Have you considered the impact of tunneling? Your rope crossings are not
perfect barriers.
On Sat, Jan 20, 2024 at 6:09 PM James Holton wrote:
> Update:
>
> I've gotten some feedback asking for clarity on what I mean by "tangled".
> I paste here a visual aid:
>
>
> The protein chains in an ense
That is a live link to sauc, but I have not updated the database from the
PDB in a while. Let me know if there is an
urgent need for an update, Otherwise I am planning one for March. I
normally build the database from COD and
the PDB, but if CCDC wishes, we can add the CSD to the mix. For the
Dear James,
I think open reviews would be a major improvement in the grants review
process. Most grant reviews are done carefully and honestly, but I have
seen some that were clearly written carelessly and dishonestly that would
not
have been submitted if the reviewers knew they would have to pu
thousands
of frames per second -- possible in the longer term.
If you are interested in attending via Zoom, please register
at:
https://www.bnl.gov/hdrmx2022/
-- Dale Kreitler, dkreit...@bnl.gov
Herbert J. Bernstein, hbernst...@bnl.gov
The zenodo policies seem to the most workable as a start. I would suggest
contacting them for the cases that go over 50GB, but at worst splitting
into 50GB chunks. -- Herbert
On Fri, Jan 18, 2019 at 10:49 AM Andreas Förster <
andreas.foers...@dectris.com> wrote:
> Hi Aaron,
>
> can you slice yo
Dear Colleagues,
May I suggest that those who are at Universities take a look at the
G-suite for Education
https://edu.google.com/products/gsuite-for-education/editions/?modal_active=none
which provides unlimited cloud storage for free to educational institutions.
Regards,
Herbert
On T
Dear James,
Perhaps it is time for us to admit that this is too large, expensive and
complex a problem for us to resolve without help from one
or more of the commercial data managers, such as Google or Amazon. I know
that dealing with ads is a nuisance, introducing
a loss of time for research,
own version locally, the source is
available in
the sauc.git repository iterate project at http://sf.net/projects/iterate at
https://sourceforge.net/p/iterate/sauc/ci/master/tree/
or on github at
https://github.com/yayahjb/sauc
-- Herbert J. Bernstein
yaya...@gmail.com
Try
http://iterate.sourceforge.net/sauc-1.0.0/
which finds 4Y42 as closest for both cells, but lots of others nearby.
On Sun, Jun 18, 2017 at 10:39 AM, James Holton
wrote:
>
> By the way. Does anyone out there have a unit cell search engine still
> running? The two mentioned on this thread s
Dear Colleagues,
The information Graeme is requesting would be very helpful in making
accurate NeXus/HDF5, minicbf, and full cbf beamline templates. We would be
happy to host the beamline photographs on the HDRMX web site (
www.medsbio.org/hdrmx). These photographs would be even more useful if
The unit cell search at
http://iterate.sf.net/sauc/
now includes 368 thousand Crystallographic Open Database (COD) cells
through 26 November 2016, as well as 111 thousand PDB cells through 18
November 2016.
Please report problems to yaya...@gmail.com
-- H. J. Bernstein
apologies,
Herbert J. Bernstein
--
Herbert J. Bernstein
Professor of Mathematics and Computer Science
Dowling College, Brookhaven Campus, A210/B205
1300 William Floyd Parkway, Shirley, NY, 11967
+1-631-244-1328
Lab: +1-631
Dear Colleagues,
This exchange is a wonderful illustration of the simple fact that
different scientists
work differently, favoring different approach and different tools. For
some, the latest
and greatest formats and support systems are what they need to be
productive. For
a surprising large n
Dear Colleagues,
Clearly, no system will be able to perfectly preserve every pixel of
every dataset collected at a cost that can be afforded. Resources are
finite and we must set priorities. I would suggest that, in order
of declining priority, we try our best to retain:
1. raw data that
Dear Colleagues,
One thing that would help is avoiding misappropriated priority of
research
results would be to join the math and physics community in their robust
use of open-access
preprints in arXiv. Such public preprints establish reliable timelines
for research credit
and help to ensu
r your detailed explanation. I had missed the important
point that it's the requirement on the authors to assent to open
access after a year, which the proposed Bill seeks to abolish, that's
critical here.
I will go and sign the petition right now!
Best wishes
-- Ian
On 16 February 2012
Dear Colleagues,
Acta participates very nicely and fully in the NIH Open Access
program. After
one year of the normal restricted access any NIH-funded paper automatically
enters the NIH open access system. The journals get to get their
revenue when
the paper is most in demand, but the com
.AC.UK] On Behalf Of Herbert
J. Bernstein
Sent: Thursday, February 16, 2012 8:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act
Dear Ian,
You are mistaken. The proposed law has nothing to do with preventing the
encouragement people to break copyright law. It
Dear Ian,
You are mistaken. The proposed law has nothing to do with preventing the
encouragement people to break copyright law. It has everything to do with
trying to kill the very reasonable NIH open access policy that properly
balances the rights of publishers with the rights of authors and
ADSC has been a leader in supporting compressed CBF's.
=
Herbert J. Bernstein
Professor of Mathematics and Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY,
the enemy of the good. James is proposing something
good.
Regards,
Herbert
=============
Herbert J. Bernstein
Professor of Mathematics and Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakda
collective nose at lossy images? Even if it means waiting
6 years for "Nielsen's Law" to make up the difference in network
bandwidth?
-James Holton
MAD Scientist
On Mon, Nov 7, 2011 at 10:01 AM, Herbert J. Bernstein
wrote:
This is a very good question. I would suggest that
option in CBFlib. Right now all the compressions
we have are lossless.
Regards,
Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
,
Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowling.edu
onal. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
s involved. This might be
a good time to try to get a consensus of the scientific community
of what approach to IP law would best serve our interests going
forward. The current situation seems a bit messy.
Regards,
Herbert
=====
Herbert J.
e do not let the perfect be the enemy of the good.
Regards,
Herbert
=============
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
s.
James
--
=====
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Brookhaven Campus, B111B
1300 William Floyd Parkway, Shirley, NY, 11967
+1-631-244-1328
Lab: +1-631-244-1935
Cell: +1-631-428-1397
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling C
Try RasMol 2.7.5, e.g.
load ../data/pdb1w0k.ent
restrict not hoh
map generate LRsurf dots
map select atom within 1.8
show selected
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
he Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax:+1-831-4593139 (fax)
--
==
up would welcome any feedback you may have on this
specification, whether through open discussion on this list or by
contacting members of the working group (see the online discussion
archive for names of the participants).
=
Herbert J. Bernstein
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowling.edu
I agree with Bernhard -- both on the soundness of the idea and on
the difficulty in finding the right home for it in NSF or NIH, but
I would suggest giving it a try. -- Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling
reate an award
in his name to be given to people who carry on his ideals. Those ideals
deserve to be encoraged and perpetuated.
With deepest condolences to his family,
Herbert
=====
Herbert J. Bernstein, Professor of Computer Science
Do
.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowling.edu
=
On Mon, 21 Sep 2009, Harry Powell
CBFlib 0.8.1 kit to address the problem in loading core
CIF data files.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631
://sbevsl.wiki.sourceforge.net/Movie+Making+Commands
Bug reports, comments, correction and suggestions would be appreciated
Please report problems to
y...@bernstein-plus-sons.com
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer
My apologies to the list. That was intended as an off-list comment.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631
FBU259 LEAD COMPUTATIONAL SCIENTIST looks like a wonderful job. Think
what Larry could do with it. It is a shame he is not portable.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Some of us have already been discussing that possibility.
-- Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631
rbert
=====
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowlin
nth from now, and we have good, if not perfect, solutions available for
many, if not all, of the technical issues involved. Is it really wise to
let this opportunity pass us by?
Regards,
Herbert
=============
Herbert J. Bernstein, Professor
Have you considered gcc under MINGW? It produced more stable
code that runs under more versions of windows than CL.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour
mp; Molecular Pharmacology and
The Sandler Center for Basic Research in Parasitic Diseases
Phone: 415-514-3426 FAX: 415-502-8193
E-mail: [EMAIL PROTECTED]
QB3/Byers Hall 508C
1700 4th Street
University of California
San Francisco, CA 94158-2550
USPS:
UCSF MC 2550
Byers Hall Room 508
1700 4th Street
package
and you may link to the functions in the CBFlib package from a
proprietary program just as you may link to glibc or to the trigonometry
functions in the libm math library.
Use it in good health.
-- Herbert J. Bernstein
--
=
Herbert J
abstract deadline is Friday, 9 May 2008 and the
handout deadline is Wednesday, 14 May 2008.
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
.
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
[EMAIL PROTECTED]
=
useful, we hope that you will consider making a
donation to help support further development via the sourceforge
donation system.
Herbert J. Bernstein
yaya-hjb at users.sourceforge.net
openrasmol.sourceforge.net
--
=
Herbert J. Bernstein, Professor
fee,
but space is limited, so registration will be required. Lunch will
be provided. If you are interested in participating, please email
[EMAIL PROTECTED] no later than 15 April 2008.
The new imgCIF workshop series has been funded in part by NSF, NIH and
DOE.
--
======
registration will be required. Lunch will
be provided. If you are interested in participating, please email
[EMAIL PROTECTED] no later than 15 April 2008.
The new imgCIF workshop series has been funded in part by NSF, NIH and
DOE.
--
=
Herbert J
ry of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 2QH
--
=========
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
r a plural is to say "each
table 1".
-- Herbert
=============
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-6
0.00 0.00 ? ? ?
? ? ? ? ? ?
?
-47 1 3 17.00 0.00 0.00 ? ? ?
? ? ? ? ? ?
--
=============
Herbert J. Bernstein, Professor of Computer Scienc
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
--
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
[EMAIL PROTECTED]
=
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
[EMAIL PROTECTED]
=
On Mon, 20
ot be unambiguously
parsed without advice from the delphic oracle.
Regards,
Herbert J. Bernstein
=====
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY,
quot;
The code changes for graphics programs are fairly
simple, since most things are in the same place
in very similar formats, just with more of a
range.
-- HJB
=====
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kram
runs from the page being down. We had a couple
of bad power failures, and that machine is
not back in service yet, but the spec is
available.
Regards,
Herbet J. Bernstein
=====
Herbert J. Bernstein, Professor of Computer Science
Dowli
your name
if you will be joining us for lunch on Tuesday, 14 August 2007
if you will be joining us for lunch on Friday, 17 August 2007
Please send this message no later than 12:00 GMT on Friday,
3 August 2007.
Thank you for your cooperation.
Rega
compatibility
with older formats is in progress, but users of
current remediated PDB entries are encouraged to
use this new version now.
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
experimental data in structural biology, these workshops may
prove interesting for you.
Thanks to funding from DOE, NSF and NIH we have some funds to help
with travel to these workshops. If you need assistance, please
contact us.
For further information and to register please contact Herbert J.
Bernstein
otron
800 Blackburn Road
Clayton, VIC 3168
Australia
Attachment converted: Macintosh HD:Untitled 15 (/) (0016B5AD)
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
"single program" is my own imprecise
term, not a specific legal wording that is under dispute.
--
Ethan A Merritt
--
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
[EMAIL PROTECTED]
=
provided. Space is limited so ...
Important: Even if you are already registered for the CFN/NSLS
meeting or are a local BNL person, it is important to contact us if
you wish to attend so we can be sure to have enough chairs and food.
Please send email to Herbert J. Bernstein and Bob Sweet at
[EMAIL
introduction to the subject, there will
also be a working lunch during the BSR meeting in Manchester. The
time and room will be announced on the MEDSBIO.org web site and at
the meeting. For further information and to register please contact
Herbert J. Bernstein and Alun Ashton at [EMAIL PROTECTED
Second imgCIF workshop (new series) at BNL after NSLS/CFN meeting:
Synchrotron Image-Data Format Workshop
Herbert J. Bernstein, [EMAIL PROTECTED]
Robert M. Sweet, [EMAIL PROTECTED]
Sponsored by DOE under grant ER64212-1027708-0011962, NSF under grant
DBI-0610407. NIH support pending.
There
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