouldn't it simply depend on which residue record comes first in the
pdb file?
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
. In practice, as Ed pointed out, it is a big mess.
Cheers,
Robbie
-Original Message-
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Wednesday, December 05, 2012 17:26
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] thanks god for pdbset
I had always assumed
Hi Peter,
Thanks for the info. I'd better go check whether my code assumes insertion
codes are not digits.
Cheers,
Robbie
Date: Wed, 5 Dec 2012 17:57:58 +
From: pkel...@globalphasing.com
Subject: Re: [ccp4bb] thanks god for pdbset
To: CCP4BB@JISCMAIL.AC.UK
Hi Robbie,
On Wed
Especially the renumber command that changes
residue insertion codes into an increment of
the impacted residue numbers.
Regards,
F.
Thanks for the many responses. I had been setting the parameters right. The problem was I was not telling xds to go
back as far as INIT in the reprocessing. JOB ALL was the answer
Best wishes
Nick
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Thanks everyone for letting me know its canister. I had a different idea of
a canister. I really appreciate all your replies.Instead of replying
individually, I am sending this common email.
Thanks again,
Ivan
Thanks to all who responded. I was able to somewhat generate the info
I needed.
Raji
Dear colleagues,
Thanks a lot for the many constructive suggestions! Attchached is
another response I got directly.
Best regards,
Mark
__
Hello Mark,
for low absorbing proteins, the Ehresmann method is a good
Thanks for all the quick replies! The problem turned
out to be that the Turbo output pdb file of my ligand
(created by using the MAKE command) somehow failed to
label all my carbon atoms as C. Instead, all my
carbons were labelled with just the number. For
example, C12 was mislabelled as 12.
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