Re: [ccp4bb] xds to mtz using pointless

[Phil Evans]

There was a bug in Pointless for XDS reading due to my  
misunderstanding of the STARTING_FRAME value, which is fixed in  
version 1.2.13, available from


ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.13.linux  (eg)

Otherwise if you send me the file I'll investigate

Phil


On 20 Feb 2008, at 09:39, Sabine Schneider wrote:


Hi everyone,

I have a fine sliced dataset consisting of 720 frames (0.25dg /  
frame). I processed them with Xds and used Pointless to convert it  
to mtz for putting it in Scala. Spacegroup is P212121 and the  
resolution ~3.2. After ~200 frames the Rmerge goes up crazy and  
after 560 it is OK again. Therefore I am trying to process the the  
data in 3 wedges (1-199, 200-560, 561-720) in XDS and see how they  
scale independently and when I sort and scale them together with  
Sortmtz and Scala. When converting the .hkl file to mtz with  
pointless there is no problem with wedge 1-199. But for the other  
two wedges I am getting a Segmentation fault in Pointless (example  
see below). Or for wedge frame 200-560 I also only got an mtz file  
with batches 200 - 360. CORRECT.LP for all three wedges looks OK (at  
least to me)?

Anyone an idea what I am missing?

Thanks for you help!

Sabine

Matrix to transform XDS axis system to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Matrix to transform XDS detector coordinates to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Rotation axis in CCP4 frame: ( 0.000  0.000  1.000)

Incident beam in CCP4 frame: ( 1.000 -0.000 -0.002)


Spacegroup information obtained from library file:
Logical Name: SYMINFO   Filename: /usr/local/share/CCP4/ccp4-6.0.2/ 
lib/data/syminfo.lib



 85329 observations accepted
   Resolution range   49.1403.016
  6107 accepted incomplete observations with PART < 0.98, minimum 0.75
  1214 observations flagged as MISFITS in XDS, kept here

Reconstructing orientation matrix [U] from  199 observations

Orientation matrix [U]:
|0.5847,0.1184,0.8026|
|   -0.4283,   -0.7951,0.4294|
| 0.689,   -0.5948,   -0.4142|
Determinant = 1.000
Segmentation fault

Re: [ccp4bb] xds to mtz using pointless

[Kay Diederichs]

Sabine,

versions of pointless before 1.2.13 have a problem with XDS_ASCII.HKL. 
Phil fixed this in 1.2.13, which can be obtained from 
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/


Why don't you use XDSCONV to go to MTZ format? (and XSCALE for merging)

best,

Kay

Sabine Schneider schrieb:

Hi everyone,

I have a fine sliced dataset consisting of 720 frames (0.25dg / frame). 
I processed them with Xds and used Pointless to convert it to mtz for 
putting it in Scala. Spacegroup is P212121 and the resolution ~3.2. 
After ~200 frames the Rmerge goes up crazy and after 560 it is OK again. 
Therefore I am trying to process the the data in 3 wedges (1-199, 
200-560, 561-720) in XDS and see how they scale independently and when I 
sort and scale them together with Sortmtz and Scala. When converting the 
.hkl file to mtz with pointless there is no problem with wedge 1-199. 
But for the other two wedges I am getting a Segmentation fault in 
Pointless (example see below). Or for wedge frame 200-560 I also only 
got an mtz file with batches 200 - 360. CORRECT.LP for all three wedges 
looks OK (at least to me)?

Anyone an idea what I am missing?

Thanks for you help!

Sabine

Matrix to transform XDS axis system to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Matrix to transform XDS detector coordinates to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Rotation axis in CCP4 frame: ( 0.000  0.000  1.000)

Incident beam in CCP4 frame: ( 1.000 -0.000 -0.002)


Spacegroup information obtained from library file:
Logical Name: SYMINFO   Filename: 
/usr/local/share/CCP4/ccp4-6.0.2/lib/data/syminfo.lib



  85329 observations accepted
Resolution range   49.1403.016
   6107 accepted incomplete observations with PART < 0.98, minimum 0.75
   1214 observations flagged as MISFITS in XDS, kept here

Reconstructing orientation matrix [U] from  199 observations

Orientation matrix [U]:
|0.5847,0.1184,0.8026|
|   -0.4283,   -0.7951,0.4294|
| 0.689,   -0.5948,   -0.4142|
 Determinant = 1.000
Segmentation fault



--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz


smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] xds to mtz using pointless

[Sabine Schneider]

Hi everyone,

I have a fine sliced dataset consisting of 720 frames (0.25dg / frame). 
I processed them with Xds and used Pointless to convert it to mtz for 
putting it in Scala. Spacegroup is P212121 and the resolution ~3.2. 
After ~200 frames the Rmerge goes up crazy and after 560 it is OK again. 
Therefore I am trying to process the the data in 3 wedges (1-199, 
200-560, 561-720) in XDS and see how they scale independently and when I 
sort and scale them together with Sortmtz and Scala. When converting the 
.hkl file to mtz with pointless there is no problem with wedge 1-199. 
But for the other two wedges I am getting a Segmentation fault in 
Pointless (example see below). Or for wedge frame 200-560 I also only 
got an mtz file with batches 200 - 360. CORRECT.LP for all three wedges 
looks OK (at least to me)?

Anyone an idea what I am missing?

Thanks for you help!

Sabine

Matrix to transform XDS axis system to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Matrix to transform XDS detector coordinates to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Rotation axis in CCP4 frame: ( 0.000  0.000  1.000)

Incident beam in CCP4 frame: ( 1.000 -0.000 -0.002)


Spacegroup information obtained from library file:
Logical Name: SYMINFO   Filename: 
/usr/local/share/CCP4/ccp4-6.0.2/lib/data/syminfo.lib



  85329 observations accepted
Resolution range   49.1403.016
   6107 accepted incomplete observations with PART < 0.98, minimum 0.75
   1214 observations flagged as MISFITS in XDS, kept here

Reconstructing orientation matrix [U] from  199 observations

Orientation matrix [U]:
|0.5847,0.1184,0.8026|
|   -0.4283,   -0.7951,0.4294|
| 0.689,   -0.5948,   -0.4142|
 Determinant = 1.000
Segmentation fault

Re: [ccp4bb] xds to mtz using pointless

[Sabine Schneider]

That solved it! I had an older version (1.2.9). Thanks a lot!

Sabine


Phil Evans wrote:
There was a bug in Pointless for XDS reading due to my 
misunderstanding of the STARTING_FRAME value, which is fixed in 
version 1.2.13, available from


ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.13.linux  (eg)

Otherwise if you send me the file I'll investigate

Phil


On 20 Feb 2008, at 09:39, Sabine Schneider wrote:


Hi everyone,

I have a fine sliced dataset consisting of 720 frames (0.25dg / 
frame). I processed them with Xds and used Pointless to convert it to 
mtz for putting it in Scala. Spacegroup is P212121 and the resolution 
~3.2. After ~200 frames the Rmerge goes up crazy and after 560 it is 
OK again. Therefore I am trying to process the the data in 3 wedges 
(1-199, 200-560, 561-720) in XDS and see how they scale independently 
and when I sort and scale them together with Sortmtz and Scala. When 
converting the .hkl file to mtz with pointless there is no problem 
with wedge 1-199. But for the other two wedges I am getting a 
Segmentation fault in Pointless (example see below). Or for wedge 
frame 200-560 I also only got an mtz file with batches 200 - 360. 
CORRECT.LP for all three wedges looks OK (at least to me)?

Anyone an idea what I am missing?

Thanks for you help!

Sabine

Matrix to transform XDS axis system to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Matrix to transform XDS detector coordinates to CCP4 frame:
|   0.00796, -0.006359,0.|
| -0.001536,-1, -0.006347|
| 1, -0.001485,  -0.00797|

Rotation axis in CCP4 frame: ( 0.000  0.000  1.000)

Incident beam in CCP4 frame: ( 1.000 -0.000 -0.002)


Spacegroup information obtained from library file:
Logical Name: SYMINFO   Filename: 
/usr/local/share/CCP4/ccp4-6.0.2/lib/data/syminfo.lib



 85329 observations accepted
   Resolution range   49.1403.016
  6107 accepted incomplete observations with PART < 0.98, minimum 0.75
  1214 observations flagged as MISFITS in XDS, kept here

Reconstructing orientation matrix [U] from  199 observations

Orientation matrix [U]:
|0.5847,0.1184,0.8026|
|   -0.4283,   -0.7951,0.4294|
| 0.689,   -0.5948,   -0.4142|
Determinant = 1.000
Segmentation fault

Re: [ccp4bb] crashing-out protein eluted from Nickel column

[Vangelis Christodoulou]

Hi Juliana,

Since you can purify some protein with IMAC, I suggest that you do a  
buffer screening with Thermofluor before running the desalting column  
(or gel filtration column) and use the buffer condition(s) that  
stabilise your protein for the next purification step and possibly  
freezing it in that buffer.


Good luck,
Vangelis


--
Vangelis Christodoulou
Analist C
Anastassis (Tassos) Perrakis lab
The Netherlands Cancer Institute
Division of Molecular Carcinogenesis - H2
Plesmanlaan 121, 1066 CX, Amsterdam
The Netherlands

tel: +31 (0)20 512 1951
fax: +31 (0)20 512 1954
Website: xtal.nki.nl/Tassos_group/

On Feb 15, 2008, at 17:47, Juliana Barbosa Coitinho wrote:



Dear all,
I am with the same problem of Jacob.
My protein is precipitating, especially when I 'freeze it'. I am  
using a His Trap HP column coupled with a desalting column. Already  
tried to elute with gradient of imidazole (that allowed an elution  
with less amount of imidazole), but even then, the protein still  
crashes-out.
I am trying to use the protein immediately after purified it, but  
this is not always possible and I am losing much protein with that.

I will try to use the tips that have already been said.
But if someone can help me more, I will thank!!!

Thanks a lot!

Juliana

Abra sua conta no Yahoo! Mail, o único sem limite de espaço para  
armazenamento!

[ccp4bb] Vista

[deena]

Hi All,
I am about to buy a laptop and find that the XP is twice the price of  
Vista. Does anyone have positive experience using Vista for  
crystallographic packages: CCP4, Coot, O, X-plor?  or must I still  
avoid it?


Thanks,

Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389

Re: [ccp4bb] Vista

[James Stroud]

My Understanding is that XP is twice the price for a reason--Vista has  
been considered a major downgrade. It seems that SP1 has not helped.


Of course, there are other options out there besides windows boxes, so  
you might also want to investigate those (OS X, Linux). Some of  
crystallographers even prefer these other options to windows boxes.




On Feb 20, 2008, at 12:11 PM, deena wrote:


Hi All,
I am about to buy a laptop and find that the XP is twice the price  
of Vista. Does anyone have positive experience using Vista for  
crystallographic packages: CCP4, Coot, O, X-plor?  or must I still  
avoid it?


Thanks,

Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389



--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA  90095

http://www.jamesstroud.com

Re: [ccp4bb] Vista

[Paul Paukstelis]

Or don't buy an OS at all. There are a number of vendors out there that 
sell OEM notebooks without OSs. I picked up a Compal IF90 with

WSXGA+ (1680x1050) for a good price.

--paul

Yi Zhou wrote:

I think we are all using Linux, so just choose the cheaper OS (you have
to delete it anyway).

Yi

On Wed, 2008-02-20 at 15:11 -0500, deena wrote:

Hi All,
I am about to buy a laptop and find that the XP is twice the price of
Vista. Does anyone have positive experience using Vista for
crystallographic packages: CCP4, Coot, O, X-plor?  or must I still
avoid it?


Thanks,


Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389






--
Paul Paukstelis, Ph.D.
Research Associate
Institute for Cellular and Molecular Biology
The University of Texas at Austin
P: 512-471-4778, F: 512-232-3420
[EMAIL PROTECTED]

Re: [ccp4bb] Vista

[Yi Zhou]

I think we are all using Linux, so just choose the cheaper OS (you have
to delete it anyway).

Yi

On Wed, 2008-02-20 at 15:11 -0500, deena wrote:
> Hi All,
> I am about to buy a laptop and find that the XP is twice the price of
> Vista. Does anyone have positive experience using Vista for
> crystallographic packages: CCP4, Coot, O, X-plor?  or must I still
> avoid it?
> 
> 
> Thanks,
> 
> 
> Deena
> 
> Deena Abells Oren, PhD
> Manager, Structural Biology Resource Center
> Rockefeller University
> 1230 York Avenue
> New York, NY 10065-6399
> phone: 212- 327-7429
> fax: 212-327-7389
> 
> 

Re: [ccp4bb] Vista

[Scott Pegan]

Deena,

If you are going to run windows, have to use XP.  I tried vista, and the
software wouldn't work.

Scott

On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote:
> Or don't buy an OS at all. There are a number of vendors out there that
> sell OEM notebooks without OSs. I picked up a Compal IF90 with
> WSXGA+ (1680x1050) for a good price.
>
> --paul
>
> Yi Zhou wrote:
>> I think we are all using Linux, so just choose the cheaper OS (you have
>> to delete it anyway).
>>
>> Yi
>>
>> On Wed, 2008-02-20 at 15:11 -0500, deena wrote:
>>> Hi All,
>>> I am about to buy a laptop and find that the XP is twice the price of
>>> Vista. Does anyone have positive experience using Vista for
>>> crystallographic packages: CCP4, Coot, O, X-plor?  or must I still
>>> avoid it?
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Deena
>>>
>>> Deena Abells Oren, PhD
>>> Manager, Structural Biology Resource Center
>>> Rockefeller University
>>> 1230 York Avenue
>>> New York, NY 10065-6399
>>> phone: 212- 327-7429
>>> fax: 212-327-7389
>>>
>>>
>>
>
> --
> Paul Paukstelis, Ph.D.
> Research Associate
> Institute for Cellular and Molecular Biology
> The University of Texas at Austin
> P: 512-471-4778, F: 512-232-3420
> [EMAIL PROTECTED]
>
>


-- 
Scott D. Pegan, Ph.D.
Visiting Senior Research Specialist
Center for Pharmaceutical
Biotechnology
University of Illinois at Chicago

Re: [ccp4bb] Vista

[Avinash Gill]

I have been using CCP4MG, Chimera, O for Windows, Wincoot, and the entire
CCP4 suite (including running Refmac and Phaser through the CCP4i interface)
on my Windows Vista laptop for the past 9-10 months without any issues. It
has worked very well for me, and I have found Vista to be much more stable
than XP.

Regards.

Avi.

On Feb 20, 2008 3:11 PM, deena <[EMAIL PROTECTED]> wrote:

> Hi All,I am about to buy a laptop and find that the XP is twice the price
> of Vista. Does anyone have positive experience using Vista for
> crystallographic packages: CCP4, Coot, O, X-plor?  or must I still avoid it?
>
> Thanks,
>
> Deena
>
> Deena Abells Oren, PhD
> Manager, Structural Biology Resource Center
> Rockefeller University
> 1230 York Avenue
> New York, NY 10065-6399
> phone: 212- 327-7429
> fax: 212-327-7389
>
>


-- 

*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,
 Avinash Gill
 Dartmouth Medical School
 Biochemistry Dept
 HB 7200 Vail Bldg
 Hanover NH 03755
 Phone: (O) 603-650-1174
*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,

Re: [ccp4bb] Vista

[Flip Hoedemaeker]

Strange, CCP4 and Coot run just fine on my Vista laptop... Have not tried
all programs though.

Flip

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Scott
Pegan
Sent: Wednesday, February 20, 2008 22:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Vista

Deena,

If you are going to run windows, have to use XP.  I tried vista, and the
software wouldn't work.

Scott

On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote:
> Or don't buy an OS at all. There are a number of vendors out there that
> sell OEM notebooks without OSs. I picked up a Compal IF90 with
> WSXGA+ (1680x1050) for a good price.
>
> --paul
>
> Yi Zhou wrote:
>> I think we are all using Linux, so just choose the cheaper OS (you have
>> to delete it anyway).
>>
>> Yi
>>
>> On Wed, 2008-02-20 at 15:11 -0500, deena wrote:
>>> Hi All,
>>> I am about to buy a laptop and find that the XP is twice the price of
>>> Vista. Does anyone have positive experience using Vista for
>>> crystallographic packages: CCP4, Coot, O, X-plor?  or must I still
>>> avoid it?
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Deena
>>>
>>> Deena Abells Oren, PhD
>>> Manager, Structural Biology Resource Center
>>> Rockefeller University
>>> 1230 York Avenue
>>> New York, NY 10065-6399
>>> phone: 212- 327-7429
>>> fax: 212-327-7389
>>>
>>>
>>
>
> --
> Paul Paukstelis, Ph.D.
> Research Associate
> Institute for Cellular and Molecular Biology
> The University of Texas at Austin
> P: 512-471-4778, F: 512-232-3420
> [EMAIL PROTECTED]
>
>


-- 
Scott D. Pegan, Ph.D.
Visiting Senior Research Specialist
Center for Pharmaceutical
Biotechnology
University of Illinois at Chicago

Re: [ccp4bb] Vista

[Scott Pegan]

My attempt was a desktop installation.  This was ~1 month ago.

Scott


On Wed, February 20, 2008 3:34 pm, Flip Hoedemaeker wrote:
> Strange, CCP4 and Coot run just fine on my Vista laptop... Have not tried
> all programs though.
>
> Flip
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> Scott
> Pegan
> Sent: Wednesday, February 20, 2008 22:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Vista
>
> Deena,
>
> If you are going to run windows, have to use XP.  I tried vista, and the
> software wouldn't work.
>
> Scott
>
> On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote:
>> Or don't buy an OS at all. There are a number of vendors out there that
>> sell OEM notebooks without OSs. I picked up a Compal IF90 with
>> WSXGA+ (1680x1050) for a good price.
>>
>> --paul
>>
>> Yi Zhou wrote:
>>> I think we are all using Linux, so just choose the cheaper OS (you have
>>> to delete it anyway).
>>>
>>> Yi
>>>
>>> On Wed, 2008-02-20 at 15:11 -0500, deena wrote:
 Hi All,
 I am about to buy a laptop and find that the XP is twice the price of
 Vista. Does anyone have positive experience using Vista for
 crystallographic packages: CCP4, Coot, O, X-plor?  or must I still
 avoid it?


 Thanks,


 Deena

 Deena Abells Oren, PhD
 Manager, Structural Biology Resource Center
 Rockefeller University
 1230 York Avenue
 New York, NY 10065-6399
 phone: 212- 327-7429
 fax: 212-327-7389


>>>
>>
>> --
>> Paul Paukstelis, Ph.D.
>> Research Associate
>> Institute for Cellular and Molecular Biology
>> The University of Texas at Austin
>> P: 512-471-4778, F: 512-232-3420
>> [EMAIL PROTECTED]
>>
>>
>
>
> --
> Scott D. Pegan, Ph.D.
> Visiting Senior Research Specialist
> Center for Pharmaceutical
> Biotechnology
> University of Illinois at Chicago
>
>


-- 
Scott D. Pegan, Ph.D.
Visiting Senior Research Specialist
Center for Pharmaceutical
Biotechnology
University of Illinois at Chicago

Re: [ccp4bb] Vista

[James Stroud]

For those who risk becoming blinded and/or deafened by the vista bells  
and whistles:


http://pcworld.co.nz/pcworld/pcw.nsf/feature/1FE803ADF0486D06CC2573990069A75D

"The bottom line: It's Vista's architecture and feature set -- Barth  
cited Volume Shadow Copy, Vista's snapshot service, as an example --  
not a lack of fine-tuning or bug fixes that makes it perform poorly on  
PCs that run Windows XP blazingly fast."


Frankly, I don't run windows (and wouldn't think of it, except on a  
VM), so I don't have any special allegiances to either XP or Vista.  
But if you *must* have windows, you should seriously consider XP for  
crystallography, especially if you think performance might be an  
issue. Also bear in mind that the time between the release of vista  
and SP1 was over a year, so performance improvements might be a ways  
off if you decide to go with Vista.


James

On Feb 20, 2008, at 1:14 PM, Avinash Gill wrote:

I have been using CCP4MG, Chimera, O for Windows, Wincoot, and the  
entire CCP4 suite (including running Refmac and Phaser through the  
CCP4i interface) on my Windows Vista laptop for the past 9-10 months  
without any issues. It has worked very well for me, and I have found  
Vista to be much more stable than XP.


Regards.

Avi.

On Feb 20, 2008 3:11 PM, deena <[EMAIL PROTECTED]> wrote:
Hi All,
I am about to buy a laptop and find that the XP is twice the price  
of Vista. Does anyone have positive experience using Vista for  
crystallographic packages: CCP4, Coot, O, X-plor?  or must I still  
avoid it?


Thanks,

Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389




--

*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,
 Avinash Gill
 Dartmouth Medical School
 Biochemistry Dept
 HB 7200 Vail Bldg
 Hanover NH 03755
 Phone: (O) 603-650-1174
*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,


--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA  90095

http://www.jamesstroud.com

Re: [ccp4bb] Vista

[Juergen Bosch]

Hi all,

sorry I couldn't help it :-)

flames on

http://movies.apple.com/movies/us/apple/getamac/apple-getamac-chooseavista_480x376.mov

flames off

Juergen

James Stroud wrote:

For those who risk becoming blinded and/or deafened by the vista bells 
and whistles:


http://pcworld.co.nz/pcworld/pcw.nsf/feature/1FE803ADF0486D06CC2573990069A75D

"The bottom line: It's Vista's architecture and feature set -- Barth 
cited Volume Shadow Copy, Vista's snapshot service, as an example -- 
not a lack of fine-tuning or bug fixes that makes it perform poorly on 
PCs that run Windows XP blazingly fast."


Frankly, I don't run windows (and wouldn't think of it, except on a 
VM), so I don't have any special allegiances to either XP or Vista. 
But if you *must* have windows, you should seriously consider XP for 
crystallography, especially if you think performance might be an 
issue. Also bear in mind that the time between the release of vista 
and SP1 was over a year, so performance improvements might be a ways 
off if you decide to go with Vista.


James

On Feb 20, 2008, at 1:14 PM, Avinash Gill wrote:

I have been using CCP4MG, Chimera, O for Windows, Wincoot, and the 
entire CCP4 suite (including running Refmac and Phaser through the 
CCP4i interface) on my Windows Vista laptop for the past 9-10 months 
without any issues. It has worked very well for me, and I have found 
Vista to be much more stable than XP.


Regards.

Avi.

On Feb 20, 2008 3:11 PM, deena <[EMAIL PROTECTED] 
> wrote:


Hi All,
I am about to buy a laptop and find that the XP is twice the
price of Vista. Does anyone have positive experience using Vista
for crystallographic packages: CCP4, Coot, O, X-plor?  or must I
still avoid it?

Thanks,

Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389




--

*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,
 Avinash Gill
 Dartmouth Medical School
 Biochemistry Dept
 HB 7200 Vail Bldg
 Hanover NH 03755
 Phone: (O) 603-650-1174
*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,



--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA  90095

http://www.jamesstroud.com






--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

[ccp4bb] XDS and overlaps

[Engin Ozkan]

Hi everyone,

I have been recently relying on XDS quite a bit, but at the same time 
worrying about how XDS treats overlaps.  We had one dataset that both 
HKL2000 and Mosflm would show to have severe overlaps, as expected due 
to unit cell parameters and the unfortunate crystal orientation in the 
loop. We always ended up with completeness percentages in the 70's.


XDS can find the same lattice, index and scale the data, but yields a 
100% complete mtz (and a nice structure). Without the HKL/Mosflm-like 
GUI, it is difficult to assess the fate of the overlapped observations 
in XDS. What I could see with VIEW was that some observations were being 
divided into several ovals, probably different reflections, but I'm not 
very certain.


So, the basic question is, how does XDS treat overlaps?  I could not 
find in the documentation an answer to this question; the single mention 
of overlaps I could find tells me that XDS can recognize overlaps, but 
does not tell me if it rejects them, or divvies them up into separate 
reflections, and if that is the case, how does it divide them, and how 
reliable is that? Depending on how it divides the overlaps, could that 
affect commonly-used intensity stats and distributions?


Thanks,

Engin

Re: [ccp4bb] Vista

[Antony Oliver]

Hear Hear.

OS X wins for me, followed by various flavours of Linux, and then - only
then - a windows box (not running Vista).

--
Dr Antony W Oliver
Cancer Research UK: DNA Repair Enzymes Group
Section of Structural Biology
The Institute of Cancer Research
237 Fulham Road
LONDON SW3 6JB

[EMAIL PROTECTED]
020 7153 5488
--
>>> Juergen Bosch <[EMAIL PROTECTED]> 02/20/08 10:44 PM >>>
Hi all,

sorry I couldn't help it :-)

flames on

http://movies.apple.com/movies/us/apple/getamac/apple-getamac-chooseavista_480x376.mov

flames off

Juergen


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

Re: [ccp4bb] Vista

[Edwin Pozharski]

I am sure Vista is probably just as good (or bad, depending on your 
point of view) as XP.  Most of this stuff should run just fine (I 
understand that Vista is probably loaded with features that will bring 
older computer to complete stop, but we are talking about brand new 
laptop here).  But let me emphasize an important point - you always run 
outdated versions on windows.  CCP4 is usually up-to-date, but if you 
want latest refmac - no windows binaries.  WinCoot is currently 0.3.3.1, 
not 0.4.1.  O - well, if you learn to work with it you are ready for 
transition to linux anyway.  X-plor (CNS) is advertised as compiled for 
WinNT/Win98, should be fine in Vista, but then the whole concept of CNS 
interface is unix-assuming (I couldn't imagine a diehard windows fan 
enjoying CNS for windows).  You can, of course, always compile (or at 
least try to compile) from source, if authors are kind enough to provide 
it.  But if you figure out how to compile coot in windows, I think you 
will not have any problem working in linux in general. 

Doing crystallography in windows is like playing hockey with a football 
- it sure does work but it's a wrong combination of tools.  The only 
reason I can think of is if laptop is always running windows because you 
use it for msword but want to open coot to take a quick look at the 
structure occasionally (without rebooting or running virtual machine).  
In which case there should be no crystallography-specific difference 
between XP and Vista.


deena wrote:

Hi All,
I am about to buy a laptop and find that the XP is twice the price of 
Vista. Does anyone have positive experience using Vista for 
crystallographic packages: CCP4, Coot, O, X-plor?  or must I still 
avoid it?


Thanks,

Deena

Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389



--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

Re: [ccp4bb] Vista

[Changrui Lu]

Hi all,

Vista has tons of compatibility issues, especially with opengl. As far as I 
know pymol, swisspdbviewer and a number of other opengl based programs do not 
work on vista. (Coot has some compatibility problem with Aeroglass, and pymol 
might have a stable release for vista soon.) More programs are being upgraded 
to support vista but you might find yourself in trouble with legacy programs 
that are no longer supoorted. I would not suggest running crystal graphic 
softwares on vista (or xp) unless you have a good reason. But to choose the 
lesser of 2 evils I would go for xp. If price is an issue then you should go 
for linux, as many of us already suggusted.

cheers,
Ray


  - Original Message - 
  From: deena 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Wednesday, February 20, 2008 3:11 PM
  Subject: [ccp4bb] Vista


  Hi All,
  I am about to buy a laptop and find that the XP is twice the price of Vista. 
Does anyone have positive experience using Vista for crystallographic packages: 
CCP4, Coot, O, X-plor?  or must I still avoid it?


  Thanks,


  Deena


  Deena Abells Oren, PhD
  Manager, Structural Biology Resource Center
  Rockefeller University
  1230 York Avenue
  New York, NY 10065-6399
  phone: 212- 327-7429
  fax: 212-327-7389

[ccp4bb] cns and refmac refinement

[yang li]

Dear All,
  I have a 3A structure, the quality of the data is not very good. Now I
have refined it to Rfree=40.7 in Refmac.
But it wonnot go further down. Then I used CNS to do annealing, then use
refmac to do rigid body refinement.
The Rfree converged to 0.34, but if I use restrain refinement it will go up
gradually. Then I use CNS refine
script to refine the anneal.pdb, then the rigid body of refmac refinement
converged at Rfree=0.33, but the refmac restrain
refinement will still increase the Rfree--given weighting=0.03, after 80
cycle Rfree is 0.38 and seems like still increasing.
Then I gave weighting=0.02, after 180 cycle, the Rfree is 0.37. I very
wonder if I give 1000 cycle to run, Rfree
will go back to 0.4. Can anybody give me some suggestions?
 By the way, it is a dimer and I didnot use NCS restarin during
refinement. Below is from refmac log:
Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
 0   0.303   0.3260.738   81869.20.0121.5750.104
 1   0.288   0.3370.722   81411.20.0131.3210.080
 2   0.284   0.3430.717   81312.90.0111.3030.081
 3   0.282   0.3470.713   81308.20.0101.3120.083
 4   0.282   0.3490.710   81326.40.0101.3130.083
 5   0.281   0.3520.708   81339.90.0101.3210.084
 6   0.280   0.3530.707   81356.40.0101.3220.085
 7   0.280   0.3550.705   81380.90.0101.3320.086
 8   0.280   0.3550.704   81390.50.0101.3300.086
 9   0.279   0.3590.702   81400.60.0101.3420.087
10   0.279   0.3570.701   81405.10.0101.3400.086
11   0.279   0.3600.700   81435.30.0101.3490.087
12   0.278   0.3580.700   81425.80.0111.3630.086
13   0.278   0.3620.698   81436.30.0101.3520.087
14   0.278   0.3610.698   81438.10.0101.3470.086
15   0.278   0.3640.696   81456.50.0101.3540.087
16   0.277   0.3630.696   81452.30.0111.3520.087
17   0.278   0.3650.695   81456.70.0101.3560.087
18   0.277   0.3630.695   81450.30.0111.3480.087
19   0.277   0.3660.694   81447.60.0101.3550.087
20   0.276   0.3640.694   81448.20.0111.3500.087
21   0.277   0.3660.693   81451.40.0101.3550.087
22   0.276   0.3640.694   81442.40.0111.3500.087
23   0.277   0.3660.693   81440.80.0101.3540.087
24   0.276   0.3640.693   81434.40.0111.3500.087
25   0.277   0.3650.693   81453.90.0101.3560.087
26   0.276   0.3630.693   81446.50.0111.3520.087
27   0.276   0.3650.693   81448.60.0101.3560.087
28   0.276   0.3630.693   81438.20.0111.3520.087
29   0.276   0.3640.693   81433.70.0101.3560.088
30   0.276   0.3620.693   81430.10.0111.3520.087
31   0.276   0.3640.692   81427.00.0101.3550.087
32   0.275   0.3620.693   81421.20.0111.3540.087
33   0.276   0.3640.692   81428.60.0101.3560.087
34   0.275   0.3620.692   81421.90.0111.3550.087
35   0.275   0.3640.691   81439.00.0101.3580.087
36   0.275   0.3620.691   81435.90.0111.3560.087
37   0.275   0.3640.691   81446.40.0101.3600.088
38   0.275   0.3620.691   81444.60.0101.3580.087
39   0.275   0.3640.690   81453.30.0101.3610.088
40   0.275   0.3620.691   81443.50.0101.3600.087
41   0.275   0.3630.690   81453.20.0101.3620.088
42   0.274   0.3620.691   81443.80.0101.3610.088
43   0.275   0.3640.690   81468.10.0101.3640.088
44   0.274   0.3620.690   81471.50.0101.3630.088
45   0.274   0.3640.689   81509.40.0101.3660.088
46   0.274   0.3630.689   81498.10.0101.3640.088
47   0.274   0.3640.689   81512.90.0101.3680.088
48   0.274   0.3630.689   81499.20.0101.3660.088
49   0.274   0.3650.688   81513.60.0101.3690.088
50   0.274   0.3630.689   81509.30.0101.3680.088
51   0.274   0.3650.688   81505.70.0101.3720.088
52   0.274   0.3630.689   8149

Re: [ccp4bb] cns and refmac refinement

[Pavel Afonine]

Hi Yang Li,

trying alternatives is always good thing to do -:)

If you have latest PHENIX installed, try this:

% phenix.refine model.pdb data.mtz 
strategy=rigid_body+individual_sites+individual_adp 
simulated_annealing=true optimize_wxc=true optimize_wxu=true 
main.number_of_macro_cycles=5


Here "data.mtz" is your reflection data file. PHENIX automatically 
recognizes most of the known file formats, so it can be MTZ, CNS or ...


This will do the following:

1) Rigid body refinement first cycle only (MZ protocol = VERY high 
convergence radius);
2) Refinement of individual xyz and b-factors every cycle with optimized 
weights;

3) Simulated annealing at 2nd and one before the last cycles;

If this does not help, you need to start thinking -:)

For more info or if you have any questions: write me or look here: 
http://www.phenix-online.org/


Cheers,
Pavel.


yang li wrote:

Dear All,
  I have a 3A structure, the quality of the data is not very good. 
Now I have refined it to Rfree=40.7 in Refmac.
But it wonnot go further down. Then I used CNS to do annealing, then 
use refmac to do rigid body refinement.
The Rfree converged to 0.34, but if I use restrain refinement it will 
go up gradually. Then I use CNS refine
script to refine the anneal.pdb, then the rigid body of refmac 
refinement converged at Rfree=0.33, but the refmac restrain
refinement will still increase the Rfree--given weighting=0.03, after 
80 cycle Rfree is 0.38 and seems like still increasing.
Then I gave weighting=0.02, after 180 cycle, the Rfree is 0.37. I very 
wonder if I give 1000 cycle to run, Rfree

will go back to 0.4. Can anybody give me some suggestions?
 By the way, it is a dimer and I didnot use NCS restarin during 
refinement. Below is from refmac log:

Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
 0   0.303   0.3260.738   81869.20.0121.575
0.104
 1   0.288   0.3370.722   81411.20.0131.321
0.080
 2   0.284   0.3430.717   81312.90.0111.303
0.081
 3   0.282   0.3470.713   81308.20.0101.312
0.083
 4   0.282   0.3490.710   81326.40.0101.313
0.083
 5   0.281   0.3520.708   81339.90.0101.321
0.084
 6   0.280   0.3530.707   81356.40.0101.322
0.085
 7   0.280   0.3550.705   81380.90.0101.332
0.086
 8   0.280   0.3550.704   81390.50.0101.330
0.086
 9   0.279   0.3590.702   81400.60.0101.342
0.087
10   0.279   0.3570.701   81405.10.0101.340
0.086
11   0.279   0.3600.700   81435.30.0101.349
0.087
12   0.278   0.3580.700   81425.80.0111.363
0.086
13   0.278   0.3620.698   81436.30.0101.352
0.087
14   0.278   0.3610.698   81438.10.0101.347
0.086
15   0.278   0.3640.696   81456.50.0101.354
0.087
16   0.277   0.3630.696   81452.30.0111.352
0.087
17   0.278   0.3650.695   81456.70.0101.356
0.087
18   0.277   0.3630.695   81450.30.0111.348
0.087
19   0.277   0.3660.694   81447.60.0101.355
0.087
20   0.276   0.3640.694   81448.20.0111.350
0.087
21   0.277   0.3660.693   81451.40.0101.355
0.087
22   0.276   0.3640.694   81442.40.0111.350
0.087
23   0.277   0.3660.693   81440.80.0101.354
0.087
24   0.276   0.3640.693   81434.40.0111.350
0.087
25   0.277   0.3650.693   81453.90.0101.356
0.087
26   0.276   0.3630.693   81446.50.0111.352
0.087
27   0.276   0.3650.693   81448.60.0101.356
0.087
28   0.276   0.3630.693   81438.20.0111.352
0.087
29   0.276   0.3640.693   81433.70.0101.356
0.088
30   0.276   0.3620.693   81430.10.0111.352
0.087
31   0.276   0.3640.692   81427.00.0101.355
0.087
32   0.275   0.3620.693   81421.20.0111.354
0.087
33   0.276   0.3640.692   81428.60.0101.356
0.087
34   0.275   0.3620.692   81421.90.0111.355
0.087
35   0.275   0.3640.691   81439.00.0101.358
0.087
36   0.275   0.3620.691   81435.90.0111.356
0.087
37   0.275   0.3640.691   81446.40.0101.360
0.088
38   0.275   0.3620.691   81444.60.0101.358
0.087
39   0.275   0.3640.690   81453.30.0101.361
0.088
40   0.275   0.362   

Re: [ccp4bb] Vista

[Anastassis Perrakis]

Vista or XP, I shamelessly admit that I personally totally fail to  
see why - ideology left aside - I would ever buy a *laptop* which is  
not a Mac.


Even for the fact that when a Mac is "asleep" you open the cover and  
it actually comes up in 1 sec, exactly where it was last evening, its  
worth it !


I run MS Office (I actually do like Word), iWork (Keynote is what PP  
might some day be ... Pages is great for eg posters),
iLife for home, Coot, O, CCP4, Phenix, ARP/wARP, Solve/Resolve,  
Phaser, Pymol, Papers (!!! a dream that will not come true for  
Windows-based scientists - http://mekentosj.com/), R, Adobe and all  
work. And you also have Xcode, the GUI builder, management tools, and  
others for development.


For the last 4 years I use a G4 as my laptop which is also my desktop  
with external monitor and keyboard/mouse -
I have dropped it a couple of times, have been around the world,  
still works. I only switched to Macs in 2001 and I am still happy.


And I did not even mention that it LOOKS better ;-))



Apologies for not answering the original question, but the discussion  
was drifting this way.


I am now waiting to see what Vista can do that Windows cannot. I am  
aware of one application I want and does not run on a Mac,
and that is the Polar Fitness software for my bike. Argh. Most  
spyware and virus detection software also do not run in a Mac btw!

For a reason: you do not need them dudes !

A.

PS And no, I don't work for Apple, I don't get free gifts from Apple,  
but if Steve is reading and he wants to send me a Mac Air for my kind  
words, please, go ahead ! ;-)))

[ccp4bb] postdoctoral positions in Xiamen

[Aidong Han]

Postdoctoral positions available

This lab conducts two aspects of research using X-ray crystallography 
and other biochemical approaches.  One is to understand how a limited 
number of transcriptional factors regulate larger amount of genes.  Our 
model is that two or more transcription factors work together and 
further recruit other protein modification factors to form high-order 
regulatory assemblies on gene promoters.  Another is to study how the 
extracellular signals are transferred to a specific set of 
transcription factors.  These projects include structural 
characterization of ligand-protein and protein-protein interaction and 
proteins associated with cell membranes.  Please refer 
http://life.xmu.edu.cn/teacher/teachersy/2008-02-18/1760.html for more 
information.


Those who have Ph.D in any biological or medical disciplines are 
strongly encouraged to apply.  Any experience in protein biochemistry 
is a plus.  Training in crystallography is welcome but not required.  
You will be provided with a standard package from Xiamen University 
including low-cost oncampus apartment, medical insurance and family 
assistance.  Additional salary will be offered to compensate your 
credentials.  Initial contract is 1-2 years and expected to start 
within 6 months.   Please send your CV including personal statement and 
contact information of three referees to Dr. Aidong Han at  
[EMAIL PROTECTED]


Xiamen is one of the most beautiful cities and the best place to live 
in China. Xiamen University, in particular, the School of Life 
Sciences, has been quickly arising with strong financial support from 
the government.  The lab is fully equipped and among the  excellent 
academic environment.