Re: [ccp4bb] Python3 and MTZ

[graeme.win...@diamond.ac.uk]

Dear Kay,

Yes, it’s writing code to be compatible with Python2 and Python3 - in real life 
they are largely idiomatically similar, with well documented differences e.g.

http://python-future.org/compatible_idioms.html

Most of this will not affect you unless you are doing a pretty major project...

Re: cctbx -> python3 - there is a roadmap at

https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap

Unlike e.g. FORTRAN where you can still compile 40 year old code, the choice 
was made in Python to fix some things which were not “right” and make Python3 a 
different dialect - since Python3 is now a decade old and only really now 
gaining traction a lot of people have found this challenging. That said, cctbx 
is > 15 years old now so has seen some changes too..

In terms of learning Python, obviously Python3 _syntax_ is the way forward - my 
daughter learns this at school! - but using Python2 _compatible_ code as per 
the idioms above will make life easier in the short term, and will allow use of 
cctbx… adding

from __future__ import division, print_function

to the very top of your source files will help this

Best wishes Graeme

On 6 Jun 2018, at 21:36, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Dear Graeme,

that sounded to me at first like xia2 and DIALS could be written in Python3 and 
still use cctbx. But thinking about it, this cannot be true; once you run your 
code, you have to run either the Python2 or the Python3 interpreter. And if you 
try to use Python3, it will not correctly run cctbx.

I think what you do in xia2 and DIALS is write code that now runs under 
Python2, but will/would still work if run under Python3 - but this requires 
converting cctbx to Python3 (which, as I saw on some webpage, is a goal for 
2018 IIUC).

Right? Pls ignore my ignorance; I'm a beginner in this area ...

best,

Kay

On Wed, 6 Jun 2018 20:22:10 +, 
graeme.win...@diamond.ac.uk 
mailto:graeme.win...@diamond.ac.uk>> wrote:

Dear Kay,


While I am obviously biased, I have to say that using cctbx (even if it is 
"old" Python) has a lot to be said for it - there are a lot of tools in there 
which are useful once you have read the reflection data & want to do 
crystallography.


Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have moved 
to writing Python which is compatible with 2.7.x and 3.x language standards - 
by and large it is not a hardship and means you can write code today which will 
continue to be useful. There is a wider push to migrate cctbx to 2.7.x and 3.x 
compatibility however it is a large code base and it's a fair amount of work. 
There's more to it than just adding brackets after print though :-)


Best wishes Graeme


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>>
Sent: 06 June 2018 19:47:07
To: ccp4bb
Subject: Re: [ccp4bb] Python3 and MTZ

Dear Nicolas,

my (our) motivation is purely that when learning Python today, and developing 
something from scratch, Python3 appears like the better choice (compared to 
version 2) - provided that basic crystallographic libraries can be used.

Just a note (for those whose operating system provides only one of the two 
Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
installed in parallel (using "Software Collections"). The user makes a choice 
by setting the PATH variable.

best,

Kay

On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS 
mailto:nicolas.f...@esrf.fr>> wrote:

Dear Kay,

depending of the motivation to develop in python3 (could be due to an OS
using python3 by default or you really prefer to work with python3). If
it's due to the OS, a possible strategy is to use virtualenv
(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
if python3 is the default version for the OS. It exist probably other
method to have a contain installation of python2 with all the library needs.

I used this strategy (virtualenv) to install ccp4 (with the installer
which needed python2) on a manjaro linux (Arch based) running python3
and that works very well.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 06/06/2018 14:25, Kay Diederichs wrote:
Dear all,

I haven't tried to read MTZ files from Python until now, but for a new
project in my lab I'd like to do that - and with Python3.

Googling around, it seems that iotbx from cctbx is not (yet)
Python3-compatible.

So, what are my options?

thanks,

Kay



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



To 

Re: [ccp4bb] Python3 and MTZ

[Kay Diederichs]

Hi Ethan,

the problem is that most tutorials or courses are Python3 nowadays. I installed 
the App "Sololearn" 
(https://play.google.com/store/apps/details?id=com.sololearn; thanks Isabel!) 
and am fascinated; this is really fun! But it is Python3. 

https://jakevdp.github.io/blog/2013/01/03/will-scientists-ever-move-to-python-3/
 states in the 2016 header: "Short version: just use Python 3. There's almost 
no reason not to any more." So the problem boils down to the word "almost".

best,

Kay


On Wed, 6 Jun 2018 12:28:20 -0700, Ethan Merritt  
wrote:

>On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote:
>> Right you are Kay. It would be very weird to start developing things on 
>> Python 2.7 right now. Its days are numbered: https://pythonclock.org/
>
>I would take a contrarian view.
>Given the instability of python development, the promise to leave version 2.7
>alone makes it more desirable than the current ever-changing version.
>You can be reasonably sure that anything you write for 2.7 will continue
>to work, since they won't change the 2.7 infrastructure underneath you.
>
>But in truth I would recommend staying away from python for new projects
>altogether, precisely because it is continually unstable.  The python
>development philosophy places low priority on backwards-compatibility.
>Combined with the explicit philosophy that python should only support one
>way of accomplishing any given task, that is a recipe for frequent and
>continual breakage.
>
>Here's an essay from a few years back that I think is still apposite.
>https://jakevdp.github.io/blog/2013/01/03/will-scientists-ever-move-to-python-3/
>
>
>   Ethan
>
>
>>
>>
>> Cheers,
>>
>> Robbie
>>
>>
>>
>> Sent from my Windows 10 phone
>>
>>
>>
>> 
>> From: CCP4 bulletin board  on behalf of Kay 
>> Diederichs 
>> Sent: Wednesday, June 6, 2018 8:47:07 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Python3 and MTZ
>>
>> Dear Nicolas,
>>
>> my (our) motivation is purely that when learning Python today, and 
>> developing something from scratch, Python3 appears like the better choice 
>> (compared to version 2) - provided that basic crystallographic libraries can 
>> be used.
>>
>> Just a note (for those whose operating system provides only one of the two 
>> Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
>> installed in parallel (using "Software Collections"). The user makes a 
>> choice by setting the PATH variable.
>>
>> best,
>>
>> Kay
>>
>> On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:
>>
>> >Dear Kay,
>> >
>> >depending of the motivation to develop in python3 (could be due to an OS
>> >using python3 by default or you really prefer to work with python3). If
>> >it's due to the OS, a possible strategy is to use virtualenv
>> >(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>> >if python3 is the default version for the OS. It exist probably other
>> >method to have a contain installation of python2 with all the library needs.
>> >
>> >I used this strategy (virtualenv) to install ccp4 (with the installer
>> >which needed python2) on a manjaro linux (Arch based) running python3
>> >and that works very well.
>> >
>> >Nicolas
>> >
>> >Nicolas Foos
>> >PhD
>> >Structural Biology Group
>> >European Synchrotron Radiation Facility (E.S.R.F)
>> >71, avenue des Martyrs
>> >CS 40220
>> >38043 GRENOBLE Cedex 9
>> >+33 (0)6 76 88 14 87
>> >+33 (0)4 76 88 45 19
>> >
>> >On 06/06/2018 14:25, Kay Diederichs wrote:
>> >> Dear all,
>> >>
>> >> I haven't tried to read MTZ files from Python until now, but for a new
>> >> project in my lab I'd like to do that - and with Python3.
>> >>
>> >> Googling around, it seems that iotbx from cctbx is not (yet)
>> >> Python3-compatible.
>> >>
>> >> So, what are my options?
>> >>
>> >> thanks,
>> >>
>> >> Kay
>> >
>> >
>> >
>> >To unsubscribe from the CCP4BB list, click the following link:
>> >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>--
>Ethan A Merritt, Dept of Biochemistry
>Biomolecular Structure Center,  K-428 Health Sciences Bldg
>MS 357742,   University of Washington, Seattle 98195-7742
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the 

Re: [ccp4bb] Python3 and MTZ

[Kay Diederichs]

Dear Graeme,

that sounded to me at first like xia2 and DIALS could be written in Python3 and 
still use cctbx. But thinking about it, this cannot be true; once you run your 
code, you have to run either the Python2 or the Python3 interpreter. And if you 
try to use Python3, it will not correctly run cctbx. 

I think what you do in xia2 and DIALS is write code that now runs under 
Python2, but will/would still work if run under Python3 - but this requires 
converting cctbx to Python3 (which, as I saw on some webpage, is a goal for 
2018 IIUC).

Right? Pls ignore my ignorance; I'm a beginner in this area ...

best,

Kay

On Wed, 6 Jun 2018 20:22:10 +, graeme.win...@diamond.ac.uk 
 wrote:

>Dear Kay,
>
>
>While I am obviously biased, I have to say that using cctbx (even if it is 
>"old" Python) has a lot to be said for it - there are a lot of tools in there 
>which are useful once you have read the reflection data & want to do 
>crystallography.
>
>
>Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have 
>moved to writing Python which is compatible with 2.7.x and 3.x language 
>standards - by and large it is not a hardship and means you can write code 
>today which will continue to be useful. There is a wider push to migrate cctbx 
>to 2.7.x and 3.x compatibility however it is a large code base and it's a fair 
>amount of work. There's more to it than just adding brackets after print 
>though :-)
>
>
>Best wishes Graeme
>
>
>From: CCP4 bulletin board  on behalf of Kay Diederichs 
>
>Sent: 06 June 2018 19:47:07
>To: ccp4bb
>Subject: Re: [ccp4bb] Python3 and MTZ
>
>Dear Nicolas,
>
>my (our) motivation is purely that when learning Python today, and developing 
>something from scratch, Python3 appears like the better choice (compared to 
>version 2) - provided that basic crystallographic libraries can be used.
>
>Just a note (for those whose operating system provides only one of the two 
>Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
>installed in parallel (using "Software Collections"). The user makes a choice 
>by setting the PATH variable.
>
>best,
>
>Kay
>
>On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:
>
>>Dear Kay,
>>
>>depending of the motivation to develop in python3 (could be due to an OS
>>using python3 by default or you really prefer to work with python3). If
>>it's due to the OS, a possible strategy is to use virtualenv
>>(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>>if python3 is the default version for the OS. It exist probably other
>>method to have a contain installation of python2 with all the library needs.
>>
>>I used this strategy (virtualenv) to install ccp4 (with the installer
>>which needed python2) on a manjaro linux (Arch based) running python3
>>and that works very well.
>>
>>Nicolas
>>
>>Nicolas Foos
>>PhD
>>Structural Biology Group
>>European Synchrotron Radiation Facility (E.S.R.F)
>>71, avenue des Martyrs
>>CS 40220
>>38043 GRENOBLE Cedex 9
>>+33 (0)6 76 88 14 87
>>+33 (0)4 76 88 45 19
>>
>>On 06/06/2018 14:25, Kay Diederichs wrote:
>>> Dear all,
>>>
>>> I haven't tried to read MTZ files from Python until now, but for a new
>>> project in my lab I'd like to do that - and with Python3.
>>>
>>> Googling around, it seems that iotbx from cctbx is not (yet)
>>> Python3-compatible.
>>>
>>> So, what are my options?
>>>
>>> thanks,
>>>
>>> Kay
>>
>>
>>
>>To unsubscribe from the CCP4BB list, click the following link:
>>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>-- 
>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
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Python3 and MTZ

[Paul Adams]

Dear Kay,

  I’m even more biased that Graeme of course, but I agree completely with what 
he says. You can write code that is compatible with both 2.7 and 3 and easily 
make use of the libraries available. Cctbx, and Phenix, are moving to python 3 
compatibility in the not so distant future.

  Cheers,
Paul 

> On Jun 6, 2018, at 4:22 PM, graeme.win...@diamond.ac.uk 
>  wrote:
> 
> Dear Kay,
> 
> 
> While I am obviously biased, I have to say that using cctbx (even if it is 
> "old" Python) has a lot to be said for it - there are a lot of tools in there 
> which are useful once you have read the reflection data & want to do 
> crystallography.
> 
> 
> Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have 
> moved to writing Python which is compatible with 2.7.x and 3.x language 
> standards - by and large it is not a hardship and means you can write code 
> today which will continue to be useful. There is a wider push to migrate 
> cctbx to 2.7.x and 3.x compatibility however it is a large code base and it's 
> a fair amount of work. There's more to it than just adding brackets after 
> print though :-)
> 
> 
> Best wishes Graeme
> 
> 
> From: CCP4 bulletin board  on behalf of Kay Diederichs 
> 
> Sent: 06 June 2018 19:47:07
> To: ccp4bb
> Subject: Re: [ccp4bb] Python3 and MTZ
> 
> Dear Nicolas,
> 
> my (our) motivation is purely that when learning Python today, and developing 
> something from scratch, Python3 appears like the better choice (compared to 
> version 2) - provided that basic crystallographic libraries can be used.
> 
> Just a note (for those whose operating system provides only one of the two 
> Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
> installed in parallel (using "Software Collections"). The user makes a choice 
> by setting the PATH variable.
> 
> best,
> 
> Kay
> 
> On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:
> 
>> Dear Kay,
>> 
>> depending of the motivation to develop in python3 (could be due to an OS
>> using python3 by default or you really prefer to work with python3). If
>> it's due to the OS, a possible strategy is to use virtualenv
>> (https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>> if python3 is the default version for the OS. It exist probably other
>> method to have a contain installation of python2 with all the library needs.
>> 
>> I used this strategy (virtualenv) to install ccp4 (with the installer
>> which needed python2) on a manjaro linux (Arch based) running python3
>> and that works very well.
>> 
>> Nicolas
>> 
>> Nicolas Foos
>> PhD
>> Structural Biology Group
>> European Synchrotron Radiation Facility (E.S.R.F)
>> 71, avenue des Martyrs
>> CS 40220
>> 38043 GRENOBLE Cedex 9
>> +33 (0)6 76 88 14 87
>> +33 (0)4 76 88 45 19
>> 
>> On 06/06/2018 14:25, Kay Diederichs wrote:
>>> Dear all,
>>> 
>>> I haven't tried to read MTZ files from Python until now, but for a new
>>> project in my lab I'd like to do that - and with Python3.
>>> 
>>> Googling around, it seems that iotbx from cctbx is not (yet)
>>> Python3-compatible.
>>> 
>>> So, what are my options?
>>> 
>>> thanks,
>>> 
>>> Kay
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> -- 
> 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
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence 
Berkeley Lab
Division Deputy for Biosciences, 

Re: [ccp4bb] Python3 and MTZ

[graeme.win...@diamond.ac.uk]

Dear Kay,


While I am obviously biased, I have to say that using cctbx (even if it is 
"old" Python) has a lot to be said for it - there are a lot of tools in there 
which are useful once you have read the reflection data & want to do 
crystallography.


Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have moved 
to writing Python which is compatible with 2.7.x and 3.x language standards - 
by and large it is not a hardship and means you can write code today which will 
continue to be useful. There is a wider push to migrate cctbx to 2.7.x and 3.x 
compatibility however it is a large code base and it's a fair amount of work. 
There's more to it than just adding brackets after print though :-)


Best wishes Graeme


From: CCP4 bulletin board  on behalf of Kay Diederichs 

Sent: 06 June 2018 19:47:07
To: ccp4bb
Subject: Re: [ccp4bb] Python3 and MTZ

Dear Nicolas,

my (our) motivation is purely that when learning Python today, and developing 
something from scratch, Python3 appears like the better choice (compared to 
version 2) - provided that basic crystallographic libraries can be used.

Just a note (for those whose operating system provides only one of the two 
Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
installed in parallel (using "Software Collections"). The user makes a choice 
by setting the PATH variable.

best,

Kay

On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:

>Dear Kay,
>
>depending of the motivation to develop in python3 (could be due to an OS
>using python3 by default or you really prefer to work with python3). If
>it's due to the OS, a possible strategy is to use virtualenv
>(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>if python3 is the default version for the OS. It exist probably other
>method to have a contain installation of python2 with all the library needs.
>
>I used this strategy (virtualenv) to install ccp4 (with the installer
>which needed python2) on a manjaro linux (Arch based) running python3
>and that works very well.
>
>Nicolas
>
>Nicolas Foos
>PhD
>Structural Biology Group
>European Synchrotron Radiation Facility (E.S.R.F)
>71, avenue des Martyrs
>CS 40220
>38043 GRENOBLE Cedex 9
>+33 (0)6 76 88 14 87
>+33 (0)4 76 88 45 19
>
>On 06/06/2018 14:25, Kay Diederichs wrote:
>> Dear all,
>>
>> I haven't tried to read MTZ files from Python until now, but for a new
>> project in my lab I'd like to do that - and with Python3.
>>
>> Googling around, it seems that iotbx from cctbx is not (yet)
>> Python3-compatible.
>>
>> So, what are my options?
>>
>> thanks,
>>
>> Kay
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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

-- 
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




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Python3 and MTZ

[Ethan Merritt]

On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote:
> Right you are Kay. It would be very weird to start developing things on 
> Python 2.7 right now. Its days are numbered: https://pythonclock.org/

I would take a contrarian view.
Given the instability of python development, the promise to leave version 2.7
alone makes it more desirable than the current ever-changing version.
You can be reasonably sure that anything you write for 2.7 will continue
to work, since they won't change the 2.7 infrastructure underneath you.

But in truth I would recommend staying away from python for new projects
altogether, precisely because it is continually unstable.  The python
development philosophy places low priority on backwards-compatibility.
Combined with the explicit philosophy that python should only support one
way of accomplishing any given task, that is a recipe for frequent and
continual breakage.  

Here's an essay from a few years back that I think is still apposite.
https://jakevdp.github.io/blog/2013/01/03/will-scientists-ever-move-to-python-3/


Ethan


> 
> 
> Cheers,
> 
> Robbie
> 
> 
> 
> Sent from my Windows 10 phone
> 
> 
> 
> 
> From: CCP4 bulletin board  on behalf of Kay Diederichs 
> 
> Sent: Wednesday, June 6, 2018 8:47:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Python3 and MTZ
> 
> Dear Nicolas,
> 
> my (our) motivation is purely that when learning Python today, and developing 
> something from scratch, Python3 appears like the better choice (compared to 
> version 2) - provided that basic crystallographic libraries can be used.
> 
> Just a note (for those whose operating system provides only one of the two 
> Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
> installed in parallel (using "Software Collections"). The user makes a choice 
> by setting the PATH variable.
> 
> best,
> 
> Kay
> 
> On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:
> 
> >Dear Kay,
> >
> >depending of the motivation to develop in python3 (could be due to an OS
> >using python3 by default or you really prefer to work with python3). If
> >it's due to the OS, a possible strategy is to use virtualenv
> >(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
> >if python3 is the default version for the OS. It exist probably other
> >method to have a contain installation of python2 with all the library needs.
> >
> >I used this strategy (virtualenv) to install ccp4 (with the installer
> >which needed python2) on a manjaro linux (Arch based) running python3
> >and that works very well.
> >
> >Nicolas
> >
> >Nicolas Foos
> >PhD
> >Structural Biology Group
> >European Synchrotron Radiation Facility (E.S.R.F)
> >71, avenue des Martyrs
> >CS 40220
> >38043 GRENOBLE Cedex 9
> >+33 (0)6 76 88 14 87
> >+33 (0)4 76 88 45 19
> >
> >On 06/06/2018 14:25, Kay Diederichs wrote:
> >> Dear all,
> >>
> >> I haven't tried to read MTZ files from Python until now, but for a new
> >> project in my lab I'd like to do that - and with Python3.
> >>
> >> Googling around, it seems that iotbx from cctbx is not (yet)
> >> Python3-compatible.
> >>
> >> So, what are my options?
> >>
> >> thanks,
> >>
> >> Kay
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] Python3 and MTZ

[Robbie Joosten]

Right you are Kay. It would be very weird to start developing things on Python 
2.7 right now. Its days are numbered: https://pythonclock.org/



Cheers,

Robbie



Sent from my Windows 10 phone




From: CCP4 bulletin board  on behalf of Kay Diederichs 

Sent: Wednesday, June 6, 2018 8:47:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Python3 and MTZ

Dear Nicolas,

my (our) motivation is purely that when learning Python today, and developing 
something from scratch, Python3 appears like the better choice (compared to 
version 2) - provided that basic crystallographic libraries can be used.

Just a note (for those whose operating system provides only one of the two 
Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
installed in parallel (using "Software Collections"). The user makes a choice 
by setting the PATH variable.

best,

Kay

On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:

>Dear Kay,
>
>depending of the motivation to develop in python3 (could be due to an OS
>using python3 by default or you really prefer to work with python3). If
>it's due to the OS, a possible strategy is to use virtualenv
>(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>if python3 is the default version for the OS. It exist probably other
>method to have a contain installation of python2 with all the library needs.
>
>I used this strategy (virtualenv) to install ccp4 (with the installer
>which needed python2) on a manjaro linux (Arch based) running python3
>and that works very well.
>
>Nicolas
>
>Nicolas Foos
>PhD
>Structural Biology Group
>European Synchrotron Radiation Facility (E.S.R.F)
>71, avenue des Martyrs
>CS 40220
>38043 GRENOBLE Cedex 9
>+33 (0)6 76 88 14 87
>+33 (0)4 76 88 45 19
>
>On 06/06/2018 14:25, Kay Diederichs wrote:
>> Dear all,
>>
>> I haven't tried to read MTZ files from Python until now, but for a new
>> project in my lab I'd like to do that - and with Python3.
>>
>> Googling around, it seems that iotbx from cctbx is not (yet)
>> Python3-compatible.
>>
>> So, what are my options?
>>
>> thanks,
>>
>> Kay
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Python3 and MTZ

[Kay Diederichs]

Dear Nicolas,

my (our) motivation is purely that when learning Python today, and developing 
something from scratch, Python3 appears like the better choice (compared to 
version 2) - provided that basic crystallographic libraries can be used.

Just a note (for those whose operating system provides only one of the two 
Python flavours): RHEL7 has Python2 as system library, but Python3 can be 
installed in parallel (using "Software Collections"). The user makes a choice 
by setting the PATH variable.

best,

Kay

On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS  wrote:

>Dear Kay,
>
>depending of the motivation to develop in python3 (could be due to an OS
>using python3 by default or you really prefer to work with python3). If
>it's due to the OS, a possible strategy is to use virtualenv
>(https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>if python3 is the default version for the OS. It exist probably other
>method to have a contain installation of python2 with all the library needs.
>
>I used this strategy (virtualenv) to install ccp4 (with the installer
>which needed python2) on a manjaro linux (Arch based) running python3
>and that works very well.
>
>Nicolas
>
>Nicolas Foos
>PhD
>Structural Biology Group
>European Synchrotron Radiation Facility (E.S.R.F)
>71, avenue des Martyrs
>CS 40220
>38043 GRENOBLE Cedex 9
>+33 (0)6 76 88 14 87
>+33 (0)4 76 88 45 19
>
>On 06/06/2018 14:25, Kay Diederichs wrote:
>> Dear all,
>>
>> I haven't tried to read MTZ files from Python until now, but for a new
>> project in my lab I'd like to do that - and with Python3.
>>
>> Googling around, it seems that iotbx from cctbx is not (yet)
>> Python3-compatible.
>>
>> So, what are my options?
>>
>> thanks,
>>
>> Kay
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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[ccp4bb] what's the difference between ccp4's coot and a normal coot?

[Murpholino Peligro]

I installed coot from here (
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/devel/build-info.html).


After installing a few libraries with `sudo dnf whatprovides missinglib`
got coot working. But it does not feel the same as ccp4's coot. It feels a
little bit slow.


I am asking if there are any differences so I can make my binary coot
behave more like ccp4's coot.

Thanks



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[ccp4bb] PhD call at the Free University of Bolzano deadline July 9th 2018

[Benini Stefano]

Dear All,
A multidisciplinary PhD call is open at the Free University of Bolzano,

In the Faculty of Science and Technology within the Mountain Environment and 
Agriculture PhD program

Selected candidates could choose among the following line of research in my 
group:

Siderophore mediated Iron uptake in Erwinia amylovora

Exopolysaccharide biosynthetic pathway in Erwinia amylovora

Pathogenicity associated proteins in Erwinia amylovora

Dihydrochalcones biosynthesis in Malus domestica

Your PhD research work will involve cloning of the genes of interest followed 
by protein expression and purification followed by structural and functional 
characterization of proteins and enzymes via X-ray crystallography and other 
techniques in collaboration with research organization such as John Innes 
Centre, DIAMOND, ELETTRA, Fondazione Edmund Mach, Medical University Innsbruck, 
etc.,

The link to the PhD program page and call:

https://www.unibz.it/en/applicants/phd-programmes/

link to Mountain Environment and Agriculture PhD program:
https://www.unibz.it/en/faculties/sciencetechnology/phd-mountain-environment-agriculture/

to apply online (compulsory) please register via:

https://unibz.gomovein.com/locallogin/5a957c2b8ba3286cdb7dd142/eng


Applicants will be ranked by an independent selection panel

Deadline for completing the application: July 9th 2018 at 1 a.m.

Bolzano is located in the North of Italy in the heart of Dolomites not far from 
historical cities like Verona, Venice etc., moreover it's only about 30-45 
minute drive from sky resorts (e.g., Obereggen, Carezza, etc.,). With a cable 
car you can reach 1200 m in 10 minutes from city centre and go hiking in the 
woods...
http://www.bolzano-bozen.it/en/bolzano.htm


for informal enquiries please contact me... @
stefano.ben...@unibz.it

Best regards
S.

Stefano Benini, Ph.D. Assistant Professor
https://sbenini.people.unibz.it/

"I don't like anything that's fake and I hate pretenders!"
*
Bioorganic chemistry and Bio-Crystallography laboratory (B2Cl)
Faculty of Science and Technology
Free University of Bolzano
Piazza Università, 5
39100 Bolzano, Italy
Office (room K2.14):  +39 0471 017128
Laboratory (room E.021): +39 0471 017910
Fax: +39 0471 017009
https://sbenini.people.unibz.it/
orcid.org/-0001-6299-888X

"ogni giorno in più è un giorno in meno..."

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In any case you may not copy or disseminate this message to anyone. Thank you.

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Re: [ccp4bb] Python3 and MTZ

[Nicolas FOOS]

Dear Kay,

depending of the motivation to develop in python3 (could be due to an OS 
using python3 by default or you really prefer to work with python3). If 
it's due to the OS, a possible strategy is to use virtualenv 
(https://virtualenv.pypa.io/en/stable/) which let you use python2 even 
if python3 is the default version for the OS. It exist probably other 
method to have a contain installation of python2 with all the library needs.


I used this strategy (virtualenv) to install ccp4 (with the installer 
which needed python2) on a manjaro linux (Arch based) running python3 
and that works very well.


Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 06/06/2018 14:25, Kay Diederichs wrote:

Dear all,

I haven't tried to read MTZ files from Python until now, but for a new
project in my lab I'd like to do that - and with Python3.

Googling around, it seems that iotbx from cctbx is not (yet)
Python3-compatible.

So, what are my options?

thanks,

Kay




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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Python3 and MTZ

[Mooers, Blaine H.M. (HSC)]

Hi Kay,

clipper_tools is python3 compliant.

https://github.com/clipper-python

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage   X-ray lab (LBSF)  COBRE in Structural Biology
SSRL UEC Facebook Page  SSRL UEC  SSRL SAC  LCLS UEC
EasyPyMOL Molecular Graphics  Small Angle Scattering
office: (405) 271-8300   lab: (405) 271-8313   e-mail: blaine-moo...@ouhsc.edu


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs 
[kay.diederi...@uni-konstanz.de]
Sent: Wednesday, June 06, 2018 7:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Python3 and MTZ

Dear all,

I haven't tried to read MTZ files from Python until now, but for a new
project in my lab I'd like to do that - and with Python3.

Googling around, it seems that iotbx from cctbx is not (yet)
Python3-compatible.

So, what are my options?

thanks,

Kay
--
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".




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Re: [ccp4bb] crysol or FoxS integration into python and pymol

[Tanner, John J.]

Dhiraj,

Download the  command line version of foxs from 
https://modbase.compbio.ucsf.edu/foxs/.

You can integrate foxs into linux scripts:

[tannerjj@dizzy ambiguity]$ cat FoXS.sh
#!/bin/bash
date
while read pdb
do
  echo "processing " $pdb
  /titan/tanner/SAXS/FoXS/foxs --max_q=0.32 $pdb $dat
done < filelist
date

You can also use wildcards: foxs *.pdb *.dat

Type foxs without arguments to get help:

[tannerjj@dizzy ~]$ foxs
/titan/tanner/SAXS/FoXS/foxs
Usage:   ...   ... :

Options:
  --helpAny number of input PDBs and profiles is
supported. Each PDB will be fitted against
each profile.
  --version FoXS (IMP applications)
Copyright 2007-2016 IMP Inventors.
All rights reserved.
License: GNU LGPL version 2.1 or later
.
Written by Dina Schneidman.
  -s [ --profile_size ] arg (=500)  number of points in the profile
  -q [ --max_q ] arg (=0.50)max q value
  --min_c1 arg (=0.99)  min c1 value
  --max_c1 arg (=1.05)  max c1 value
  --min_c2 arg (=-2.00) min c2 value
  --max_c2 arg (=4.00)  max c2 value
  -h [ --hydrogens ]explicitly consider hydrogens in PDB files
(default = false)
  -r [ --residues ] fast coarse grained calculation using CA
atoms only (default = false)
  -b [ --background_q ] arg (=0)background adjustment, not used by default.
if enabled, recommended q value is 0.2
  -o [ --offset ]   use offset in fitting (default = false)
  -p [ --write-partial-profile ]write partial profile file (default = false
)
  -m [ --multi-model-pdb ] arg (=1) 1 - read the first MODEL only (default), 2
- read each MODEL into a separate structure
, 3 - read all models into a single structu
re
  -v [ --volatility_ratio ] calculate volatility ratio score (default =
false)
  -l [ --score_log ]use log(intensity) in fitting and scoring
(default = false)
  -g [ --gnuplot_script ]   print gnuplot script for gnuplot viewing
(default = false)




On Jun 6, 2018, at 1:25 AM, Srivastava, Dhiraj 
mailto:dhiraj-srivast...@uiowa.edu>> wrote:

Hi All
 sorry for asking non-crystallography related question. Is it possible 
to integrate crysol or FoxS in python and pymol? I have generated thousands of 
models of my protein that I want to test against SAXS and other biochemical 
data. The ability to integrate the comparison of experimental and calculated 
X-ray scattering profile into python and pymol will be really helpful as I can 
easily calculate other parameter of my protein in pymol and compare it to other 
biochemical data. There is a pymol plugin available for SAXS but its not 
helpful for me as its not practical to use plugins for so many different 
models. I am looking for script that can automate the calculation.
 if anyone has script that can do this and is willing to share with 
me, that will be really helpful.

thank you
Dhiraj


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John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Interim Chair, Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html







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[ccp4bb] Python3 and MTZ

[Kay Diederichs]

Dear all,

I haven't tried to read MTZ files from Python until now, but for a new
project in my lab I'd like to do that - and with Python3.

Googling around, it seems that iotbx from cctbx is not (yet)
Python3-compatible.

So, what are my options?

thanks,

Kay
-- 
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
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Description: S/MIME Cryptographic Signature

Re: [ccp4bb] crysol or FoxS integration into python and pymol

[amin sagar]

Hi. If you really want to use a python based script, then you can probably
look at IMP (https://integrativemodeling.org/). However, would it not work
if you download FOXS and run it on thousands of models automatically.
Regards,
Amin.


On Wed, Jun 6, 2018 at 8:25 AM, Srivastava, Dhiraj <
dhiraj-srivast...@uiowa.edu> wrote:

> Hi All
>
>  sorry for asking non-crystallography related question. Is it
> possible to integrate crysol or FoxS in python and pymol? I have generated
> thousands of models of my protein that I want to test against SAXS and
> other biochemical data. The ability to integrate the comparison of
> experimental and calculated X-ray scattering profile into python and pymol
> will be really helpful as I can easily calculate other parameter of my
> protein in pymol and compare it to other biochemical data. There is a pymol
> plugin available for SAXS but its not helpful for me as its not practical
> to use plugins for so many different models. I am looking for script that
> can automate the calculation.
>
>  if anyone has script that can do this and is willing to share
> with me, that will be really helpful.
>
>
> thank you
>
> Dhiraj
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] crysol or FoxS integration into python and pymol

[Srivastava, Dhiraj]

Hi All

 sorry for asking non-crystallography related question. Is it possible 
to integrate crysol or FoxS in python and pymol? I have generated thousands of 
models of my protein that I want to test against SAXS and other biochemical 
data. The ability to integrate the comparison of experimental and calculated 
X-ray scattering profile into python and pymol will be really helpful as I can 
easily calculate other parameter of my protein in pymol and compare it to other 
biochemical data. There is a pymol plugin available for SAXS but its not 
helpful for me as its not practical to use plugins for so many different 
models. I am looking for script that can automate the calculation.

 if anyone has script that can do this and is willing to share with 
me, that will be really helpful.


thank you

Dhiraj



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