Re: [ccp4bb] Mac mini advice

[James Stroud]

I meant c.2006 iMac, of course.

James

On Jan 22, 2013, at 11:05 PM, James Stroud wrote:

> Get a quad-core. If you have iTunes going, some website running javascript 
> without your knowing it, and you have a computational job running, then 
> you've used up your dual core and things get sluggish. It happens to me all 
> the time on my c. 1996 iMac, which is still (barely) good enough for me.
> 
> On Mac v. Linux where calculations come secondary to office-type 
> calculations, you have to weigh your level of vendor lock-in. Do you run 
> Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? 
> Etc. If you are locked-in to commercial products and haven't migrated to open 
> source, then you may want to think twice about a Linux box. Macs are very 
> seamless for an office environment, but I don't know if they are appropriate 
> for heavy-duty calculations given that you'll trade horsepower for the Mac 
> experience.
> 
> James
> 
> 
> 
> On Jan 22, 2013, at 10:59 AM, Cara Vaughan wrote:
> 
>> Dear CCP4BB
>> 
>> I'm thinking about buying a Mac Mini and was looking for advice from people 
>> who have used these for crystallography.
>> 
>> We don't need the computer to do serious number-crunching as we have 
>> back-end servers that can do this for us, so it is primarily for running 
>> coot for model building, etc. and low intensity crystallography jobs.
>> 
>> I've seen from the archive that some people do use the Mac Mini for 
>> crystallography and I've got two questions:
>> 1. Do I need the Quad core or is a Dual core processor enough?
>> 2. Is the intergrated Intel HD graphics card OK for crystallography 
>> requirements?
>> 
>> All the best,
>> Cara.
>> 
>> 
>> Cara Vaughan
>> Lecturer in Structural Biology
>> Institute of Structural and Molecular Biology
>> Birkbeck College and UCL
>> London UK
>> 
>> 
>> This message was sent using IMP, the Internet Messaging Program.
> 

Re: [ccp4bb] Mac mini advice

[Nat Echols]

On Tue, Jan 22, 2013 at 10:05 PM, James Stroud  wrote:
> On Mac v. Linux where calculations come secondary to office-type 
> calculations, you have to weigh your level of vendor lock-in. Do you run 
> Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? 
> Etc. If you are locked-in to commercial products and haven't migrated to open 
> source, then you may want to think twice about a Linux box. Macs are very 
> seamless for an office environment, but I don't know if they are appropriate 
> for heavy-duty calculations given that you'll trade horsepower for the Mac 
> experience.

In my experience, yes they are (depending on your definition of
"heavy-duty" - everything I work with is either small or
low-resolution).  The real difficulty is integrating Macs into a
Linux-centric environment, for example configuring NFS, NIS, etc.
Far, far more painful than it needs to be, and for this reason I would
avoid Macs for shared workstations or (even worse) servers.  But they
make excellent standalone systems,  are very easy to maintain, and
while they may be relatively pricey, some of the premium features
(like SSDs) really do make a big difference, and the performance is
quite adequate even for the "low-end" laptops like the Air.  A $400
Celeron PC laptop, on the other hand, is probably large, heavy, and a
piece of junk.

-Nat

Re: [ccp4bb] Mac mini advice

[kaiser]

Well said, James Stroud!
  May I add that the "MAC- experience" is like walking to Jerusalem with dry 
peas in your shoes? It's possible, you might opt to do it for religious 
reasons, but it is far from the most logical or efficient course of action.
 Just my 2 cents,

Jens




- Reply message -
From: "James Stroud" 
Date: Tue, Jan 22, 2013 10:05 pm
Subject: [ccp4bb] Mac mini advice
To: 

Get a quad-core. If you have iTunes going, some website running javascript 
without your knowing it, and you have a computational job running, then you've 
used up your dual core and things get sluggish. It happens to me all the time 
on my c. 1996 iMac, which is still (barely) good enough for me.

On Mac v. Linux where calculations come secondary to office-type calculations, 
you have to weigh your level of vendor lock-in. Do you run Libreoffice or 
Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? Etc. If you are 
locked-in to commercial products and haven't migrated to open source, then you 
may want to think twice about a Linux box. Macs are very seamless for an office 
environment, but I don't know if they are appropriate for heavy-duty 
calculations given that you'll trade horsepower for the Mac experience.

James



On Jan 22, 2013, at 10:59 AM, Cara Vaughan wrote:

> Dear CCP4BB
> 
> I'm thinking about buying a Mac Mini and was looking for advice from people 
> who have used these for crystallography.
> 
> We don't need the computer to do serious number-crunching as we have back-end 
> servers that can do this for us, so it is primarily for running coot for 
> model building, etc. and low intensity crystallography jobs.
> 
> I've seen from the archive that some people do use the Mac Mini for 
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?
> 2. Is the intergrated Intel HD graphics card OK for crystallography 
> requirements?
> 
> All the best,
> Cara.
> 
> 
> Cara Vaughan
> Lecturer in Structural Biology
> Institute of Structural and Molecular Biology
> Birkbeck College and UCL
> London UK
> 
> 
> This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Mac mini advice

[James Stroud]

Get a quad-core. If you have iTunes going, some website running javascript 
without your knowing it, and you have a computational job running, then you've 
used up your dual core and things get sluggish. It happens to me all the time 
on my c. 1996 iMac, which is still (barely) good enough for me.

On Mac v. Linux where calculations come secondary to office-type calculations, 
you have to weigh your level of vendor lock-in. Do you run Libreoffice or 
Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? Etc. If you are 
locked-in to commercial products and haven't migrated to open source, then you 
may want to think twice about a Linux box. Macs are very seamless for an office 
environment, but I don't know if they are appropriate for heavy-duty 
calculations given that you'll trade horsepower for the Mac experience.

James



On Jan 22, 2013, at 10:59 AM, Cara Vaughan wrote:

> Dear CCP4BB
> 
> I'm thinking about buying a Mac Mini and was looking for advice from people 
> who have used these for crystallography.
> 
> We don't need the computer to do serious number-crunching as we have back-end 
> servers that can do this for us, so it is primarily for running coot for 
> model building, etc. and low intensity crystallography jobs.
> 
> I've seen from the archive that some people do use the Mac Mini for 
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?
> 2. Is the intergrated Intel HD graphics card OK for crystallography 
> requirements?
> 
> All the best,
> Cara.
> 
> 
> Cara Vaughan
> Lecturer in Structural Biology
> Institute of Structural and Molecular Biology
> Birkbeck College and UCL
> London UK
> 
> 
> This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Mac mini advice

[Dmitry Rodionov]

AFAIK there is no problem mixing and matching different timing RAM: system will 
run at the speed of the slowest module.
I don't think anybody will notice the difference with CAS latency Coot'ing and 
Refmac'ing.

I don't think there is much sense in having more than 4 GB of RAM per physical 
core on a Mac.
Majority of the Mac flock does not really care for where the RAM modules come 
from.
As for Mac Pro's- they use ECC RAM with proprietary heat sensors, so that's a 
completely different story. You can still use generic ECC RAM in a MAC PRO at 
the cost of the fan being stuck in hurricane mode.

The bottleneck of pretty much any modern system is the HDD. Apple-branded HDDs 
were known to have somewhat modified firmware, causing problems at times 
(mostly with AppleRAID, if not using an Apple-branded HDD)
An end user most definitely will notice an SSD VS HDD, which brings up TRIM 
support on OS X, which is limited to controllers sold by Apple.

Upgradeability-wise Apple is not the way to go in any case. 

DISCLAIMER:  The rest may be much more inflammatory.

Personally, I am not convinced OS X and Apple is the way to go log term (having 
been surrounded by MACs for the past 4-5 years)
I am not happy with the direction OS X is going. Too much emphasis on eye candy 
and not enough on underlying technology.
ZFS (long ago), Xgrid and X11 have been ditched, which I find disturbing. I 
don't see Apple investing in computers given current revenue from that sector.

Linux in a virtual machine of your choice might be a better bang for the buck. 
Or, Windows in a virtual machine on a Linux box for that matter.

Don't kick me,
DIR



On 2013-01-22, at 7:22 PM, Bryan Lepore  wrote:

> On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey  wrote:
> I don't think that anybody has shown a significant performance difference on 
> Apple memory vs a reasonable 3rd party supplier.  Apple may potentially have 
> better quality controls but places like Crucial essentially have lifetime 
> warranties on their memory.  I use Crucial at home and at work. [...]
> 
> sure, I agree with all this
> 
> the only other point I really wanted to make is to be cautious when 
> configuring a computer on the Apple website, where they might say for memory 
> "DDR3 ECC SDRAM" (checked this for a Mac Pro just now) but that is a 
> non-obvious way of, from what I can tell, selling only high end memory when 
> e.g. different CAS latency is available elsewhere - again, not obvious what 
> their CL is (perhaps it is listed somewhere). and maybe other specs apply.

Re: [ccp4bb] Mac mini advice

[Bryan Lepore]

On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey wrote:

> I don't think that anybody has shown a significant performance difference
> on Apple memory vs a reasonable 3rd party supplier.  Apple may potentially
> have better quality controls but places like Crucial essentially have
> lifetime warranties on their memory.  I use Crucial at home and at work.
> [...]


sure, I agree with all this

the only other point I really wanted to make is to be cautious when
configuring a computer on the Apple website, where they might say for
memory "DDR3 ECC SDRAM" (checked this for a Mac Pro just now) but that is a
non-obvious way of, from what I can tell, selling only high end memory when
e.g. different CAS latency is available elsewhere - again, not obvious what
their CL is (perhaps it is listed somewhere). and maybe other specs apply.

[ccp4bb] Workshop announcement: From Computational Biophysics to Systems Biology (CBSB13)

[Franklin A. Hays]

Dear colleague,

We invite you to participate in the upcoming workshop
on biological physics and systems biology entitled

"From Computational Biophysics to Systems Biology 2013 (CBSB13)"

which will take place at the University of Oklahoma Conference Center
in Norman, OK (USA) May 19 through May 21, 2013.

* There are opportunities for oral presentations, and*
* students/postdocs are eligible for travel fellowships. *
* More details can be found below or at  *
*http://www.hansmann-lab.com/cbsb13*

CBSB13 is organized in conjunction with the Stephenson Life
Sciences Research Center at the University of Oklahoma, and will
continue a series of successful workshops that have been held
since 2006 in both Germany and the USA.

As in previous years, the workshop aims to bring together
expertise from physics, biology, and computer science to
discuss current trends in computational biophysics and
systems biology. Topics of CBSB13 will include folding
and aggregation, protein-protein complexes, supramolecular
assemblies, cellular environments and interaction networks.

A list of confirmed speakers includes as keynote speakers:

* Hans Frauenfelder (Los Alamos National Laboratory)
* Klaus Schulten (Univ. Illinois Urbana-Champaign)
* Dan Stanzione (Univ. Texas, Austin, and IPlant Collaborative)

and as further invited speakers:

* Ana-Nicoleta Bondar (Free University Berlin)
* Boris Demeler ((Univ. of Texas Health Science Center at San Antonio)
* Don Hamelberg (Georgia State Univ.)
* Rohit Pappu (Washington Univ., St. Louis)
* Carol Post (Purdue Univ.)
* Harold Scheraga (Cornell Univ.)
* Art Voter (Los Alamos National Laboratory)
* Eberhard Voit (Georgia Inst. of Technol.)
* Feng Wang (Univ. of Arkansas)
* Tom Woolf (John Hopkins Univ.)
 
We especially encourage participation by students and

postdocs, and we are able to offer financial support for
selected students and postdocs on a competitive basis.

Five students/postdocs will be selected to receive a

"CBSB13 Young Researcher Award"

which we expect to include a $450 travel fellowship, free registration,
and the opportunity to give a featured oral presentation.

Contingent on availability of funds, 15 additional students/postdocs
will receive travel awards of $250 each and free registration,
and will compete for  additional oral presentation slots. Another
20 students/postdocs will receive $100 each to cover their registration fee.

All accepted applicants will be able to present their research
in poster form.

The *registration deadline is April 15* to be considered for an oral
or poster presentation. Acceptance letters and notifications of
fellowship awards will be sent out by April 22, 2013.

The registration fee is $100 if paid by May 1, and $150 after this date.

Please circulate this announcement among your colleagues, students, and
postdocs; and contact us with any questions you might have by sending email
tocbs...@ou.edu.

With best regards,

Ulrich H.E. Hansmann
Franklin A Hays
Henry Neeman
George Richter-Addo

.


---
Franklin A. Hays, Ph.D.
Assistant Professor, Department of Biochemistry and Molecular Biology
Adjunct Assistant Professor, Department of Nutritional Sciences
Member, Stephenson Oklahoma Cancer Center
University of Oklahoma Health Sciences Center
940 Stanton L. Young Blvd.
BMSB 937A (Office) or BMSB 937 (Lab)
Oklahoma City, OK 73104
405-271-2227 X61213
Franklin-Hays AT OUHSC.edu
-

Re: [ccp4bb] Mac mini advice

[Bosch, Juergen]

> Any reason for the Mac Mini over the iMac

A zalman monitor ir can you hook up a second monitor in stereo mode to your 
iMac ?

Jürgen 

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://lupo.jhsph.edu

On Jan 22, 2013, at 15:13, "Antony Oliver"  wrote:

> Hi Cara, 
> 
> Any reason for the Mac Mini over the iMac? - presumably as you've got a 
> suitable monitor / keyboard already? 
> 
> We're pretty much exclusively iMac of late (ditched the towers) and finding 
> them absolutely fine for both fairly intensive jobs (refinement) and 
> visualisation/building (Coot / PyMOL). 
> 
> We working with the quad-core i7's - but a lower spec is probably ok too - 
> just boost the memory if you can. 
> 
> With regards, 
> 
> Tony. 
> 
> Sent from my iPhone
> 
> On 22 Jan 2013, at 18:00, "Cara Vaughan"  
> wrote:
> 
>> Dear CCP4BB
>> 
>> I'm thinking about buying a Mac Mini and was looking for advice from people 
>> who have used these for crystallography.
>> 
>> We don't need the computer to do serious number-crunching as we have 
>> back-end servers that can do this for us, so it is primarily for running 
>> coot for model building, etc. and low intensity crystallography jobs.
>> 
>> I've seen from the archive that some people do use the Mac Mini for 
>> crystallography and I've got two questions:
>> 1. Do I need the Quad core or is a Dual core processor enough?
>> 2. Is the intergrated Intel HD graphics card OK for crystallography 
>> requirements?
>> 
>> All the best,
>> Cara.
>> 
>> 
>> Cara Vaughan
>> Lecturer in Structural Biology
>> Institute of Structural and Molecular Biology
>> Birkbeck College and UCL
>> London UK
>> 
>> 
>> This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Mac mini advice

[Antony Oliver]

Hi Cara, 

Any reason for the Mac Mini over the iMac? - presumably as you've got a 
suitable monitor / keyboard already? 

We're pretty much exclusively iMac of late (ditched the towers) and finding 
them absolutely fine for both fairly intensive jobs (refinement) and 
visualisation/building (Coot / PyMOL). 

We working with the quad-core i7's - but a lower spec is probably ok too - just 
boost the memory if you can. 

With regards, 

Tony. 

Sent from my iPhone

On 22 Jan 2013, at 18:00, "Cara Vaughan"  wrote:

> Dear CCP4BB
> 
> I'm thinking about buying a Mac Mini and was looking for advice from people 
> who have used these for crystallography.
> 
> We don't need the computer to do serious number-crunching as we have back-end 
> servers that can do this for us, so it is primarily for running coot for 
> model building, etc. and low intensity crystallography jobs.
> 
> I've seen from the archive that some people do use the Mac Mini for 
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?
> 2. Is the intergrated Intel HD graphics card OK for crystallography 
> requirements?
> 
> All the best,
> Cara.
> 
> 
> Cara Vaughan
> Lecturer in Structural Biology
> Institute of Structural and Molecular Biology
> Birkbeck College and UCL
> London UK
> 
> 
> This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Mac mini advice

[Phil Jeffrey]

I don't think that anybody has shown a significant performance 
difference on Apple memory vs a reasonable 3rd party supplier.  Apple 
may potentially have better quality controls but places like Crucial 
essentially have lifetime warranties on their memory.  I use Crucial at 
home and at work.


I'd echo Nat's suggestion of going 3rd party for the memory and putting 
in as much as you can afford.


(Modern Mac Minis and even my 13" Macbook Pro outperform my older 
octacore tower on a per-core basis.  They're quite capable machines.)


Phil Jeffrey
Princeton

On 1/22/13 1:26 PM, Bryan Lepore wrote:

On Jan 22, 2013, at 13:08, Nat Echols  wrote:


On Tue, Jan 22, 2013 at 9:59 .

I would definitely recommend maxing out the memory, but don't buy it
from Apple - we were able to get 16GB from CDW for less than $100.


I think it is just that Apple only offers the highest end memory - CL and all 
that.

-Bryan

Re: [ccp4bb] Mac mini advice

[Bryan Lepore]

On Jan 22, 2013, at 13:08, Nat Echols  wrote:

> On Tue, Jan 22, 2013 at 9:59 .
> 
> I would definitely recommend maxing out the memory, but don't buy it
> from Apple - we were able to get 16GB from CDW for less than $100.

I think it is just that Apple only offers the highest end memory - CL and all 
that.

-Bryan

Re: [ccp4bb] Mac mini advice

[Nat Echols]

On Tue, Jan 22, 2013 at 9:59 AM, Cara Vaughan
 wrote:
> I've seen from the archive that some people do use the Mac Mini for
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?

You can survive with the dual, but I would definitely spring for the
quad if you can afford it - but I suppose it depends on how you work.
I like to run multiple of jobs at once if possible, and still have a
core left for the web browser, etc.  Some programs will also take
advantage of multiple processors, for that matter.

I would definitely recommend maxing out the memory, but don't buy it
from Apple - we were able to get 16GB from CDW for less than $100.

> 2. Is the intergrated Intel HD graphics card OK for crystallography
> requirements?

It depends on your requirements, but I've been using Coot and PyMOL
frequently on a MacBook Air for the last year, and usually the
graphics chip (also Intel HD) isn't the bottleneck.

-Nat

Re: [ccp4bb] Mac mini advice

[Bosch, Juergen]

Current Mac minis outperform my 2009 models with which I am still happy. So 
dual core I guess would be sufficient no need for upgrade on graphics card.

Jürgen 

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://lupo.jhsph.edu

On Jan 22, 2013, at 11:59, "Cara Vaughan"  
wrote:

> Dear CCP4BB
> 
> I'm thinking about buying a Mac Mini and was looking for advice from  
> people who have used these for crystallography.
> 
> We don't need the computer to do serious number-crunching as we have  
> back-end servers that can do this for us, so it is primarily for  
> running coot for model building, etc. and low intensity  
> crystallography jobs.
> 
> I've seen from the archive that some people do use the Mac Mini for  
> crystallography and I've got two questions:
> 1. Do I need the Quad core or is a Dual core processor enough?
> 2. Is the intergrated Intel HD graphics card OK for crystallography  
> requirements?
> 
> All the best,
> Cara.
> 
> 
> Cara Vaughan
> Lecturer in Structural Biology
> Institute of Structural and Molecular Biology
> Birkbeck College and UCL
> London UK
> 
> 
> This message was sent using IMP, the Internet Messaging Program.

[ccp4bb] Mac mini advice

[Cara Vaughan]

Dear CCP4BB

I'm thinking about buying a Mac Mini and was looking for advice from  
people who have used these for crystallography.


We don't need the computer to do serious number-crunching as we have  
back-end servers that can do this for us, so it is primarily for  
running coot for model building, etc. and low intensity  
crystallography jobs.


I've seen from the archive that some people do use the Mac Mini for  
crystallography and I've got two questions:

1. Do I need the Quad core or is a Dual core processor enough?
2. Is the intergrated Intel HD graphics card OK for crystallography  
requirements?


All the best,
Cara.


Cara Vaughan
Lecturer in Structural Biology
Institute of Structural and Molecular Biology
Birkbeck College and UCL
London UK


This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Superposing nucleic acids

[Phoebe A. Rice]

As already pointed out, it depends on what you're trying to show / figure out.

But my generic advice would be to go with just C1' because the backbone can 
vary quite a bit even in more-or-less-B-form DNA.

If you feel like getting a little fancier, add the atom on the other end of the 
glycosidic bond (note the atom number is different for pyrimidines vs. 
purines).  The sublime thing about W:C pairing is that it keeps the orientation 
glycosidic bonds constant.



++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

773 834 1723; pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/

http://www.rsc.org/shop/books/2008/9780854042722.asp


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Barry Finzel 
[finze...@umn.edu]
Sent: Tuesday, January 22, 2013 9:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Superposing nucleic acids

Minimally,  I believe you want to use P and C1'.
(This has been done by others, including Pabo and Pabo & Nekludova, J.Mol. 
Biol., 301:597-694 (2000).

I actually prefer to use all backbone atoms: P O5' C5' C4' O3' C3' C2' C1' O1'


Barry Finzel
Medicinal Chemistry Department
2-160C Weaver-Densford
Tel: (612) 626-5979
Lab: (612) 626-5226
Fax: (612) 624-0139
finze...@umn.edu



On Jan 22, 2013, at 9:00 AM, Alan Cheung wrote:

Dear all - is there a convention for superposing nucleic acids duplexes of 
unrelated sequence?

i.e. which atoms should be superposed : C4' of the sugar, P of the backbone, 
O3'/O5' of the backbone, or some combination thereof?

Alan


--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de

[ccp4bb] Off-topic: ITC - what to buy?

[Wulf Blankenfeldt]

Dear all:

we are looking into buying an isothermal titration calorimeter, but are 
only aware of two manufacturers: TA Instruments and MicroCal (GE 
Healthcare). Are there any more?


Do you have any recommendations (brand, model etc.) for us?

Thanks in advance,


Wulf

--
Prof. Dr. Wulf Blankenfeldt
NW-I, 2.0.U1.09Universitaet Bayreuth
fon:+49-(0)921-55-2427  Lehrstuhl fuer Biochemie
fax:+49-(0)921-55-2432   Universitaetsstrasse 30
e-mail: wulf.blankenfeldt [at] uni-bayreuth.de95447 Bayreuth
web:www.biochemie.uni-bayreuth.deGermany

Re: [ccp4bb] Superposing nucleic acids

[Barry Finzel]

Minimally,  I believe you want to use P and C1'.
(This has been done by others, including Pabo and Pabo & Nekludova,  
J.Mol. Biol., 301:597-694 (2000).


I actually prefer to use all backbone atoms: P O5' C5' C4' O3' C3' C2'  
C1' O1'



Barry Finzel
Medicinal Chemistry Department
2-160C Weaver-Densford
Tel: (612) 626-5979
Lab: (612) 626-5226
Fax: (612) 624-0139
finze...@umn.edu



On Jan 22, 2013, at 9:00 AM, Alan Cheung wrote:

Dear all - is there a convention for superposing nucleic acids  
duplexes of unrelated sequence?


i.e. which atoms should be superposed : C4' of the sugar, P of the  
backbone, O3'/O5' of the backbone, or some combination thereof?


Alan


--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de

Re: [ccp4bb] Superposing nucleic acids

[Ho,Shing]

Dear Alan,

This depends very much on whether the structures are similar in the
helical conformations or not, and on what question you are trying to
address.  If these are nearly identical structures, it really does not
matter much what atoms you use for superposition, as long as they lie
along the backbone. Indeed, for general superpositions, you could use all
the atoms of the backbone.  The most common single atom type would be the
C1' carbons of the sugar, since the C1' to C1' distances should be
constant across Watson-Crick paired bases and should be similar along the
individual strands regardless of the sequence.  This would allow you to
compare the helical core of the structures without worrying about
variations along the backbone, such as sugar puckers, phosphate
orientations, etc.

However, if you are comparing across conformations (e.g., between A-
versus B- type helices), there would not be many atoms that would be
highly superimposable, in which case a general all atom superpositioning
would probably be most appropriate (although I am not sure what you would
learn from that other than general orientation).

P. Shing Ho, Ph.D.
Professor & Chair
Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Fort Collins, CO 80523-1870
970-491-0569 (phone)





On 1/22/13 8:00 AM, "Alan Cheung"  wrote:

>Dear all - is there a convention for superposing nucleic acids duplexes
>of unrelated sequence?
>
>i.e. which atoms should be superposed : C4' of the sugar, P of the
>backbone, O3'/O5' of the backbone, or some combination thereof?
>
>Alan
>
>
>-- 
>Alan Cheung
>Gene Center
>Ludwig-Maximilians-University
>Feodor-Lynen-Str. 25
>81377 Munich
>Germany
>Phone:  +49-89-2180-76845
>Fax:  +49-89-2180-76999
>E-mail: che...@lmb.uni-muenchen.de

[ccp4bb] Superposing nucleic acids

[Alan Cheung]

Dear all - is there a convention for superposing nucleic acids duplexes 
of unrelated sequence?


i.e. which atoms should be superposed : C4' of the sugar, P of the 
backbone, O3'/O5' of the backbone, or some combination thereof?


Alan


--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de

Re: [ccp4bb] EF motif

[Pavšič , Miha]

Dear Kris,

Letters A, B, C, D, E, F, ... refer to the helices in parvalbumin where the 
motif was first described. See http://www.ncbi.nlm.nih.gov/pubmed/4700463

Best,
Miha

On 22. 1. 2013, at 14:09, K Singh  wrote:

> Dear All,
> While going through Ca2+ binding site, I came across helix-loop-helix
> motif known as EF-motif, where E and F represents respective helices.
> What I am not able to follow why it is known as "EF" or is it
> something EF abbreviates for?
> With best regards
> Kris

Re: [ccp4bb] EF motif

[K Singh]

Thanks Berta
but Thats exactly what I am asking that what E and F refers to in
naming the respective helices...
why it was not any other set of alphabets?

With best regards,
Kris

On Tue, Jan 22, 2013 at 6:43 PM, Berta Martins
 wrote:
> Dear Kris,
>
> E and F are the helices names.
> Look at the book Introduction to Protein Structure from Branden & Tooze.
> They have great pictures and a very good introduction to fold names.
>
> Kind regards,
> Berta Martins
>
>
>
> On Jan 22, 2013, at 2:09 PM, K Singh wrote:
>
> Dear All,
> While going through Ca2+ binding site, I came across helix-loop-helix
> motif known as EF-motif, where E and F represents respective helices.
> What I am not able to follow why it is known as "EF" or is it
> something EF abbreviates for?
> With best regards
> Kris
>
>

[ccp4bb] protein solubility predictions

[Careina Edgooms]

Dear ccp4

Apologies for the off topic question. I was wondering whether anyone could 
suggest a good tool or methodology to use to predict protein solubility and 
ability to fold from the sequence? I am working with a large protein of 
multiple domains. I would like to work with as close to the full length protein 
as possible without affecting its solubility and ability to fold correctly. I 
know there are web based tools where you can upload a sequence and see the 
predicted solubility but I wonder if there is any good strategy to use to 
determine how best to construct the truncated protein? ie which parts of the 
sequence to keep and which to remove so as to maximise solubility. Also I have 
an eye to crystallising this protein in the future and I wonder if there are 
any specific things I should look out for with that in mind? I'm sure 
minimising flexible loops is one such thing.
All help appreciated
Best
Careina

Re: [ccp4bb] perfect twin

[Randy Read]

Just to follow up on what has already been said:

The twinning tests in truncate, phenix.xtriage and (since recently) in Phaser 
should give you a good idea whether the data might be twinned.  If you have 
merged the data with too high symmetry, there won't be a potential twin 
operator (because it has been interpreted as a crystallographic symmetry 
operator) so you can't use things like the L test, but the moment tests are 
still useful.

If these tests do indicate twinning, then the true symmetry is probably lower, 
and there are many subgroups for P6222 that could be the true space group.  You 
could investigate them systematically, but with a 42% identical model you might 
be able to sort it out by molecular replacement.  In a number of cases we've 
succeeded in solving a structure using data merged in P1, and then using the 
symmetry of the resulting model to determine the space group.  It's worth a 
try, especially if the MR attempts in P6222 gave a reasonable peak for the 
rotation search.  

Best wishes,

Randy Read

On 22 Jan 2013, at 06:25, LISA wrote:

> Hi all,
> Does anyone know how to check a data is twin and how to detwin?
> My data is 3.3 A with space group P6222 or P6422? But I can not solve this 
> structue by molecular replacement with the model has 42% sequence identity. I 
> am wondering my data maybe twin.
> Thanks
> Lisa

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] perfect twin

[Herman . Schreuder]

Hi Lisa,
 
The problem you have can be very tricky. Here my comments:
 
-What do you mean by "I can not solve the structure by molecular replacement"?. 
Moleculare replacement programs usually produce some solution, even if it is 
wrong. Do the R-factors stay around 50%, is the electron density very bad? If 
you do not get a solution at all, the solution might be rejected because of 
clashes. In this case you may want to cut out some variable loops from the 
model or increase the maximum number of allowed clashes.
-What does the Matthews number tell you? If you get a very dense crystal 
packing even with one molecule in the asymmetric unit, you most likely have 
twinning.
-3.3 Å means rather poor data. This means that the statistics you get on your 
space group and on the twinning will be tentative and you have to test all 
possibilities. Also you may have pseudo crystallographic NCS making the 
apparent space group look different from the true space group. This means that 
in molecular replacement, you have to test all possibilities, e.g. P622, P6122, 
P6222, P6322 etc. Most molecular replacement programs have an option to 
automatically test them all.
-Considering twinning, you have to process the data in the lower symmetry space 
group, presumably P6 and submit the data to a twin server, as Fred suggested. I 
would also run molecular replacement on the lower symmetry data. Even with 
perfect twinning, one usuallly gets two solutions, corresponding to the two 
twin domains.
 
Good luck!
Herman




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
LISA
Sent: Tuesday, January 22, 2013 7:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] perfect twin


Hi all,

Does anyone know how to check a data is twin and how to detwin?

My data is 3.3 A with space group P6222 or P6422? But I can not solve 
this structue by molecular replacement with the model has 42% sequence 
identity. I am wondering my data maybe twin.

Thanks

Lisa