[ccp4bb] 2nd International Workshop on Pontin/RUVBL1 & Reptin/RUVBL2 - 3rd Announcement

[Pedro M. Matias]

Dear CCP4ers,

We would like to remind you that the registration for this workshop, 
that will take place in very nice surroundings in Oeiras (Portugal) 
next October 10-12, is still open.


The Workshop will divided into 5 sessions covering the following topics:

- Structural Biology
- Chromatin remodeling and pre-rRNA processing
- Regulation of gene expression
- Transcription
- Pathophysiology

Each session will be structured as follows:

- Invited lecture 35 minutes
- Invited lecture 35 minutes
- Coffee/Tea break 50 minutes
- Selected talks from Abstracts

Poster sessions will be held during coffee/tea and lunch breaks.

Please visit http://pontinreptin2014.itqb.unl.pt where you will find 
regularly updated information on this meeting.


A lot has happened since the exciting First Workshop in 2012 that 
gathered people from 15 countries in Bordeaux in 2012. For those of 
you who did not attend, you can get a flavor of it by reading its 
Proceedings (Sci. Signal. 2013; 6, mr1).


Whether Pontin/RUVBL1 & Reptin/RUVBL2 are at the core of your 
studies, or whether you recently fell upon them in the course of your 
research, this Workshop will allow you to meet all the specialists in 
this complex field and find collaborations.


To take advantage of the reduced registration fee, please register 
until June 30. There are still many open slots for oral 
communications besides invited speakers.


Important dates:

Early registration deadline - June 30 (150 Eur PhD students / 200 Eur 
PhD holders)

Registration deadline - July 31 (200 Eur PhD students / 250 Eur PhD holders)
Registration fee & accomodation payment deadline - August 15
Abstract submission deadline - August 31

We have secured a special single room rate of 50 Eur/night at nearby 
Hotel Riviera () - this rate is good until August 15.


We look forward to meeting you soon in Portugal!

The local organizing committee,

Pedro Matias
Tiago Bandeiras
Sara Silva


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] 2nd International Workshop on Pontin/RUVBL1 & Reptin/RUVBL2 - 2nd Announcement

[Pedro M. Matias]

Dear CCP4ers,

It is our great pleasure to announce that the registration for this 
workshop, that will take place in very nice surroundings in Oeiras 
(Portugal) next October 10-12, is now open.


The Workshop will divided into 5 sessions covering the following topics:

- Structural Biology
- Chromatin remodeling and pre-rRNA processing
- Regulation of gene expression
- Transcription
- Pathophysiology

Each session will be structured as follows:

- Invited lecture 35 minutes
- Invited lecture 35 minutes
- Coffee/Tea break 50 minutes
- Selected talks from Abstracts

Poster sessions will be held during coffee/tea and lunch breaks.

Please visit http://pontinreptin2014.itqb.unl.pt where you will find 
regularly updated information on this meeting.


A lot has happened since the exciting First Workshop in 2012 that 
gathered people from 15 countries in Bordeaux in 2012. For those of 
you who did not attend, you can get a flavor of it by reading its 
Proceedings (Sci. Signal. 2013; 6, mr1).


Whether Pontin/RUVBL1 & Reptin/RUVBL2 are at the core of your 
studies, or whether you recently fell upon them in the course of your 
research, this Workshop will allow you to meet all the specialists in 
this complex field and find collaborations.


Register early to benefit from a reduced rate and to make sure that 
you will be in. There are still many open slots for oral 
communications besides invited speakers.


Important dates:

Early registration deadline - June 30 (150 Eur PhD students / 200 Eur 
PhD holders)

Registration deadline - July 31 (200 Eur PhD students / 250 Eur PhD holders)
Registration fee & accomodation payment deadline - August 15
Abstract submission deadline - August 31

We have secured a special single room rate of 50 Eur/night at nearby 
Hotel Riviera () - this rate is good until August 15.


We look forward to meeting you soon in Portugal!

The local organizing committee,

Pedro Matias
Tiago Bandeiras
Sara Silva


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

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

[Pedro M. Matias]

Can non-US residents sign this petition? You need a Whitehouse.gov 
account and in order to register you have to provide a U.S. (I 
presume) zipcode.


At 15:37 16-02-2012, Ian Tickle wrote:

Dear Herbert

Thanks for 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 15:24, Herbert J. Bernstein
 wrote:
> The bill summary says:
>
> Research Works Act - Prohibits a federal agency from adopting, maintaining,
> continuing, or otherwise engaging in any policy, program, or other activity
> that: (1) causes, permits, or authorizes network dissemination of any
> private-sector research work without the prior consent of the publisher; or
> *(2) requires that any actual or prospective author, or the author's
> employer, assent to such network dissemination. *
>
> Defines "private-sector research work" as an article intended to be
> published in a scholarly or scientific publication, or any version of such
> an article, that is not a work of the U.S. government, describing or
> interpreting research funded in whole or in part by a federal agency and to
> which a commercial or nonprofit publisher has made or has entered into an
> arrangement to make a value-added contribution, including peer review or
> editing, but does not include progress reports or raw data 
outputs routinely
> required to be created for and submitted directly to a funding 
agency in the

> course of research.
>
> ==
>
> It is the second provision that really cuts the legs out from the NIH open
> access policy. What the NIH policy does is to make open access 
publication a

> condition imposed on the grant holders in publishing work that the NIH
> funded. This has provided the necessary lever for NIH-funded authors to be
> able to publish in well-respected journals and still to be able to require
> that, after a year, their work be available without charge to the 
scientific

> community. Without that lever we go back to the unlamented old system (at
> least unlamented by almost everybody other than Elsevier) in 
which pubishers

> could impose an absolute copyright transfer that barred the authors from
> ever posting copies of their work on the web. People affiliated with
> libraries with the appropriate subscriptions to the appropriate archiving
> services may not have noticed the difference, but for the significant
> portions of both researchers and students who did not have such access, the
> NIH open access policy was by itself a major game changer, making much more
> literature rapidly accessible, and even more importantly changed the
> culture, making open access much more respectable.
>
> The NIH policy does nothing more than put grant-sponsored 
research on almost
> the same footing as research done directly by the government 
which has never

> been subject to copyright at all, on the theory that, if the tax-payers
> already paid for the research, they should have open access to 
the fruits of

> that research. This law would kill that policy. This would be a major step
> backwards.
>
> Please read:
>
> 
http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/

>
> http://www.taxpayeraccess.org/action/action_access/12-0106.shtml
>
> http://www.care2.com/causes/open-access-under-threat-hr-3699.html
>
> Please support the petition. This is a very bad bill. It is not about
> protecting copyright, it is an effort to restrict the free flow of
> scientific information in our community.
>
> Regards,
> Herbert
>
> On 2/16/12 9:02 AM, Fischmann, Thierry wrote:
>>
>> Herbert
>>
>> I don't see how the act could affect the NIH open access policy. Could you
>> please shed some light on that?
>>
>> What I read seems reasonable and I intend to ask my representatives to
>> support this text. But obviously I am missing something and like to learn
>> from you first.
>>
>> Regards
>> Thierry
>>
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.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 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 the
>> interests of
>> the scientific community.  Most publishers fare quite well under a
>> policy that
>> gives them a year of exclusive control over papers, followed by open
>> access.
>>
>>It is, unfortunately, a standard ploy in current American politi

[ccp4bb] Reference for JLigand

[Pedro M. Matias]

Dear CCP4 Developers,

What is the correct reference for JLigand to include in a publication ?

Thanks & best regards,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] frm2frm

[Pedro M. Matias]

You need to register at their site first, I suppose. Have you tried 
to ask them for the software ?


At 06:06 26-10-2011, khuchtumur bumerdene wrote:

Hello,

Does anyone know where I could download frm2frm utility from Bruker? 
Is it even possible to do so?


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] Laptop stereo

[Pedro M. Matias]

There are several laptops which are compatible with the Nvidia 3D 
vision system. However, I only know of laptops with GeForce type 
cards, whereas Coot and Pymol require OpenGL and a Quadro graphics 
card to work in stereo. In fact, the hardware requirements for 
Windows (Vista and 7) are less strict than for Linux in that you can 
buy a less expensive card, but it still needs to be a Quadro.


I've tried to interest the Coot windows developer to make a port of 
Coot from OpenGL stereo to DirectX stereo but that apparently it is 
not a straightforward proposition.


So, for the moment (and until NVIDIA releases compatible drivers) 
that option is grayed out...


Pedro

At 14:01 20-10-2011, David Schuller wrote:
There are a some models of laptop which contain a stereo-capable 
screen, but since the make & model of the laptop were not mentioned, 
it is not clear that Claude's equipment is on that list.


http://www.nvidia.com/object/3d-vision-system-requirements.html


He also does not mention which OS he is running, which is the next question.


On 10/20/11 08:37, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Claude,

why do you expect stereo to work with a laptop? Usually it requires
special equipment, e.g. a shutter system or polarizing screen and
goggles, like the Zalman 3D monitors.

Maybe you want to let us know more about your setup.

Tim

On 10/20/2011 02:33 PM, Claude Didierjean wrote:

Dear All,

I just bought a new laptop with the graphics card "NVIDIA GeForce GTX
460M" with 1.5GB memory.
Unfortunately the stereo does not work with Coot (Windows or Linux).

Can Anyone help me ?
Thanks in advance,
Claude.

- -- - --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

[Pedro M. Matias]

Well played, Ethan!

At 07:06 01-04-2011, Ethan Merritt wrote:

Hi to all on ccp4bb:

What better day to announce the availability of a breakthrough technique
in macromolecular crystallography?

Given recent discussion and in particular James Holton's suggestion that
the problem of disordered sidechains is a problem akin to the difficulty
of describing dark matter and dark energy...

I am happy to announce a new crystallographic tool that can improve your
model by accounting for an often-neglected physical property. A detailed
explanation, references, and a preliminary implementation of the program
can be downloaded from

http://skuld.bmsc.washington.edu/DarkMatter

--
Ethan A Merritt
Karmic Diffraction Project
Fine crystallography since April 1, 2011
"What goes around, comes around - usually as a symmetry equivalent"


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

[Pedro M. Matias]

Have you noticed the date ? It's April 1!

At 10:31 01-04-2011, Frank von Delft wrote:
I'm pretty sure Coot has been displaying it all along.  In the early 
days it displayed it much better, I must say, which is why it tended to crash.




Maybe the next version of coot as well as pymol/ Raster3D could also display
virtual particles. This would really flashily push the quality of our models,
especially on the title pages of the electronic versions of journals. There
could even be a special July-14th-mode
(http://de.wikipedia.org/w/index.php?title=Datei:DESYNebelkammer.jpg&filetimestamp=20090223134909).

Cheers, Tim


On Fri, Apr 01, 2011 at 11:15:36AM +0200, Flip Hoedemaeker wrote:

Dear Ethan,

I would really really like to enhance all my PDB files, but I am
concerned I will create a black hole in my hard drive. I hope you
can convince me of the safety of your tool, thx

Flip

On 4/1/2011 8:06, Ethan Merritt wrote:

Hi to all on ccp4bb:

What better day to announce the availability of a breakthrough technique
in macromolecular crystallography?

Given recent discussion and in particular James Holton's suggestion that
the problem of disordered sidechains is a problem akin to the difficulty
of describing dark matter and dark energy...

I am happy to announce a new crystallographic tool that can improve your
model by accounting for an often-neglected physical property. A detailed
explanation, references, and a preliminary implementation of the program
can be downloaded from

http://skuld.bmsc.washington.edu/DarkMatter


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Pedro M. Matias]

Yes, we recently installed such a system and it works very well.

Minor drawback: the 3D Vision system interferes with the older 3D 
stereo (NuVision) system - we have 4 stereo workstations in the same 
room, 3 old and one new.
We don't know yet whether there are interference problems between 
machines with 3D Vision in the same room.


Regards,

Pedro Matias

At 09:14 01-03-2011, Andreas Eichinger wrote:

Dear colleagues,

We are currently setting up a new 3D workstation with a Samsung
SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a
Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,
Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on
Linux if it is connected via a 3-pin mini-DIN stereo connector. Has
somebody experience with such a setup?

Any help is kindly appreciated. Thanks in advance.

Andreas Eichinger


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

[Pedro M. Matias]

No, it requires a native system (Windows/Linux) installed. The 
graphics drivers installed by VMWare do not emulate the full HW 
capabilities of the Quadro card.


Pedro Matias

At 12:36 24-01-2011, Amir Khan wrote:

Hi,

Does newer 3-D hardware work using VMWare/Windows on a Mac?

Thanks!
Amir


___ _
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim 
Fairman [fairman@gmail.com]

Sent: Monday, January 24, 2011 6:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D 
LCD displays?


Forgot to mention that this is only for the newer 120 Hz LCDs using 
the Nvidia 3D Vision system.  You'll have to stick with your CRT for 
now or switch to Linux/Win for the newer hardware.


On Mon, Jan 24, 2011 at 1:10 AM, Jim Fairman 
mailto:fairman@gmail.com>> wrote:
Stereoscopic 3D driven by OpenGL via an Nvidia Quadro FX card is 
only available on Linux and Windows.  You'll have to beg the Nvidia 
gods for drivers for Mac.



On Mon, Jan 24, 2011 at 12:56 AM, Luecke, Hartmut 
mailto:hu...@uci.edu>> wrote:

My apologies if this has been discussed before.

Has anyone got this to work?  Preferably with a Mac?  We would love to hear
the configuration.


Cheers, Hudel

Hartmut Luecke
Director, Center for Biomembrane Systems
Depts. of Biochemistry, Biophysics & Computer Science
3205 McGaugh Hall
University of California
Irvine, CA 92697-3900
hu...@uci.edu http://bass.bio.uci.edu/~hudel/



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--
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Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab
Lab: 1-301-594-9229
E-mail: fairman@gmail.com 
james.fair...@nih.gov





--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab
Lab: 1-301-594-9229
E-mail: fairman@gmail.com 
james.fair...@nih.gov


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
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Apartado 127
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Re: [ccp4bb] deposited SF (or not)?

[Pedro M. Matias]

At 00:15 10-01-2011, Bernhard Rupp (Hofkristallrat a.D.) wrote:

Yes, exactly. 2002 papers, the question is how to
1) assure consistent deposition verification
2) how to fix omissions in earlier entries

Best, BR

PS: How did the EO confirm deposition - just ask you or the PDB, or some
more automated mechanism?


I don't know exactly. I sent them a copy of the release confirmation 
from PDB at EBI. I assume they did a direct check on the web, based 
on the entry IDs I sent them.




-Original Message-
From: mat...@itqb.unl.pt [mailto:mat...@itqb.unl.pt]
Sent: Sunday, January 09, 2011 3:35 PM
To: hofkristall...@gmail.com
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] deposited SF (or not)?

Hi, Bernhard,

I recently published a paper in JBC that was published online only after
the Editorial Office confirmed release of PDB coordinates and structure
factors. Maybe those structures you mention are older and their internal
checking procedures were not yet fully developed ?

Cheers,

Pedro.

> Dear All,
>
> during a random search for a model structure I found a situation where the
> journal article clearly states that coordinates and SFs were deposited for
> a
> series of structures. EDS and SF files were absent and I confirmed with
> PDB
> that no SFs were ever deposited.
>
> I have no feeling for how frequent this is nor do I suggest anything more
> than book-keeping errors. Nevertheless I wonder if there is a way to
> crosscheck this in an automatic fashion (maybe PDB has some tools to do
> that?) or whose responsibility it is to ensure consistency here. JBC
> editors
> have not responded so far.
>
> Best, BR
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> hofkristall...@gmail.com
> http://www.ruppweb.org/
> -
> No animals were hurt or killed during the production of this email.
> -
>


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
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Re: [ccp4bb] bruker smart and mosflm

[Pedro M. Matias]

Hi,

That utility is available within the Bruker Suite. We have a Proteum 
system and it is available from the Bruker software, although there 
is a standalone version. A while back, I was able to convert some 
images so that they could be read by MOSFLM and XDS, but I was never 
successful in processing them with those programs.


Cheers,

Pedro.

At 02:12 09-11-2010, Iain Kerr wrote:

Hi Ed,

Bruker used to supply a utility called FRM2FRM that would "unwarp" 
their images so that they were readable by Mosflm. You may want to 
consult them directly; Matt Benning (I believe he's still there) was 
most helpful when I was having problems with Bruker images a few years ago.


HTH,
Iain

On 11/8/2010 12:01 PM, Ed Pozharski wrote:

I am trying to read Bruker's Smart 6000 images with mosflm and it fails.
Based on some limited googlearch I feel that "NPIXELB:1" is a relevant
information and when these files were processed in HKL (not by me), the
relevant detector line says "format ccd bruker smart6000 binned".  I see
from mosflm website that I might be in trouble here although it says
that in recent version handling of bruker smart has been improved.  In
the mosflm crash file I get this

  From information in the image file, the detector has been
  recognized as: Bruker SMART
  If this is incorrect you must supply a DETECTOR keyword

So my question is how do I figure out if this particular format is
supported or not?

Cheers,

Ed.


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] arp_warp 7.1 and CCP4 6.1.3

[Pedro M. Matias]

Hi.

I don't know whether other people had this problem, but I've tried to 
install arp_warp 7.1 with CCP4 6.1.3 and the installation failed 
because the refmac version is 5.5.0109. There's a conditional branch 
in the installation script that extracts the "0109" from this and 
does not like the leading zero.


Solution (to be tried): re-compile refmac5 changing the version 
number to 5.5.109


Pedro Matias

Re: [ccp4bb] Error while compiling ccp4-6.0.99e from source

[Pedro M. Matias]

I think I figured out the problem: the directory path where I had 
unpacked the source tree was different from that defined in ccp4.setup


I guess I forgot once again that Linux and Windows are quite 
different operating systems...



Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] Error while compiling ccp4-6.0.99e from source

[Pedro M. Matias]

Dear CCP4ers,

I am compiling ccp4-6.0.99e from source and get the errors listed 
below when the compilation gets to lib/ccif/libccif.a. I re-ran 
configure with the --with-rxdispencer option as recommended but the 
error persists.


My system is a Fedora Core 8
Linux xtal2.itqb.unl.pt 2.6.23.1-42.fc8 #1 SMP Tue Oct 30 13:55:12 
EDT 2007 i686 i686 i386 GNU/Linux


What can I do to overcome this error ? Is there any system component 
missing, or did I miss something obvious?


Thanks in advance,

Pedro.


rxdispencer routines being added to library
make[1]: *** No rule to make target 
`/home/xtal/ccp4-6.0.99e/lib/data/cif_mm.dic', needed by 
`cif_mmdic.lib'.  Stop.
make[1]: Leaving directory 
`/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif'
make[1]: Entering directory 
`/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif'
if test -f 
/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx/librx.a; 
then \

  rm -rf rx.dir; mkdir rx.dir; \
  echo 'rxdispencer routines being added to library'; \
  cp 
/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx/librx.a 
rx.dir; cd rx.dir; \

  ar -x librx.a; cd ..; \
  ar r libccif.a rx.dir/*.o; \
  ranlib libccif.a; rm -rf rx.dir; \
fi
rxdispencer routines being added to library
gcc -O -w -DGFORTRAN -DPROTOTYPE 
-I/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx 
-DHAVE_SIGNAL_H=1 -DHAVE_TIME_H=1 -DHAVE_ASSERT_H=1 -DUPDATE_WARN=1 
-DUSER_ZZMODE_STACK=1 -D_XOPEN_SOURCE=500 -D_XOPEN_SOURCE_EXTENDED=1 
-DHAVE_MMAP=1 
-I/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif 
-o cifdic_to_symtab cifdic_to_symtab.o -lm -L`pwd` -lccif -lm 
-L/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx 
-lrx
make[1]: *** No rule to make target 
`/home/xtal/ccp4-6.0.99e/lib/data/cif_mm.dic', needed by 
`cif_mmdic.lib'.  Stop.
make[1]: Leaving directory 
`/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif'

make: *** [cciflib] Error 2




Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] Zalman 3D LCD Monitors

[Pedro M. Matias]

Dear All,

I've recently come across the information that 
Zalman manufactures 2 LCD monitors with 3D stereo 
capability at very affordable prices (between 500 and 700 €).


http://www.zalman.co.kr/ENG/product/Product_Read.asp?idx=217

I'd like to know whether anyone in this community 
has had the opportunity to use one of these 
monitors for 3D stereo modelling, and if so, what is your opinion.
With the demise of the CRT monitors, and the 
horribly expensive LCD alternatives available so 
far, this seems almost too good to be true!


Regards,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

Hi, Jeroen

The Vuzix VR920 should provide a cheap 3D stereo alternative to CRT 
monitors, because it contains two small LCD screens - if one displays 
a right eye view and the other a left eye view we'd have a situation 
similar to older display systems, with side-by-side stereo and a 3D 
viewer with mirrors. Afterglow and flicker wouldn't be a problem 
because each LCD would always receive the same eye view. In Linux 
with an NVIDIA Quadro card, this might (?) be achieved by option "4" 
TwinView clone mode stereo, provided each LCD can be perceived as a 
single display.


Regards,

Pedro.

At 14:24 04-02-2008, Jeroen Mesters wrote:

Dear Pedro,

there is no cheap solution for now, the 3D community has to wait for a
few years more I think to be presented with a good stereo-capable LCD.
The problem is not the refresh rate (as low as 5 ms nowadays) but it is
the after glow effect... that is one of the reasons why LCDs provide a
stable picture at just 60 Hz refresh rate in contrast to CRTs that look
stable at 85 - 100 Hz.

The cheapest solution is still the good old CRT (there are still a few
around) with nuvision stereo glasses.
For example, you can still buy the Samsung SyncMaster 1100MB that has
sufficient rates (Vert x Hori 160 Hz x 130 kHz) to do the job.

If you can, wait a few years ...

Jeroen.

p.s. There are also some (more expensive) active stereo beamers around
(we own an Infocus DepthQ) and they provide a nice active stereo picture
on the wall:
- http://www.digital-image.de/
- http://www.depthq.com/



Pedro M. Matias wrote:
> At USD 7000 it's not exactly the cheap solution I was looking for...
>
> At 10:46 04-02-2008, Andrew Raine wrote:
>> Anastassis Perrakis wrote:
>>
>>> While we are on the subject, does anyone in general have working in
>>> their labs a stereo-3D solution that does not require CRT monitors
>>> but works on LCD and preferably with Linux or OSX ? (any windows
>>> hints are welcome as well).
>>
>> Yes indeed.  We have a 20" one of these:
>>
>> 
http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3

>>
>>
>> on one of our Linux workstations.  After the original Acer screens
>> were swapped for Samsung ones it is excellent.  People like it for
>> the lack of flicker and consequent lack of headaches!  It has a wide
>> angle of view, and several people can see stereo on the same screen
>> at the same time, and there is no cross-talk between different
>> displays in the same room.
>>
>> It needs to be driven by an nVidia FX-series graphics card, with dual
>> DVI outputs.  Other cards with dual outputs can be made to work, but
>> the nVidia driver can intercept the conventional quad-buffered screen
>> swapping instructions and divert the two eye views tot he different
>> displays.  Thus most software that is already stereo-capable will
>> work without modification.
>>
>> In case this sounds a little too glowing, I should point out that I
>> have no connection with the suppliers or the manufacturers, except as
>> a customer!
>>
>> Andrew
>>
>> --
>> Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
>> Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
>> phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
>> web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>   (351-21) 446-9669 (direct)
> Fax   : (351-21) 441-1277 or 443-3644
>
> email : [EMAIL PROTECTED]
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Apartado 127
> 2781-901 OEIRAS
> Portugal


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

At USD 7000 it's not exactly the cheap solution I was looking for...

At 10:46 04-02-2008, Andrew Raine wrote:

Anastassis Perrakis wrote:

While we are on the subject, does anyone in general have working in 
their labs a stereo-3D solution that does not require CRT monitors 
but works on LCD and preferably with Linux or OSX ? (any windows 
hints are welcome as well).


Yes indeed.  We have a 20" one of these:

http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_omnia_mimo&SubCatID_=3

on one of our Linux workstations.  After the original Acer screens 
were swapped for Samsung ones it is excellent.  People like it for 
the lack of flicker and consequent lack of headaches!  It has a wide 
angle of view, and several people can see stereo on the same screen 
at the same time, and there is no cross-talk between different 
displays in the same room.


It needs to be driven by an nVidia FX-series graphics card, with 
dual DVI outputs.  Other cards with dual outputs can be made to 
work, but the nVidia driver can intercept the conventional 
quad-buffered screen swapping instructions and divert the two eye 
views tot he different displays.  Thus most software that is already 
stereo-capable will work without modification.


In case this sounds a little too glowing, I should point out that I 
have no connection with the suppliers or the manufacturers, except 
as a customer!


Andrew

--
Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

[Pedro M. Matias]

Dear Colleagues,

I found out that eDimensional sells the Vuzix HMD 3D glasses, but 
their stereo drivers only work in windows. I suppose that they should 
also work under Linux with the Nvidia stereo drivers. However because 
we must pay by purchase order and bank transfer, they will not honor 
the 30-day money back warranty in case the glasses don't work, and 
that would be an expensive mistake.


Therefore, I'm asking whether anybody in this community has had any 
experience with these glasses, in either Windows or Linux 
environments, using programs such as Coot for 3D stereo 
visualization. I know there are other such system out there but these 
seem to be the cheapest I found so far.


Thanks in advance,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal

[ccp4bb] Crystal Imaging Systems - possibilities and recommendations

[Pedro M. Matias]

Dear Colleagues,

We are currently contemplating the acquisition of 
an automated imaging system for crystallization screen plates (96-well).
I am aware that Molecular Dimensions sells these 
systems ranging in price between 47 and 71 k€ and 
I am inviting your opinions, comments and advice 
on these and other commercially available 
systems, in particular regarding price, reliability and ease of use.


Thanks in advance,

Pedro Matias


Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
Fax   : (351-21) 441-1277 or 443-3644

email : [EMAIL PROTECTED]

Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal