Re: [ccp4bb] mmCIF as working format?

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

[ccp4bb] Comments needed CBF X-axis definition ambiguity

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

Re: [ccp4bb] very informative - Trends in Data Fabrication

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

Re: [ccp4bb] very informative - Trends in Data Fabrication

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

[ccp4bb] imgCIF workshop at BNL on 24 May 2007

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

[ccp4bb] imgCIF workshop (new series) at BSR 2007

an 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

Re: [ccp4bb] The CCP4 license is ambiguous

-- = 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] =

Re: [ccp4bb] The CCP4 license is ambiguous

HD:Untitled 15 (/) (0016B5AD) -- = 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

[ccp4bb] imgCIF workshops, 14 and 17 Aug 2007

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

[ccp4bb] imgCIF workshops at BSR 2007

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. Regards, Herbert J. Bernstein

Re: [ccp4bb] PDB format survey?

... 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, Kramer Science

Re: [ccp4bb] PDB format survey?

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 Dowling College, Kramer

Re: [ccp4bb] converting structure factor files to mtz files

? ? ? ? ? ? ? ? ? ? -47 1 3 17.00 0.00 0.00 ? ? ? ? ? ? ? ? ? -- = Herbert J. Bernstein, Professor of Computer Science Dowling College

Re: [ccp4bb] bond lengths, angles, ideality and refinements

. -- 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 [EMAIL PROTECTED

Re: [ccp4bb] Missing fonts...

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 +1-631-244-3035

[ccp4bb] Workshop on Raw Image Formats in Structural Biology

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

[ccp4bb] RasMol: 2.7.4.2 binaries updated

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

[ccp4bb] Registration deadline Workshop on Raw Image Format

. -- = 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] =

[ccp4bb] LGPL for more of CBFlib

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

Re: [ccp4bb] Non-sequential residue numbering?

: [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 San Francisco, CA 94158 -- = Herbert J. Bernstein, Professor of Computer Science

Re: [ccp4bb] cl.exe

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

Re: [ccp4bb] images

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 of Computer Science Dowling

Re: [ccp4bb] images

= 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

Re: [ccp4bb] images

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

[ccp4bb] Important proposed changes in CIF

on this list or by contacting members of the working group (see the online discussion archive for names of the participants). = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour

Re: [ccp4bb] Whither pymol?

phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) -- = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale

Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues

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

Re: [ccp4bb] Mac OSX 10.7 Lion

Biology, Hills Road, Cambridge, CB2 0QH -- = 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

Re: [ccp4bb] IUCr committees, depositing images

-- = 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 y

Re: [ccp4bb] IUCr committees, depositing images

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 +1-631-244-3035 y...@dowling.edu

Re: [ccp4bb] To archive or not to archive, that's the question!

. 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. Bernstein

Re: [ccp4bb] To archive or not to archive, that's the question!

gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** -- = Herbert J. Bernstein

Re: [ccp4bb] To archive or not to archive, that's the question!

, 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

Re: [ccp4bb] image compression

it as an 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

Re: [ccp4bb] image compression

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 y...@bernstein-plus-sons.com wrote: This is a very good question. I would suggest that both versions of the old data are useful. If was is being done

Re: [ccp4bb] image compression

something good. Regards, Herbert = Herbert J. Bernstein Professor of Mathematics and Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035

Re: [ccp4bb] image compression

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, 11769

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 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

Re: [ccp4bb] Fwd: HR3699, Research Works Act

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 has everything to do

Re: [ccp4bb] Fwd: HR3699, Research Works Act

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 15:24, Herbert J. Bernstein y

Re: [ccp4bb] 3 positions available in the CCP4 core group

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

Re: [ccp4bb] 3 positions available in the CCP4 core group

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

[ccp4bb] Testers needed for RasMol 2.7.5

://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

Re: [ccp4bb] Warren DeLano

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 Dowling

Re: [ccp4bb] Refining against images instead of only reflections

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

Re: [ccp4bb] lossy compression of diffraction images

= 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

[ccp4bb] SAUC cell search now includes COD cells as well as PDB

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

Re: [ccp4bb] similar unit cell

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

[ccp4bb] Updated SAUC Cell Database

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

Re: [ccp4bb] Should we still keep copies of all raw data?

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,

Re: [ccp4bb] Open Access Repositories for Big Data?

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

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

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

[ccp4bb] HDRMX virtual meeting 27-28 April 2022

-- in the 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

Re: [ccp4bb] open review?

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

Re: [ccp4bb] nearestcell

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

Re: [ccp4bb] Introducing the UNTANGLE Challenge

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