Re: [ccp4bb] Sortwater NCS Matrix input

[Phil Evans]

I should maybe add some code to orthonormalise the matrix if it's not too far 
off (which would be approximate). I haven't looked at this program for a long 
time (nor indeed used it), so don't hold your breath

Phil

On 1 Apr 2015, at 22:52, Shane Caldwell  wrote:

> Hi ccp4bb,
> 
> I'm trying to solve a problem I never quite figured out in the past. I'd like 
> to use the sortwater utility to send my picked waters to various protein 
> chains, and to give them the same residue number if they are NCS-equivalent, 
> as the manual outlines.
> 
> http://www.ccp4.ac.uk/html/sortwater.html
> 
> The first part goes off perfectly, partitioning the waters into their 
> respective chains. Where I run into problems is bringing in NCS. I can't get 
> the program to recognize the transformation matrix. I can calculate the 
> matrix using superpose, and manually input these (limited precision) values 
> into my script, which looks like:
> 
> NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004 -0.994 
> 37.502 -35.283 81.276
> 
> and it returns 
> 
>  WARNING:   Matrix is not orthonormal 
> 
> 
> My linear algebra is very limited, and I don't know exactly what this means 
> in the context of this program, though I suspect it could be either linked to 
> converting to fractional coordinates (I'm in a monoclinic system), or a 
> product of the limited precision of the matrix values. 
> 
> Using the identity matrix, like so: 
> 
> NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0 
> 0.0 1.0 0.000 0.000 0.000
> 
> doesn't trigger the warning. These values have more digits, but adding extra 
> zeroes to the original matrix as a very crude workaround still returns the 
> error.
> 
> So, I'm now stuck trying to parse what's going on. I know sortwater also 
> takes O datablocks as matrix input, and that's something I could look into 
> (especially if calculating in a different program might get me better 
> precision). Although, I'm not sure the format is a factor given the identity 
> matrix is accepted as a keyword input.
> 
> Skimming the archives, I get the sense this isn't something that many users 
> do any more. I have quite a few structures with hundreds of waters each and 
> I'd like to get the waters organized, but doing it by hand will take a very 
> long time. Any help getting this program running would be greatly appreciated!
> 
> 
> Shane Caldwell
> McGill University

Re: [ccp4bb] Sortwater NCS Matrix input

[Phil Evans]

the test limit is perhaps over-tight

data eps/0.0001/

Phil


On 2 Apr 2015, at 00:34, Dale Tronrud  wrote:

>   I think you are on the right track - There are not enough decimal
> points in your matrix elements to pass the orthonormal test.  This test
> checks that the length of each row (x^2+y^2+z^2) is equal to one and the
> dot product of each row with every other row is equal to zero.  If the
> values on your NCS statement are in row order I calculate 0.999337 for
> the length of the first row.  If the program is testing if this is equal
> to one to four decimal points you lose.
> 
>   You have to add more digits, but just adding zeros isn't going to
> accomplish much.  The best solution is to get your ncs program to report
> its matrix with more digits -- three is pitiful.  Failing that you could
> calculate one element of each row from the other two to ensure the
> length is equal to one at a higher level of precision and hope this
> doesn't mess up the dot product test.  You'll end up with one number in
> each row having more than three decimal places.
> 
> Dale Tronrud
> 
> On 4/1/2015 2:52 PM, Shane Caldwell wrote:
>> Hi ccp4bb,
>> 
>> I'm trying to solve a problem I never quite figured out in the past. I'd
>> like to use the *sortwater* utility to send my picked waters to various
>> protein chains, and to give them the same residue number if they are
>> NCS-equivalent, as the manual outlines.
>> 
>> http://www.ccp4.ac.uk/html/sortwater.html
>> 
>> The first part goes off perfectly, partitioning the waters into their
>> respective chains. Where I run into problems is bringing in NCS. I can't
>> get the program to recognize the transformation matrix. I can calculate
>> the matrix using *superpose*, and manually input these (limited
>> precision) values into my script, which looks like:
>> 
>> NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004
>> -0.994 37.502 -35.283 81.276
>> 
>> and it returns
>> 
>> WARNING:   Matrix is not orthonormal 
>> 
>> 
>> My linear algebra is very limited, and I don't know exactly what this
>> means in the context of this program, though I suspect it could be
>> either linked to converting to fractional coordinates (I'm in a
>> monoclinic system), or a product of the limited precision of the matrix
>> values.
>> 
>> Using the identity matrix, like so:
>> 
>> NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0
>> 0.0 1.0 0.000 0.000 0.000
>> 
>> doesn't trigger the warning. These values have more digits, but adding
>> extra zeroes to the original matrix as a very crude workaround still
>> returns the error.
>> 
>> So, I'm now stuck trying to parse what's going on. I know *sortwater*
>> also takes O datablocks as matrix input, and that's something I could
>> look into (especially if calculating in a different program might get me
>> better precision). Although, I'm not sure the format is a factor given
>> the identity matrix is accepted as a keyword input.
>> 
>> Skimming the archives, I get the sense this isn't something that many
>> users do any more. I have quite a few structures with hundreds of waters
>> each and I'd like to get the waters organized, but doing it by hand will
>> take a very long time. Any help getting this program running would be
>> greatly appreciated!
>> 
>> 
>> Shane Caldwell
>> McGill University

[ccp4bb] CCP4-6.5 Update 006

[Charles Ballard]

Dear CCP4 Users

An update for the CCP4-6.5 series has just been released, consisting
of the following changes

* ccp4-progs
- rwcontents: support for strict NCS records, via pdb header

* blend
- update to 0.6.3

* ccp4mg
- addition of pdbview (except windows)

* pointless
- Bug fixes
- update to 1.9.29

* prelyscar
- Bug fixes, documentation fixes

* 'imosflm
- fix for issue with 0 oscillation angle

* acedrg
- major update

* atoms_electron.lib
- Electron scattering terms for use in refmac (cyro-EM)


Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team

Re: [ccp4bb] CCP4-6.5 Update 007

[Charles Ballard]

Dear All

for the record, this is, of course, Update 006

Charles

On 14 Mar 2015, at 10:51, Charles Ballard wrote:

> Dear CCP4 Users
> 
> An update for the CCP4-6.5 series has just been released, consisting
> of the following changes
> 
> * ccp4-progs
> - areaimol - bug fixes
> - r500 - update=
> - standard_geometry.cif - update
> 
> * imosflm/mosflm
> - update to 7.1.3
> 
> * Molrep
> - fix for bug in multi-copy search
> 
> * aimless
> - 0.5.7, bug fixes
> 
> * privateer
> - extended support for disaccharides
> - added support for external validation strings
> 
> * prosmart
> - minor update to h-bond restaint generation
> 
> * mmdb2
> - update to rwbrook interface
> 
> * ccp4i'
> - updated autoSHARP interface
> 
> Please report any bugs to c...@stfc.ac.uk.
> 
> Many thanks for using CCP4.
> 
> The CCP4 Core Team
> 
> 

[ccp4bb] Renormalize a matrix

[Gert Vriend]

This matrix-renormalizer comes from WHAT IF. Feel free to use it any way 
you want:


  SUBROUTINE GVSREN (RMAT)
C+++
C---
C   

C RMAT IS A REAL MATRIX DIMENSIONED 
(3,3).  
C GVSEIG can be any eigenvalue calculator. Ask me if you want the 
WHAT IF one.
C   


C---
C===
  IMPLICIT  NONE
  INTEGER   I, J, K, L
  REAL  A(6), RMAT(3,3), S(3,3), T(3,3), X(3,3), Y
C
C FORM THE PRODUCT OF RMAT * RMAT(TRANSPOSE)
C
  L=0
  DO 30 I=1,3
 DO 20 J=1,I
L=L+1
A(L)=0.0
DO 10 K=1,3
   A(L)=A(L)+RMAT(I,K)*RMAT(J,K)
   10   CONTINUE
   20CONTINUE
   30 CONTINUE
C
C CALCULATE THE EIGENVALUES AND THE EIGENVECTORS OF A
C
  CALL GVSEIG (A,X,3,0)
C
C SMALL PRECAUTION AGAINST FUTURE OVERFLOWS
C
  A(1)=1.0/SQRT(AMAX1(A(1),1.E-12))
  A(2)=1.0/SQRT(AMAX1(A(3),1.E-12))
  A(3)=1.0/SQRT(AMAX1(A(6),1.E-12))
C
C FORM THE PRODUCT OF X * A
C
  DO 50 I=1,3
 DO 40 J=1,3
S(I,J)=X(I,J)*A(J)
   40CONTINUE
   50 CONTINUE
C
C TRANSPOSE X
C
  DO 70 I=2,3
 DO 60 J=1,I-1
Y=X(I,J)
X(I,J)=X(J,I)
X(J,I)=Y
   60CONTINUE
   70 CONTINUE
C
C CALCULATE THE RENORMALIZED RMAT AS S * X * RMAT
C
  CALL GVS3X3 (T,X,RMAT)
  CALL GVS3X3 (RMAT,S,T)

  RETURN
  END

Re: [ccp4bb] Sortwater NCS Matrix input

[Kay Diederichs]

On Wed, 1 Apr 2015 17:52:44 -0400, Shane Caldwell  
wrote:

>Hi ccp4bb,
>
>I'm trying to solve a problem I never quite figured out in the past. I'd
>like to use the *sortwater* utility to send my picked waters to various
>protein chains, and to give them the same residue number if they are
>NCS-equivalent, as the manual outlines.
>
>http://www.ccp4.ac.uk/html/sortwater.html
>
>The first part goes off perfectly, partitioning the waters into their
>respective chains. Where I run into problems is bringing in NCS. I can't
>get the program to recognize the transformation matrix. I can calculate the
>matrix using *superpose*, and manually input these (limited precision)
>values into my script, which looks like:
>
>NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004 -0.994
>37.502 -35.283 81.276

I'd try the following:
calculate 
delta1=(1 - (0.072^2 + 0.997^2 + 0.012^2) ) / 2 and add it to 0.997; use the 
result instead of 0.997
delta2=(1- (0.991^2 + 0.073^2 + 0.113^2)) / 2 and add it to 0.991; use the 
result instead of 0.991
delta3=(1 - (0.113^2 + 0.004^2 + 0.994^2)) / 2 and add it to -0.994; use the 
result instead of -0.994

I think (but didn't verify!) these operations would adjust the lengths of the 
"vectors" towards 1.000, while keeping their dot product close to zero.

best,

Kay 


>
>and it returns
>
> WARNING:   Matrix is not orthonormal 
>
>
>My linear algebra is very limited, and I don't know exactly what this means
>in the context of this program, though I suspect it could be either linked
>to converting to fractional coordinates (I'm in a monoclinic system), or a
>product of the limited precision of the matrix values.
>
>Using the identity matrix, like so:
>
>NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0
>0.0 1.0 0.000 0.000 0.000
>
>doesn't trigger the warning. These values have more digits, but adding
>extra zeroes to the original matrix as a very crude workaround still
>returns the error.
>
>So, I'm now stuck trying to parse what's going on. I know *sortwater* also
>takes O datablocks as matrix input, and that's something I could look into
>(especially if calculating in a different program might get me better
>precision). Although, I'm not sure the format is a factor given the
>identity matrix is accepted as a keyword input.
>
>Skimming the archives, I get the sense this isn't something that many users
>do any more. I have quite a few structures with hundreds of waters each and
>I'd like to get the waters organized, but doing it by hand will take a very
>long time. Any help getting this program running would be greatly
>appreciated!
>
>
>Shane Caldwell
>McGill University
>

[ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[xaravich ivan]

Hello everyone,
I am planing to buy a new Mac laptop (price no bar) which will let me run
all xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular
Modelling (1000 to 1 decoys) softwares smoothly.

What in your opinion is the best configuration. (RAM, memory, number and
speed  of processors, graphics card etc.) Also I am buying a Mac display
separately so that I have a big screen for easy visualization of models,
COOT etc.

I know that powerful Mac desktops can make life much easier but here I am
specifically interested in Mac laptops only.

As always thanks in advance and I will post all the suggestions anonymously
for others with same query.

ivan

Re: [ccp4bb] nVidia quadro

[Oganesyan, Vaheh]

Kay and others,

I think Quadro 5000 available @
http://www.amazon.com/PNY-VCQ5000-PB-DisplayPort-Profesional-Graphics/dp/B003X26T7K
is a better option both price wise and need of transforming the output into 
3-pin mini DIN. Having said that I should mention difference: the memory is 
2.5GB for 5000 model while K4200 has 4 GB. I believe the memory shouldn't be an 
issue at that level since my 10 years old FX1400 has only 1 GB and I did not 
encounter problems so far.



Vaheh Oganesyan
www.medimmune.com


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Wednesday, April 01, 2015 3:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] nVidia quadro

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
 wrote:

>On 3/25/2015 18:10, Kay Diederichs wrote:
>> On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  
>> wrote:
>>
>>> You could check the nVidia page of officially supported displays. It
>>> includes a search tab so you can check for "Built-in Emitter."
>>> http://www.nvidia.com/object/3d-vision-displays.html
>>>
>>> Performing that search brings up 5 contenders. Good luck finding any
>>> of these products still for sale.
>> Unfortunately, this NVidia page has not been updated for years.
>>
>> The qualifier "3D-fähig (aktiv)" at 
>> http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top
>>  should indicate a built-in emitter, but I looked at some of the 
>> descriptions of these 11 monitors and was unable to confirm that they indeed 
>> have a built-in emitter. So one has to research every specific case.
>>
>> I changed the wording on the wiki page.
>>
>> Kay
>>
>I went through the specs for the monitors on the Heise list, and none
>of them seems to have a built in emitter compatible with Nvidia 3D
>Vision 2. It looks like it is a bad time to buy a 3D monitor. At this
>point it might be easier to just go for a Quadro with 3-pin connector.
>
>Best,
>Andreas
>

I asked the company who runs the price info site to check their assignments, 
and they fixed the categories: http://geizhals.eu/?cat=monlcd19wide now has a 
"inkl. 3D-emitter" attribute. This currently only returns the Asus 278HR which 
can only be bought in Poland, or through EBay.

The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo connector 
(needed for Linux) is the K4200 
(http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at 
~ €700.

best,

Kay
To the extent this electronic communication or any of its attachments contain 
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be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
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cooperation.

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[Mark van Raaij]

Hi Ivan, 
Being in the same boat, I have investigated a bit. It seems to be a straight trade-off between more processing power, more RAM and less partability Macbook, Macbook Air, 13" Macbook Pro, 15" Macbook Pro. 
For running Rosetta I think you will be thankful for the faster processors and extra RAM of the Pro...and only the 15" has quadcore. You can put 16 Gb RAM in the 13" Pro but it has only dual-core.
The 15" is quite a bit bigger to lug around...nevertheless I'll probably go for that one. 
I don't know if there are any updates to the Macbook forthcoming, but I have to wait a bit anyway for financial reasons.
Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaij
On 2 Apr 2015 15:03, xaravich ivan  wrote:Hello everyone,I am planing to buy a new Mac laptop (price no bar) which will let me run all xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular Modelling (1000 to 1 decoys) softwares smoothly.What in your opinion is the best configuration. (RAM, memory, number and speed  of processors, graphics card etc.) Also I am buying a Mac display separately so that I have a big screen for easy visualization of models, COOT etc.I know that powerful Mac desktops can make life much easier but here I am specifically interested in Mac laptops only.As always thanks in advance and I will post all the suggestions anonymously for others with same query.ivan

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[Jurgen Bosch]

You two should absolutely invest in the 1TB SSD option as well, I have 
essentially the machine you describe, but it is now already 14 months old. So 
the newer models will be maybe 30% more powerful in overall performance.
The geek bench score of my Macpro 2010 (48GB RAM, dual hexa core) corresponds 
to my current laptop.
J?rgen

..
J?rgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

On Apr 2, 2015, at 09:33, Mark van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:


Hi Ivan,
Being in the same boat, I have investigated a bit. It seems to be a straight 
trade-off between more processing power, more RAM and less partability Macbook, 
Macbook Air, 13" Macbook Pro, 15" Macbook Pro.
For running Rosetta I think you will be thankful for the faster processors and 
extra RAM of the Pro...and only the 15" has quadcore. You can put 16 Gb RAM in 
the 13" Pro but it has only dual-core.
The 15" is quite a bit bigger to lug around...nevertheless I'll probably go for 
that one.
I don't know if there are any updates to the Macbook forthcoming, but I have to 
wait a bit anyway for financial reasons.

Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaij

On 2 Apr 2015 15:03, xaravich ivan 
mailto:xaravich.i...@gmail.com>> wrote:
Hello everyone,
I am planing to buy a new Mac laptop (price no bar) which will let me run all 
xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular Modelling 
(1000 to 1 decoys) softwares smoothly.

What in your opinion is the best configuration. (RAM, memory, number and speed  
of processors, graphics card etc.) Also I am buying a Mac display separately so 
that I have a big screen for easy visualization of models, COOT etc.

I know that powerful Mac desktops can make life much easier but here I am 
specifically interested in Mac laptops only.

As always thanks in advance and I will post all the suggestions anonymously for 
others with same query.

ivan

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[Scott Thomas Walsh]

Dear Mac Lovers:

I would have to agree with Jurgen with SSD drives.  These fast drives
have breathed new life into my old Macs (2011 Macbook Pro, 2009 Mac mini,
and yes a 2006 Mac Pro (has 8 cores and just keeps running)).

In addition, all these Macs are maxed out with RAM.

Cheers,

Scott


Scott T. R. Walsh, PhD
Assistant Professor
University of Maryland
IBBR/CBMG
3127E CARB-2
9600 Gudelsky Drive
Rockville, MD  20850  USA
phone: (240) 314-6478
fax: (240) 314-6225
email: swals...@umd.edu

On Apr 2, 2015, at 9:43 AM, Jurgen Bosch 
mailto:jbos...@jhu.edu>> wrote:

You two should absolutely invest in the 1TB SSD option as well, I have 
essentially the machine you describe, but it is now already 14 months old. So 
the newer models will be maybe 30% more powerful in overall performance.
The geek bench score of my Macpro 2010 (48GB RAM, dual hexa core) corresponds 
to my current laptop.
Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

On Apr 2, 2015, at 09:33, Mark van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:


Hi Ivan,
Being in the same boat, I have investigated a bit. It seems to be a straight 
trade-off between more processing power, more RAM and less partability Macbook, 
Macbook Air, 13" Macbook Pro, 15" Macbook Pro.
For running Rosetta I think you will be thankful for the faster processors and 
extra RAM of the Pro...and only the 15" has quadcore. You can put 16 Gb RAM in 
the 13" Pro but it has only dual-core.
The 15" is quite a bit bigger to lug around...nevertheless I'll probably go for 
that one.
I don't know if there are any updates to the Macbook forthcoming, but I have to 
wait a bit anyway for financial reasons.

Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaij

On 2 Apr 2015 15:03, xaravich ivan 
mailto:xaravich.i...@gmail.com>> wrote:
Hello everyone,
I am planing to buy a new Mac laptop (price no bar) which will let me run all 
xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular Modelling 
(1000 to 1 decoys) softwares smoothly.

What in your opinion is the best configuration. (RAM, memory, number and speed  
of processors, graphics card etc.) Also I am buying a Mac display separately so 
that I have a big screen for easy visualization of models, COOT etc.

I know that powerful Mac desktops can make life much easier but here I am 
specifically interested in Mac laptops only.

As always thanks in advance and I will post all the suggestions anonymously for 
others with same query.

ivan

Re: [ccp4bb] Sortwater NCS Matrix input

[Edward A. Berry]

On 04/01/2015 08:47 PM, Shane Caldwell wrote:


I guess the next, probably more general question for the bb is: which utilities 
export an NCS transformation matrix with more precision?


TAJones' "O" program allows you to specify output format like
write .LSQ_RT_m2m ncs.odb (3f16.10)
which gives 10 places after the decimal and is probably greater precision than 
"under the hood"
Anyway i never have orthonormality problems with this format

Calculate the operator with ls_explicit command.

Re: [ccp4bb] nVidia quadro

[mesters]

Be aware though, the option 3-pin + USB for Nvidia 3D Vision 2 glasses 
is not running/supported under Linux!


For linux boxes and Nvidia 3D Vision 2 glasses:
You have to buy an 120Hz ASUS VG287HR (there is no other useful option 
in my opinion at the moment) and whatever quadro card you buy, make sure 
the card posesses a "DVI-I Dual-Link Connector" (also termed DVI-D / 
DVI-I DL instead of a simple DVI) because the ASUS VG287HR comes with a 
DVI-D port (no displayport 1.2 and VGA is not usefull if you are going 
for 1920x1080@120hz). If the quadro card has display ports 1.2 only, you 
will need a Club-3D CAC-1051 active DisplayPort/Dual-Link DVI Adapter 
330MHz for about 110 € (do not buy the 270 mhz model, it will not work 
as the bandwidth is too low for 1920x1080@120hz) or for miniDisplay port 
cards, the Club-3D CAC-1151 active miniDisplayPort/Dual-Link DVI Adapter 
330MHz.


It is better anyway to operate the glasses via the emitter of the 
VG287HR monitor (no lagging behind at all) and you can forget about 
getting a card with a 3-pin connector. The new entry k420 (192 cuda 
cores for ± 120 €, similar to older quadro 2000) or k620 will do just 
more than fine (386 cuda cores for ± 200 € is more than fast enough, 
similar to oder quadro 4000).


For windows and Nvidia 3D Vision 2 glasses:
You can buy a 144Hz monitor such as the ASUS VG278HE WITHOUT build-in 
emitter, but you will need to spend considerably more money for a new 
card with 3-pin stereo (or buy an old model such as fx3800) to operate 
the glasses by emitter in conjunction with the USB port. This is a 
windows only option.



Jeroen

Am 02.04.15 um 15:17 schrieb Oganesyan, Vaheh:

Kay and others,

I think Quadro 5000 available @
http://www.amazon.com/PNY-VCQ5000-PB-DisplayPort-Profesional-Graphics/dp/B003X26T7K
is a better option both price wise and need of transforming the output into 
3-pin mini DIN. Having said that I should mention difference: the memory is 
2.5GB for 5000 model while K4200 has 4 GB. I believe the memory shouldn't be an 
issue at that level since my 10 years old FX1400 has only 1 GB and I did not 
encounter problems so far.



Vaheh Oganesyan
www.medimmune.com


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Wednesday, April 01, 2015 3:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] nVidia quadro

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
 wrote:


On 3/25/2015 18:10, Kay Diederichs wrote:

On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  wrote:


You could check the nVidia page of officially supported displays. It
includes a search tab so you can check for "Built-in Emitter."
http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any
of these products still for sale.

Unfortunately, this NVidia page has not been updated for years.

The qualifier "3D-fähig (aktiv)" at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top 
should indicate a built-in emitter, but I looked at some of the descriptions of these 11 
monitors and was unable to confirm that they indeed have a built-in emitter. So one has to 
research every specific case.

I changed the wording on the wiki page.

Kay


I went through the specs for the monitors on the Heise list, and none
of them seems to have a built in emitter compatible with Nvidia 3D
Vision 2. It looks like it is a bad time to buy a 3D monitor. At this
point it might be easier to just go for a Quadro with 3-pin connector.

Best,
Andreas


I asked the company who runs the price info site to check their assignments, and they 
fixed the categories: http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 
3D-emitter" attribute. This currently only returns the Asus 278HR which can only be 
bought in Poland, or through EBay.

The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo connector 
(needed for Linux) is the K4200 
(http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at 
~ €700.

best,

Kay
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Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lüb

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[Rob Gruninger]

Keep in mind the updated 15" MacBook Pro is slated to come out soon (sounds
like early summer). Probably won't have more RAM but is supposed to have a
new processor. If you can hold off for a couple months I would suggest
waiting as these haven't been updated in almost a year.

Rob

On Thu, Apr 2, 2015 at 7:03 AM, xaravich ivan 
wrote:

> Hello everyone,
> I am planing to buy a new Mac laptop (price no bar) which will let me run
> all xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular
> Modelling (1000 to 1 decoys) softwares smoothly.
>
> What in your opinion is the best configuration. (RAM, memory, number and
> speed  of processors, graphics card etc.) Also I am buying a Mac display
> separately so that I have a big screen for easy visualization of models,
> COOT etc.
>
> I know that powerful Mac desktops can make life much easier but here I am
> specifically interested in Mac laptops only.
>
> As always thanks in advance and I will post all the suggestions
> anonymously for others with same query.
>
> ivan
>

[ccp4bb] [SUSPECTED SPAM] Re: [ccp4bb] nVidia quadro Update for Linux

[mesters]

After Kay send me an email today to have a look at the wiki at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo to 
add my findings, I researched things further.


I remember I wrote to the ccp4bb March 1st, 2013, asking about Nvidia 3D 
Vision under Linux via USB/3-pin because back then for the first time 
options for USB suggested this constellation might work under Linux as 
well. Nobody could confirm it worked back then so I did not go for that 
option and bought an ASUS VG278HR. But because monitors with build-in 
emitters are becoming extinct, we/I need the alternative employing the 
Nvidia 3D Vision 2 glasses under Linux I guess.


Apparently this option is working, see
http://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/

otherwise the following at Nvidia would not make much sense, see

http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html /
and
ftp://download.nvidia.com/XFree86/Linux-x86/256.44/README/xconfigoptions.html 
(search for USB and you will find it)


So, I ask the question again, can somebody confirm the Nvidia 3D Vision 
2 glasses with USB/3-pin now work under Linux? If so, I withdraw my 
previous email.


Jeroen

Am 02.04.15 um 17:34 schrieb mesters:
Be aware though, the option 3-pin + USB for Nvidia 3D Vision 2 glasses 
is not running/supported under Linux!


For linux boxes and Nvidia 3D Vision 2 glasses:
You have to buy an 120Hz ASUS VG287HR (there is no other useful option 
in my opinion at the moment) and whatever quadro card you buy, make 
sure the card posesses a "DVI-I Dual-Link Connector" (also termed 
DVI-D / DVI-I DL instead of a simple DVI) because the ASUS VG287HR 
comes with a DVI-D port (no displayport 1.2 and VGA is not usefull if 
you are going for 1920x1080@120hz). If the quadro card has display 
ports 1.2 only, you will need a Club-3D CAC-1051 active 
DisplayPort/Dual-Link DVI Adapter 330MHz for about 110 € (do not buy 
the 270 mhz model, it will not work as the bandwidth is too low for 
1920x1080@120hz) or for miniDisplay port cards, the Club-3D CAC-1151 
active miniDisplayPort/Dual-Link DVI Adapter 330MHz.


It is better anyway to operate the glasses via the emitter of the 
VG287HR monitor (no lagging behind at all) and you can forget about 
getting a card with a 3-pin connector. The new entry k420 (192 cuda 
cores for ± 120 €, similar to older quadro 2000) or k620 will do just 
more than fine (386 cuda cores for ± 200 € is more than fast enough, 
similar to oder quadro 4000).


For windows and Nvidia 3D Vision 2 glasses:
You can buy a 144Hz monitor such as the ASUS VG278HE WITHOUT build-in 
emitter, but you will need to spend considerably more money for a new 
card with 3-pin stereo (or buy an old model such as fx3800) to operate 
the glasses by emitter in conjunction with the USB port. This is a 
windows only option.



Jeroen

Am 02.04.15 um 15:17 schrieb Oganesyan, Vaheh:

Kay and others,

I think Quadro 5000 available @
http://www.amazon.com/PNY-VCQ5000-PB-DisplayPort-Profesional-Graphics/dp/B003X26T7K
is a better option both price wise and need of transforming the output into 
3-pin mini DIN. Having said that I should mention difference: the memory is 
2.5GB for 5000 model while K4200 has 4 GB. I believe the memory shouldn't be an 
issue at that level since my 10 years old FX1400 has only 1 GB and I did not 
encounter problems so far.



Vaheh Oganesyan
www.medimmune.com


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Wednesday, April 01, 2015 3:31 PM
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] nVidia quadro

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas 
Schenk  wrote:


On 3/25/2015 18:10, Kay Diederichs wrote:

On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  wrote:


You could check the nVidia page of officially supported displays. It
includes a search tab so you can check for "Built-in Emitter."
http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any
of these products still for sale.

Unfortunately, this NVidia page has not been updated for years.

The qualifier "3D-fähig (aktiv)" 
athttp://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top  
should indicate a built-in emitter, but I looked at some of the descriptions of these 11 
monitors and was unable to confirm that they indeed have a built-in emitter. So one has to 
research every specific case.

I changed the wording on the wiki page.

Kay


I went through the specs for the monitors on the Heise list, and none
of them seems to have a built in emitter compatible with Nvidia 3D
Vision 2. It looks like it is a bad time to buy a 3D monitor. At this
point it might be easier to just go for a Quadro with 3-pin connector.

Best,
Andreas


I asked the company who runs the price info site to check their assignments, and they 
fixed the categories:http://geizha

Re: [ccp4bb] nVidia quadro Update for Linux

[mesters]

Great, so for stereo 10 to work under Linux you compiled a Linux kernel 
built with USB device filesystem (usbfs) and USB 2.0 support?


I see you did not implement the following, Option "3DVisionUSBPath" 
"/sys/bus/usb/devices/1-1" , right?


Jeroen

Am 02.04.15 um 23:31 schrieb Lukasz Salwinski:

On 04/02/2015 02:05 PM, mesters wrote:

After Kay send me an email today to have a look at the wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo to 
add my

findings, I researched things further.

I remember I wrote to the ccp4bb March 1st, 2013, asking about Nvidia 
3D Vision
under Linux via USB/3-pin because back then for the first time 
options for USB
suggested this constellation might work under Linux as well. Nobody 
could
confirm it worked back then so I did not go for that option and 
bought an ASUS
VG278HR. But because monitors with build-in emitters are becoming 
extinct, we/I
need the alternative employing the Nvidia 3D Vision 2 glasses under 
Linux I guess.


Apparently this option is working, see
http://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/ 



otherwise the following at Nvidia would not make much sense, see

http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html /
and
ftp://download.nvidia.com/XFree86/Linux-x86/256.44/README/xconfigoptions.html 


(search for USB and you will find it)

So, I ask the question again, can somebody confirm the Nvidia 3D 
Vision 2
glasses with USB/3-pin now work under Linux? If so, I withdraw my 
previous email.


Jeroen


See the attached snapshots. Both coot & pymol run happily in 3D
with nVidia emitter (hooked up through both USB and 3-pin cable)
and 3D vision 2 glasses.

the relevant snippet of my xorg.conf reads:

-
Section "Device"
Identifier "Device0"
Driver "nvidia"
VendorName "NVIDIA Corporation"
EndSection

Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor"Monitor0"
DefaultDepth24
Option "UBB" "1"
Option "Stereo" "10"
Option "AllowDFPStereo" "1"
SubSection "Display"
Depth   24
EndSubSection
EndSection

Section "Extensions"
Option "Composite" "Disable"
EndSection
--


cheers,
lukasz







--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-5004065 (secretariate -5004061)
fax: +49-451-5004068

http://www.biochem.uni-luebeck.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 


--
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and which will not, speak then to me who neither beg nor fear 
(Shakespeare's Macbeth, Act I, Scene 3)

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Re: [ccp4bb] nVidia quadro Update for Linux

[Lukasz Salwinski]

On 04/02/2015 02:47 PM, mesters wrote:

Great, so for stereo 10 to work under Linux you compiled a Linux
kernel built with USB device filesystem (usbfs) and USB 2.0 support?


nope... I'm just using stock Centos 6.6 (installed, quite a while ago,
as version 6.3 and occasionally updated) and a relatively recent driver
from nVidia.


I see you did not implement the following, Option "3DVisionUSBPath"
"/sys/bus/usb/devices/1-1" , right?


I didn't have to do anything special about USB. no extra packages to
install, nothing to compile, no need for the 3DVisionUSBPath option you
mention.

lukasz


Jeroen






--
-
 Lukasz Salwinski PHONE:310-825-1402
 UCLA-DOE Institute for Genomics & Proteomics   FAX:310-206-3914
 UCLA, Los AngelesEMAIL: luk...@mbi.ucla.edu
-

Re: [ccp4bb] nVidia quadro Update for Linux

[Ethan A Merritt]

On Thursday, 02 April, 2015 23:47:12 mesters wrote:
> Great, so for stereo 10 to work under Linux you compiled a Linux kernel 
> built with USB device filesystem (usbfs) and USB 2.0 support?

usbfs was removed from linux starting with kernel version 3.5 (July 2012).
  
Some linux distros with "extended life" support for old kernels 
may still allow you to enable usbfs, but it's not a tenable requirement
going forward.  Whatever script or component was using this should
be updated to query /sys/kernel/debug/usb/...  instead.

Ethan

> 
> I see you did not implement the following, Option "3DVisionUSBPath" 
> "/sys/bus/usb/devices/1-1" , right?
> 
> Jeroen
> 
> Am 02.04.15 um 23:31 schrieb Lukasz Salwinski:
> > On 04/02/2015 02:05 PM, mesters wrote:
> >> After Kay send me an email today to have a look at the wiki at
> >> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo to 
> >> add my
> >> findings, I researched things further.
> >>
> >> I remember I wrote to the ccp4bb March 1st, 2013, asking about Nvidia 
> >> 3D Vision
> >> under Linux via USB/3-pin because back then for the first time 
> >> options for USB
> >> suggested this constellation might work under Linux as well. Nobody 
> >> could
> >> confirm it worked back then so I did not go for that option and 
> >> bought an ASUS
> >> VG278HR. But because monitors with build-in emitters are becoming 
> >> extinct, we/I
> >> need the alternative employing the Nvidia 3D Vision 2 glasses under 
> >> Linux I guess.
> >>
> >> Apparently this option is working, see
> >> http://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/
> >>  
> >>
> >>
> >> otherwise the following at Nvidia would not make much sense, see
> >>
> >> http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html /
> >> and
> >> ftp://download.nvidia.com/XFree86/Linux-x86/256.44/README/xconfigoptions.html
> >>  
> >>
> >> (search for USB and you will find it)
> >>
> >> So, I ask the question again, can somebody confirm the Nvidia 3D 
> >> Vision 2
> >> glasses with USB/3-pin now work under Linux? If so, I withdraw my 
> >> previous email.
> >>
> >> Jeroen
> >
> > See the attached snapshots. Both coot & pymol run happily in 3D
> > with nVidia emitter (hooked up through both USB and 3-pin cable)
> > and 3D vision 2 glasses.
> >
> > the relevant snippet of my xorg.conf reads:
> >
> > -
> > Section "Device"
> > Identifier "Device0"
> > Driver "nvidia"
> > VendorName "NVIDIA Corporation"
> > EndSection
> >
> > Section "Screen"
> > Identifier "Screen0"
> > Device "Device0"
> > Monitor"Monitor0"
> > DefaultDepth24
> > Option "UBB" "1"
> > Option "Stereo" "10"
> > Option "AllowDFPStereo" "1"
> > SubSection "Display"
> > Depth   24
> > EndSubSection
> > EndSection
> >
> > Section "Extensions"
> > Option "Composite" "Disable"
> > EndSection
> > --
> >
> >
> > cheers,
> > lukasz
> >
> >
> >
> >
> 
> 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)

[dusan turk]

Shane,

After you define which segments share proper or improper all NCS their 
parameters in MAIN environment, they will be calculated and stored in such 
macro files. 

$ cat mol_A_to_B.com 
! SAVING RMS FIT DATA: 
set matrix MAT_ROT number - 
  0.959598  -0.031620  -0.279592 - 
 -0.029443   0.976927  -0.211536 - 
  0.279830   0.211222   0.936526 
set vari XTRAN global real = 3.66 
set vari YTRAN global real =   105.12 
set vari ZTRAN global real =   -33.40 
return 

If you want to renormalize your matrices, you not only need to ensure that the 
length of your lines or columns is equal to 1, but also that they are 
orthogonal to each other, which is the easiest achieved by calculating the 
cross products of the matrix lines (a,b,c): (a * b = c ) through which you 
calculate first c and then either a or b.  I would not do it, because  the 
limited precision distorts the transformation and making in orthogonal will 
distort the accuracy of superimposition.

best,
dusan



> On Apr 3, 2015, at 1:00 AM, CCP4BB automatic digest system 
>  wrote:
> 
> 
> Date:Wed, 1 Apr 2015 20:47:25 -0400
> From:Shane Caldwell 
> Subject: Re: Sortwater NCS Matrix input
> 
> Alright, thanks! It's a good thing, then, I spent the afternoon brushing up
> on matrices.
> 
> I guess the next, probably more general question for the bb is: which
> utilities export an NCS transformation matrix with more precision?
> *superpose* and *gesamt* only export three decimals, though I'm sure they
> use greater precision under the hood. I'm not opposed to exporting from
> coot or pymol either, I just haven't figured out how to do this yet - what
> would be the simplest way to calculate and export an NCS transformation
> matrix?
> 
> Shane
> 

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS "Jozef Stefan"
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com