Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Thorn, Dr. Andrea]

Renato and Stuart McNicholls wrote exactly the right thing: deleting this file 
resolved the issue. Thank you very much!

-Original Message-
From: CCP4 bulletin board  On Behalf Of Renato Weiße
Sent: 08 May 2024 16:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Hi Andrea,

concerning Log #1: there is a log file 
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is 
probably empty. If it is, then deleting it should resolve the error. I have 
seen this problem from time to time on students laptops, but could not figure 
out, for what reason it occurs.

Cheers,
Renato


Zitat von "Thorn, Dr. Andrea" <d000cdf57279-dmarc-requ...@jiscmail.ac.uk>:

> Dear all,
> My ccp4i2 installation stopped working - it does not start up  
> properly anymore (see Log #1 below for the output).
> I started ccp4i which brought up the update manager and ran  
> outstanding updates. This did not fix the issue. I also sourced the  
> source file manually, just to make sure.
> Then I ran ./find-missing-libs.sh and fixed some issues, but got  
> stuck (see Log #2 below).
> Deleting the ccp4 folder and re-install also did not help.
> The system is Ubuntu in a virtual box.
> I would be grateful for any advice.
> Best wishes,
>
> Andrea.
>
> __
>
> LOG #1:
>
> Running CCP4i2 browser from:  
> /opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
> Python 3.7.12 (default, Jan  6 2022, 21:30:12)
> [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
> Qt version 5.15.2
>
> Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use  
> QT_QPA_PLATFORM=wayland to run on Wayland anyway.
> Sandboxing disabled by user.
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.browser.py'
> [0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
> application directory...
> Qt WebEngine locales directory not found at location  
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path  
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]  
> locale_file_path.empty() for locale
> ccp4i2 version 1.1.0
> ccp4i2 source revision 6539
> CPrintHandler saving print output to directory:  
> /home/athorn/.CCP4I2/logs/started_1715177113
> None
> None
> Starting Project Manager
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> Starting Project Manager - DONE
> Starting Job Controller
> Starting Job Controller - DONE
> 
> isDarkMode? False
> 
> Starting   0.00048089027404785156
> StyleSheet screen size: 1920 1089
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> CCP4i2 starti

Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Renato Weiße]

Hi Andrea,

concerning Log #1: there is a log file  
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which  
is probably empty. If it is, then deleting it should resolve the  
error. I have seen this problem from time to time on students laptops,  
but could not figure out, for what reason it occurs.


Cheers,
Renato


Zitat von "Thorn, Dr. Andrea" <d000cdf57279-dmarc-requ...@jiscmail.ac.uk>:


Dear all,
My ccp4i2 installation stopped working - it does not start up  
properly anymore (see Log #1 below for the output).
I started ccp4i which brought up the update manager and ran  
outstanding updates. This did not fix the issue. I also sourced the  
source file manually, just to make sure.
Then I ran ./find-missing-libs.sh and fixed some issues, but got  
stuck (see Log #2 below).

Deleting the ccp4 folder and re-install also did not help.
The system is Ubuntu in a virtual box.
I would be grateful for any advice.
Best wishes,

Andrea.

__

LOG #1:

Running CCP4i2 browser from:  
/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2

Python 3.7.12 (default, Jan  6 2022, 21:30:12)
[GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
Qt version 5.15.2

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use  
QT_QPA_PLATFORM=wayland to run on Wayland anyway.

Sandboxing disabled by user.
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.browser.py'
[0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying  
application directory...
Qt WebEngine locales directory not found at location  
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback  
directory... Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path  
'/home/athorn/.QtWebEngineProcess'
[0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]  
locale_file_path.empty() for locale

ccp4i2 version 1.1.0
ccp4i2 source revision 6539
CPrintHandler saving print output to directory:  
/home/athorn/.CCP4I2/logs/started_1715177113

None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
Starting Job Controller
Starting Job Controller - DONE

isDarkMode? False

Starting   0.00048089027404785156
StyleSheet screen size: 1920 1089
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
CCP4i2 starting HTTP server on 127.0.0.1 port 43434

Retrieving status  
file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml

Traceback (most recent call last):
  File  
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",  
line 266, in openFileToEtree

tree = parse_from_unicode(s,useLXML=useLXML)
  File  
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py",  
line 255, in parse_from_unicode

return etree.fromstring(s, parser=utf8_parser)
  File "src/lxml/etree.pyx", line 3211, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
  File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
 

[ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Thorn, Dr. Andrea]

Dear all,
My ccp4i2 installation stopped working - it does not start up properly anymore 
(see Log #1 below for the output).
I started ccp4i which brought up the update manager and ran outstanding 
updates. This did not fix the issue. I also sourced the source file manually, 
just to make sure.
Then I ran ./find-missing-libs.sh and fixed some issues, but got stuck (see Log 
#2 below).
Deleting the ccp4 folder and re-install also did not help.
The system is Ubuntu in a virtual box.
I would be grateful for any advice.
Best wishes,

Andrea.

__

LOG #1:

Running CCP4i2 browser from: 
/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
Python 3.7.12 (default, Jan  6 2022, 21:30:12)
[GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
Qt version 5.15.2

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use 
QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Sandboxing disabled by user.
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path '/home/athorn/.browser.py'
[0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application 
directory...
Qt WebEngine locales directory not found at location 
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory... 
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path 
'/home/athorn/.QtWebEngineProcess'
[0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)] 
locale_file_path.empty() for locale
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
CPrintHandler saving print output to directory: 
/home/athorn/.CCP4I2/logs/started_1715177113
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
Starting Job Controller
Starting Job Controller - DONE

isDarkMode? False

Starting   0.00048089027404785156
StyleSheet screen size: 1920 1089
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
CCP4i2 starting HTTP server on 127.0.0.1 port 43434

Retrieving status 
file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
Traceback (most recent call last):
  File 
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line 
266, in openFileToEtree
tree = parse_from_unicode(s,useLXML=useLXML)
  File 
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line 
255, in parse_from_unicode
return etree.fromstring(s, parser=utf8_parser)
  File "src/lxml/etree.pyx", line 3211, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
  File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
  File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc
  File "src/lxml/parser.pxi", line 601, in 
lxml.etree._ParserContext._handleParseResultDoc
  File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
  File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
  File "", line 1
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1

During handling of the above exce

[ccp4bb] Advice on crystal imaging systems

[Marko Hyvonen]

Dear colleagues,

We are looking to replace our aging crystal imaging system (Formulatrix Rock 
Imager). Any advice on the latest offerings? Anyone using JANSi UVEXps and 
happy to share their experiences?

Feel free to email directly as well, I'll post an anonymised & moderated 
summary of the responses back to CCP4bb (w/o comments that are asked to be kept 
confidential).

Thanks in advance, Marko
-
Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@cam.ac.uk




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Advice on DNA negative staining

[Artem Evdokimov]

Hiya

*Half an hour in the library saves a month of research.* That's what my
late advisor Dr. Frolow used to say a lot and he was not wrong.

Erenpreisa J. 1981. Staining of DNA with uranlyacetate in hydrolyzed
ultrathin sections. Acta histochem 68(1): 22-26

there are several very clever methods, using depurination and various
chemical treatments (e.g. phenylhydrazine) followed by staining with
various heavy atoms (tungsten derivatives)

In general, shadowing with tungsten is a highly adequate method, see for
example gorgeous images of replicaiton forks here:

https://www.jbc.org/content/285/18/13349.full.pdf

Artem

- Cosmic Cats approve of this message


On Tue, Aug 4, 2020 at 7:11 AM Panne, Daniel (Prof.) <
daniel.pa...@leicester.ac.uk> wrote:

> Hi Meytal,
>
> 1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml
> are used.
> 2. Uranyl ions react with phosphate groups resulting in positive stain.
> The resulting contrast is frequently poor.
> 3. Rotary shadowing can be used to enhance contrast.
>
> Best,
> Daniel
>
>
> On 4 Aug 2020, at 11:20, Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Dear Meytal,
>
> Suggestion: Apply a strong high-pass filter to the images before visually
> judging them!
>
> Marin
>
> On Tue, Aug 4, 2020 at 3:50 AM Meytal Galilee 
> wrote:
>
>> Hi Arunabh Athreya,
>> Sure (this is the linear 2200 b.p. at 175uM)
>> 
>>
>>
>>
>> Get Outlook for Android
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fghei36&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736273265&sdata=1JpwGUyNpGCO3IlNY8y0eXKdGulww020ZzJLc93idfo%3D&reserved=0>
>>
>>
>> --
>> *From:* Arunabh Athreya 
>> *Sent:* Tuesday, August 4, 2020, 12:54
>> *To:* CCP4BB@JISCMAIL.AC.UK; Meytal Galilee
>> *Subject:* Re: Advice on DNA negative staining
>>
>> Hi Meytal
>>
>> Do you have an EM image snapped from your negative staining sample?
>>
>> Get Outlook for Android
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fghei36&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736273265&sdata=1JpwGUyNpGCO3IlNY8y0eXKdGulww020ZzJLc93idfo%3D&reserved=0>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736283221&sdata=QooLJZLuHXjOPYtWFVQXnLB4CShQRxG3u5EX%2FACb%2FuQ%3D&reserved=0>
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736283221&sdata=QooLJZLuHXjOPYtWFVQXnLB4CShQRxG3u5EX%2FACb%2FuQ%3D&reserved=0>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Advice on DNA negative staining

[Panne, Daniel (Prof.)]

Hi Meytal,

1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml are 
used.
2. Uranyl ions react with phosphate groups resulting in positive stain. The 
resulting contrast is frequently poor.
3. Rotary shadowing can be used to enhance contrast.

Best,
Daniel


On 4 Aug 2020, at 11:20, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>>
 wrote:


Dear Meytal,

Suggestion: Apply a strong high-pass filter to the images before visually 
judging them!

Marin

On Tue, Aug 4, 2020 at 3:50 AM Meytal Galilee 
mailto:meytal.gali...@gmail.com>> wrote:
Hi Arunabh Athreya,
Sure (this is the linear 2200 b.p. at 175uM)




Get Outlook for 
Android<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fghei36&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736273265&sdata=1JpwGUyNpGCO3IlNY8y0eXKdGulww020ZzJLc93idfo%3D&reserved=0>



From: Arunabh Athreya mailto:arun...@iisc.ac.in>>
Sent: Tuesday, August 4, 2020, 12:54
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>; Meytal Galilee
Subject: Re: Advice on DNA negative staining

Hi Meytal

Do you have an EM image snapped from your negative staining sample?

Get Outlook for 
Android<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fghei36&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736273265&sdata=1JpwGUyNpGCO3IlNY8y0eXKdGulww020ZzJLc93idfo%3D&reserved=0>





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736283221&sdata=QooLJZLuHXjOPYtWFVQXnLB4CShQRxG3u5EX%2FACb%2FuQ%3D&reserved=0>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cdaniel.panne%40leicester.ac.uk%7C1d84ebc5b8674ad1d62b08d838601d22%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637321332736283221&sdata=QooLJZLuHXjOPYtWFVQXnLB4CShQRxG3u5EX%2FACb%2FuQ%3D&reserved=0>




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Advice on DNA negative staining

[Arunabh Athreya]

Hi Meytal

Do you have an EM image snapped from your negative staining sample?

Get Outlook for Android




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Advice on DNA negative staining

[Meytal Galilee]

Dear All,
I am new to negative staining (and hopefully cryoEM soon) and wanted to ask for 
your advice before I proceed.
I am trying to visualize DNA, both circular and linear (2200b.p.), I am using 
2% Uranyl Acetate and regular carbon grids. I’ve been getting unclear images 
under TEM, some strings which I doubt are what I am looking for.
I would highly appreciate any advice, for example what are the DNA 
concentrations I should work with? What dye? How long should I let the DNA stay 
on the grid prior to staining? Is there an optimal size for a plasmid ?
Thank you,
Meytal




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Goldman, Adrian]

I tend to agree - though I am still using a 15” machine myself - the lab has 
13” machines and at their desks they have a big monitor as well.  

Adrian

> On 8 Jun 2020, at 17:37, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> I’d make the decision based largely on where I was going to use it, and how 
> much I was going to have to carry it (and if I ever wanted to use it in coach 
> class). If it was going to be my machine for “on the road”, I’d go for the 
> 13” one, but if it was going to sit on my desk most of the time (and do what 
> a traditional desktop does), I’d go for the larger one. 
> 
> I “traded down” to a 13” after many years using 15”+ laptops a few years ago 
> and have never regretted it, even when I have to put my reading glasses on to 
> read what’s on the screen.
> 
> However, if you _really_ need 64GB RAM, you don’t have much of a choice.
> 
> Just my two ha’porth
> 
> Harry
> 
>> On 8 Jun 2020, at 17:07, Diana Tomchick  
>> wrote:
>> 
>> Make sure the 13” display is large enough to display all the GUIs for 
>> program suites that you are interested in.
>> 
>> For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 
>> GUI. Requirements are found here:
>> 
>> https://hkl-xray.com/hardware-operating-systems
>> 
>> Diana
>> 
>> **
>> Diana R. Tomchick
>> Professor
>> Departments of Biophysics and Biochemistry
>> UT Southwestern Medical Center
>> 5323 Harry Hines Blvd.
>> Rm. ND10.214A
>> Dallas, TX 75390-8816
>> diana.tomch...@utsouthwestern.edu
>> (214) 645-6383 (phone)
>> (214) 645-6353 (fax)
>> 
>> On Jun 8, 2020, at 10:56 AM, Scott Pegan  wrote:
>> 
>> 
>> EXTERNAL MAIL
>> 
>> 
>> Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
>> welcome any input or being put in the direction of some related to the 
>> following:
>> 
>> 13" versus 16"
>> 
>> I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
>> that finds that it works well? If so, what were the specs
>> 
>> Memory for the 16"
>> 
>> Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a 
>> premium for the 32 gb, but some say that now with the SSD's it's not as big 
>> of a deal. Any thoughts?
>> 
>> GPU
>> 
>> For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience 
>> on these for running CCP4 and other Xtal software on these?
>> 
>> Thanks for your help in advance, looking to get something that is a Mac, 
>> robust to last a while spec wise.  However, not looking to buy something 
>> that is the equivalent of a small car in price and overkill.
>> 
>> Scott
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>> 
>> 
>> CAUTION: This email originated from outside UTSW. Please be cautious of 
>> links or attachments, and validate the sender's email address before 
>> replying.
>> 
>> 
>> 
>> 
>> UT Southwestern 
>> 
>> Medical Center
>> 
>> The future of medicine, today.
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Harry Powell - CCP4BB]

Hi

I’d make the decision based largely on where I was going to use it, and how 
much I was going to have to carry it (and if I ever wanted to use it in coach 
class). If it was going to be my machine for “on the road”, I’d go for the 13” 
one, but if it was going to sit on my desk most of the time (and do what a 
traditional desktop does), I’d go for the larger one. 

I “traded down” to a 13” after many years using 15”+ laptops a few years ago 
and have never regretted it, even when I have to put my reading glasses on to 
read what’s on the screen.

However, if you _really_ need 64GB RAM, you don’t have much of a choice.

Just my two ha’porth

Harry

> On 8 Jun 2020, at 17:07, Diana Tomchick  
> wrote:
> 
> Make sure the 13” display is large enough to display all the GUIs for program 
> suites that you are interested in.
> 
> For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 
> GUI. Requirements are found here:
> 
> https://hkl-xray.com/hardware-operating-systems
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> On Jun 8, 2020, at 10:56 AM, Scott Pegan  wrote:
> 
> 
> EXTERNAL MAIL
> 
> 
> Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
> welcome any input or being put in the direction of some related to the 
> following:
> 
> 13" versus 16"
> 
> I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
> that finds that it works well? If so, what were the specs
> 
> Memory for the 16"
> 
> Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a premium 
> for the 32 gb, but some say that now with the SSD's it's not as big of a 
> deal. Any thoughts?
> 
> GPU
> 
> For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience 
> on these for running CCP4 and other Xtal software on these?
> 
> Thanks for your help in advance, looking to get something that is a Mac, 
> robust to last a while spec wise.  However, not looking to buy something that 
> is the equivalent of a small car in price and overkill.
> 
> Scott
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> 
> CAUTION: This email originated from outside UTSW. Please be cautious of links 
> or attachments, and validate the sender's email address before replying.
> 
> 
> 
> 
> UT Southwestern 
> 
> Medical Center
> 
> The future of medicine, today.
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Diana Tomchick]

Make sure the 13” display is large enough to display all the GUIs for program 
suites that you are interested in.

For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 GUI. 
Requirements are found here:

https://hkl-xray.com/hardware-operating-systems

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jun 8, 2020, at 10:56 AM, Scott Pegan 
mailto:scott.d.pe...@gmail.com>> wrote:


EXTERNAL MAIL

Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
welcome any input or being put in the direction of some related to the 
following:

13" versus 16"

I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
that finds that it works well? If so, what were the specs

Memory for the 16"

Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a premium 
for the 32 gb, but some say that now with the SSD's it's not as big of a deal. 
Any thoughts?

GPU

For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience on 
these for running CCP4 and other Xtal software on these?

Thanks for your help in advance, looking to get something that is a Mac, robust 
to last a while spec wise.  However, not looking to buy something that is the 
equivalent of a small car in price and overkill.

Scott






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and validate the sender's email address before replying.





UT Southwestern


Medical Center



The future of medicine, today.




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Scott Pegan]

Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I
would welcome any input or being put in the direction of some related to
the following:

13" versus 16"

I know the 16" has a better and standalone GPU.  Is there anyone using a
13" that finds that it works well? If so, what were the specs

Memory for the 16"

Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a
premium for the 32 gb, but some say that now with the SSD's it's not as big
of a deal. Any thoughts?

GPU

For the 15", apple has two 4 gb and an 8 gb. Does anyone have any
experience on these for running CCP4 and other Xtal software on these?

Thanks for your help in advance, looking to get something that is a Mac,
robust to last a while spec wise.  However, not looking to buy something
that is the equivalent of a small car in price and overkill.

Scott



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Advice on Cryo-Synchrotron use during early 1990s HIV Protease Inhibitor development

[David Haas]

Hi,

I am studying how HIV-1 Protease Inhibitors were developed so rapidly, 
3-5 years vs. normal 10-15 years, enabling the HAART Drug Therapy to be 
introduced in 1996?    Can you suggest articles or contacts on how 
/_cryocrystallography_/ (with synchrotrons) accelerated the first HIV 
Protease Inhibitor development, employing Structure Based Drug Design.  
In particular, how Macromolecular Cryo Crystallography accelerated the 
introduction of the HIV Protease Inhibitors in 1996, which lead to the 
Lazarus Effect, saving thousands of lives.These new Inhibitors were 
essential in leading


to the successful introduction of the HAART HIV Drug Therapy.Any advice, 
articles or knowledgeable-individuals relating to this topic would be 
appreciated?


Email:da...@teccocorp.com <mailto:da...@teccocorp.com>

David Haas

Suffern NY




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] [ccp4bb] Remittance advice - Invitation to edit

[Anindito Sen]

my point exactly.

Andy


> On Dec 12, 2016, at 2:49 AM, Laura Spagnolo  
> wrote:
> 
> Isn't this mailing list moderated?
> Laura 
> 
> Sent from my iPhone
> 
> On 11 Dec 2016, at 17:48, Bonsor, Daniel  <mailto:dbon...@som.umaryland.edu>> wrote:
> 
>> The Nigerian Prince wants your money.
>> 
>> Get Outlook for Android <https://aka.ms/ghei36>
>> From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Anindito Sen 
>> mailto:andysen.to...@gmail.com>>
>> Sent: Sunday, December 11, 2016 12:45:16 PM
>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>> Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit
>>  
>> Guys 
>> 
>> are you all receiving the same??? What on earth is this ?
>> 
>> Andy
>> 
>> 
>> 
>>> Begin forwarded message:
>>> 
>>> From: Hai-fu Fan mailto:fanha...@gmail.com>>
>>> Subject: [ccp4bb] Remittance advice - Invitation to edit
>>> Date: December 12, 2016 at 2:31:56 AM GMT+9
>>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>>> Reply-To: Hai-fu Fan mailto:fanha...@gmail.com>>
>>> 
>>> Please find attached for your review.
>>> Regards.
>>> 
>>> Hai-fu Fan
>> 
>> 

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

[Laura Spagnolo]

Isn't this mailing list moderated?
Laura

Sent from my iPhone

On 11 Dec 2016, at 17:48, Bonsor, Daniel 
mailto:dbon...@som.umaryland.edu>> wrote:


The Nigerian Prince wants your money.

Get Outlook for Android<https://aka.ms/ghei36>


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Anindito Sen 
mailto:andysen.to...@gmail.com>>
Sent: Sunday, December 11, 2016 12:45:16 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

Guys

are you all receiving the same??? What on earth is this ?

Andy



Begin forwarded message:

From: Hai-fu Fan mailto:fanha...@gmail.com>>
Subject: [ccp4bb] Remittance advice - Invitation to edit
Date: December 12, 2016 at 2:31:56 AM GMT+9
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Reply-To: Hai-fu Fan mailto:fanha...@gmail.com>>

Please find attached for your review.
Regards.

Hai-fu Fan

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

[Tristan Croll]

Phishing spam. Don't click.

T

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 11 Dec 2016, at 17:45, Anindito Sen  wrote:
> 
> Guys 
> 
> are you all receiving the same??? What on earth is this ?
> 
> Andy
> 
> 
> 
>> Begin forwarded message:
>> 
>> From: Hai-fu Fan 
>> Subject: [ccp4bb] Remittance advice - Invitation to edit
>> Date: December 12, 2016 at 2:31:56 AM GMT+9
>> To: CCP4BB@JISCMAIL.AC.UK
>> Reply-To: Hai-fu Fan 
>> 
>> Please find attached for your review.
>> Regards.
>> 
>> Hai-fu Fan
> 
> 

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

[Bonsor, Daniel]

The Nigerian Prince wants your money.

Get Outlook for Android<https://aka.ms/ghei36>


From: CCP4 bulletin board  on behalf of Anindito Sen 

Sent: Sunday, December 11, 2016 12:45:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

Guys

are you all receiving the same??? What on earth is this ?

Andy



Begin forwarded message:

From: Hai-fu Fan mailto:fanha...@gmail.com>>
Subject: [ccp4bb] Remittance advice - Invitation to edit
Date: December 12, 2016 at 2:31:56 AM GMT+9
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Reply-To: Hai-fu Fan mailto:fanha...@gmail.com>>

Please find attached for your review.
Regards.

Hai-fu Fan

Re: [ccp4bb] Remittance advice - Invitation to edit

[Artem Evdokimov]

https://www.youtube.com/watch?v=m0gVZm5QR_Q

Hermes: You dumb stumps. Don't you realize you're being scammed?

Zoidberg: That is low, Hermes. Just because you don't have a body, you
don't want anyone else to be prince of Nigeria. Well, try and stop me from
wiring that money.

(Futurama)

Artem
www.harkerbio.com
(a legitimate company)

- Cosmic Cats approve of this message

On Mon, Dec 5, 2016 at 2:57 PM, Folmer Fredslund  wrote:

> Dear all,
>
> Just to point out the obvious (I hope) this is spam and points to a scam
> site trying to acquire your Google account password (in case you have one).
>
> Sorry to spam the list, just writing in case anyone stumbles upon it and
> thinks it's legit.
>
> Best regards,
> Folmer
>
>
> On 2016-12-05 14:34, Yong-Fu Li wrote:
>
> Please find attached for your review.
> Regards.
>
> Y.-F. Li
>
>
>

Re: [ccp4bb] Remittance advice - Invitation to edit

[Folmer Fredslund]

Dear all,

Just to point out the obvious (I hope) this is spam and points to a scam 
site trying to acquire your Google account password (in case you have one).


Sorry to spam the list, just writing in case anyone stumbles upon it and 
thinks it's legit.


Best regards,
Folmer


On 2016-12-05 14:34, Yong-Fu Li wrote:

Please find attached for your review.
Regards.

Y.-F. Li

Re: [ccp4bb] advice on screen dispensing?

[Olga Moroz]

Many thanks to all who replied!

I got emails from people who are also interested, asking to summarise the 
results, so here is what I’ve got so far:

1) Liquidator 96 200mkl from Rainin. Everyone agrees it works well and is easy 
to use, but tips from Rainin are required.

2) Integra VIAFLO 96. Tips also needed, but not specialised ones. It is also 
automatic, which Liquidator apparently is not.

3) Multichannel pipettes, ranging from 96 - 12 to even 8 channel

4) Old Hydra

More expensive options, and more versatile robots than can dispense screens in 
addition to other functions:

5) Art Robbins Scorpion
6) Gryphon
7) Phoenix

If I find out something else, I’ll let you know.

Best wishes,
Olga

Re: [ccp4bb] advice on screen dispensing?

[clare stevenson (JIC)]

Olga,

We use the liquidator96 and are very happy with it.  You have to use their own 
tips but they fit well and as long as you use it properly it works really well. 
 I trialled a few other makes but this works well for us.

Best wishes

Clare

Dr Clare E.M. Stevenson
John Innes Centre
Norwich Research Park
Colney Lane
Norwich
NR4 7UH
Tel 01603 450734


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Olga Moroz
Sent: 01 December 2016 00:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] advice on screen dispensing?

Dear All,
It looks like our old Hydra died of old age, and new Hydras seem quite 
expensive. We are now looking for an optimal way to transfer crystallisation 
screens from the deep well blocks into crystallisation plates.  We were told 
Liquidator96 from Rainin, 5-200mkl worked well and was very easy to use.
Are there any other suggestions - what do you use in your labs, how much did 
the instruments cost, are you happy with them?
Thanks a lot!
Olga

[ccp4bb] advice on screen dispensing?

[Olga Moroz]

Dear All,
It looks like our old Hydra died of old age, and new Hydras seem quite 
expensive. We are now looking for an optimal way to transfer crystallisation 
screens
from the deep well blocks into crystallisation plates.  We were told 
Liquidator96 from Rainin, 5-200mkl worked well and was very easy to use.
Are there any other suggestions - what do you use in your labs, how much did 
the instruments cost, are you happy with them?
Thanks a lot!
Olga

Re: [ccp4bb] Advice for Structure Determination

[David Hall]

Diamond and a variety of other SRs have these devices. Check out their webpages 
for available equipment or contact directly.

Dave

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: 05 October 2015 09:59
To: ccp4bb
Subject: Re: [ccp4bb] Advice for Structure Determination

Xe at longish wavelength (> 1.5Å), if you can find a pressure device (LURE 
maybe?)

Phil

> On 5 Oct 2015, at 09:08, Marc Graille  wrote:
> 
> Dear Monica,
> 
> I had solved couple of structures using anomalous signal for tungsten. I have 
> incubated the proteins with 25-50mM NaWO3 and set-up the crystallization 
> trays. 
> If you are lucky, WO3 might interact with your protein as SO4 ions do 
> sometimes and you might be able to get anomalous signals.
> This works fine for nucleic acid binding proteins.
> 
> Otherwise, I have also solved a structure of a protein expressed in Pichia 
> using anomalous signal from SeMet. It might be time-consuming and complicated 
> to get labeled protein in Pichia but could be faster than heavy atoms 
> derivatives.
> Here is a link to the publication describing the SeMet labeling procedure.
> http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/26082394
> 
> Hope it helps,
> 
> Good luck,
> 
> Marc
> 
>> Le 5 oct. 2015 à 09:38, Monica Mittal  a écrit :
>> 
>> Dear all,
>> 
>> I need a general advice. I don't have a suitable Model (Lets say only with a 
>> similarity of 15%) and no other model to solve the structure by MR. Then i 
>> think of anomalous experiments, but soaking with heavy metals is not good 
>> for the crystals. Since the protein is being expressed in Pichia cells, 
>> growth in Seleno-media is cumbersome. There are no ligands or ions that i 
>> can use for anomalous scattering of protein crystals. I am trying to express 
>> it in bacteria but have some issues. What is the option that i can choose to 
>> solve the structure of such a protein ? Your suggestions are highly 
>> recommended.
>> 
>> Thanks in advance.
>> Monica
> 
> Marc GRAILLE, PhD
> Directeur de recherche CNRS
> 
> Laboratoire de Biochimie
> ECOLE POLYTECHNIQUE - UMR7654 CNRS
> 91128 PALAISEAU CEDEX
> 
> 
> 
> Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09
> 
> Email: marc.grai...@polytechnique.edu
> 
> Team: Translation and degradation of eukaryotic mRNAs
> http://bioc.polytechnique.fr/spip.php?rubrique117
> Team supported by the ATIP-Avenir CNRS program
> 
> 
> 

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] Advice for Structure Determination

[Graeme Winter]

Dear Monica

Given you have eliminated all other phasing possibilities I would try phasing 
from native atoms e.g. sulphur. If you have reasonable resolution and you can 
collect data at a long wavelength from many samples (which has been shown to 
improve the phasing signals under some circumstances) you may be able to get 
yourself phases or at least a decent amount of signal which could be combined 
with highly partial MR solutions to bootstrap your way.

There are also methods which allow phasing from highly incomplete MR models 
given good data ™ however your mileage may vary. There was a discussion on this 
subject on this very forum recently.

Your problem here if your crystals do not diffract so well is “hard” so your 
cumbersome alternative could be necessary. However in the meantime effort in 
optimising the crystals you can obtain already is probably well spent.

Best wishes Graeme




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Monica 
Mittal
Sent: 05 October 2015 08:39
To: ccp4bb
Subject: [ccp4bb] Advice for Structure Determination

Dear all,

I need a general advice. I don't have a suitable Model (Lets say only with a 
similarity of 15%) and no other model to solve the structure by MR. Then i 
think of anomalous experiments, but soaking with heavy metals is not good for 
the crystals. Since the protein is being expressed in Pichia cells, growth in 
Seleno-media is cumbersome. There are no ligands or ions that i can use for 
anomalous scattering of protein crystals. I am trying to express it in bacteria 
but have some issues. What is the option that i can choose to solve the 
structure of such a protein ? Your suggestions are highly recommended.

Thanks in advance.
Monica

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Antonio Ariza]

>Burning/frying the crystal is never the right strategy, at least not if you 
>use a Pilatus detector.

>Burning/frying is a strategy that results from the widespread misunderstanding 
>of using Rsym

>as a criterion of data quality.

I apologise if I didn't make myself clear. The point I tried to make is that it 
is ok to strive to obtain higher resolution with native data sets ... and yes, 
"fry" is a poor choice of a word on my side as it implies damage to the 
crystal, which is not what I meant. I simply tried to emphasise that going for 
high resolution is ok when collecting native data sets but not when collecting 
anomalous ones. The rest of my message made a point of collecting data with 
high attenuation and fast shutter speed at a lower resolution to keep the 
anomalous signal high in as many images as possible before X-ray damage sets in 
lowers it.



Tony



--
Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

On Mon, 20 Apr 2015 23:15:17 +, Keller, Jacob  
wrote:


>>I have processed test data sets (measured at the SLS) which have only a few 
>>non-zero pixels on each frame. Can be nicely integrated - but it was insulin. 
 
>What were the values of the non-zero pixels, I wonder? How many total counts 
>per image? And this was, I assume, Pilatus? Sounds pretty amazing, even for 
>insulin... 
 
>JPK

Pilatus 2M. This is the histogram of a random frame I picked:
  counts  number
   0 2211457  thus 97% of all pixels have zero counts
   1   65154that's 2.8% of all pixels
   22107
   3  96
   4  20
   5  12
   6   3
   7   5
   9   2
  10   2
  11   3
  12   4
  14   2
  15   1
  29   1
all other counts are zero. The average count is 0.03.  Processing was done with 
the March-2015 version of XDS; older versions do not work well with average 
counts below about 0.5 .

best,

Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Keller, Jacob]

>I have processed test data sets (measured at the SLS) which have only a few 
>non-zero pixels on each frame. Can be nicely integrated - but it was insulin.

What were the values of the non-zero pixels, I wonder? How many total counts 
per image? And this was, I assume, Pilatus? Sounds pretty amazing, even for 
insulin...

JPK

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

On Fri, 17 Apr 2015 15:00:12 +, Keller, Jacob  
wrote:


>>Finally, there is simply no downside in collecting more degrees with 
>>proportionally lower dose on the Pilatus. Merging the data recovers the 
>>_same_ signal. It has only advantages - so many that I won't write them up 
>>here with 1 finger on my tablet. 
 
> ...Up to the point at which one can no longer index/refine the frames 
> reliably. 

I agree. In addition, one also needs some reflections significantly higher than 
the noise to build up the reference profiles.
 
> And it would be interesting to try to figure out what that point is, or how 
> to push it to even fewer photons. 
 
I have processed test data sets (measured at the SLS) which have only a few 
non-zero pixels on each frame. Can be nicely integrated - but it was insulin.

> JPK 
 
best,

Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

On Fri, 17 Apr 2015 13:02:01 +, Antonio Ariza  
wrote:

>Hi,
>
>I agree with Kay, try to fry your native crystals to get the highest overall 
>resolution possible, 

since you mention my name in your sentence: no, this is not what I think (nor 
said). Burning/frying the crystal is never the right strategy, at least not if 
you use a Pilatus detector. Burning/frying is a strategy that results from the 
widespread misunderstanding of using Rsym as a criterion of data quality.

best,

Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[John R Helliwell]

Hi,
Re " Has anybody ever used xenon? Can anyone share the starting pressure
and time for optimization? "
This paper :-
doi:10.1107/S0907444901009350 <http://dx.doi.org/10.1107/S0907444901009350>
offers you details.
Best wishes,
John

On Fri, Apr 17, 2015 at 2:11 AM, joy yang  wrote:

> Hi All,
>
> Thanks a lot for the advice from Mark.
>
> 1. For the comment to use a attenuated beam, the major concern here is
> resolution, since at full beam,  the resolution is already somewhere
> between 3.5-4.2, I assume that significant attenuation will bring down the
> resolution dramatically, and also decrease the I/Sigma which might  lead to
> more errors in |F|?
>
> 2.  We used TaBr because as a large electron dense cluster, it is good for
> low resolution phasing. This derivative, in the best scenario, give a 4.8A
> data set (a resolution that is supposed to be enough to find the huge
> cluster) which only has 0.1~0.2A unit cell difference to a native data set
> collected on the same beam, theoretically, this dataset should give
> prominent peaks on hacker section (the crystal is green, and fluoresence
> scan give moderate signal), but what I find is only two small peaks (6-7
> sigma, boarder line) (maybe occupancy too low?), and using Hyss to find the
> HA only result in a FOM of 0.20. This is what triggers me to wonder if a
> high scaling error model (0.05-0.1) is also detrimental for isomorphous
> phasing?
>
> 3. speaking of Se. Is it possible to use Se as a second derivative for MIR
> in my case (500 amino acid, 18 Met)? my concern is that Se might be too
> “light” for my protein, and 4.5A resolution is NOT much better than the 7A
> Mark has mentioned.
>
> 4. Has anybody ever used xenon? Can anyone share the starting pressure and
> time for optimization?
>
> Thank you again,
>
> Bei
>



-- 
Professor John R Helliwell DSc

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Jurgen Bosch]

I’m sure James Holton has an option for that :-)

By the way, zero photon data sets exist and have been published before (some of 
them had to be retracted though).

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 17, 2015, at 11:00 AM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Finally, there is simply no downside in collecting more degrees with 
proportionally lower dose on the Pilatus. Merging the data recovers the _same_ 
signal. It has only advantages - so many that I won't write them up here with 1 
finger on my tablet.

...Up to the point at which one can no longer index/refine the frames reliably.

And it would be interesting to try to figure out what that point is, or how to 
push it to even fewer photons.

JPK







With a CCD it's a different story.

Best,

Kay

Am 17. April 2015 15:49:21 MESZ, schrieb Jurgen Bosch 
mailto:jbos...@jhu.edu>>:
I would disagree.
My philosophy is: assume this is your only diffracting crystal,
maximize the outcome by investing some thoughts into it before being
sorry. Therefore, run strategy and optimize for anomalous pairs being
collected as close in time as possible.
If you have the luxury of having multiple crystals you know diffract,
then it;s a different story.

Regarding the 1degree option, I think that dates back to the dinosaurs
of crystallography, when only non-decimal numbers were an option to be
entered in the CLI, yes there was no GUI before :-) Also the
goniometers are much more accurate these days. More seriously, I think
this had something to do perhaps with the cost of storage, remember 50
MB was a lot of space 20 years ago. Your average Pilatus data set today
comes at 3-5 GB, considering a 6TB drive costs about 250$ today that’s
nothing. Or reading the files from a DAT4 drive took ages, so you
really didn’t want to collect fine sliced data.

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 17, 2015, at 9:25 AM, Kay Diederichs
mailto:kay.diederi...@uni-konstanz.de>>
wrote:

Hi Jürgen,

sorry - that's what I get when mailing while boarding ... No, I'd just
collect 360 degrees, and if the crystal is still ok, another 360, ...
This way one
- obtains high completeness and multiplicity
- can discard frames with "too much" radiation damage
- does not have to worry about the starting point of data collection.
To make the most of the second 360°, you should change some parameter:
wavelength, rotation axis (requires a BL with kappa or Prigo), or at
least distance (by few percent).

When I read that 1° frames are collected, I just wonder why? Because it
used to be done like that in the good old times?

HTH,

Kay

On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch
mailto:jbos...@jhu.edu>> wrote:

Just to clarify, I think what Kay meant with "strategy" is that you
don't just shoot at the crystal and collect. You should figure out what
is the optimum start and end point of your data collection. Best to be
cautious and not immediately go for highest resolution and not fry your
crystal. A 4 A complete anomalous data set is better than a partial
3.2A one.
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 17, 2015, at 06:37, Kay Diederichs
mailto:kay.diederi...@uni-konstanz.de>>
wrote:

Hi,
I'd say using a Pilatus detector in fine-slicing mode and lowdose/high
multiplicity will give you better chances to solve the structure. The
right strategy makes a difference ...
Best,
Kay

--
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Keller, Jacob]

>Finally, there is simply no downside in collecting more degrees with 
>proportionally lower dose on the Pilatus. Merging the data recovers the _same_ 
>signal. It has only advantages - so many that I won't write them up here with 
>1 finger on my tablet.

...Up to the point at which one can no longer index/refine the frames reliably.

And it would be interesting to try to figure out what that point is, or how to 
push it to even fewer photons.

JPK







With a CCD it's a different story.

Best,

Kay

Am 17. April 2015 15:49:21 MESZ, schrieb Jurgen Bosch :
>I would disagree.
>My philosophy is: assume this is your only diffracting crystal, 
>maximize the outcome by investing some thoughts into it before being 
>sorry. Therefore, run strategy and optimize for anomalous pairs being 
>collected as close in time as possible.
>If you have the luxury of having multiple crystals you know diffract, 
>then it;s a different story.
>
>Regarding the 1degree option, I think that dates back to the dinosaurs 
>of crystallography, when only non-decimal numbers were an option to be 
>entered in the CLI, yes there was no GUI before :-) Also the 
>goniometers are much more accurate these days. More seriously, I think 
>this had something to do perhaps with the cost of storage, remember 50 
>MB was a lot of space 20 years ago. Your average Pilatus data set today 
>comes at 3-5 GB, considering a 6TB drive costs about 250$ today that’s 
>nothing. Or reading the files from a DAT4 drive took ages, so you 
>really didn’t want to collect fine sliced data.
>
>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 17, 2015, at 9:25 AM, Kay Diederichs 
>mailto:kay.diederi...@uni-konstanz.de>>
>wrote:
>
>Hi Jürgen,
>
>sorry - that's what I get when mailing while boarding ... No, I'd just 
>collect 360 degrees, and if the crystal is still ok, another 360, ...
>This way one
>- obtains high completeness and multiplicity
>- can discard frames with "too much" radiation damage
>- does not have to worry about the starting point of data collection.
>To make the most of the second 360°, you should change some parameter:
>wavelength, rotation axis (requires a BL with kappa or Prigo), or at 
>least distance (by few percent).
>
>When I read that 1° frames are collected, I just wonder why? Because it 
>used to be done like that in the good old times?
>
>HTH,
>
>Kay
>
>On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch 
>mailto:jbos...@jhu.edu>> wrote:
>
>Just to clarify, I think what Kay meant with "strategy" is that you 
>don't just shoot at the crystal and collect. You should figure out what 
>is the optimum start and end point of your data collection. Best to be 
>cautious and not immediately go for highest resolution and not fry your 
>crystal. A 4 A complete anomalous data set is better than a partial 
>3.2A one.
>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 17, 2015, at 06:37, Kay Diederichs 
>mailto:kay.diederi...@uni-konstanz.de>>
>wrote:
>
>Hi,
>I'd say using a Pilatus detector in fine-slicing mode and lowdose/high 
>multiplicity will give you better chances to solve the structure. The 
>right strategy makes a difference ...
>Best,
>Kay

--
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

But if you only have a single diffracting crystal, then you don't know the 
space group before the experiment, and you have to collect 180 (native) or 360 
(anom) anyway.
Plus, I have seen too many sorry cases where people thought they had a certain 
space group, and later it turned out to be lower symmetry -  happens e.g. for 
twinned crystals. These cases ended up with severely incomplete datasets.
Finally, there is simply no downside in collecting more degrees with 
proportionally lower dose on the Pilatus. Merging the data recovers the _same_ 
signal. It has only advantages - so many that I won't write them up here with 1 
finger on my tablet.

With a CCD it's a different story.

Best,

Kay

Am 17. April 2015 15:49:21 MESZ, schrieb Jurgen Bosch :
>I would disagree.
>My philosophy is: assume this is your only diffracting crystal,
>maximize the outcome by investing some thoughts into it before being
>sorry. Therefore, run strategy and optimize for anomalous pairs being
>collected as close in time as possible.
>If you have the luxury of having multiple crystals you know diffract,
>then it;s a different story.
>
>Regarding the 1degree option, I think that dates back to the dinosaurs
>of crystallography, when only non-decimal numbers were an option to be
>entered in the CLI, yes there was no GUI before :-) Also the
>goniometers are much more accurate these days. More seriously, I think
>this had something to do perhaps with the cost of storage, remember 50
>MB was a lot of space 20 years ago. Your average Pilatus data set today
>comes at 3-5 GB, considering a 6TB drive costs about 250$ today that’s
>nothing. Or reading the files from a DAT4 drive took ages, so you
>really didn’t want to collect fine sliced data.
>
>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 17, 2015, at 9:25 AM, Kay Diederichs
>mailto:kay.diederi...@uni-konstanz.de>>
>wrote:
>
>Hi Jürgen,
>
>sorry - that's what I get when mailing while boarding ... No, I'd just
>collect 360 degrees, and if the crystal is still ok, another 360, ...
>This way one
>- obtains high completeness and multiplicity
>- can discard frames with "too much" radiation damage
>- does not have to worry about the starting point of data collection.
>To make the most of the second 360°, you should change some parameter:
>wavelength, rotation axis (requires a BL with kappa or Prigo), or at
>least distance (by few percent).
>
>When I read that 1° frames are collected, I just wonder why? Because it
>used to be done like that in the good old times?
>
>HTH,
>
>Kay
>
>On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch
>mailto:jbos...@jhu.edu>> wrote:
>
>Just to clarify, I think what Kay meant with "strategy" is that you
>don't just shoot at the crystal and collect. You should figure out what
>is the optimum start and end point of your data collection. Best to be
>cautious and not immediately go for highest resolution and not fry your
>crystal. A 4 A complete anomalous data set is better than a partial
>3.2A one.
>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 17, 2015, at 06:37, Kay Diederichs
>mailto:kay.diederi...@uni-konstanz.de>>
>wrote:
>
>Hi,
>I'd say using a Pilatus detector in fine-slicing mode and lowdose/high
>multiplicity will give you better chances to solve the structure. The
>right strategy makes a difference ...
>Best,
>Kay

-- 
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Jurgen Bosch]

I would disagree.
My philosophy is: assume this is your only diffracting crystal, maximize the 
outcome by investing some thoughts into it before being sorry. Therefore, run 
strategy and optimize for anomalous pairs being collected as close in time as 
possible.
If you have the luxury of having multiple crystals you know diffract, then it;s 
a different story.

Regarding the 1degree option, I think that dates back to the dinosaurs of 
crystallography, when only non-decimal numbers were an option to be entered in 
the CLI, yes there was no GUI before :-) Also the goniometers are much more 
accurate these days. More seriously, I think this had something to do perhaps 
with the cost of storage, remember 50 MB was a lot of space 20 years ago. Your 
average Pilatus data set today comes at 3-5 GB, considering a 6TB drive costs 
about 250$ today that’s nothing. Or reading the files from a DAT4 drive took 
ages, so you really didn’t want to collect fine sliced data.

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 17, 2015, at 9:25 AM, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Hi Jürgen,

sorry - that's what I get when mailing while boarding ... No, I'd just collect 
360 degrees, and if the crystal is still ok, another 360, ... This way one
- obtains high completeness and multiplicity
- can discard frames with "too much" radiation damage
- does not have to worry about the starting point of data collection.
To make the most of the second 360°, you should change some parameter: 
wavelength, rotation axis (requires a BL with kappa or Prigo), or at least 
distance (by few percent).

When I read that 1° frames are collected, I just wonder why? Because it used to 
be done like that in the good old times?

HTH,

Kay

On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch 
mailto:jbos...@jhu.edu>> wrote:

Just to clarify, I think what Kay meant with "strategy" is that you don't just 
shoot at the crystal and collect. You should figure out what is the optimum 
start and end point of your data collection. Best to be cautious and not 
immediately go for highest resolution and not fry your crystal. A 4 A complete 
anomalous data set is better than a partial 3.2A one.
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 17, 2015, at 06:37, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Hi,
I'd say using a Pilatus detector in fine-slicing mode and lowdose/high 
multiplicity will give you better chances to solve the structure. The right 
strategy makes a difference ...
Best,
Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Antonio Ariza]

Something else you could try is using a kappa goniometer. There were a couple 
of presentations at the last CCP4 meeting where they discussed that alignment 
along the appropriate axis using a Kappa goniometer often worked much better 
than the inverse beam mode. By aligning the crystal with the beam in such a way 
that one of the cell axes lies perpendicular to the beam, you can obtain 
diffraction images that have bilateral symmetry and where both parts of a 
Friedel pair are visible on the same image. This way the differences between 
each pair are easily measured and compared and, because they are measured at 
the same time, the differences cannot be due to X-ray damage, scaling or 
anisotropy that result when the two parts of a Friedel pair are measured from 
different images taken from different positions on the crystal at different 
times.

At the Diamond Light Source they have started to implement these goniometers on 
some of the macromolecular beam lines. You simply take 2 to 4 test images 
between 0 and 90 degrees and the software automatically spits out the theta and 
kappa angles you need to orient the goniometer. After you align the crystal and 
collect the data set you should collect a second data set where you misalign 
all the crystal axes. This is useful since the first data set will have no data 
for the aligned axis and it will help determine the correct space group if 
there are systematic absences along that plane. By integrating both data sets 
and then merging and scaling them together you will also obtain much better 
completeness.

Tony



--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

Hi Jürgen,

sorry - that's what I get when mailing while boarding ... No, I'd just collect 
360 degrees, and if the crystal is still ok, another 360, ... This way one 
- obtains high completeness and multiplicity
- can discard frames with "too much" radiation damage
- does not have to worry about the starting point of data collection.
To make the most of the second 360°, you should change some parameter: 
wavelength, rotation axis (requires a BL with kappa or Prigo), or at least 
distance (by few percent).

When I read that 1° frames are collected, I just wonder why? Because it used to 
be done like that in the good old times?

HTH,

Kay

On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch  wrote:

>Just to clarify, I think what Kay meant with "strategy" is that you don't just 
>shoot at the crystal and collect. You should figure out what is the optimum 
>start and end point of your data collection. Best to be cautious and not 
>immediately go for highest resolution and not fry your crystal. A 4 A complete 
>anomalous data set is better than a partial 3.2A one.
>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 17, 2015, at 06:37, Kay Diederichs 
>mailto:kay.diederi...@uni-konstanz.de>> wrote:
>
>Hi,
>I'd say using a Pilatus detector in fine-slicing mode and lowdose/high 
>multiplicity will give you better chances to solve the structure. The right 
>strategy makes a difference ...
>Best,
>Kay
>

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Antonio Ariza]

Hi,

I agree with Kay, try to fry your native crystals to get the highest overall 
resolution possible, but go for low resolution if your crystals decay rapidly, 
particularly when collecting anomalous data. A high overall resolution is 
always desirable, but during anomalous phasing you can potentially solve good 
data (no twinning, pseudo-translational NCS symmetry, etc...) even at an 
anomalous resolution (NOT overall resolution) as low as 5 to 6 Angstroms, 
though in practice you generally need at least 3 to 4 Angstroms of anomalous 
resolution for a straight forward solution. Once you have solved the 
substructure and have initial phases and an acceptable build, you can swap to 
your native data to build the structure using higher resolution data.

Obviously, there are a number of factors that influence the result: If your 
crystals are stable, decay very slowly in the X-ray beam and you have a high 
symmetry space group, you can attempt MAD phasing. However, if your crystals 
decay rapidly and you have a low symmetry space group you should try SAD 
phasing. In this case it's best to collect a lot of data (360 to 720 degrees) 
close to the peak wavelength with high attenuation, fast exposure times and 
slightly larger oscillations than usual (1 to 2 degrees). My own experience 
with this has been that larger oscillations work better in this case than fine 
slicing, which doesn't seem logical. I've seen this with the last three 
structures I solved by anomalous phasing where 1 degree oscillations gave 
better anomalous signal that 0.2 degree oscillations with a Pilatus detector at 
0.035 second exposures. Maybe it's to do with the fact that you collect more 
complete data (as in degrees collected) this way compared to fine slicing 
(where you will cover fewer degrees using the same dose before the crystal 
decays).



You already tried merging several data sets collected from different positions 
of the same crystal, but if your crystals are isomorphous you can also merge 
the data from several crystals to improve your SAD phasing as the anomalous 
resolution often increases with high multiplicity (the overall resolution does 
not). For this you need to take into account that the heavy metal atoms will be 
damaged first at the wavelength at which they produce anomalous diffraction, so 
the best anomalous resolution will be provided by the images at the start of 
the data even if the overall resolution doesn't seem to decrease. So, check if 
you get better data by discarding the images to the end of each individual data 
set before you merge them. Merging and then scaling the data sets together 
might increase the overall error and not improve the high resolution data, but 
I have found this will boost the signal of week anomalous scatterers found in 
the same positions in all the crystals.

I hope this helped.



Tony



--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Jurgen Bosch]

Just to clarify, I think what Kay meant with "strategy" is that you don't just 
shoot at the crystal and collect. You should figure out what is the optimum 
start and end point of your data collection. Best to be cautious and not 
immediately go for highest resolution and not fry your crystal. A 4 A complete 
anomalous data set is better than a partial 3.2A one.
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 17, 2015, at 06:37, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Hi,
I'd say using a Pilatus detector in fine-slicing mode and lowdose/high 
multiplicity will give you better chances to solve the structure. The right 
strategy makes a difference ...
Best,
Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[Kay Diederichs]

Hi,
I'd say using a Pilatus detector in fine-slicing mode and lowdose/high 
multiplicity will give you better chances to solve the structure. The right 
strategy makes a difference ...
Best,
Kay

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[joy yang]

Hi All,

Thanks a lot for the advice from Mark.

1. For the comment to use a attenuated beam, the major concern here is
resolution, since at full beam,  the resolution is already somewhere
between 3.5-4.2, I assume that significant attenuation will bring down the
resolution dramatically, and also decrease the I/Sigma which might  lead to
more errors in |F|?

2.  We used TaBr because as a large electron dense cluster, it is good for
low resolution phasing. This derivative, in the best scenario, give a 4.8A
data set (a resolution that is supposed to be enough to find the huge
cluster) which only has 0.1~0.2A unit cell difference to a native data set
collected on the same beam, theoretically, this dataset should give
prominent peaks on hacker section (the crystal is green, and fluoresence
scan give moderate signal), but what I find is only two small peaks (6-7
sigma, boarder line) (maybe occupancy too low?), and using Hyss to find the
HA only result in a FOM of 0.20. This is what triggers me to wonder if a
high scaling error model (0.05-0.1) is also detrimental for isomorphous
phasing?

3. speaking of Se. Is it possible to use Se as a second derivative for MIR
in my case (500 amino acid, 18 Met)? my concern is that Se might be too
“light” for my protein, and 4.5A resolution is NOT much better than the 7A
Mark has mentioned.

4. Has anybody ever used xenon? Can anyone share the starting pressure and
time for optimization?

Thank you again,

Bei

[ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

[joy yang]

Hi all,

I am working a extremely difficult crystal whose resolution is low (3.5-4 A
for native ) and could not be solved by MR. I am looking for some advice on
data collection strategies, bellow are the details:

Say that I have a rod shaped xtal which is 50 um * 150 um * 20 uM, and if i
use a 15um * 15 um beam size to shoot it, hopefully we can have 8 different
site along the length to collect data. say that it take 60 frames (1 degree
each ) before xtal decays significantly, if I collect 0-15 and 180-195 on
the first site, and 15-30 (195-210) successively …., it is true that for
each site, the Friedel paris are collected in a identical or close
conditions, however how about the diffrences between each site? For my
xtal, the unit cell and diffraction intensities could vary much from one
end of the rod to the other end. Actually in my last attempt to collect on
3 different site of a single crystal, the scale factor and B-scale changes
dramatically between the three site, as a consequence, high error model
were used in scaling (0.1), and I assume that such a high error model is
also detrimental for the small difference between Friedel pairs as when
scaling the data from different site together, the signals get averaged
out, am I right? Could anyone give me some advice on data collection
strategy to maximize the possibility to get a useful peak dataset?

I am also wondering if a high error model is also detrimental if I went for
isomorphous phasing instead of anomalous phasing?

Thank you for everyone’s wonderful advises in advance!

Bei

Dr. Bei Yang

Postdoctoral Scholar
UC Berkeley, QB3
360 Stanley Hall
Berkeley, CA 94720

[ccp4bb] Advice on set-up for stereo projection of PyMol sessions in lecture theatre

[Ruth Brenk]

Hi,

we are looking for a set-up that allows us to project PyMol sessions in 
stereo in a lecture theatre for about 100 students.

Due to the cost, the system should run with passive glasses.
Does anybody have any advice on which projector to use and which 
hardware we need on the PC side (the PC will be a windows system)?


Cheers

Ruth



--
Jun.-Prof. Dr. Ruth Brenk
Johannes Gutenberg-Universität Mainz
Institut für Pharmazie und Biochemie
Staudinger Weg 5
D-55128 Mainz

Phone:  +49 (6131) 39-25726
Fax:  +49 (6131) 39-25670
http://www.pharmazie.uni-mainz.de/AK-Brenk

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Sergei Strelkov]

I wanted to thank everyone who responded,
for a whole bunch of advice and suggestions!
Sergei



On 29-Jul-13 12:22 PM, Sergei Strelkov wrote:

Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete 
NFS-based

cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei



--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Mark van der Woerd]

Dear Sergei,

Many have already given good advice. A somewhat different approach:

You might want to consider using a NAS for user file and program storage. We 
have run a group of Linux PCs for years that way and we are quite pleased with 
it. The NAS would take the place of your file server PC.

Although I don't quite have enough experience with it yet to fully recommend 
it, I do think you might want to consider using FreeNAS (just Google it), 
rather than buying a physical NAS. In a nutshell:

1) It is a free NAS setup, as the name suggests.
2) You need a PC with disk bays, a fair CPU and LOTS of memory. Add number and 
size of the disks you want. The PC generally should be a 64-bit system or else 
you will not be able to install enough memory.  
3) You download the operating system on a USB drive (it does not go on your 
data disks) - this is very easy to do
4) Follow setup instructions and you are ready to start testing. 

FreeNAS offers many options, such as mirroring, striping etc. Different kinds 
of RAIDS are possible. My experience has been that it is very nice to have a 
RAID system that allows for one disk to go bad and you still have a working 
system. It has happened 2-3 times in 5 years, on 3 NASes combined, that we have 
had a disk fail without notice. The FreeNAS home page will lead you to all the 
RAID options you have, how "safe" they are, what the read and write performance 
is etc. 

It is a good idea to build a second system in a different building for backup. 
We use Rsync for backup at night and this works well (it is slow but it does 
not matter). 

You might want to do a resource analysis what your limiting factor is in 
processing crystallographic data. My experience is that the network generally 
is not the limiting factor and disk access generally is not the limit either - 
but it can be, if you are transferring a large number of images from a 
synchrotron. Typically, in my experience, CPU is still the limiting factor. 

Hope this helps.

Mark
 

 

 

 

-Original Message-
From: Sergei Strelkov 
To: CCP4BB 
Sent: Mon, Jul 29, 2013 4:22 am
Subject: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster


Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete NFS-based
cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei

-- 
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

 

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Dmitry Rodionov]

Sorry, my "P4" statement came out wrong.
What I meant was that one does not need a high-end modern machine for such a 
server.
The workstation we use is dual-processor Dell Precision 470 with ECC RAM. As it 
happens, we also have an identical computer sitting around in case of a 
failure. )
I absolutely agree that reliability is paramount.

CPU load-wise:
our software Raid6 with 8 members does not produce CPU loads of >50% when 
writing 1 TB. I think 50% of 2x3.2 GHz Prescott-2M CPUs from 2005 is not all 
that much, though older single-core processor will struggle in such situation.

Best regards,
Dmitry

On 2013-07-29, at 11:08 AM, Georg Zocher wrote:

> Dear Sergei,
> 
> I agree in principle with the setup suggested by Dmitry.
> 
> But I would not use an old P4 system to serve as central device for all other 
> workstations. Keep in mind that such an old system might have a higher chance 
> to fail. As this is your central unit which keeps the work of all other 
> members running, I would not trust in such an old machine (beside there is no 
> money). Lifetime should be more expensive than hardware...
> 
> If you go for such a cheap setup, I would at least configure a second P4 
> system, that you can plug-in directly after a hardware failure of system-1. 
> Depending on the RAID-level and the number of hard disks, I assume that a P4 
> single core will not be sufficient in a setup with several users, especially 
> with a software raid setup (although I do not have solid data for it).
> 
> I would highly recommend to buy a system which is designed to do a 24/7/365 
> job. I installed such a machine in our workgroup three years ago including a 
> 3x RAID6 hardware setup for all /home/$USERNAME, diffraction data, and 
> crystallographic software. Workstations are attached via 2x1GBit network 
> connections (bonding) and are diskless. They get their image from the server 
> using tftpboot. This substantially reduces the administration time. 
> Especially, it allows you to "setup" a new workstation by simply adding it to 
> your dhcp.conf on the server...
> 
> All the best,
> Georg
> 
> 
> 
> 
> 
> 
> Am 29.07.2013 15:38, schrieb Dmitry Rodionov:
>> Dear Sergei,
>> 
>> IMO, the easiest way to achieve your goals is good old NIS and NFS with a 
>> centralized server on wired gigabit network. You could go with LDAP instead 
>> of NIS, but it is considerably more difficult to set up.
>> One computer would act as a server, containing the user database, homes and 
>> programs.
>> Hardware RAID is not worth it. You are better off getting a Linux-supported 
>> SAS/SATA HBA (e.g. Dell SAS 6/iR) and making a software RAID 5 with mdadm 
>> out of a bunch of inexpensive consumer-grade SATA disks. You need a minimum 
>> of 4 drives for RAID5. An external HDD enclosure might be necessary 
>> depending on server's chassis and the desired number of drives.
>> We built our server from an old P4 workstation with a couple gigs of RAM (8 
>> clients). Having two or more cores is a benefit.
>> If I am not mistaken, software RAID 5 is not bootable, so you would need an 
>> extra drive (can be very small) for the core part of the OS.
>> Export /home and /usr/local with NFS, mount them from client machines, hook 
>> the clients up to NIS and you are done. Some programs might not reside in 
>> /usr/local in which case you would have to export and mount more directories.
>> Ubuntu community has pretty good and easy to follow guides for NIS, NFS and 
>> mdadm.
>> 
>> Bets regards,
>>  Dmitry
>> 
>> On 2013-07-29, at 6:22 AM, Sergei Strelkov wrote:
>> 
>>> Dear all,
>>> 
>>> In old times I, just like about any protein crystallographer,
>>> used to work on a cluster of SGI/IRIX workstations with complete NFS-based
>>> cross-mounting of hard disks.
>>> 
>>> A typical operation included:
>>> 1. A single home directory location for every user:
>>> if my home directory was on workstation X, I would by default use
>>> it after logging on any of the workstations in the cluster.
>>> 2. A single location for all software for general use.
>>> (And, obviously, 3. The ability to log on any node from
>>> any terminal; today this is done via the 'ssh -X' command).
>>> 
>>> I wondered if someone could give us an advice on a painless
>>> setup enabling 1. and 2., for a small cluster of Ubuntu computers.
>>> We (will) have about five similar Dell computers in a local (192.168.*.*)
>>> network (wired/wireless). Any tips on the hardware (especially the
>>> LAN and networ

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Dmitry Rodionov]

Dear Sergei,

IMO, the easiest way to achieve your goals is good old NIS and NFS with a 
centralized server on wired gigabit network. You could go with LDAP instead of 
NIS, but it is considerably more difficult to set up.
One computer would act as a server, containing the user database, homes and 
programs.
Hardware RAID is not worth it. You are better off getting a Linux-supported 
SAS/SATA HBA (e.g. Dell SAS 6/iR) and making a software RAID 5 with mdadm out 
of a bunch of inexpensive consumer-grade SATA disks. You need a minimum of 4 
drives for RAID5. An external HDD enclosure might be necessary depending on 
server's chassis and the desired number of drives.
We built our server from an old P4 workstation with a couple gigs of RAM (8 
clients). Having two or more cores is a benefit.
If I am not mistaken, software RAID 5 is not bootable, so you would need an 
extra drive (can be very small) for the core part of the OS. 
Export /home and /usr/local with NFS, mount them from client machines, hook the 
clients up to NIS and you are done. Some programs might not reside in 
/usr/local in which case you would have to export and mount more directories.
Ubuntu community has pretty good and easy to follow guides for NIS, NFS and 
mdadm.

Bets regards,
Dmitry

On 2013-07-29, at 6:22 AM, Sergei Strelkov wrote:

> Dear all,
> 
> In old times I, just like about any protein crystallographer,
> used to work on a cluster of SGI/IRIX workstations with complete NFS-based
> cross-mounting of hard disks.
> 
> A typical operation included:
> 1. A single home directory location for every user:
> if my home directory was on workstation X, I would by default use
> it after logging on any of the workstations in the cluster.
> 2. A single location for all software for general use.
> (And, obviously, 3. The ability to log on any node from
> any terminal; today this is done via the 'ssh -X' command).
> 
> I wondered if someone could give us an advice on a painless
> setup enabling 1. and 2., for a small cluster of Ubuntu computers.
> We (will) have about five similar Dell computers in a local (192.168.*.*)
> network (wired/wireless). Any tips on the hardware (especially the
> LAN and network disks) are also welcome.
> 
> Many thanks,
> Sergei
> 
> -- 
> Prof. Sergei V. Strelkov
> Laboratory for Biocrystallography
> Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
> Herestraat 49 bus 822, 3000 Leuven, Belgium
> Work phone: +32 16 330845   Mobile: +32 486 294132
> Lab pages: http://pharm.kuleuven.be/anafar



smime.p7s
Description: S/MIME cryptographic signature

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Sergei,

if you are happy with NIS and NFS version 3, the setup is very simple.
For NFS you pick one of the computers as server and list the
directories (e.g. /home and /xtal) in /etc/exports (syntax examples
are usually within that file).
The syntax for mounting might actually be the same as on IRIX.

For NIS you install the package nis on all machines and define the
server as server and all other machines as clients. It helps to define
the server by IP-address in /etc/ypclient.conf on the client machines.

If you want NFS version 4 with kerberos protection and / or and
LDAP-system instead of NIS, you should really be interested in these
technologies and refer to one of the howto's available on the net. But
I would not recommend it since you only want to work with a small network.

Regards,
Tim

On 07/29/2013 12:22 PM, Sergei Strelkov wrote:
> Dear all,
> 
> In old times I, just like about any protein crystallographer, used
> to work on a cluster of SGI/IRIX workstations with complete
> NFS-based cross-mounting of hard disks.
> 
> A typical operation included: 1. A single home directory location
> for every user: if my home directory was on workstation X, I would
> by default use it after logging on any of the workstations in the
> cluster. 2. A single location for all software for general use. 
> (And, obviously, 3. The ability to log on any node from any
> terminal; today this is done via the 'ssh -X' command).
> 
> I wondered if someone could give us an advice on a painless setup
> enabling 1. and 2., for a small cluster of Ubuntu computers. We
> (will) have about five similar Dell computers in a local
> (192.168.*.*) network (wired/wireless). Any tips on the hardware
> (especially the LAN and network disks) are also welcome.
> 
> Many thanks, Sergei
> 

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFR9m+8UxlJ7aRr7hoRAo27AJ9rU6K/P9vCqNcb/5gmnqD7DQsWnwCbBO84
PCPO1SgbawtlaDyIU7BkZ4I=
=DZ8L
-END PGP SIGNATURE-

[ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Sergei Strelkov]

Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete NFS-based
cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei

--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] Microseeding technique advice

[Kelly Daughtry]

DLadakis,
The seed stock solution should be your crystallization solution with a
slight (5% maybe) increase in the precipitant. In my experience, I have not
needed additional protein to stabilize the nano-crystals, but as with all
things, every protein is different.

The idea is the crystals should be stable in the stock solution and not
dissolve. I generally place one crystal in 500 microL of seed stock (with
the little ball for crushing). Once I've vortexed for 5 minutes and a
13,000 rpm centrifuge spin for 5 minutes, I then prepare 3 1000-fold
dilutions (i.e. 1000-fold, 1 million fold and 1 billion fold). All can be
stored at -20 degrees C for extended periods of time.
When I setup the drops I generally either add 0.2 microL to a protein +
well drop (assuming 2 microL drop), or instead of adding the well solution,
I add the seed stock (or dilution) in equivalent volumes to the protein.

Another option is streak seeding, where you streak a cat (horse, etc)
whisker (or purchase the Hampton Research equivalent) across a crystal,
then streak the whisker through your crystallization drops, with each
successive drop being a dilution of the first streak (4 - 6 drops per
streak).

Hope this helps,
Kelly Daughtry




<http://walk.avonfoundation.org/site/TR?px=7043512&pg=personal&fr_id=2260&s_src=BF_emailbadge>

***
Kelly Daughtry, Ph.D.
IRTA Fellow
Mechanisms of Mutation Group
Molecular Genetics Laboratory, MD E-301
National Institute of Environmental Health Sciences
111 TW Alexander Drive
Research Triangle Park, NC 27709
Tel. (919) 541-3452
***


On Thu, May 30, 2013 at 5:15 AM, dladakis  wrote:

> Dear all
> I would like your advice on preparing a seed stock for microseeding.
> Should the seed stabilizing stock soltion include soluble protein as well.
> If it doesn't will the seeds eventually disolve leading to an unsuccesfull
> screen?
> Also how is the seedstock supposed to look under the microscope, clear?
> Thanks for your help
> DLadakis
>

Re: [ccp4bb] Microseeding technique advice

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear DLadakis,

you are probably thinking of using a robot for seeding. For manual
seeding you would overcome the problem of a stock solution by using a
cat whisker for seeding. Manual seeding also has the advantage of
getting a much better feeling for your crystals and the
crystallisation conditions.

Cheers,
Tim

On 05/30/2013 11:15 AM, dladakis wrote:
> Dear all I would like your advice on preparing a seed stock for
> microseeding. Should the seed stabilizing stock soltion include
> soluble protein as well. If it doesn't will the seeds eventually
> disolve leading to an unsuccesfull screen? Also how is the
> seedstock supposed to look under the microscope, clear? Thanks for
> your help DLadakis

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD4DBQFRpzRmUxlJ7aRr7hoRApQbAJYwWw/E8ijqD68BFIAOwBy12mU1AJ9UsuNj
85BRAKLZwwtjuANz54nmmg==
=8L1b
-END PGP SIGNATURE-

[ccp4bb] Microseeding technique advice

[dladakis]

Dear all
I would like your advice on preparing a seed stock for microseeding.
Should the seed stabilizing stock soltion include soluble protein as well. If 
it doesn't will the seeds eventually disolve leading to an unsuccesfull screen?
Also how is the seedstock supposed to look under the microscope, clear?
Thanks for your help
DLadakis

Re: [ccp4bb] Mac mini advice

[Chris Richardson]

On 23 Jan 2013, at 14:05, Bosch, Juergen wrote:

> I assume nobody of you is running an actual Osx server ? I mean the upgrade 
> to a full server version of the commonly distributed normal Osx releases ?

At the moment we have two OS X servers.  One runs open directory for user 
authentication.  The other is an AFP server for network home directories.  They 
are elderly Xeon-based XServes and will be retired as soon as possible.

We're getting rid of the authentication server because of unrelated changes to 
the way user authentication will be handled.

We're getting rid of the file server because it's old and needs replacing.  It 
will, however, be replaced by a Linux server.  In my opinion, Apple's 
abandonment of its rack-mountable server line shows a lack of commitment to 
servers.  The Promise RAID storage they resell is considerably more expensive 
than the equivalent from our Windows/Linux supplier.  Finally, the other Mac 
admins in my organisation haven't been saying nice things about mountain lion 
server.  If you look at forums like AFP548.com it's apparent that many other 
people are moving away from OS X server.

Moving to OS X servers does simplify some aspects of administration.  In the 
past, there was the added bonus that it was easy to get Linux and Windows 
machines to talk to a Mac server.  Creeping changes made by Apple since OS X 
server 10.4 mean that this is less true.  In particular, the horrible way Apple 
sets up SMB make its use a nightmare with other modern operating systems.

Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk

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] Mac mini advice

[Sidhu, Khushwant S. (Dr.)]

Hi,

I'm running a mac mini server.
The file sharing seems to work fine - I'm not running NIS.

There is a lag in software starting up - up to 20-30 s but once the software is 
loaded, it runs fine.

We did some benchmarking with phaser last week & there was no perceivable 
difference in running it of the server or locally (on a Mac Pro)

Software may require fiddling with to ensure that paths point to where the 
software is mounted.

This may be referred to as 'hacking' … so I wouldn't do it :-)

Sid


Dr K S Sidhu
Department of Biochemistry
1/61 Henry Wellcome Building
Lancaster Road
Leicester
LE1 9HN

Tel: 0116 229 7237




On 23 Jan 2013, at 14:05, "Bosch, Juergen" 
mailto:jubo...@jhsph.edu>> wrote:

I assume nobody of you is running an actual Osx server ? I mean the upgrade to 
a full server version of the commonly distributed normal Osx releases ?

I have not done it yet but I do think many of the issues mentioned regarding 
NFS/NIS could be addressed there. Regarding the missing macpro upgrades I 
expect to see new machines with thunderbolt connectivity in the next 4 months. 
And I will buy my third macpro then to run it as a true server.

Jürgen

Sent from my iPad

On Jan 23, 2013, at 5:21, "Peter Keller" 
mailto:pkel...@globalphasing.com>> wrote:

On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote:
On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
The real difficulty is integrating Macs into a
Linux-centric environment, for example configuring NFS, NIS, etc.

That's because NFS and NIS are antiquities left over from the days of
mainframes. Distributed file systems and user information databases
are designed for an environment of many workers and few machines, when
the typical graphics workstation cost $50,000. These days, we argue
whether to spend an extra $200 on a $500 computer. We have moved to a
new paradigm: many workers with many more machines, with each machine
having essentially mainframe levels of storage and computing power.

Technically there is something in what you say as a pattern for
day-to-day work (for some people, although not all), but I think that
describing the debate in terms of modern vs. antiquated is missing the
point completely. The real difference between local vs. centralised
storage is to do with responsibility for the hardware and the data that
it contains.

Local workstation storage is OK for the following kinds of cases:

(i) the data that are stored locally have no value, so it doesn't matter
if they are lost (either through hardware failure, misbehaving software
or accidental deletion).

(ii) the user has the expertise and the time to set up and maintain a
strategy for recovering data that are lost from local disks

(iii) the institution that the user works for allows the user to include
data on local workstation disks in the institution's regular backup
operations

When none of these apply, there is a real, contemporary case for using
something like NFS, where the storage is centrally maintained and backed
up. The cost of storage has fallen of course, but what that means is
that the real questions now are about the value of the data. In some
fields, you could store your entire career's data on a few USB memory
sticks, but I doubt that many people would want to do that without
having made other copies somewhere else, and the same applies to local
workstation storage too :-).

There are other considerations in favour of connecting a workstation to
networked services: if you use more than one machine it can be an
incredible pain to be constantly moving data around from one to the
other, and to keep track of what the authoritative versions are. Having
independent, local user id's and passwords on every workstation can also
cause difficulties. I could go on

In other words, instead of NFS, you should run git.

This is simply not an option for many crystallographers, who do not have
a background in software development or data management. Advocating and
supporting git (or indeed any content/version management system) for
those kind of users is a losing battle: they see it as an unnecessary
complication to their daily work, and will avoid using it as far as they
can.

Regards,
Peter.

--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom

Re: [ccp4bb] Mac mini advice

[Dmitry Rodionov]

We have 10.5&10.6 servers and briefly tested 10.7 server.
Last time I tried, Ubuntu 12.04 box would not authenticate users registered on 
the OS X Open Directory server.
Before that, 10.04 clients would cause random user lockouts.
NFS GUI is gone as of 10.7

Regards,
Dmitry

On 2013-01-23, at 9:05 AM, Bosch, Juergen wrote:

> I assume nobody of you is running an actual Osx server ? I mean the upgrade 
> to a full server version of the commonly distributed normal Osx releases ?
> 
> I have not done it yet but I do think many of the issues mentioned regarding 
> NFS/NIS could be addressed there. Regarding the missing macpro upgrades I 
> expect to see new machines with thunderbolt connectivity in the next 4 
> months. And I will buy my third macpro then to run it as a true server.
> 
> Jürgen 
> 
> Sent from my iPad
> 
> On Jan 23, 2013, at 5:21, "Peter Keller"  wrote:
> 
>> On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote:
>>> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
 The real difficulty is integrating Macs into a
 Linux-centric environment, for example configuring NFS, NIS, etc.
>>> 
>>> That's because NFS and NIS are antiquities left over from the days of
>>> mainframes. Distributed file systems and user information databases
>>> are designed for an environment of many workers and few machines, when
>>> the typical graphics workstation cost $50,000. These days, we argue
>>> whether to spend an extra $200 on a $500 computer. We have moved to a
>>> new paradigm: many workers with many more machines, with each machine
>>> having essentially mainframe levels of storage and computing power.
>> 
>> Technically there is something in what you say as a pattern for
>> day-to-day work (for some people, although not all), but I think that
>> describing the debate in terms of modern vs. antiquated is missing the
>> point completely. The real difference between local vs. centralised
>> storage is to do with responsibility for the hardware and the data that
>> it contains.
>> 
>> Local workstation storage is OK for the following kinds of cases:
>> 
>> (i) the data that are stored locally have no value, so it doesn't matter
>> if they are lost (either through hardware failure, misbehaving software
>> or accidental deletion).
>> 
>> (ii) the user has the expertise and the time to set up and maintain a
>> strategy for recovering data that are lost from local disks
>> 
>> (iii) the institution that the user works for allows the user to include
>> data on local workstation disks in the institution's regular backup
>> operations
>> 
>> When none of these apply, there is a real, contemporary case for using
>> something like NFS, where the storage is centrally maintained and backed
>> up. The cost of storage has fallen of course, but what that means is
>> that the real questions now are about the value of the data. In some
>> fields, you could store your entire career's data on a few USB memory
>> sticks, but I doubt that many people would want to do that without
>> having made other copies somewhere else, and the same applies to local
>> workstation storage too :-).
>> 
>> There are other considerations in favour of connecting a workstation to
>> networked services: if you use more than one machine it can be an
>> incredible pain to be constantly moving data around from one to the
>> other, and to keep track of what the authoritative versions are. Having
>> independent, local user id's and passwords on every workstation can also
>> cause difficulties. I could go on
>> 
>>> In other words, instead of NFS, you should run git.
>> 
>> This is simply not an option for many crystallographers, who do not have
>> a background in software development or data management. Advocating and
>> supporting git (or indeed any content/version management system) for
>> those kind of users is a losing battle: they see it as an unnecessary
>> complication to their daily work, and will avoid using it as far as they
>> can.
>> 
>> Regards,
>> Peter.
>> 
>> -- 
>> Peter Keller Tel.: +44 (0)1223 353033
>> Global Phasing Ltd., Fax.: +44 (0)1223 366889
>> Sheraton House,
>> Castle Park,
>> Cambridge CB3 0AX
>> United Kingdom

Re: [ccp4bb] Mac mini advice

[Anastassis Perrakis]

We did work with a full blown OSX Server in 2004 - indeed many issues on NFS 
were Ok, but NIS was a problem - or we could not figure it out.
We used it as server for developers, running X-grid, SVN, WebObjects servers 
for a couple of EC networks, but never deployed it fully
as a departmental-level server, due to the NIS issues. For a while it also 
hosted the protein-ccd server. 
We wanted to move to Kerberos if I recall correctly, but since my colleague 
Serge Cohen moved out and our IT are mac-o-phobic I opted to continue with 
Linux.

The Server was decommissioned a few weeks ago, and will likely get a second 
life in Soleil/Ipanema, 
but I think as an electric heat generator - almost as good on it as my old 
8-proc Alpha (2000) ;-)

A.

On 23 Jan 2013, at 15:05, Bosch, Juergen wrote:

> I assume nobody of you is running an actual Osx server ? I mean the upgrade 
> to a full server version of the commonly distributed normal Osx releases ?
> 
> I have not done it yet but I do think many of the issues mentioned regarding 
> NFS/NIS could be addressed there. Regarding the missing macpro upgrades I 
> expect to see new machines with thunderbolt connectivity in the next 4 
> months. And I will buy my third macpro then to run it as a true server.
> 
> Jürgen 
> 
> Sent from my iPad
> 
> On Jan 23, 2013, at 5:21, "Peter Keller"  wrote:
> 
>> On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote:
>>> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
 The real difficulty is integrating Macs into a
 Linux-centric environment, for example configuring NFS, NIS, etc.
>>> 
>>> That's because NFS and NIS are antiquities left over from the days of
>>> mainframes. Distributed file systems and user information databases
>>> are designed for an environment of many workers and few machines, when
>>> the typical graphics workstation cost $50,000. These days, we argue
>>> whether to spend an extra $200 on a $500 computer. We have moved to a
>>> new paradigm: many workers with many more machines, with each machine
>>> having essentially mainframe levels of storage and computing power.
>> 
>> Technically there is something in what you say as a pattern for
>> day-to-day work (for some people, although not all), but I think that
>> describing the debate in terms of modern vs. antiquated is missing the
>> point completely. The real difference between local vs. centralised
>> storage is to do with responsibility for the hardware and the data that
>> it contains.
>> 
>> Local workstation storage is OK for the following kinds of cases:
>> 
>> (i) the data that are stored locally have no value, so it doesn't matter
>> if they are lost (either through hardware failure, misbehaving software
>> or accidental deletion).
>> 
>> (ii) the user has the expertise and the time to set up and maintain a
>> strategy for recovering data that are lost from local disks
>> 
>> (iii) the institution that the user works for allows the user to include
>> data on local workstation disks in the institution's regular backup
>> operations
>> 
>> When none of these apply, there is a real, contemporary case for using
>> something like NFS, where the storage is centrally maintained and backed
>> up. The cost of storage has fallen of course, but what that means is
>> that the real questions now are about the value of the data. In some
>> fields, you could store your entire career's data on a few USB memory
>> sticks, but I doubt that many people would want to do that without
>> having made other copies somewhere else, and the same applies to local
>> workstation storage too :-).
>> 
>> There are other considerations in favour of connecting a workstation to
>> networked services: if you use more than one machine it can be an
>> incredible pain to be constantly moving data around from one to the
>> other, and to keep track of what the authoritative versions are. Having
>> independent, local user id's and passwords on every workstation can also
>> cause difficulties. I could go on
>> 
>>> In other words, instead of NFS, you should run git.
>> 
>> This is simply not an option for many crystallographers, who do not have
>> a background in software development or data management. Advocating and
>> supporting git (or indeed any content/version management system) for
>> those kind of users is a losing battle: they see it as an unnecessary
>> complication to their daily work, and will avoid using it as far as they
>> can.
>> 
>> Regards,
>> Peter.
>> 
>> -- 
>> Peter Keller Tel.: +44 (0)1223 353033
>> Global Phasing Ltd., Fax.: +44 (0)1223 366889
>> Sheraton House,
>> Castle Park,
>> Cambridge CB3 0AX
>> United Kingdom

Re: [ccp4bb] Mac mini advice

[Bosch, Juergen]

I assume nobody of you is running an actual Osx server ? I mean the upgrade to 
a full server version of the commonly distributed normal Osx releases ?

I have not done it yet but I do think many of the issues mentioned regarding 
NFS/NIS could be addressed there. Regarding the missing macpro upgrades I 
expect to see new machines with thunderbolt connectivity in the next 4 months. 
And I will buy my third macpro then to run it as a true server.

Jürgen 

Sent from my iPad

On Jan 23, 2013, at 5:21, "Peter Keller"  wrote:

> On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote:
>> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
>>> The real difficulty is integrating Macs into a
>>> Linux-centric environment, for example configuring NFS, NIS, etc.
>> 
>> That's because NFS and NIS are antiquities left over from the days of
>> mainframes. Distributed file systems and user information databases
>> are designed for an environment of many workers and few machines, when
>> the typical graphics workstation cost $50,000. These days, we argue
>> whether to spend an extra $200 on a $500 computer. We have moved to a
>> new paradigm: many workers with many more machines, with each machine
>> having essentially mainframe levels of storage and computing power.
> 
> Technically there is something in what you say as a pattern for
> day-to-day work (for some people, although not all), but I think that
> describing the debate in terms of modern vs. antiquated is missing the
> point completely. The real difference between local vs. centralised
> storage is to do with responsibility for the hardware and the data that
> it contains.
> 
> Local workstation storage is OK for the following kinds of cases:
> 
> (i) the data that are stored locally have no value, so it doesn't matter
> if they are lost (either through hardware failure, misbehaving software
> or accidental deletion).
> 
> (ii) the user has the expertise and the time to set up and maintain a
> strategy for recovering data that are lost from local disks
> 
> (iii) the institution that the user works for allows the user to include
> data on local workstation disks in the institution's regular backup
> operations
> 
> When none of these apply, there is a real, contemporary case for using
> something like NFS, where the storage is centrally maintained and backed
> up. The cost of storage has fallen of course, but what that means is
> that the real questions now are about the value of the data. In some
> fields, you could store your entire career's data on a few USB memory
> sticks, but I doubt that many people would want to do that without
> having made other copies somewhere else, and the same applies to local
> workstation storage too :-).
> 
> There are other considerations in favour of connecting a workstation to
> networked services: if you use more than one machine it can be an
> incredible pain to be constantly moving data around from one to the
> other, and to keep track of what the authoritative versions are. Having
> independent, local user id's and passwords on every workstation can also
> cause difficulties. I could go on
> 
>> In other words, instead of NFS, you should run git.
> 
> This is simply not an option for many crystallographers, who do not have
> a background in software development or data management. Advocating and
> supporting git (or indeed any content/version management system) for
> those kind of users is a losing battle: they see it as an unnecessary
> complication to their daily work, and will avoid using it as far as they
> can.
> 
> Regards,
> Peter.
> 
> -- 
> Peter Keller Tel.: +44 (0)1223 353033
> Global Phasing Ltd., Fax.: +44 (0)1223 366889
> Sheraton House,
> Castle Park,
> Cambridge CB3 0AX
> United Kingdom

Re: [ccp4bb] Mac mini advice

[Peter Keller]

On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote:
> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
> > The real difficulty is integrating Macs into a
> > Linux-centric environment, for example configuring NFS, NIS, etc.
> 
> That's because NFS and NIS are antiquities left over from the days of
> mainframes. Distributed file systems and user information databases
> are designed for an environment of many workers and few machines, when
> the typical graphics workstation cost $50,000. These days, we argue
> whether to spend an extra $200 on a $500 computer. We have moved to a
> new paradigm: many workers with many more machines, with each machine
> having essentially mainframe levels of storage and computing power.

Technically there is something in what you say as a pattern for
day-to-day work (for some people, although not all), but I think that
describing the debate in terms of modern vs. antiquated is missing the
point completely. The real difference between local vs. centralised
storage is to do with responsibility for the hardware and the data that
it contains.

Local workstation storage is OK for the following kinds of cases:

(i) the data that are stored locally have no value, so it doesn't matter
if they are lost (either through hardware failure, misbehaving software
or accidental deletion).

(ii) the user has the expertise and the time to set up and maintain a
strategy for recovering data that are lost from local disks

(iii) the institution that the user works for allows the user to include
data on local workstation disks in the institution's regular backup
operations

When none of these apply, there is a real, contemporary case for using
something like NFS, where the storage is centrally maintained and backed
up. The cost of storage has fallen of course, but what that means is
that the real questions now are about the value of the data. In some
fields, you could store your entire career's data on a few USB memory
sticks, but I doubt that many people would want to do that without
having made other copies somewhere else, and the same applies to local
workstation storage too :-).

There are other considerations in favour of connecting a workstation to
networked services: if you use more than one machine it can be an
incredible pain to be constantly moving data around from one to the
other, and to keep track of what the authoritative versions are. Having
independent, local user id's and passwords on every workstation can also
cause difficulties. I could go on

> In other words, instead of NFS, you should run git.

This is simply not an option for many crystallographers, who do not have
a background in software development or data management. Advocating and
supporting git (or indeed any content/version management system) for
those kind of users is a losing battle: they see it as an unnecessary
complication to their daily work, and will avoid using it as far as they
can.

Regards,
Peter.

-- 
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom

Re: [ccp4bb] Mac mini advice (rapidly veering off topic)

[Chris Richardson]

In the great internet tradition I'll chip in with my opinion even though it 
doesn't differ substantially from those already stated earlier in the thread.

I'm responsible for a mixed bag of Windows, Linux and Mac boxen used for 
crystallography and structural electron microscopy.

In terms of setting up the infrastructure and getting things working, Linux 
wins by a mile.  It's easy to buy cheap, powerful machines as desktops or 
servers.  There's a wealth of resources to help the sysadmin.  The ubiquity of 
Linux means that if you're trying to do something, there's almost always 
someone who has done it already and posted about it on a forum or blog.

In terms of getting people to use the machines, OS X wins hands down.  Putting 
people in front of linux machines requires more hand-holding on my part, 
especially for people who are inexperienced or even afraid of computers.  This 
is becoming more of an issue: gone are the days when most crystallographers had 
a favourite shell and were happy editing scripts.  Linux has come on in leaps 
and bounds but it's still not quite user-friendly enough; even something as 
simple as copying and pasting still doesn't have a uniform implementation.  
People familiar with commercial software struggle with the open source 
equivalents.

I won't cover Windows as I have an irrational hatred of it.

Having said all that, I too am worried about the way Apple is going.  They 
haven't released a proper Mac Pro upgrade in ages, and seem to be concentrating 
on making iMacs as wafer thing as possible at the expense of other practical 
considerations.  Their move to using the App Store for everything has 
concentrated on individual users and hasn't included support for "corporate" 
IT. Support for NFS and other UNIXy under-the-hood features is changed or 
dropped seemingly on a whim with no real documentation.  Their habit of making 
every change or new release a big surprise makes it difficult to plan for the 
future.

I'm glad I've got that off my chest.  Now I can do something productive.

Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk

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] Mac mini advice

[Ashley Buckle]

Cara you have re-ignited the perennial Mac v PC debate!!! You'll be asking 
about depositing raw diffraction data next ;)

Cheers
Ashley

Sent from my iPhone

On 23/01/2013, at 10:29 PM, Anastassis Perrakis  wrote:

> I am of the opinion that the truth lies somewhere in between ...
> 
> Here are my two cents based on personal experience ...
> 
> For example, I am happy myself using a MacBook Pro, which is sufficient for 
> all my activities, and has all software and data that I need.
> Thus, I am myself on the 'new' paradigm side, having a machine with 
> "mainframe levels of storage and computing power" (I do not run git,
> but time machine in a mac has the bits I need from the git idea - as far as I 
> know git that is).
> 
> In the department, we have about 20-25 scientists. These people need to 
> ''maintain" and be proficient in many software suites, many more than
> a traditional crystallographer (like me in my PhD time for example) would 
> need:
> vector design software for cloning, databases for keeping track of clones, 
> sequencing viewing software for their clones, 
> interfaces for crystallisation and biophysical equipment, analysis suites 
> like Graphpad/Prism, Origin, Kintek (etc etc)  for biophysical experiments 
> ... 
>  and lets not forget SAXS software ... Our experience, is that most of 
> these people like to use a Windows workstation for these (the choice is free),
> others prefer a Mac, thats not my point here. Many of that software also 
> needs to "maintained" by these people...
> Also, for a variety of reasons which have to do with IT "support" 
> restrictions, the Windows machines
> we have for them are miss-configured with ancient versions of the windows 
> "operating" system, but still Ok for many things, but not for really 
> straightforward use of CCP4/Phenix ...
> 
> My point here is, that these people are less likely to be keen of the idea to 
> also install and run ccp4/coot/phenix/buster in their machines 
> (they use pymol/yassara/chimera though locally since they can copy/paste to 
> their presentations and papers then). 
> So, we find it useful to keep an old fashioned setup running in parallel. 
> Linux boxes, hooked to Zalmans or really
> big or double LCDs, in a specific room ... People like these for data 
> processing, all data of many years back are online, incremental backup is 
> running etc.
> For historical reasons we even run NFS/NIS there (I agree its not a great 
> choice if one would start now).
> 
> My conclusion and advice for labs or departments that have more than 5-6 
> people, and are doing crystallography but not as their
> "full-time" business is that besides personal PC/Mac, a common room with a 
> few relatively powerful machines with nice, big, double,
> screens, likely also Stereo, is useful for a few reasons:
> 
> 1. Easier to make sure everybody is using the same software more or less
> 2. Same machine to everybody - not the situation that a new student gets a 
> new machine at year 0, which is redundant by graduation time at +3 years 
> (...or +5,6,7...)
> 3. Mixing of people in the room and ability for people to "look over the 
> shoulder" of others, the point that my colleague Titia Sixma always favours,
> which has indeed proved great for teaching others and learning from others.
> 4. Centralised "real" backup, availability of diffraction data on-line with 
> less "mounts"...
> 
> For these machines, centralised user account information and 'home' sharing 
> is in my view essential, as it allows to "blindly" choose any of the
> machines that is available at a time ... and, being a Mac fun, I think Linmux 
> is better suited for that purpose, financially and practically...
> 
> These said, it reminds me that we need to update the OS, buy a few new 
> machines, new LCDs ... argh.
> 
> Sorry of this lecture was outside the scope of the original thread.
> 
> Tassos
> 
> 
> 
> On 23 Jan 2013, at 9:54, James Stroud wrote:
> 
>> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
>>> The real difficulty is integrating Macs into a
>>> Linux-centric environment, for example configuring NFS, NIS, etc.
>> 
>> That's because NFS and NIS are antiquities left over from the days of 
>> mainframes. Distributed file systems and user information databases are 
>> designed for an environment of many workers and few machines, when the 
>> typical graphics workstation cost $50,000. These days, we argue whether to 
>> spend an extra $200 on a $500 computer. We have moved to a new paradigm: 
>> many workers with many more machines, with each machine having 
>> essentiallymainframe levels of storage and computing power. In other words, 
>> instead of NFS, you should run git.
>> 
>> James

Re: [ccp4bb] Mac mini advice

[Anastassis Perrakis]

I am of the opinion that the truth lies somewhere in between ...

Here are my two cents based on personal experience ...

For example, I am happy myself using a MacBook Pro, which is sufficient for all 
my activities, and has all software and data that I need.
Thus, I am myself on the 'new' paradigm side, having a machine with "mainframe 
levels of storage and computing power" (I do not run git,
but time machine in a mac has the bits I need from the git idea - as far as I 
know git that is).

In the department, we have about 20-25 scientists. These people need to 
''maintain" and be proficient in many software suites, many more than
a traditional crystallographer (like me in my PhD time for example) would need:
vector design software for cloning, databases for keeping track of clones, 
sequencing viewing software for their clones, 
 interfaces for crystallisation and biophysical equipment, analysis suites like 
Graphpad/Prism, Origin, Kintek (etc etc)  for biophysical experiments ... 
 and lets not forget SAXS software ... Our experience, is that most of 
these people like to use a Windows workstation for these (the choice is free),
others prefer a Mac, thats not my point here. Many of that software also needs 
to "maintained" by these people...
Also, for a variety of reasons which have to do with IT "support" restrictions, 
the Windows machines
we have for them are miss-configured with ancient versions of the windows 
"operating" system, but still Ok for many things, but not for really 
straightforward use of CCP4/Phenix ...

My point here is, that these people are less likely to be keen of the idea to 
also install and run ccp4/coot/phenix/buster in their machines 
(they use pymol/yassara/chimera though locally since they can copy/paste to 
their presentations and papers then). 
So, we find it useful to keep an old fashioned setup running in parallel. Linux 
boxes, hooked to Zalmans or really
big or double LCDs, in a specific room ... People like these for data 
processing, all data of many years back are online, incremental backup is 
running etc.
For historical reasons we even run NFS/NIS there (I agree its not a great 
choice if one would start now).

My conclusion and advice for labs or departments that have more than 5-6 
people, and are doing crystallography but not as their
"full-time" business is that besides personal PC/Mac, a common room with a few 
relatively powerful machines with nice, big, double,
screens, likely also Stereo, is useful for a few reasons:

1. Easier to make sure everybody is using the same software more or less
2. Same machine to everybody - not the situation that a new student gets a new 
machine at year 0, which is redundant by graduation time at +3 years (...or 
+5,6,7...)
3. Mixing of people in the room and ability for people to "look over the 
shoulder" of others, the point that my colleague Titia Sixma always favours,
which has indeed proved great for teaching others and learning from others.
4. Centralised "real" backup, availability of diffraction data on-line with 
less "mounts"...

For these machines, centralised user account information and 'home' sharing is 
in my view essential, as it allows to "blindly" choose any of the
machines that is available at a time ... and, being a Mac fun, I think Linmux 
is better suited for that purpose, financially and practically...

These said, it reminds me that we need to update the OS, buy a few new 
machines, new LCDs ... argh.

Sorry of this lecture was outside the scope of the original thread.

Tassos



On 23 Jan 2013, at 9:54, James Stroud wrote:

> On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
>> The real difficulty is integrating Macs into a
>> Linux-centric environment, for example configuring NFS, NIS, etc.
> 
> That's because NFS and NIS are antiquities left over from the days of 
> mainframes. Distributed file systems and user information databases are 
> designed for an environment of many workers and few machines, when the 
> typical graphics workstation cost $50,000. These days, we argue whether to 
> spend an extra $200 on a $500 computer. We have moved to a new paradigm: many 
> workers with many more machines, with each machine having 
> essentiallymainframe levels of storage and computing power. In other words, 
> instead of NFS, you should run git.
> 
> James

Re: [ccp4bb] Mac mini advice

[James Stroud]

On Jan 22, 2013, at 11:20 PM, Nat Echols wrote:
> The real difficulty is integrating Macs into a
> Linux-centric environment, for example configuring NFS, NIS, etc.

That's because NFS and NIS are antiquities left over from the days of 
mainframes. Distributed file systems and user information databases are 
designed for an environment of many workers and few machines, when the typical 
graphics workstation cost $50,000. These days, we argue whether to spend an 
extra $200 on a $500 computer. We have moved to a new paradigm: many workers 
with many more machines, with each machine having essentially mainframe levels 
of storage and computing power. In other words, instead of NFS, you should run 
git.

James

Re: [ccp4bb] Mac mini advice

[Antony Oliver]

Dmitry... everyone is of course entitled to their opinion - but as one of the 
brain-washed masses I feel I need to at least reply (!). Sorry Cara...

>>> I am not happy with the direction OS X is going. Too much emphasis on eye 
>>> candy and not enough on underlying technology.

Fair enough, but it does seem to be the way that most of the UIs/OSes are 
going. Erm, Windows 8, Unity...

Also Apple are *constantly* innovating under the hood - albeit mainly hardware 
- Lightning connectors, Fusion hard-drives etc... so they are one of the few 
computer manufacturers actually innovating at all(!)

>>> 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.

I sort of agree with you here - but on the other hand at least it is still a 
Unix variant underneath and we still have Xquartz.  X11/X window is itself 
becoming quite an old beast and I'm pretty sure there's ever going to be an 
X12. Hence the probable rise and prevalence of Qt - so you can run any OS you 
like...

>>> 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.

Or, ( controversially ) a Mac running Linux and Windows in virtual boxes !?

Tony.

Sent from my iPhone

On 23 Jan 2013, at 03:03, "Dmitry Rodionov" 
mailto:d.rodio...@gmail.com>> wrote:

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 
mailto:bryanlep...@gmail.com>> wrote:

On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey 
mailto:pjeff...@princeton.edu>> 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

[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.

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.

[ccp4bb] Advice on Enzyme Kinetics (substrate bound plate format)

[Stephen Connelly]

I am looking for some expert advice on enzyme kinetics but for an assay in 
plate format which has the substrate bound. This is different that the usual 
homogeneous plate assays or heterogeneous assays where the enzyme (catalyst) is 
plate bound. 

In short I am trying to look at the Ki of a compound and wish to use a plate 
assay as the compound absorbs at the same wavelength as the typical 
para-nitroanaline substrate that is usually used.

Is it possible to do normal Michaelis Menten kinetics in a plate format given 
the substrate is bound and not homogeneous despite rigorous shaking? 

We believe the inhibitor is mixed in its mechanism, it binds non covalently but 
does seem to react, albeit poorly with the Cys nucleophile in the protease. We 
have shown this through a few different studies but wish to obtain a Ki and 
generate a graph that will provide evidence of either competitive or mixed 
inhibition.

Hoping to hear form you all!!!

Thanks - Steve - Email:conne...@scripps.edu

Re: [ccp4bb] advice on spectrometric instruments choice

[Scott Thomas Walsh]

Hi Sebastiano,

We have a Chirascan instrument with all the attachments (fluorescence, stopped 
flow, multi-cell attachment, etc).  It is by far the best CD 
instrument that I have used.  I have experience in the past with Aviv, Jasco, 
and Olis instruments.

Cheers,

Scott


Scott T. R. Walsh, Ph.D.
Assistant Professor
University of Maryland
IBBR/CBMG
Rm 3127E CARB-2
9600 Gudelsky Drive
Rockville, MD 20850
email: swals...@umd.edu
phone: (240) 314-6478
fax: (240) 314-6255

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sebastiano 
Pasqualato [sebastiano.pasqual...@gmail.com]
Sent: Friday, July 20, 2012 8:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] advice on spectrometric instruments choice

Dear all,
I'm looking for some advices on the choice of some spectroscopic equipment for 
our lab.

What we would like to have is the possibility of measuring Circular Dichroism 
spectra, and perform kinetic analysis in fluorescence, possibly also with a 
stopped-flow set up, for pre-steady state kinetics.

Would you reckon a single instrument would be capable of fulfilling these 
tasks, or would you rather advice the investment on two instruments?

Could you guys please give me suggestions on piece of instruments that you're 
happy (or unhappy) with?
I've been currently considering the Chirascan from Applied Photophysics, or the 
Jasco J-815, so far. Any comment on those?

Thanks a lot in advance,
best regards,
ciao,
s

--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu<mailto:sebastiano.pasqual...@ieo.eu>

[ccp4bb] advice on spectrometric instruments choice

[Sebastiano Pasqualato]

Dear all,
I'm looking for some advices on the choice of some spectroscopic equipment for 
our lab.

What we would like to have is the possibility of measuring Circular Dichroism 
spectra, and perform kinetic analysis in fluorescence, possibly also with a 
stopped-flow set up, for pre-steady state kinetics.

Would you reckon a single instrument would be capable of fulfilling these 
tasks, or would you rather advice the investment on two instruments?

Could you guys please give me suggestions on piece of instruments that you're 
happy (or unhappy) with?
I've been currently considering the Chirascan from Applied Photophysics, or the 
Jasco J-815, so far. Any comment on those?

Thanks a lot in advance,
best regards,
ciao,
s

-- 
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

Re: [ccp4bb] Low resolution structure determination advice

[Eleanor Dodson]

Are thw Se SAd and native data isomorphous - because if so you can just 
cad the data sets together - generate phases for the Se set, then use 
those as a starting set for the native data to phase extend. Parrot is 
the more up to date version of DM which does this in the GUI.


The AutoSHARP will use SOLOMON I believe to do this.

Eleanor

 On 09/01/2011 08:28 PM, Bosch, Juergen wrote:

How about phase extension using DM, sure you say you only have one mol per asu 
but it might still be worth trying various approaches of solvent 
flattening/flipping.
Don't know what you used to detect your sites and refine them, but it also 
might be worth sticking them into Sharp with your partial model and see if the 
phases improve.
You say you have 450/750 residues what makes you believe that you placed them 
correctly ?
Also do you have space from the crystal lattice packing for the additional 300 
residues ? In other words are you certain that what you have crystalized is the 
full length version of your protein ?
Adding side chains leading to worse Rfactors would suggest that you are most 
likely not in frame.
Since you have a partial backbone you could try finding a "homolog" via EBI SSM 
to serve as a better starting model, aligning your sequence to it and replacing the side 
chains accordingly.

Another suggestion keep changing programs don't stick to Refmac visit Phenix or 
the other way round, and as a last resort you could give GraphENT a try.

Jürgen

On Sep 1, 2011, at 3:00 PM, Pete Meyer wrote:

Hi,
Depending on how many zn sites you have, you may be able to do zn-mad
for your native crystals.  You don't mention if you've tried combining
your various sources of phase information; if not, it's worth looking into.

You may also want to look into various multi-crystal techniques
(averaging, phasing and/or merging) - I've had decent luck with
multi-crystal phasing off zn at low resolutions.

Good luck,
Pete

Basudeb Bhattacharyya wrote:
Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project).
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

..
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://web.mac.com/bosch_lab/

Re: [ccp4bb] Low resolution structure determination advice

[Tanner, John J.]

Did you try density modification starting with the sad phases with phase 
extension to 2.7 A followed by auto-tracing?  The model should be better than 
the one built from the 3.7 A sad map.



Sent from Jack's iPad

On Sep 1, 2011, at 11:24 PM, "Kianoush Sadre-Bazzaz" 
mailto:ksad...@yahoo.com>> wrote:

Hi Basu,

You mentioned molecular replacement was not successful for this project. Which 
model was used for this procedure? Have you tried your partially built 
structure as a model to obtain preliminary phases for your native (2.7A) data 
set? If there is  any luck with that, you might be able to combine phases from 
this procedure with the Selenium SAD phases, as already suggested.

Kianoush

--- On Thu, 9/1/11, Basudeb Bhattacharyya 
mailto:bbhattach...@wisc.edu>> wrote:

From: Basudeb Bhattacharyya 
mailto:bbhattach...@wisc.edu>>
Subject: [ccp4bb] Low resolution structure determination advice
To: <mailto:CCP4BB@JISCMAIL.AC.UK> 
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Date: Thursday, September 1, 2011, 9:31 AM

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project).
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

Re: [ccp4bb] Low resolution structure determination advice

[Kianoush Sadre-Bazzaz]

Hi Basu,
You mentioned molecular replacement was not successful for this project. Which 
model was used for this procedure? Have you tried your partially built 
structure as a model to obtain preliminary phases for your native (2.7A) data 
set? If there is  any luck with that, you might be able to combine phases from 
this procedure with the Selenium SAD phases, as already suggested.
Kianoush
--- On Thu, 9/1/11, Basudeb Bhattacharyya  wrote:

From: Basudeb Bhattacharyya 
Subject: [ccp4bb] Low resolution structure determination advice
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, September 1, 2011, 9:31 AM

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project). 
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

Re: [ccp4bb] Low resolution structure determination advice

[Bosch, Juergen]

How about phase extension using DM, sure you say you only have one mol per asu 
but it might still be worth trying various approaches of solvent 
flattening/flipping.
Don't know what you used to detect your sites and refine them, but it also 
might be worth sticking them into Sharp with your partial model and see if the 
phases improve.
You say you have 450/750 residues what makes you believe that you placed them 
correctly ?
Also do you have space from the crystal lattice packing for the additional 300 
residues ? In other words are you certain that what you have crystalized is the 
full length version of your protein ?
Adding side chains leading to worse Rfactors would suggest that you are most 
likely not in frame.
Since you have a partial backbone you could try finding a "homolog" via EBI SSM 
to serve as a better starting model, aligning your sequence to it and replacing 
the side chains accordingly.

Another suggestion keep changing programs don't stick to Refmac visit Phenix or 
the other way round, and as a last resort you could give GraphENT a try.

Jürgen

On Sep 1, 2011, at 3:00 PM, Pete Meyer wrote:

Hi,
Depending on how many zn sites you have, you may be able to do zn-mad
for your native crystals.  You don't mention if you've tried combining
your various sources of phase information; if not, it's worth looking into.

You may also want to look into various multi-crystal techniques
(averaging, phasing and/or merging) - I've had decent luck with
multi-crystal phasing off zn at low resolutions.

Good luck,
Pete

Basudeb Bhattacharyya wrote:
Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project).
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

..
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://web.mac.com/bosch_lab/

Re: [ccp4bb] Low resolution structure determination advice

[Pete Meyer]

Hi,
Depending on how many zn sites you have, you may be able to do zn-mad 
for your native crystals.  You don't mention if you've tried combining 
your various sources of phase information; if not, it's worth looking into.


You may also want to look into various multi-crystal techniques 
(averaging, phasing and/or merging) - I've had decent luck with 
multi-crystal phasing off zn at low resolutions.


Good luck,
Pete

Basudeb Bhattacharyya wrote:

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best maps--clear density and visible secondary structures--we get are off Se SAD).  We have one monomer per AU (and we have secondary structure coverage over our entire protein based on looking at conserved domains of our protein--unfortunately, MR is not working for this project). 
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 and P31, which haven't worked).  We also have a native set down to 2.7 angstroms.  We are able to place our working model into the native data set, but we are unable to further refine the structure in Refmac (density doesn’t improve and the stats creep up).  Addition of side chains only makes our stats worse.  The data sets are clean (no twinning, etc.).  While we understand that we may need more phasing information (i.e. our initial model may still be quite inaccurate given resolution and size of the protein among other things--we are trying to improve this), we're wondering if anyone might have some other suggestions or insights about how we can move forward given the data that we currently have. Thanks in advance for any advice.


Sincerely,

Basu

[ccp4bb] Low resolution structure determination advice

[Basudeb Bhattacharyya]

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project). 
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

Re: [ccp4bb] Stereo Microscope advice

[Artem Evdokimov]

'White' LED light produced by most integrated white LED packages is in fact
a mixture of blue (~460nm), produced by the LED itself and a
broad-band yellow (560nm), produced by a secondary phosphor, typically
directly coating the semiconductor that emits the primary light. The net
effect is a single-source mixed-wavelength light. The eye does not
immediately notice the dip in the spectrum around the green (notably, the
eye is in fact tuned into green for maximum sensitivity so the spectrum
'appears' smooth to us when in fact it's anything but). These LEDs are
awesome for many applications and they indeed do not generate as much heat
as incandescent lightbulbs do, but several folks I know have noted that
their eyes are more tired after viewing LED-illuminated samples under a
microscope.
http://powerelectronics.com/power_management/led_drivers/Fig-2-white-LED-vs-RGB-LED-spectrum.jpg

Other types of 'white' LED lights employ carefully balanced mixtures of
three primary colors, each produced by a separate quantum well.
Unfortunately these lights tend to shift colors with temperature and with
age and appear different from different angles - feedback compensation is
required for precision use. These tend to be much easier on the eye (at
least to me), but I am not sure whether any scopes come with these composite
LEDs installed.

Artem

On Sun, Jan 23, 2011 at 7:35 PM, Kevin Corbett
wrote:

> Hi everyone,
>
>I'm looking to buy a new stereo microscope for looking at crystal
> trays, and was wondering if anyone could help me answer a few questions:
>
> 1) Does anyone have experience with LED illumination in the microscope
> base? I'm worried that there might be excessive heating of the base, as this
> is a huge problem with integrated halogen lamps. Also, can these stands with
> LED's accommodate polarizers?
>
> 2) Any really good (or really bad) experiences with specific
> manufacturer/models?
>
> Any advice is much appreciated. Thanks very much,
>
> Kevin
>
> Kevin Corbett, Ph.D.
> Stephen C. Harrison Lab
> Harvard University Medical School
> corbett (at) crystal.harvard.edu
> (617)-432-5605
>

Re: [ccp4bb] Stereo Microscope advice

[Adrian Goldman]

Just one comment on LEDs as we have them as part of an imaging system. While it 
is true that the LEDs themselves emit cool light, the associated electronics is 
hotter than I would have expected.  FYI. 

Adrian

Sent from my iPhone

On 24 Jan 2011, at 19:24, "Sampson, Jared"  wrote:

> Hi Kevin - 
> 
> 1) I can only imagine that LEDs would produce vastly less heat than halogen 
> lamps.  In general, they are small, efficient, long-lasting and don't produce 
> a lot of heat.  Here's a start for more information 
> http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got 
> me this page http://www.tedpella.com/mscope_html/2282.htm which has what 
> appears to be all the options you mentioned.  I'm sure other manufacturers 
> have similar models.
> 
> 2) We are generally satisfied with our older model Olympus .  If you will be 
> looking at drops smaller than 1μl total volume (e.g. from a mosquito or other 
> sub-μl liquid handler) I'd recommend at least a 2x objective lens.  Some 
> models (like the one linked above) have an option to direct the light to a 
> camera mount instead of the eyepieces--get one of these if possible!  Trying 
> to hold a camera (or smartphone) steady in front of one of the eyepieces gets 
> old after a while.
> 
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> New York, NY 10016
> 212-263-7898
> 
> 
> On Jan 23, 2011, at 8:35 PM, Kevin Corbett wrote:
> 
>> Hi everyone,
>> 
>>I'm looking to buy a new stereo microscope for looking at crystal trays, 
>> and was wondering if anyone could help me answer a few questions:
>> 
>> 1) Does anyone have experience with LED illumination in the microscope base? 
>> I'm worried that there might be excessive heating of the base, as this is a 
>> huge problem with integrated halogen lamps. Also, can these stands with 
>> LED's accommodate polarizers?
>> 
>> 2) Any really good (or really bad) experiences with specific 
>> manufacturer/models?
>> 
>> Any advice is much appreciated. Thanks very much,
>> 
>> Kevin
>> 
>> Kevin Corbett, Ph.D.
>> Stephen C. Harrison Lab
>> Harvard University Medical School
>> corbett (at) crystal.harvard.edu
>> (617)-432-5605
> 
> 
> 
> This email message, including any attachments, is for the sole use of the 
> intended recipient(s) and may contain information that is proprietary, 
> confidential, and exempt from disclosure under applicable law. Any 
> unauthorized review, use, disclosure, or distribution is prohibited. If you 
> have received this email in error please notify the sender by return email 
> and delete the original message. Please note, the recipient should check this 
> email and any attachments for the presence of viruses. The organization 
> accepts no liability for any damage caused by any virus transmitted by this 
> email.
> =

Re: [ccp4bb] Stereo Microscope advice

[Andrew T. Torelli]

Hi Kevin,

We have 3 Olympus microscopes  with three different lighting options.  
The three variations we have on our microscopes are:
 1. a microscope with a reflective light base (internal mirror) that reflects 
light directed into the microscope base from an external halogen light-box.
 2. a microscope with an integrated, low-power (30 watt) halogen light source 
(still has a mirror for the trans-illumination)
 3. a microscope with an LED light source

In general, the LED light source in our microscope produces very little 
heat so crystal trays should be safe for viewing for quite some time without 
heating.  And, instead of a mirror, the base has a series of filters/diffusers 
to modulate the intensity of the light directed through the sample, or a 
"dark-field" filter.  That can be helpful.  However, the spectrum of light 
output by our LED light source is very blue (as opposed to the warmer 
"yellow-heavy" output from halogen or incandescent light sources).  I don't 
like the "cold", blue tones of the light and find that it contributes to eye 
fatigue.  I also find that this light doesn't offer as high a contrast for 
viewing certain drop conditions.  By that I mean that I occasionally find drop 
conditions for which I feel I can see differences in edge transitions or object 
boundaries better using the microscopes with the halogen light sources (i.e. 
comparing same drop with different microscope/light-source combinations).  This 
doesn't happen often and does not dramatically affect my ability to rate the 
drop, but it's notable to me.  In summary, I prefer alternatives to the LED 
light sources, but my dislike of the output spectrum is a matter of opinion.
NOTE: My understanding is that the "blue-heavy" spectral output of 
white-light LEDs is a recognized property of LEDs (i.e. it's hard to achieve a 
true white light with LEDs).  However, the ability to produce LEDs that have a 
more natural spectra is improving and I know at least Olympus is very close to 
offering such a version (more $$).

With regards to polarizers, we just use "screw-on" polarizing filters 
that attach to a channel/groove near the bottom of our objective lenses.  These 
are convenient and inexpensive (works with any light source).  They won't, 
however, fit on all objective lenses depending on the presence of the necessary 
groove.

-Andy Torelli


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin 
Corbett
Sent: Sunday, January 23, 2011 8:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Stereo Microscope advice

Hi everyone,

I'm looking to buy a new stereo microscope for looking at crystal 
trays, and was wondering if anyone could help me answer a few questions:

1) Does anyone have experience with LED illumination in the microscope base? 
I'm worried that there might be excessive heating of the base, as this is a 
huge problem with integrated halogen lamps. Also, can these stands with LED's 
accommodate polarizers?

2) Any really good (or really bad) experiences with specific 
manufacturer/models?

Any advice is much appreciated. Thanks very much,

Kevin

Kevin Corbett, Ph.D.
Stephen C. Harrison Lab
Harvard University Medical School
corbett (at) crystal.harvard.edu
(617)-432-5605

Re: [ccp4bb] Stereo Microscope advice

[Sampson, Jared]

Hi Kevin - 

1) I can only imagine that LEDs would produce vastly less heat than halogen 
lamps.  In general, they are small, efficient, long-lasting and don't produce a 
lot of heat.  Here's a start for more information 
http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got me 
this page http://www.tedpella.com/mscope_html/2282.htm which has what appears 
to be all the options you mentioned.  I'm sure other manufacturers have similar 
models.

2) We are generally satisfied with our older model Olympus .  If you will be 
looking at drops smaller than 1μl total volume (e.g. from a mosquito or other 
sub-μl liquid handler) I'd recommend at least a 2x objective lens.  Some models 
(like the one linked above) have an option to direct the light to a camera 
mount instead of the eyepieces--get one of these if possible!  Trying to hold a 
camera (or smartphone) steady in front of one of the eyepieces gets old after a 
while.

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
212-263-7898


On Jan 23, 2011, at 8:35 PM, Kevin Corbett wrote:

> Hi everyone,
> 
>   I'm looking to buy a new stereo microscope for looking at crystal 
> trays, and was wondering if anyone could help me answer a few questions:
> 
> 1) Does anyone have experience with LED illumination in the microscope base? 
> I'm worried that there might be excessive heating of the base, as this is a 
> huge problem with integrated halogen lamps. Also, can these stands with LED's 
> accommodate polarizers?
> 
> 2) Any really good (or really bad) experiences with specific 
> manufacturer/models?
> 
> Any advice is much appreciated. Thanks very much,
> 
> Kevin
> 
> Kevin Corbett, Ph.D.
> Stephen C. Harrison Lab
> Harvard University Medical School
> corbett (at) crystal.harvard.edu
> (617)-432-5605



This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain information that is proprietary, 
confidential, and exempt from disclosure under applicable law. Any unauthorized 
review, use, disclosure, or distribution is prohibited. If you have received 
this email in error please notify the sender by return email and delete the 
original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
=

[ccp4bb] Stereo Microscope advice

[Kevin Corbett]

Hi everyone,

I'm looking to buy a new stereo microscope for looking at crystal 
trays, and was wondering if anyone could help me answer a few questions:

1) Does anyone have experience with LED illumination in the microscope base? 
I'm worried that there might be excessive heating of the base, as this is a 
huge problem with integrated halogen lamps. Also, can these stands with LED's 
accommodate polarizers?

2) Any really good (or really bad) experiences with specific 
manufacturer/models?

Any advice is much appreciated. Thanks very much,

Kevin

Kevin Corbett, Ph.D.
Stephen C. Harrison Lab
Harvard University Medical School
corbett (at) crystal.harvard.edu
(617)-432-5605

Re: [ccp4bb] summary: off topic: advice for crystallography workstation/server

[Ronnie Berntsson]

Hi,

First of all, thanks for all the suggestions and comments! I'll sum up a few of 
the replies here.

It seems that most people would favor going for the route of having multiple, 
individual computers (iMacs, mac minis, etc) instead of having one workhorse. 
This mainly due to the fact that anything 3D would be needed to be run locally. 
This is indeed the way we have things setup currently, and it is working fine. 
However, as some of the computers are getting older (and our structures getting 
bigger), especially the number crunching takes a hit. My idea was then 
revolving around buying new laptops/deskops, or continue using the ones we have 
(which do work fine) and buy a singe workhorse (mac pro).
My initial idea was indeed using the Mac Pro as Jürgen described, thus mainly 
as a number crunching workhorse, with all building in Coot etc done locally on 
the existing laptops. This can be done just by using ssh and running the normal 
os x on the machine, and not using vnc (or similar). I believe this might work 
quite well in our lab, but I'll need to give some thought. 

Again, thanks for your suggestions.

Cheers,
Ronnie




On Dec 15, 2010, at 20:07, Bosch, Juergen wrote:

> We have a slightly different approach to this.
> 
> Local machines are laptops if you want to do model building you can do it 
> locally either 2d or connected to a Zalman in 3D.
> 
> I have one Mac mini hooked up to a Zalman as "permanent" 3D station. The dual 
> HexaCore MacPro (16 GB RAM) is connected also to a Zalman but is mostly used 
> remotely via ssh in X11. Since you most likely want to use the MacPro for 
> number crunching the ssh connection is fast enough, also for bringing up the 
> ccp4I interface it still works fine even from home. I have a second 8core 
> MacPro in my office used the same way, although right now I only have a 2D 
> display connected to it, but the cores are accessible for number crunching. 
> We are not using OSX Server, multiple users can have simultaneous ssh 
> sessions. I link to a central .bashrc script so that every user has access to 
> all software as soon as they log in. This requires me when setting up a new 
> user to change the local .bashrc file to instead read the /etc/.bashrc that's 
> all.
> 
> So not sure if you really need OSX Server for your purposes.
> 
> Maybe if you could specify what types of things you want to run on those 
> machines it would be easier to make suggestions.
> 
> I would not built in Coot over the network, that's just frustratingly slow 
> and you don't get the benefit of graphics acceleration.
> 
> Here's an incomplete list of stuff on those MacPros:
> USF stuff e.g Moleman etc.
> Coot, Pymol
> Docking software
> CCP4 package
> Phenix
> XDS
> 
> 
> 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://web.mac.com/bosch_lab/
> 
> On Dec 15, 2010, at 12:51 PM, Francis E Reyes wrote:
> 
>> 
>>> Dear all,
>>> 
>>> We are currently considering buying a computer which can be used by  
>>> multiple people, via our existing network, as a workstation for  
>>> crystallography purposes. My thoughts are currently going towards a  
>>> 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server,  
>>> which in theory should be able to handle multiple (up to 4) users  
>>> simultaneously running crystallography software. The idea would be  
>>> to have the users access this computer using their own laptops  
>>> (starting their own virtual sessions?) connected to the same network.
>>> 
>>> Does this sound like a viable strategy, or should it be setup in a  
>>> different way? In that case how? Would it need advanced setup and  
>>> maintenance, or would it be possible to jsut set up a number of user  
>>> accounts in OS X Server, and let it run? I'm reasonably computer  
>>> savvy, but haven't really done something like this before, so I  
>>> would very much appreciate your advice or personal experiences  
>>> regarding this matter.
>>> 
>>> I know that I could probably get a cheaper computer if I went for a  
>>> pc with linux, but I have more experience with OS X, and would  
>>> therefore want to stay with it.
>>> 
>>> Thank you in advance,
>>> Ronnie Berntsson
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Ronnie B

Re: [ccp4bb] off topic: advice for crystallography workstation/server

[Bosch, Juergen]

We have a slightly different approach to this.

Local machines are laptops if you want to do model building you can do it 
locally either 2d or connected to a Zalman in 3D.

I have one Mac mini hooked up to a Zalman as "permanent" 3D station. The dual 
HexaCore MacPro (16 GB RAM) is connected also to a Zalman but is mostly used 
remotely via ssh in X11. Since you most likely want to use the MacPro for 
number crunching the ssh connection is fast enough, also for bringing up the 
ccp4I interface it still works fine even from home. I have a second 8core 
MacPro in my office used the same way, although right now I only have a 2D 
display connected to it, but the cores are accessible for number crunching. We 
are not using OSX Server, multiple users can have simultaneous ssh sessions. I 
link to a central .bashrc script so that every user has access to all software 
as soon as they log in. This requires me when setting up a new user to change 
the local .bashrc file to instead read the /etc/.bashrc that's all.

So not sure if you really need OSX Server for your purposes.

Maybe if you could specify what types of things you want to run on those 
machines it would be easier to make suggestions.

I would not built in Coot over the network, that's just frustratingly slow and 
you don't get the benefit of graphics acceleration.

Here's an incomplete list of stuff on those MacPros:
USF stuff e.g Moleman etc.
Coot, Pymol
Docking software
CCP4 package
Phenix
XDS


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://web.mac.com/bosch_lab/<http://web.me.com/bosch_lab/>

On Dec 15, 2010, at 12:51 PM, Francis E Reyes wrote:


Dear all,

We are currently considering buying a computer which can be used by
multiple people, via our existing network, as a workstation for
crystallography purposes. My thoughts are currently going towards a
8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server,
which in theory should be able to handle multiple (up to 4) users
simultaneously running crystallography software. The idea would be
to have the users access this computer using their own laptops
(starting their own virtual sessions?) connected to the same network.

Does this sound like a viable strategy, or should it be setup in a
different way? In that case how? Would it need advanced setup and
maintenance, or would it be possible to jsut set up a number of user
accounts in OS X Server, and let it run? I'm reasonably computer
savvy, but haven't really done something like this before, so I
would very much appreciate your advice or personal experiences
regarding this matter.

I know that I could probably get a cheaper computer if I went for a
pc with linux, but I have more experience with OS X, and would
therefore want to stay with it.

Thank you in advance,
Ronnie Berntsson




--
Ronnie Berntsson, PhD
PostDoctoral Fellow
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
& Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands

-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu<http://pgp.mit.edu> --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] off topic: advice for crystallography workstation/server

[Francis E Reyes]

Ronnie

Just a few comments..

There are no 'true' virtual sessions for OS X Server. (Well there is,  
but it's developed by a separate company and they charge per seat ==  
expensive). What I define as a 'virtual session' is that you get a  
login window and your own desktop all running over VNC. (and you can  
do this for multiple users). The Apple Remote Desktop software only  
shares one screen/one user.


Just as the other commenter said, multiple users on a crystallographic  
workstation is moot if you need 3d or even graphics intensive  
visualization (as each computer would benefit from having coot/pymol  
run locally).


The number of programs taking advantage of multiple processors is  
growing, but far from mainstream (support, software usability,  
benefits etc). Much of crystallography remains to be a 'serial' rather  
than a 'parallel' experience.


That being said, each your money may be better spent giving each user  
a Mac Mini (the price for 3-4 Minis == 1 Lowest end Mac Pro) .. and if  
you truly want multiple user management get a Mini Server that does  
manages user accounts/policies with  local home directories. You could  
even keep the software on the main server and map it to the clients so  
you have version control over the xtal packages.



F




On Dec 15, 2010, at 9:26 AM, Ronnie Berntsson wrote:


Dear all,

We are currently considering buying a computer which can be used by  
multiple people, via our existing network, as a workstation for  
crystallography purposes. My thoughts are currently going towards a  
8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server,  
which in theory should be able to handle multiple (up to 4) users  
simultaneously running crystallography software. The idea would be  
to have the users access this computer using their own laptops  
(starting their own virtual sessions?) connected to the same network.


Does this sound like a viable strategy, or should it be setup in a  
different way? In that case how? Would it need advanced setup and  
maintenance, or would it be possible to jsut set up a number of user  
accounts in OS X Server, and let it run? I'm reasonably computer  
savvy, but haven't really done something like this before, so I  
would very much appreciate your advice or personal experiences  
regarding this matter.


I know that I could probably get a cheaper computer if I went for a  
pc with linux, but I have more experience with OS X, and would  
therefore want to stay with it.


Thank you in advance,
Ronnie Berntsson




--
Ronnie Berntsson, PhD
PostDoctoral Fellow
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
& Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands


-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] off topic: advice for crystallography workstation/server

[Ronnie Berntsson]

Dear all,

We are currently considering buying a computer which can be used by multiple 
people, via our existing network, as a workstation for crystallography 
purposes. My thoughts are currently going towards a 8-core Apple Pro (or 
12-core) with a lot of RAM, with OS X Server, which in theory should be able to 
handle multiple (up to 4) users simultaneously running crystallography 
software. The idea would be to have the users access this computer using their 
own laptops (starting their own virtual sessions?) connected to the same 
network.

Does this sound like a viable strategy, or should it be setup in a different 
way? In that case how? Would it need advanced setup and maintenance, or would 
it be possible to jsut set up a number of user accounts in OS X Server, and let 
it run? I'm reasonably computer savvy, but haven't really done something like 
this before, so I would very much appreciate your advice or personal 
experiences regarding this matter. 

I know that I could probably get a cheaper computer if I went for a pc with 
linux, but I have more experience with OS X, and would therefore want to stay 
with it. 

Thank you in advance,
Ronnie Berntsson




--
Ronnie Berntsson, PhD
PostDoctoral Fellow
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
& Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands

Re: [ccp4bb] off topic: advice for crystallography workstation/server

[Roger Rowlett]

  
  
Ronnie,
  
  The main rub is that any of the graphical software will have to be
  run on the local CPU to take advantage of accelerated video
  graphics. The approach I've taken is to have a central
server (which is actually my office workstation) that serves up a
home and software directories to satellite workstations that then
run software on their own CPUs. Users get a portable desktop this
way. The data traffic to my server is actually quite low. I'm
running Linux, though. My central server (which is really nothing
special in terms of hardware) has extra disk storage and a quad-core
CPU, and handles the nightly backups. The clients all have dual core
CPUs and their own accelerated graphics cards.

Cheers.

On 12/15/2010 11:26 AM, Ronnie Berntsson wrote:

  Dear all,

We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network.

Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. 

I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. 

Thank you in advance,
Ronnie Berntsson




--
Ronnie Berntsson, PhD
PostDoctoral Fellow
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
& Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands


-- 
  

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
  

  

Re: [ccp4bb] Practical MR advice

[Roger Rowlett]

  
  
Ding ding ding ding...we have a winner:

  A search model with 30% identity was submitted to the Phyre
server which returned a target sequence-corrected model
  The Phyre monomer was "dimerized" in Pymol using symmetry
operators from a previous MR solution using a dimer of the
original homolog protein
  The Phyre dimer was used in Phaser to find a new MR solution
using the dimer (4 dimers placed, as expected, packs well in
unit cell.)
  
  This solution was Chainsawed to poly-Ala and then subjected to
refinement with 8-fold NCS symmetry averaging in Refmac to
generate phases. R=0.466, Rfree=0.460, FOM=0.219
  This model was fed to Parrot for 5 rounds of density
modification with 8-fold NCS symmetry averaging, improving FOM
to 0.770
  Parrot phases were fed into Buccaneer for 5 rounds of
autobuilding using the full target gene sequence and strict
sequence probability matching. The final Buccaneer model had
R=0.313, Rfree=0.345, and FOM=0.848, and the maps are readily
interpretable.

Omitting the Chainsaw step resulted in a much less satisfactory
solution, although perhaps usable, with R=0.41 and FOM=0.75, but the
map was not as interpretable, and had many problem areas and
possible mis-registrations.

My second choice of approach was going to be DM with phase extension
(Keller et al., 2006, Acta Cryst., D62, 1564-1570) which was
suggested by David Lawson. The MR challenge described in that paper
is eerily similar to mine. I may yet try this for kicks to see how
well it works ( may need this trick someday) but was too lazy to
feed all the NCS matrices into DM. Parrot will extract NCS operators
directly from the MR model, which is nice. :)

Thanks for all the very helpful advice!

On 9/2/2010 7:10 AM, Dima Klenchin wrote:

  
  1. Chainsaw the currrent solution, and
attempt to identify and build in the correct register of the
side chains. after refinement.

2. Do a low resolution refinement of the poly-Ala/Gly model to
better thread the main chain?

3. Try EPMR with the Phyre model or the poly-Ala/Gly model

4. Give up and get real phases (but I'm so close now!?)

  
  
  Roger,
  
  
  Here is what I'd do if I were you:
  
  
  1. Try both with and without Chainsaw.
  
  2. Refine current solution with tight NCS averaging.
  
  3. Feed the resulting phases into Parrot.
  
  4. Feed the output to Buccaneer.
  
  
  Since Phaser built "correct" tetramer, I'd be very surprised if
  the above procedure won't resolve registration issue.
  
  
  Good luck,
  
  
  Dima
  
  

-- 
  

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
  

  

Re: [ccp4bb] Practical MR advice

[David Briggs]

Hi Roger,

I think your ideas are sound, but I would add some "prime-and-switch"
density modification in resolve plus/minus ncs to try and improve the maps
and cut down on phase bias.

Hth,

Dave

--
Hand delivered by Androids

On 1 Sep 2010 16:12, "Roger Rowlett"  wrote:

 I am trying to find a MR solution for a large unit cell (R3:H, 158x158x196)
with a relatively poor, but I think workable search model (30% identity, 50%
similarity). The data set is decent to 2.4 A. I might be able to get better
if necessary. I submitted the  sequence of the target to the Phyre server,
and it returned a PDB file derived from what I had already identified as the
most likely successful search model. Phaser finds a reasonable solution with
four dimers (Z=9-15 depending on the data set) for which the unit cell
packing looks good. Phaser even assembles what looks like "correct"
biological tetramers in the ASU and across the symmetry interfaces. The main
chain appears to be mostly traceable, but the side chains are not all
well-resolved, and I suspect from the better-defined regions, that the chain
is misregistered by a residue or two throughout most of the structure.

Assuming that an MR solution is possible, what is a good approach from here?
FWIW, Phaser does not correctly place a poly-Ala/Gly model, although it may
place three chains similarly to the MR solution I have with the Phyre model.
My first thought is to:

1. Chainsaw the currrent solution, and attempt to identify and build in the
correct register of the side chains. after refinement.
2. Do a low resolution refinement of the poly-Ala/Gly model to better thread
the main chain?
3. Try EPMR with the Phyre model or the poly-Ala/Gly model
4. Give up and get real phases (but I'm so close now!?)

Thanks in advance.

-- 
 --
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu

Re: [ccp4bb] Practical MR advice

[Dirk Kostrewa]

 Hi Roger,

personally, I would take the four dimers from Phaser, strip off all side 
chains (make a poly-ala/gly), do a ML refinement with tight NCS 
restraints. The resulting map could then be on-the-fly 
real-space-averaged with Coot. At your resolution, I would expect to see 
the real register of at least some side chains either in the 2mfodfc-map 
or in one of the real-space-averaged 2mfodfc-maps.


Good luck,

Dirk.

Am 01.09.10 17:12, schrieb Roger Rowlett:
I am trying to find a MR solution for a large unit cell (R3:H, 
158x158x196) with a relatively poor, but I think workable search model 
(30% identity, 50% similarity). The data set is decent to 2.4 A. I 
might be able to get better if necessary. I submitted the  sequence of 
the target to the Phyre server, and it returned a PDB file derived 
from what I had already identified as the most likely successful 
search model. Phaser finds a reasonable solution with four dimers 
(Z=9-15 depending on the data set) for which the unit cell packing 
looks good. Phaser even assembles what looks like "correct" biological 
tetramers in the ASU and across the symmetry interfaces. The main 
chain appears to be mostly traceable, but the side chains are not all 
well-resolved, and I suspect from the better-defined regions, that the 
chain is misregistered by a residue or two throughout most of the 
structure.


Assuming that an MR solution is possible, what is a good approach from 
here? FWIW, Phaser does not correctly place a poly-Ala/Gly model, 
although it may place three chains similarly to the MR solution I have 
with the Phyre model. My first thought is to:


1. Chainsaw the currrent solution, and attempt to identify and build 
in the correct register of the side chains. after refinement.
2. Do a low resolution refinement of the poly-Ala/Gly model to better 
thread the main chain?

3. Try EPMR with the Phyre model or the poly-Ala/Gly model
4. Give up and get real phases (but I'm so close now!?)

Thanks in advance.

--
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu 


--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] Practical MR advice

[Roger Rowlett]

I am trying to find a MR solution for a large unit
cell (R3:H, 158x158x196) with a relatively poor, but I think workable
search model (30% identity, 50% similarity). The data set is decent to
2.4 A. I might be able to get better if necessary. I submitted the 
sequence of the target to the Phyre server, and it returned a PDB file
derived from what I had already identified as the most likely
successful search model. Phaser finds a reasonable solution with four
dimers (Z=9-15 depending on the data set) for which the unit cell
packing looks good. Phaser even assembles what looks like "correct"
biological tetramers in the ASU and across the symmetry interfaces. The
main chain appears to be mostly traceable, but the side chains are not
all well-resolved, and I suspect from the better-defined regions, that
the chain is misregistered by a residue or two throughout most of the
structure.

Assuming that an MR solution is possible, what is a good approach from
here? FWIW, Phaser does not correctly place a poly-Ala/Gly model,
although it may place three chains similarly to the MR solution I have
with the Phyre model. My first thought is to:

1. Chainsaw the currrent solution, and attempt to identify and build in
the correct register of the side chains. after refinement.
2. Do a low resolution refinement of the poly-Ala/Gly model to better
thread the main chain?
3. Try EPMR with the Phyre model or the poly-Ala/Gly model
4. Give up and get real phases (but I'm so close now!?)

Thanks in advance.

-- 

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu

Re: [ccp4bb] advice for processing data from multiple small wedges

[Kay Diederichs]

Hi Tony,

in my experience it is not uncommon for crystals that diffract to
resolution worse than 3 A to be anisomorphous - after all, there is a
reason for diffracting badly, and that must be the lattice defects.

Lattice defects e.g. often lead to differences in cell parameters, and
in that case the merging R-factors are bad, because the molecular
transform is sampled at different positions in reciprocal space.

So this may be a problem inherent to the current state of your project,
and not strictly curable in software.

Concerning XDS, my advice for such projects can be found in the XDS wiki
in the "Small molecules" article. In essence,
a) give XDS _less_ parameters to fit and adjust (people tend to let the
programs fit everything, but the results are better if as few free
parameters as possible are used)
b) iterate a few times (recycling GXPARM.XDS and the _E.S.D.
parameters), each time monitoring ISa [(I/sigma)^asymptotic]
c) for scaling in XSCALE, use the result of the iteration with highest ISa
d) maybe discard the most disagreeing wedges.

HTH,

Kay

Tony Wu schrieb:
>   I am having problems processing data from multiple wedges of 5-20
> degrees each. I am working with data from microcrystals collected at a
> minibeam. I want to use the data for molecular replacement. I can
> usually only collect about 10-15 frames before the crystal is obviously
> radiation damaged. I need to scale and merge the data from multiple
> crystals. I typically get poor diffraction, maybe to 4A. I have been
> able to process the data with xds/xscale, but the final statistics are
> worse than I would expect. For example, I can see fairly strong spots
> out to 4A, but xds might say the data only goes to 5A. This might be
> accurate, but I would like to also try the data with mosflm and scala. I
> can usually get mosflm to autoindex if I give it 3+ frames, but the
> results are not as robust as with xds. Usually the residual is poor, >
> 0.3 mm. When I try scala (tried multiple options) with just one wedge,
> it fails with "too few reflections", "no observations", or "negative
> scales".
> 
>  xds says the crystals are fairly isomorphous, < 1%. Symmetry is
> low, space group C2.
> 
>  Does anyone have some advice for processing this kind of data
> successfully?


-- 
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".



smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] advice for processing data from multiple small wedges

[Tony Wu]

  I am having problems processing data from multiple wedges of 5-20
degrees each. I am working with data from microcrystals collected at a
minibeam. I want to use the data for molecular replacement. I can usually
only collect about 10-15 frames before the crystal is obviously radiation
damaged. I need to scale and merge the data from multiple crystals. I
typically get poor diffraction, maybe to 4A. I have been able to process the
data with xds/xscale, but the final statistics are worse than I would
expect. For example, I can see fairly strong spots out to 4A, but xds might
say the data only goes to 5A. This might be accurate, but I would like to
also try the data with mosflm and scala. I can usually get mosflm to
autoindex if I give it 3+ frames, but the results are not as robust as with
xds. Usually the residual is poor, > 0.3 mm. When I try scala (tried
multiple options) with just one wedge, it fails with "too few reflections",
"no observations", or "negative scales".

 xds says the crystals are fairly isomorphous, < 1%. Symmetry is low,
space group C2.

 Does anyone have some advice for processing this kind of data
successfully?