Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Taka,

I really appreciate this information! I do have Displayport cable and can
connect the card and Asus VG248QE both via the DP cable, somehow on the
Nvidia control panel in Windows 10, I do not have an option of choosing
"120HZ" or "144Hz", I only have option choosing "60Hz" or below, which
sounds weird to me. Windows 10 should make things easier not harder. If
CentOS 6 works then Windows 10 should work, I guess I have to go back to
Windows 7 if needed, but as I already ordered the DP to DVI active cable,
I'll test this cable first and update CCP4bb later.

On Mon, Jan 30, 2017 at 7:50 PM,  wrote:

> Xiao,
>
>
>
> If you connect the board and monitor by DisplayPort cable directly, it
> should work.
>
> I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not
> tested on Windows.
>
>
>
> Taka
>
>
>
> *From:* Xiao Lei [mailto:xiaolei...@gmail.com]
> *Sent:* Tuesday, January 31, 2017 10:08 AM
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> I changed my mind, I should order the usb- powered DP to DVI dual link...
>
>
>
> On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee  wrote:
>
> Hi Xiao,
>
>
>
> I can confirm you need to buy an active adapter if you want to convert the
> display port on the graphics card to DVI. The one that they supply with the
> graphics card is passive and won't work. I was in the same boat about a
> year ago. I bought a USB powered active adapter which allowed 120htz. My
> monitor only had DVI input so I didn't try a direct display port
> connection. I can't comment on why that didn't work.
>
>
>
> Cheers
>
> Christine
>
>
>
> Sent from my iPhone
>
>
> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami 
> wrote:
>
> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *On Behalf Of *Xiao Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Takaaki Fukami]

Xiao,

If you connect the board and monitor by DisplayPort cable directly, it should 
work.
I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not tested 
on Windows.

Taka

From: Xiao Lei [mailto:xiaolei...@gmail.com]
Sent: Tuesday, January 31, 2017 10:08 AM
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under 
Windows 10

I changed my mind, I should order the usb- powered DP to DVI dual link...

On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee 
> wrote:
Hi Xiao,

I can confirm you need to buy an active adapter if you want to convert the 
display port on the graphics card to DVI. The one that they supply with the 
graphics card is passive and won't work. I was in the same boat about a year 
ago. I bought a USB powered active adapter which allowed 120htz. My monitor 
only had DVI input so I didn't try a direct display port connection. I can't 
comment on why that didn't work.

Cheers
Christine


Sent from my iPhone

On Jan 30, 2017, at 4:25 PM, Takaaki Fukami 
> wrote:
Dear Xiao,

You need an active converter from DP to DVI.  You can't get 120Hz if you use a 
passive converter, even with a DVI dual link cable.  If you used an adapter 
come with the board, it's probably passive.

Taka


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
Sent: Tuesday, January 31, 2017 9:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 
10

Dear All,

I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro 
M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 
3D monitor. I tried to connect  the graphics card with the monitor through 
displayport to displayport connection and displayport to DVI-D dual link 
connection but failed to set the monitor run on 120Hz. It seems I have to 
follow the old way of using  DVI-D dual link connection for both graphic card 
and monitor, but the problem is that the graphics card does not have a DVI-D 
dual link socket, it only have displayport.

I appreciate any suggestions.

Re: [ccp4bb] variation in freerflag

[Tim Gruene]

Hi Robbie,

I had long wondered how to flag the fields in game minesweeper with a 
deterministic algorithm. When I read about 'random sort and bin' I though this 
was quite a beautiful way. I wonder if there is any reason behind not doing it 
this way in freerflag.

Assigning the flags randomly this way in a manual manner (CAD?) probably 
requires some tedious scripting, doesn't it?

Best,
Tim

On Monday, January 30, 2017 9:45:40 PM CET Robbie Joosten wrote:
> Hi Tim,
> 
> 
> 
> I was discussing that with a student today, because we observe the same
> thing when we make test sets for k-fold cross validation. It is an
> implementation choice. You can random sort and then bin, or you can assign
> a random number to each reflection and translate that to a bin. The latter
> is fine for large bins, but not for small ones like the ones you are
> making.
> 
> 
> 
> Cheers,
> 
> Robbie
> 
> 
> 
> 
> 
> 
> 
> Sent from my Windows 10 phone
> 
> 
> 
> Van: Tim Gruene
> Verzonden: maandag 30 januari 2017 21:03
> Aan: CCP4BB@JISCMAIL.AC.UK
> Onderwerp: [ccp4bb] variation in freerflag
> 
> 
> 
> Dear all,
> 
> when I ran freerflag with the keyword FREERFRAC 0.002, the number of 
> reflection per flag (between 0 and 500) is very high, it varies between 17
> and 1.
> 
> Why is there such a high variation, instead of flagging always the same
> number of reflections per flag (6-7 in my case)? Can the distribution be
> made evenly?
> 
> Best regards,
> Tim
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

I changed my mind, I should order the usb- powered DP to DVI dual link...

On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee  wrote:

> Hi Xiao,
>
> I can confirm you need to buy an active adapter if you want to convert the
> display port on the graphics card to DVI. The one that they supply with the
> graphics card is passive and won't work. I was in the same boat about a
> year ago. I bought a USB powered active adapter which allowed 120htz. My
> monitor only had DVI input so I didn't try a direct display port
> connection. I can't comment on why that didn't work.
>
> Cheers
> Christine
>
>
> Sent from my iPhone
>
> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami 
> wrote:
>
> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *On Behalf Of *Xiao Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

OK thanks, I'll update!

On Mon, Jan 30, 2017 at 4:57 PM,  wrote:

> Dear Xiao,
>
>
>
> I think it would work, though I'm not sure because it's smaller and
> cheaper than what I used (https://www.amazon.co.uk/
> Dell-BizLink-DisplayPort-Adapter-Powered/dp/B003XYBA72), which have
> worked well since I bought them 5 years ago, though some of them broke in 2
> or 3 years.
>
>
>
> Please let us know if you succeed with the cheaper one.
>
>
>
> Regards,
>
>
>
>
>
> *Sent:* Tuesday, January 31, 2017 9:41 AM
> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
> under Windows 10
>
>
>
> Dear Taka,
>
>
>
> Thank you for the information! For the active converter from DP to DVI, is
> it something like  StarTech.com DisplayPort to DVI Active Adapter (
> https://www.amazon.com/StarTech-com-DP2DVIS-DisplayPort-Active-Adapter/dp/
> B004SUO1GM) ?
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Christine Gee]

Hi Xiao,

I can confirm you need to buy an active adapter if you want to convert the 
display port on the graphics card to DVI. The one that they supply with the 
graphics card is passive and won't work. I was in the same boat about a year 
ago. I bought a USB powered active adapter which allowed 120htz. My monitor 
only had DVI input so I didn't try a direct display port connection. I can't 
comment on why that didn't work. 

Cheers
Christine


Sent from my iPhone

> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami  
> wrote:
> 
> Dear Xiao,
>  
> You need an active converter from DP to DVI.  You can't get 120Hz if you use 
> a passive converter, even with a DVI dual link cable.  If you used an adapter 
> come with the board, it's probably passive.
>  
> Taka
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
> Sent: Tuesday, January 31, 2017 9:10 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under 
> Windows 10
>  
> Dear All,
>  
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro 
> M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 
> 3D monitor. I tried to connect  the graphics card with the monitor through 
> displayport to displayport connection and displayport to DVI-D dual link 
> connection but failed to set the monitor run on 120Hz. It seems I have to 
> follow the old way of using  DVI-D dual link connection for both graphic card 
> and monitor, but the problem is that the graphics card does not have a DVI-D 
> dual link socket, it only have displayport.
>  
> I appreciate any suggestions.
>  
>  

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Dear Taka,

Thank you for the information! For the active converter from DP to DVI, is
it something like  StarTech.com DisplayPort to DVI Active Adapter (
https://www.amazon.com/StarTech-com-DP2DVIS-DisplayPort-Active-Adapter/dp/B004SUO1GM)
?

On Mon, Jan 30, 2017 at 4:25 PM,  wrote:

> Dear Xiao,
>
>
>
> You need an active converter from DP to DVI.  You can't get 120Hz if you
> use a passive converter, even with a DVI dual link cable.  If you used an
> adapter come with the board, it's probably passive.
>
>
>
> Taka
>
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Tuesday, January 31, 2017 9:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under
> Windows 10
>
>
>
> Dear All,
>
>
>
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
> M4000 graphics card, the card has four displayport. I also has a Asus 24
> inch 3D monitor. I tried to connect  the graphics card with the monitor
> through displayport to displayport connection and displayport to DVI-D dual
> link connection but failed to set the monitor run on 120Hz. It seems I have
> to follow the old way of using  DVI-D dual link connection for both graphic
> card and monitor, but the problem is that the graphics card does not have a
> DVI-D dual link socket, it only have displayport.
>
>
>
> I appreciate any suggestions.
>
>
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Takaaki Fukami]

Dear Xiao,

You need an active converter from DP to DVI.  You can't get 120Hz if you use a 
passive converter, even with a DVI dual link cable.  If you used an adapter 
come with the board, it's probably passive.

Taka


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
Sent: Tuesday, January 31, 2017 9:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 
10

Dear All,

I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro 
M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 
3D monitor. I tried to connect  the graphics card with the monitor through 
displayport to displayport connection and displayport to DVI-D dual link 
connection but failed to set the monitor run on 120Hz. It seems I have to 
follow the old way of using  DVI-D dual link connection for both graphic card 
and monitor, but the problem is that the graphics card does not have a DVI-D 
dual link socket, it only have displayport.

I appreciate any suggestions.

[ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Xiao Lei]

Dear All,

I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro
M4000 graphics card, the card has four displayport. I also has a Asus 24
inch 3D monitor. I tried to connect  the graphics card with the monitor
through displayport to displayport connection and displayport to DVI-D dual
link connection but failed to set the monitor run on 120Hz. It seems I have
to follow the old way of using  DVI-D dual link connection for both graphic
card and monitor, but the problem is that the graphics card does not have a
DVI-D dual link socket, it only have displayport.

I appreciate any suggestions.

Re: [ccp4bb] variation in freerflag

[Robbie Joosten]

Hi Tim,



I was discussing that with a student today, because we observe the same thing 
when we make test sets for k-fold cross validation. It is an implementation 
choice. You can random sort and then bin, or you can assign a random number to 
each reflection and translate that to a bin. The latter is fine for large bins, 
but not for small ones like the ones you are making.



Cheers,

Robbie







Sent from my Windows 10 phone



Van: Tim Gruene
Verzonden: maandag 30 januari 2017 21:03
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] variation in freerflag



Dear all,

when I ran freerflag with the keyword FREERFRAC 0.002, the number of  reflection
per flag (between 0 and 500) is very high, it varies between 17 and 1.

Why is there such a high variation, instead of flagging always the same number
of reflections per flag (6-7 in my case)? Can the distribution be made evenly?

Best regards,
Tim
--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

[ccp4bb] variation in freerflag

[Tim Gruene]

Dear all,

when I ran freerflag with the keyword FREERFRAC 0.002, the number of  
reflection 
per flag (between 0 and 500) is very high, it varies between 17 and 1.

Why is there such a high variation, instead of flagging always the same number 
of reflections per flag (6-7 in my case)? Can the distribution be made evenly?

Best regards,
Tim
-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Abraham Szöke

[Debanu Das]

Dear Bill,

So sorry to hear this news and the passing of another wonderful
scientist and contributor in our field. It was very interesting
reading your obituary. May his soul rest in peace.

I first heard about John and Abraham as a graduate student and later
on when I joined Sung-Hou for postdoc training. I was interested in
their holographic method for x-ray structure determination as I was
dealing with a case where I had density for the partial molecule from
molecular replacement and experimental structure factors for the
entire protein/DNA complex and was looking at ways to recover density
for the missing portion in addition to experimental phasing.

"Holographic methods in X-ray crystallography. IV. A fast algorithm
and its application to macromolecular crystallography"
http://scripts.iucr.org/cgi-bin/paper?S0108767395002315

Best,
Debanu
---
LinkedIn: www.linkedin.com/in/debanudas
Cal Alumni: cal.berkeley.edu/debanudas


On Sun, Jan 29, 2017 at 8:17 PM, William G. Scott  wrote:
> Dear Colleagues:
>
> Is is with great sadness that I report the recent passing of Abraham Szöke, a 
> friend, colleague, informal mentor, and an exceptionally intelligent and 
> energetic source of boundless intellectual enthusiasm.
>
> Abraham was a physicist at Livermore who helped to design nuclear weapons for 
> a living, but he had many other interests. One of these was X-ray 
> crystallography, and with his wife and collaborator Hanna Szöke, as well as 
> John Somoza, he developed an approach to crystallographic real-space 
> electron-density refinement and optimization, implemented in a program called 
> EDEN, that produces electron density maps with minimal model bias in a robust 
> manner. The source code, along with a brief explanation and extensive user's 
> manual, is freely available:
>
> https://code.google.com/archive/p/edencrystallography/
>
> https://github.com/wgscott/edencrystallography
>
> EDEN is written in C and is easy to compile on any unix platform. A fink 
> package for OS X is also available, as are packages for various linux 
> distributions.
>
> John and I first met Abraham and Hanna Szöke when we were graduate students 
> at Berkeley. A few years later, I had the opportunity to collaborate with 
> them and to put EDEN to the test. A single-particle version of EDEN was also 
> under development, for use with electron microscopy. Abraham had a wide 
> variety of interests in addition to electron density reconstruction, 
> including many novel ideas about the origin of life. He enjoyed a multitude 
> of fruitful and productive collaborations throughout a period most normal 
> people would consider retirement. He passed away on Thursday at age 87 from 
> an opportunistic infection while combatting lymphoma.
>
>
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
>
> http://scottlab.ucsc.edu

[ccp4bb] Residential School on Medicinal Chemistry and Biology in Drug Discovery (ResMed): A Comprehensive One-Week Course

[Strickland, Corey]

All,

I was asked by the meeting organizers to let the CCP4 community 
know about the 2017 Residential School on Medicinal Chemistry and Biology in 
Drug Discovery.See below for information about the course and contact 
information..

Sincerely,
Corey

-

Dear all,

The 31st Annual ResMed: Residential School on Medicinal Chemistry and Biology 
in Drug Discovery, www.drew.edu/resmed will be held 
on June 12 - June 16, 2017 at Drew University, Madison NJ.  However, all 
resident attendees will be staying at The Madison 
Hotel and will be bussed to and from campus 
all week. ResMed is co-sponsored by the ACS MEDI Division.

ResMed is a week-long graduate level course organized to provide an accelerated 
program for chemists, biologists and other industrial and academic scientists 
who wish to broaden their knowledge of drug discovery and development.  The 
School's aim is to concentrate on the fundamentals that are useful in drug 
discovery spanning initial target validation through clinical development. The 
program provides ample opportunity for discussions with distinguished faculty 
from industry and academia.

The purpose of the School is to provide a strong background in the principles 
of drug discovery and development to enhance collaborative drug discovery 
programs. Previous attendees with backgrounds in macromolecular crystallography 
have found the course of great value in their research projects.

The tuition rate for Hotel Residents will include hotel stay, ResMed tuition, 
course materials, and all meals. Information regarding ResMed can be accessed 
on our website: www.drew.edu/resmed including our 
program and application.

Please join us in our 31st year. We look forward to seeing you.

Sincerely,
Co-organizers,
William J. Greenlee, Ph.D
Vincent P. Gullo, Ph.D.
Ronald J. Doll, Ph.D.


Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.

Re: [ccp4bb] Abraham Szöke

[Napoleao Fonseca Valadares]

I'm really sad to hear that. Rest in peace. 

One of his articles, which has William as the first author, is very 
interesting, well-written, easy to read, and I use it to illustrate and open 
the mind of biochemistry students regarding several important topics. Works 
like a charm. 

RNA Catalysis, Thermodynamics and the Origin of Life 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187163/ 

- Mensagem original -

> De: "William G. Scott" 
> Para: CCP4BB@JISCMAIL.AC.UK
> Enviadas: Segunda-feira, 30 de Janeiro de 2017 2:17:10
> Assunto: [ccp4bb] Abraham Szöke

> Dear Colleagues:

> Is is with great sadness that I report the recent passing of Abraham
> Szöke, a friend, colleague, informal mentor, and an exceptionally
> intelligent and energetic source of boundless intellectual
> enthusiasm.

> Abraham was a physicist at Livermore who helped to design nuclear
> weapons for a living, but he had many other interests. One of these
> was X-ray crystallography, and with his wife and collaborator Hanna
> Szöke, as well as John Somoza, he developed an approach to
> crystallographic real-space electron-density refinement and
> optimization, implemented in a program called EDEN, that produces
> electron density maps with minimal model bias in a robust manner.
> The source code, along with a brief explanation and extensive user's
> manual, is freely available:

> https://code.google.com/archive/p/edencrystallography/

> https://github.com/wgscott/edencrystallography

> EDEN is written in C and is easy to compile on any unix platform. A
> fink package for OS X is also available, as are packages for various
> linux distributions.

> John and I first met Abraham and Hanna Szöke when we were graduate
> students at Berkeley. A few years later, I had the opportunity to
> collaborate with them and to put EDEN to the test. A single-particle
> version of EDEN was also under development, for use with electron
> microscopy. Abraham had a wide variety of interests in addition to
> electron density reconstruction, including many novel ideas about
> the origin of life. He enjoyed a multitude of fruitful and
> productive collaborations throughout a period most normal people
> would consider retirement. He passed away on Thursday at age 87 from
> an opportunistic infection while combatting lymphoma.

> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA

> http://scottlab.ucsc.edu

[ccp4bb] Time to submit abstracts for ACA 2017 (May 26-30 in New Orleans)

[Terwilliger, Thomas Charles]

Dear Friends and Colleagues!



Mark your calendars and join us in May for the 67th Annual Meeting of the 
American Crystallographic Association  (ACA), to be held May 26-30 in New 
Orleans, LA, at the Hyatt Regency Hotel. The abstract submission is opened now 
till February 15th.

http://www.amercrystalassn.org/2017-meeting-homepage


Back by popular demand - New Orleans ACA Meeting T-shirts with designs on the 
front and back. Don't be a square and get yours today. Hurry! They can be 
pre-ordered during the registration or at direct link: 
https://www.booster.com/aca-meeting-in-new-orleans



The meeting will launch with a full day of 
workshops on four different 
topics followed by an Opening Ceremony with a plenary lecture by Sir James 
Fraser Stoddart, 2016 Nobel Laureate in Chemistry.



The theme of this year's Transactions Symposium is Cryo Electron Microscopy 
that will feature lectures by the world's leading researchers and experts. New 
this year will be a session on NMR crystallography. Both are dedicated to 
covering topics of importance to scientists with a wide range of professional 
backgrounds and designed to emphasize our need for collaboration and 
cooperation.



 Young researchers will 
benefit from special and free events such as Career Development, Networking 
Mixer, Diversity and Inclusion, Communicating Science to Public, Undergraduate 
Research Symposium as well as educational sessions and workshops. You are 
encouraged to apply for funding support through travel grants before February 
15th, by volunteering, or just contact us if you are many students coming from 
the same lab.



Best regards,

Tom T

Tom Terwilliger

ACA Past President

Re: [ccp4bb] !SPAM: [ccp4bb] secondary structure assignment to PDB file

[Edward A. Berry]

As I understood the problem, it is that automatic assignment comes out 
differently for different structures of the same protein or proteins so close 
that they should have the same secondary structure, due to differences in 
quality of the structures. The question then is not how to determine secondary 
structure more accurately, but how to override automatic secondary structure in 
the graphics program and assign secondary structure from the best structure to 
all the others.

And the answer may be in the wording of the question: "assign secondary structure to 
the PDB file" (emphasis on FILE). If the PDB file has HELIX and SHEET records I 
believe most applications will respect them rather than re-determining secondary 
structure. So if you have a high resolution structure file that has helix and sheet 
records, copy them to the other structures. If their is only one structure that is 
getting assigned differently in different applications, check if it has HELIX and SHEET 
records, and if not edit them in according to your best idea of the secondary structure.


On 01/30/2017 04:08 AM, Tim Gruene wrote:

Dear J. Vitali,

there are tools that have been mentioned by others, that assist with the
assignment. The final decision depends on you as researcher. You should
visually check the hydrogen bonding whether the boundaries are consistent with
the automated assignment.

People often seem to think that secondary structure is program driven, but
it's your structure that provides that data, and the researcher to make the
final decision.

Kind regards,
Tim

On Sunday 29 January 2017 11:41:49 AM chemocev marker wrote:

Hi
Is there any tool that can assign secondary structure to the PDB file. The
problem is if I used different modelling tools, there are regions in the
protein which does not remain consistent and looks different in different
application.

best

J. Vitali

[ccp4bb] Ultrafast X-ray Summer School in Hamburg: 12-15 June 2017

[Thomas White]

Hi all,

The Ultrafast X-ray Summer School (UXSS) 2017 will take place at DESY in
Hamburg, Germany, 12-15 June 2017.

UXSS is an annual event jointly organized by the Center for
Free-Electron Laser Science (CFEL) at DESY and the PULSE institute at
SLAC National Accelerator Laboratory.  As you can see from the list of
speakers below, the program will be highly interdisciplinary, with
topics ranging from accelerator physics to molecular biology.  There
will also be a coursework exercise involving a mock proposal for the
European XFEL, with the help of experienced mentors.

The UXSS 2017 website is now online with more information:
https://conferences.cfel.de/uxss2017/

Registration will open on the 31st January 2017 (tomorrow!).  Please
note that the number of summer school participants will be limited. In
order to facilitate the selection of participants, we ask applicants to
provide a short description of their educational and scientific
background and their motivation for applying for participation in UXSS
2017.  The registration deadline will be the 31 March 2017.

Financial support for UXSS 2017 is very kindly provided by the Joachim
Herz Stiftung, meaning that participants will be asked to pay a
registration fee of only 100 EUR.  Accepted applicants will receive
a financial contribution towards travel and accommodation expenses.

We hope to see many of you in Hamburg this Summer!

Thomas White, CFEL, DESY
Amy Cordones-Hahn, PULSE
Co-chairs, UXSS 2017

List of lecturers:
Rasmus Ischebeck (PSI), FEL diagnostics
Hae Ja Lee (SLAC), matter in extreme conditions
Filipe Maia (Uppsala University), coherent diffractive imaging
Giorgio Margaritondo (EPFL), fundamentals of X-ray sources
Arwen Pearson (CUI & University of Hamburg), structural biology
Robin Santra (DESY, University of Hamburg), x-ray - matter interactions
Joachim Stohr (SLAC, Stanford University), condensed matter and magnetism
Simone Techert (DESY & Göttingen Campus), structural dynamics
Linda Young (Argonne/UChicago), atomic and molecular physics

[ccp4bb] Richard E. "Dick" Marsh

[Bernard D Santarsiero]

Dear Colleagues:

I also wanted to recognize the recent passing of Dick Marsh on January 3 at the 
age of 94.  

https://www.caltech.edu/news/remembering-caltech-crystallographer-richard-marsh-53554
 


He wrote a memoir that is posted in the ACA archives

http://www.amercrystalassn.org/h-Marsh 

Dick was a remarkable individual, always positive, helpful, kind, and 
exceptionally brilliant. It was a joy to have an office next to him for six 
years, and to have the opportunity to share hundreds of lunches and coffee 
breaks with him at Caltech. He was an integral part of that early structural 
group at Caltech when Chemistry, Biochemistry, and Molecular Biology research 
at the Gates and Crellin Laboratories included gas and single crystal 
diffraction, the beginnings in the understanding and use of quantum chemistry, 
and automated computing, with a group that included Linus Pauling, Verner 
Schomaker, Sten Samson, Bill Schaefer, Eddie Hughes, and countless others. 

http://www.iucr.org/gallery/1947/caltech 

His group developed one of the first integrated packages for structure 
refinement, CRYM, in the early 1960’s. Dick’s more recent claim to fame was his 
insight into reading an article in the Journal of the American Chemical Society 
or Inorganic Chemistry that contained a crystallographic structure and 
recognizing an error in the choice of space group of “unnecessarily low 
symmetry.”  He often saw patterns in the incorrect choices of space groups, and 
helped in the development of programs like PLATON, POINTLESS, ZANUDA, for the 
automated determination of space group. He was an avid tennis player and 
golfer, and lived close enough to Caltech to ride in on his bicycle almost 
every day until about a decade ago. 

He will be greatly missed. 

Bernie Santarsiero

[ccp4bb] Thanks!

[Carter, Charlie]

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

Re: [ccp4bb] !SPAM: [ccp4bb] secondary structure assignment to PDB file

[Tim Gruene]

Dear J. Vitali,

there are tools that have been mentioned by others, that assist with the 
assignment. The final decision depends on you as researcher. You should 
visually check the hydrogen bonding whether the boundaries are consistent with 
the automated assignment.

People often seem to think that secondary structure is program driven, but 
it's your structure that provides that data, and the researcher to make the 
final decision.

Kind regards,
Tim

On Sunday 29 January 2017 11:41:49 AM chemocev marker wrote:
> Hi
> Is there any tool that can assign secondary structure to the PDB file. The
> problem is if I used different modelling tools, there are regions in the
> protein which does not remain consistent and looks different in different
> application.
> 
> best
> 
> J. Vitali
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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Description: This is a digitally signed message part.

Re: [ccp4bb] secondary structure assignment to PDB file

[Daniel Rigden]

A variety of alternatives to DSSP are easily available here

http://2struc.cryst.bbk.ac.uk/

As has been pointed out, methods other than the well-known DSSP may be 
particularly appropriate at lower-resolution or with model structures 
where perfect geometry, H-bond formation etc are not to be expected.


Dan


On 29/01/17 17:11, Pavel Afonine wrote:
Tools like DSSP and such rely on model geometry to annotate SS 
elements, so GIGO applies. For example, something that by eye looks 
like an obvious helix but has enough distortions is unlikely to be 
annotated correctly.

Pavel

On Sun, Jan 29, 2017 at 3:50 AM, Antonio Ariza 
> wrote:


I always use DSSP, which I believe has been the gold standard for
secondary structure assignment from pdb files for many years.
PYMOL also has a DSSP plugin that can be used to override its own
secondary structure assignment, which is nowhere near as good as DSSP.

Best

Tony

--
*
Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE*
**
*Links to my public profiles:*
ResearchGate 
LinkedIn 
GoogleScholar

ORCID 

*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK
] on behalf of chemocev marker
[jirivit...@gmail.com ]
*Sent:* 29 January 2017 10:41
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] secondary structure assignment to PDB file

Hi
Is there any tool that can assign secondary structure to the PDB
file. The problem is if I used different modelling tools, there
are regions in the protein which does not remain consistent and
looks different in different application.

best

J. Vitali




--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.