Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Folks,

Re: docs for elderly programs

cd $CBIN/html

In here you will find the ccp4 program docs probably going back ~ 20+ years for 
the old programs - for _your_ version of ccp4

It’s probably got greater coverage on the old command line stuff than the 
newfangled i2 things

Cheers Graeme (who still uses scripts to run ccp4 things)

On 8 Jul 2020, at 19:17, Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:

I didn’t expect it to be so lively!

I completely understand the reasons why there are changes, it looks quite good 
and I think it benefits new users greatly. Its just for us “old-fashioned” folk 
it just becomes a bit tedious to find out where the programs are now, as long 
as they are there!

However, is there a link anywhere to the old 7.0 versions? I installed 7.1 but 
removed 7.0…. I found one on google, but it led me back to 7.1.



On Jul 7, 2020, at 9:12 PM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

I really didnt mean to start this discussion - actually you did, Lau! I am so 
grateful to the modern developers who have provided GUIs to guide our work, and 
now semi-automated pipelines which mean structures can be solved routinely and 
quickly..

 Certainly it is easy enough to bypass fft to generate a map, and COOT has many 
many more facilities than the tools I quoted..
But there are some common sense oversights in all software, and it is often 
easier to find an outdated procedure to get round the difficulties than to 
influence the developers to alter their code.
One example is software which put solutions for heavy atoms, or molecular 
replacement distant from the origin . Crystallographically this is irrelevant 
but it can lead to problems in visualisation or building assemblies..
Enough - Eleanor

Cheers anyway

On Tue, 7 Jul 2020 at 19:36, Dominika Borek 
mailto:domin...@work.swmed.edu>> wrote:

I remember when I started using ccp4 programs, that frustration of writing 
scripts to run programs, and a relief when the first version of the GUI became 
available.  I have to say that there is a joy in knowing that students in 2020 
will have to also write scripts to run unsupported programs (who would guess 
that fft will be the one of those?).

Does CCP4online provide an access to all these programs? I was hesitant to 
switch, but it might be the push I needed.

What about discussing these "not taken lightly" decisions on this forum with, 
you know, users... Asking couple thousands people with combined expertise of a 
few thousands of "X-ray crystallography" years, should provide deeper insight 
into needs of community, than asking programmers around.

D.

On 2020-07-07 12:17 PM, Eleanor Dodson wrote:

I dont expect anyone to install these in the interface, and indeed if COOT told 
you the symmetry operators in a comprehensive way the distang style searches 
would be almost redundant .. But sometimes it helps to have textual 
information.. clearer andeasier to record than graphical messages..
E



On Tue, 7 Jul 2020 at 17:42, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:
I understand that one is used to the programs one is familiar with and Eleanor 
especially is very fond of these things, but there are several things which can 
be done for example in Coot (symmetry coordinates etc) . It is just another way 
to do it. I had the chance and pleasure to work for a while with the 
programmers of some of these programs in one building and such decisions are 
not taken lightly. But one cannot support all programs and write for every 
program interfaces or even keep two interfaces alive. There are just not enough 
people and money to do that. Also most scientific programmers don't get paid to 
keep the things just running. Would it be better to have also programmers to 
keep legacy up to date and write and update GUI's, maybe? But again someone 
needs to pay for that.
Just my 2 cents.

Cheers
Christian


On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
... and how all these changes being justified?

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

Yes - there are things I use all the time which are not part of the CCP4I2 list
pdbset to generate symmetry equivalents  or find the centre of mass etc etc
coordconv to turn orthogonal coordinates to fractional - after all we are 
crystallographers and need to relate models to unit cells..
distang to do a quick check on crystal contacts..
nd there must be more..
Eleanor

On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
mailto:p...@uni-greifswald.de>> wrote:
For occasions like Laus, it would be useful to further on have access to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian 

Re: [ccp4bb] Domain Motion Analysis

[00000c2488af9525-dmarc-request]

Hello Tony, I think CueMol gives you the screw rotation and translation when you fit domains. Jon CooperOn 8 Jul 2020 18:53, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:Well - I use standard software.Use GESANT or some such program to fit Structure 2 A to Structure ! A only - output wilh have all A B C but only A has been fitted//Now fit Structure 2 B from fitted structure to Structur 1 B .It will give you a PHI CHI Kappa needed to rotate B2 to B1 Is that clear enough - I can send an example..EleanorOn Wed, 8 Jul 2020 at 18:09, kazi nasrin sultana  wrote:Hi,You can try elNemo server.Regards,NasrinPhD scholarOn Wed, Jul 8, 2020, 10:16 PM Antony Oliver  wrote:







Dear CCP4bb
 
Is anyone kindly able to point me at a server or recommend software that might help me analyse relative domain movements – by comparison of two structures?
 
Structure 1 has molecules A and B. 

Structure 2 has molecules A, B and C.
 
I am interested in the induced movements, and a description thereof, that the presence of molecule C produces in molecules A and B.
 
I am aware of DynDom – but I can’t seem to make it produce a readily interpretable output (undoubtedly my fault).
 
Many thanks for your help in advance.
 
Antony.
 


 

Antony W Oliver
FHEA, PhD
Faculty Senior Research Fellow
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

 





(office): +44 (0)1273 678349
(lab): +44 (0)1273 677512

 

antony.oliver@sussex.ac.uk
https://www.sussex.ac.uk/lifesci/oliverlab
https://tinyurl.com/aw-oliver
https://orcid.org/-0002-2912-8273

http://www.sussex.ac.uk/lifesci/internal/staff/support



 
 
 


 





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Re: [ccp4bb] Looking for suggestions with protein expression

[Lau Kelvin]

Hello Umar,

I would not pin down your difficulties solely due to an Fe-S proteins. I have 
produced some with no fusion partners and they work wonderfully. They were 
expressed in an aerobic environment and then reduced in an anaerobic one before 
usage in reactions.

1) On the Fe-S side, there are plasmids you can co-transform to increase Fe-S 
production. This plasmid pH151 has the synthetic genes necessary for Fe-S 
formation.
https://www.jbc.org/content/279/33/34721.abstract

2) On the general protein side, have you hhpred your protein? Different 
constructs (not just tags), temperature? Strain? Media?

3) For these proteins we typically use His Excel (or Protein Ark Ni2+ Advance) 
that is resistant to most chelators since more often than not, they contain 
other metals and can snatch Ni2+ from normal Ni-NTA resins. Strep tags also 
work well.

On Jun 27, 2020, at 9:14 AM, Umar Farook 
mailto:umarfaroo...@gmail.com>> wrote:

Dear All,

Sorry for an offtopic question, your suggestions are highly appreciated.

We have been working on iron sulfur cluster binding protein, which is usually 
expressed as a nice soluble protein expressed in BL21 cells but aggregated in 
the affinity column itself and unable to recover from it. We had made n number 
of truncations and fused to soluble tags such as MBP, but always ended up in 
large aggregates. Anyone has experience in working with iron-sulfur cluster 
binding protein before, please let us know the critical steps in purification 
of such proteins, whether you have completely done the expression, purification 
and crystallization in anaerobic conditions? or else changing the expression 
system to eukaryotic system such as Baculo or HEK 293T would help?

Please share your valuable experience, thank you.



--
Best Regards,
Umar Farook



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Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Boaz Shaanan]

Hi, Just in case nobody has pointed this out yet (which I doubt) "google ccp4 documentaion" or just "doc" will give you several lists+docs  of current and old ccp4 programs, included and absent from ccp4i2.
Cheers,
Boaz


Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel



On Jul 8, 2020 21:17, Lau Kelvin  wrote:


I didn’t expect it to be so lively!


I completely understand the reasons why there are changes, it looks quite good and I think it benefits new users greatly. Its just for us “old-fashioned” folk it just becomes a bit tedious to find out where the programs are now, as long as they
 are there!


However, is there a link anywhere to the old 7.0 versions? I installed 7.1 but removed 7.0…. I found one on google, but it led me back to 7.1.





On Jul 7, 2020, at 9:12 PM, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:


I really didnt mean to start this discussion - actually you did, Lau! I am so grateful to the modern developers who have provided GUIs to guide our work, and now semi-automated pipelines which mean structures can be solved routinely
 and quickly..


 Certainly it is easy enough to bypass fft to generate a map, and COOT has many many more facilities than the tools I quoted..
But there are some common sense oversights in all software, and it is often easier to find an outdated procedure to get round the difficulties than to influence the developers to alter their code.
One example is software which put solutions for heavy atoms, or molecular replacement distant from the origin . Crystallographically this is irrelevant but it can lead to problems in visualisation or building assemblies..
Enough - Eleanor


Cheers anyway 



On Tue, 7 Jul 2020 at 19:36, Dominika Borek  wrote:



I remember when I started using ccp4 programs, that frustration of writing scripts to run programs, and a relief when the first version of the GUI became available.  I have to say that there is a joy in knowing that students in 2020 will have to
 also write scripts to run unsupported programs (who would guess that fft will be the one of those?). 
Does CCP4online provide an access to all these programs? I was hesitant to switch, but it might be the push I needed.
What about discussing these "not taken lightly" decisions on this forum with, you know, users... Asking couple thousands people with combined expertise of a few thousands of "X-ray crystallography" years, should provide deeper insight
 into needs of community, than asking programmers around.
D.
On 2020-07-07 12:17 PM, Eleanor Dodson wrote:

I dont expect anyone to install these in the interface, and indeed if COOT told you the symmetry operators in a comprehensive way the distang style searches would be almost redundant .. But sometimes it helps to have textual information..
 clearer andeasier to record than graphical messages..
E

 





On Tue, 7 Jul 2020 at 17:42, Christian Roth  wrote:


I understand that one is used to the programs one is familiar with and Eleanor especially is very fond of these things, but there are several things which can be done for example in Coot (symmetry coordinates etc) . It is just another way to do
 it. I had the chance and pleasure to work for a while with the programmers of some of these programs in one building and such decisions are not taken lightly. But one cannot support all programs and write for every program interfaces or even keep two interfaces
 alive. There are just not enough people and money to do that. Also most scientific programmers don't get paid to keep the things just running. Would it be better to have also programmers to keep legacy up to date and write and update GUI's, maybe? But again
 someone needs to pay for that.
Just my 2 cents.
 
Cheers
Christian
 



On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh  wrote:



... and how all these changes being justified?
 
From: CCP4 bulletin board 
On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: 
CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2
 

Yes - there are things I use all the time which are not part of the CCP4I2 list

pdbset to generate symmetry equivalents  or find the centre of mass etc etc


coordconv to turn orthogonal coordinates to fractional - after all we are crystallographers and need to relate models to unit cells..


distang to do a quick check on crystal contacts..


nd there must be more..


Eleanor


 


On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried  wrote:




For occasions like Laus, it would be useful to further on have access to the

CCP4 v7.0 Program Documentation, 


even if the programs are not updated as Christian explained.


I 

Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Lau Kelvin]

I didn’t expect it to be so lively!

I completely understand the reasons why there are changes, it looks quite good 
and I think it benefits new users greatly. Its just for us “old-fashioned” folk 
it just becomes a bit tedious to find out where the programs are now, as long 
as they are there!

However, is there a link anywhere to the old 7.0 versions? I installed 7.1 but 
removed 7.0…. I found one on google, but it led me back to 7.1.



On Jul 7, 2020, at 9:12 PM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

I really didnt mean to start this discussion - actually you did, Lau! I am so 
grateful to the modern developers who have provided GUIs to guide our work, and 
now semi-automated pipelines which mean structures can be solved routinely and 
quickly..

 Certainly it is easy enough to bypass fft to generate a map, and COOT has many 
many more facilities than the tools I quoted..
But there are some common sense oversights in all software, and it is often 
easier to find an outdated procedure to get round the difficulties than to 
influence the developers to alter their code.
One example is software which put solutions for heavy atoms, or molecular 
replacement distant from the origin . Crystallographically this is irrelevant 
but it can lead to problems in visualisation or building assemblies..
Enough - Eleanor

Cheers anyway

On Tue, 7 Jul 2020 at 19:36, Dominika Borek 
mailto:domin...@work.swmed.edu>> wrote:

I remember when I started using ccp4 programs, that frustration of writing 
scripts to run programs, and a relief when the first version of the GUI became 
available.  I have to say that there is a joy in knowing that students in 2020 
will have to also write scripts to run unsupported programs (who would guess 
that fft will be the one of those?).

Does CCP4online provide an access to all these programs? I was hesitant to 
switch, but it might be the push I needed.

What about discussing these "not taken lightly" decisions on this forum with, 
you know, users... Asking couple thousands people with combined expertise of a 
few thousands of "X-ray crystallography" years, should provide deeper insight 
into needs of community, than asking programmers around.

D.

On 2020-07-07 12:17 PM, Eleanor Dodson wrote:

I dont expect anyone to install these in the interface, and indeed if COOT told 
you the symmetry operators in a comprehensive way the distang style searches 
would be almost redundant .. But sometimes it helps to have textual 
information.. clearer andeasier to record than graphical messages..
E



On Tue, 7 Jul 2020 at 17:42, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:
I understand that one is used to the programs one is familiar with and Eleanor 
especially is very fond of these things, but there are several things which can 
be done for example in Coot (symmetry coordinates etc) . It is just another way 
to do it. I had the chance and pleasure to work for a while with the 
programmers of some of these programs in one building and such decisions are 
not taken lightly. But one cannot support all programs and write for every 
program interfaces or even keep two interfaces alive. There are just not enough 
people and money to do that. Also most scientific programmers don't get paid to 
keep the things just running. Would it be better to have also programmers to 
keep legacy up to date and write and update GUI's, maybe? But again someone 
needs to pay for that.
Just my 2 cents.

Cheers
Christian


On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
... and how all these changes being justified?

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

Yes - there are things I use all the time which are not part of the CCP4I2 list
pdbset to generate symmetry equivalents  or find the centre of mass etc etc
coordconv to turn orthogonal coordinates to fractional - after all we are 
crystallographers and need to relate models to unit cells..
distang to do a quick check on crystal contacts..
nd there must be more..
Eleanor

On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
mailto:p...@uni-greifswald.de>> wrote:
For occasions like Laus, it would be useful to further on have access to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian explained.
I was for instance looking for translating coordinates as in pdbset, but 
couldn't find a replacement in the ccp4i2 gui.
Greetings
  Gottfried


On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote:

Ah I see! Great I can run it that way

And yes, Eleanor, after I realized that list was gone, I was panicking that 
there are some random things I used to do with those programs would no longer 
be possible. Good 

Re: [ccp4bb] Domain Motion Analysis

[Eleanor Dodson]

Well - I use standard software.
Use GESANT or some such program to fit Structure 2 A to Structure ! A only
- output wilh have all A B C but only A has been fitted//
Now fit Structure 2 B from fitted structure to Structur 1 B .
It will give you a PHI CHI Kappa needed to rotate B2 to B1
Is that clear enough - I can send an example..
Eleanor

On Wed, 8 Jul 2020 at 18:09, kazi nasrin sultana 
wrote:

> Hi,
>
> You can try elNemo server.
>
>
> Regards,
> Nasrin
> PhD scholar
>
>
>
>
> On Wed, Jul 8, 2020, 10:16 PM Antony Oliver 
> wrote:
>
>> Dear CCP4bb
>>
>>
>>
>> Is anyone kindly able to point me at a server or recommend software that
>> might help me analyse relative domain movements – by comparison of two
>> structures?
>>
>>
>>
>> Structure 1 has molecules A and B.
>>
>> Structure 2 has molecules A, B and C.
>>
>>
>>
>> I am interested in the induced movements, and a description thereof, that
>> the presence of molecule C produces in molecules A and B.
>>
>>
>>
>> I am aware of DynDom – but I can’t seem to make it produce a readily
>> interpretable output (undoubtedly my fault).
>>
>>
>>
>> Many thanks for your help in advance.
>>
>>
>>
>> Antony.
>>
>>
>>
>>
>>
>> *Antony W Oliver* FHEA, PhD
>> Faculty Senior Research Fellow
>>
>> Genome Damage and Stability Centre
>> Science Park Road
>> University of Sussex
>> Falmer, Brighton, BN1 9RQ
>>
>>
>>
>>
>>
>>
>>
>> (office): +44 (0)1273 678349
>> (lab): +44 (0)1273 677512
>>
>>
>>
>>
>> *antony.oli...@sussex.ac.uk  *
>> https://www.sussex.ac.uk/lifesci/oliverlab
>> https://tinyurl.com/aw-oliver
>> https://orcid.org/-0002-2912-8273
>>
>> http://www.sussex.ac.uk/lifesci/internal/staff/support
>>
>> [image: A close up of a logo Description automatically generated]
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
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Re: [ccp4bb] AcTEV protease

[Chun Luo]

AcTEV protease is a TEV protease catalytic domain with a stabilizing mutation. 
There is a patent on the mutation, although most people ignore the patent.

 

We have TurboTEV (http://accelagen.com/TurboTEV.htm) which is not stabilized by 
the patented mutations. It costs a fraction of the price of AcTEV and is more 
user friendly.

 

Chun

 

From: CCP4 bulletin board  On Behalf Of Gloria Borgstahl
Sent: Wednesday, July 8, 2020 8:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AcTEV protease

 

Another protein purification question:  Does anyone know what is AcTEV protease 
that is sold by Thermofisher Scientific?  Is this the same as SuperTEV?

It works well but is so expensive.

Thanks for any advice, Gloria

 

  _  

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Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

[Christian Roth]

Exactly, on point David.  All programs are still there and accessible, but
maybe not actively supported or developed. Similar to Moleman I used from
time to time. However they are not in the interface list (i2) because they
are not with an interface and therefore cannot be used in that way.  But
there is always the command line or whatever script someone wrote for
themselves.  The programs don't get thrown away so to speak, but again if
there is a solution, which works and is implemented in i2, than the chance
that someone writes an additional interface for another program is not too
high on the list or at least not a priority.

Cheers
Christian

On Wed, Jul 8, 2020 at 5:17 PM David Waterman  wrote:

> Hi all,
>
> Please be reassured that there are no plans at the moment to remove
> programs from CCP4, at least none of which I am aware. The newer GUIs might
> not provide interfaces to run all of these programs, but they are still
> there to run from the command line. There is currently no good reason to
> remove them (they constitute a tiny part of the full install size, after
> all) and the policy of the core team is to keep anything that passes the
> "if it ain't broke" test.
>
> I know this because I once suggested that pdbset should be removed and
> replaced with a script that uses Gemmi. This is because pdbset has some
> problems (it removes LINK records for example). However removing it was
> strongly resisted by others in the core team. The maintenance burden of
> removing such a program far outweighs the negligible cost of simply keeping
> it around.
>
> Cheers
> -- David
>
>
> On Wed, 8 Jul 2020 at 15:36, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>> I fully agree, I have some old scripts I infrequently use. Making these
>> programs inaccessible would break these scripts, forcing me to reinvent a
>> couple of wheels.
>>
>>
>>
>> My 2 cnts worth of junk to your mailbox,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board  *Im Auftrag von 
>> *Oganesyan,
>> Vaheh
>> *Gesendet:* Mittwoch, 8. Juli 2020 16:23
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] Re: [ccp4bb] Accessing full list of programs in
>> CCP4I2
>>
>>
>>
>> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>>
>>
>>
>> Thank you for explanation. There are many small programs in CCP4 that
>> have not been updated for years and they still work despite being in
>> unsupported folder. By making them inaccessible (or more difficult to
>> access) nobody gets easier/cheaper life. Even if there are newer programs
>> that may do the same it is not a good reason to forget the old ones. It is
>> like forgetting the history and the culture. Then making new discoveries
>> just to find that it is the same old “wheel” just a bit more round. It is
>> probably very personal, but I do not throw away old edition of
>> Thermodynamics text book when new one is coming out. And I’m not a hoarder,
>> do not have OCD or ADHD.
>>
>>
>>
>> This is already 4 cents together. Sorry to clutter your mailbox.
>>
>>
>>
>> Vaheh (CCP4 user since 1992)
>>
>>
>>
>> *From:* Christian Roth 
>> *Sent:* Tuesday, July 7, 2020 12:42 PM
>> *To:* Oganesyan, Vaheh 
>> *Cc:* CCP4BB@jiscmail.ac.uk
>> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>>
>>
>>
>> I understand that one is used to the programs one is familiar with and
>> Eleanor especially is very fond of these things, but there are several
>> things which can be done for example in Coot (symmetry coordinates etc) .
>> It is just another way to do it. I had the chance and pleasure to work for
>> a while with the programmers of some of these programs in one building and
>> such decisions are not taken lightly. But one cannot support all programs
>> and write for every program interfaces or even keep two interfaces alive.
>> There are just not enough people and money to do that. Also most scientific
>> programmers don't get paid to keep the things just running. Would it be
>> better to have also programmers to keep legacy up to date and write and
>> update GUI's, maybe? But again someone needs to pay for that.
>>
>> Just my 2 cents.
>>
>>
>>
>> Cheers
>>
>> Christian
>>
>>
>>
>>
>>
>> On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh <
>> vaheh.oganes...@astrazeneca.com> wrote:
>>
>> … and how all these changes being justified?
>>
>>
>>
>> *From:* CCP4 bulletin board  *On Behalf Of *Eleanor
>> Dodson
>> *Sent:* Tuesday, July 7, 2020 12:25 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>>
>>
>>
>> Yes - there are things I use all the time which are not part of the
>> CCP4I2 list
>>
>> pdbset to generate symmetry equivalents  or find the centre of mass etc
>> etc
>>
>> coordconv to turn orthogonal coordinates to fractional - after all we are
>> crystallographers and need to relate models to unit cells..
>>
>> distang to do a quick check on crystal contacts..
>>
>> nd there must be more..
>>
>> Eleanor
>>
>>
>>
>> On 

[ccp4bb] Time-Resolved Structural Biology workshop

[Thomas Ursby]

*Time Resolved Structural Biology – Seeing the structure of motions*

The workshop in Time Resolved Structural Biology 
 
organized by LINXS  and originally planned for 
this spring will be held in Lund, Sweden, November 23-25, 2020. Note 
that it will take place those dates but the final decision if it will be 
a fully online or partly onsite meeting will be taken in the autumn. The 
maximum number of participants, length and timetable of the meeting 
might also be adjusted.


The workshop will cover different aspects of studying the molecular 
structure of biological macromolecules using time-resolved experimental 
techniques or computational methods - What can we learn? What method is 
best for a certain question and how do they complement each other? The 
workshop aims to broaden concepts of time-resolved structural biology 
and it will encourage discussion between the participants.


Confirmed speakers
Abbas Ourmazd - University of Wisconsin-Milwaukee
Sebastian Westenhoff - University of Gothenburg
Ana-Nicoleta Bondar - Freie Universität Berlin
Hongyi Xu - Stockholm University
Jakob Andreasson - ELI Beamlines
Jörg Standfuss - Paul Scherrer Institute
Linda C Johansson - University of Gothenburg
Mikael Akke - Lund University
Jörg Pieper - University of Tartu
Gleb Bourenkov - EMBL@PETRA III, Hamburg
Vania Calandrini - Forschungszentrum Juelich
Ran Friedman - Linnaeus University, Kalmar

LINXS  (Lund Institute of Advanced Neutron and 
X-Ray Science; www.linxs.se) is a recently formed institute in Lund 
whose mission is to promote science and education focusing on the use of 
neutrons and X-rays, as well as complementary methodologies, to attract 
world-leading scientists for short- and long-term focused research 
visits, and to create international networks.


For more information see: 
https://www.linxs.se/events/2020/2/10/npkhmhgvkss0ngdds5nd8ss52mnt23







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[ccp4bb] AcTEV protease

[Gloria Borgstahl]

Another protein purification question:  Does anyone know what is AcTEV
protease that is sold by Thermofisher Scientific?  Is this the same as
SuperTEV?
It works well but is so expensive.
Thanks for any advice, Gloria



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Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

[David Waterman]

Hi all,

Please be reassured that there are no plans at the moment to remove
programs from CCP4, at least none of which I am aware. The newer GUIs might
not provide interfaces to run all of these programs, but they are still
there to run from the command line. There is currently no good reason to
remove them (they constitute a tiny part of the full install size, after
all) and the policy of the core team is to keep anything that passes the
"if it ain't broke" test.

I know this because I once suggested that pdbset should be removed and
replaced with a script that uses Gemmi. This is because pdbset has some
problems (it removes LINK records for example). However removing it was
strongly resisted by others in the core team. The maintenance burden of
removing such a program far outweighs the negligible cost of simply keeping
it around.

Cheers
-- David


On Wed, 8 Jul 2020 at 15:36, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> I fully agree, I have some old scripts I infrequently use. Making these
> programs inaccessible would break these scripts, forcing me to reinvent a
> couple of wheels.
>
>
>
> My 2 cnts worth of junk to your mailbox,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Oganesyan,
> Vaheh
> *Gesendet:* Mittwoch, 8. Juli 2020 16:23
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Accessing full list of programs in
> CCP4I2
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Thank you for explanation. There are many small programs in CCP4 that have
> not been updated for years and they still work despite being in unsupported
> folder. By making them inaccessible (or more difficult to access) nobody
> gets easier/cheaper life. Even if there are newer programs that may do the
> same it is not a good reason to forget the old ones. It is like forgetting
> the history and the culture. Then making new discoveries just to find that
> it is the same old “wheel” just a bit more round. It is probably very
> personal, but I do not throw away old edition of Thermodynamics text book
> when new one is coming out. And I’m not a hoarder, do not have OCD or ADHD.
>
>
>
> This is already 4 cents together. Sorry to clutter your mailbox.
>
>
>
> Vaheh (CCP4 user since 1992)
>
>
>
> *From:* Christian Roth 
> *Sent:* Tuesday, July 7, 2020 12:42 PM
> *To:* Oganesyan, Vaheh 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>
>
>
> I understand that one is used to the programs one is familiar with and
> Eleanor especially is very fond of these things, but there are several
> things which can be done for example in Coot (symmetry coordinates etc) .
> It is just another way to do it. I had the chance and pleasure to work for
> a while with the programmers of some of these programs in one building and
> such decisions are not taken lightly. But one cannot support all programs
> and write for every program interfaces or even keep two interfaces alive.
> There are just not enough people and money to do that. Also most scientific
> programmers don't get paid to keep the things just running. Would it be
> better to have also programmers to keep legacy up to date and write and
> update GUI's, maybe? But again someone needs to pay for that.
>
> Just my 2 cents.
>
>
>
> Cheers
>
> Christian
>
>
>
>
>
> On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
>
> … and how all these changes being justified?
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Eleanor
> Dodson
> *Sent:* Tuesday, July 7, 2020 12:25 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2
>
>
>
> Yes - there are things I use all the time which are not part of the CCP4I2
> list
>
> pdbset to generate symmetry equivalents  or find the centre of mass etc etc
>
> coordconv to turn orthogonal coordinates to fractional - after all we are
> crystallographers and need to relate models to unit cells..
>
> distang to do a quick check on crystal contacts..
>
> nd there must be more..
>
> Eleanor
>
>
>
> On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
> wrote:
>
> For occasions like Laus, it would be useful to further on have access to
> the
> CCP4 v7.0 Program Documentation,
>
> even if the programs are not updated as Christian explained.
>
> I was for instance looking for translating coordinates as in pdbset, but
> couldn't find a replacement in the ccp4i2 gui.
>
> Greetings
>
>   Gottfried
>
>
>
>
> On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote:
>
> Ah I see! Great I can run it that way
>
>
>
> And yes, Eleanor, after I realized that list was gone, I was panicking
> that there are some random things I used to do with those programs would no
> longer be possible. Good to know that the command line versions are still
> there in the 7.1 distro.
>
>
>
> Best,
>
>
>
> Kelvin
>
>
>
> --
> Kelvin Lau
>
> https://people.epfl.ch/kelvin.lau
> 

Re: [ccp4bb] Commercial source of His-tagged protein

[Mark J van Raaij]

Dear All,

many thanks to you all for your suggestions and help! I learned about some 
interesting small companies producing proteins and had other useful 
suggestions, some already shared with the list. Another example of the 
wonderful CCP4bb community.
In the end it looks like we will go for His-tagged GFP, because it will have 
specific advantages for the experiments, and someone can produce it locally 
here for what will be a good price (don't have an exact quote yet and won't 
advertise the outfit unless they desire this).

Lesser known (at least not previously known to me) companies that were 
recommended are:
http://www.molirom.com/ 
https://www.37cbio.com/ 
https://www.novusbio.com/ 
Acrobiosystems.com 
(I'm think I can be sure that they are happy to be named)
 
Best wishes,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 2 Jul 2020, at 11:50, Tristan Croll  wrote:
> 
> Thermo Fisher sells His-tagged GFP quite cheaply. 
> https://www.thermofisher.com/order/catalog/product/A42611#/A42611 
> 
> Tristan
> 
>  
> 
> 
> On 2020-07-02 10:31, Mark J van Raaij wrote:
> 
>> Dear All,
>>  
>> Wondering if anyone knows of an economical commercial source of a soluble 
>> His-tagged protein. In principle any His-tagged protein would suffice, 
>> because it's for testing coupling to a surface via the His-tag. Asking for 
>> an international collaborator, who don't have access/expertise of a 
>> molecular biology lab (except us :-). 
>> We can and will make the His-tagged proteins of interest for them, but if 
>> there is an economical and reliable commercial source, it might be worth 
>> using that for initial tests.
>>  
>> Best wishes,
>>  
>> Mark
>>  
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> Section Editor Acta Crystallographica F
>> https://journals.iucr.org/f/ 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
>> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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[ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

[Schreuder, Herman /DE]

I fully agree, I have some old scripts I infrequently use. Making these 
programs inaccessible would break these scripts, forcing me to reinvent a 
couple of wheels.

My 2 cnts worth of junk to your mailbox,
Herman

Von: CCP4 bulletin board  Im Auftrag von Oganesyan, Vaheh
Gesendet: Mittwoch, 8. Juli 2020 16:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Accessing full list of programs in CCP4I2


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Thank you for explanation. There are many small programs in CCP4 that have not 
been updated for years and they still work despite being in unsupported folder. 
By making them inaccessible (or more difficult to access) nobody gets 
easier/cheaper life. Even if there are newer programs that may do the same it 
is not a good reason to forget the old ones. It is like forgetting the history 
and the culture. Then making new discoveries just to find that it is the same 
old “wheel” just a bit more round. It is probably very personal, but I do not 
throw away old edition of Thermodynamics text book when new one is coming out. 
And I’m not a hoarder, do not have OCD or ADHD.

This is already 4 cents together. Sorry to clutter your mailbox.

Vaheh (CCP4 user since 1992)

From: Christian Roth 
mailto:christianroth...@gmail.com>>
Sent: Tuesday, July 7, 2020 12:42 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

I understand that one is used to the programs one is familiar with and Eleanor 
especially is very fond of these things, but there are several things which can 
be done for example in Coot (symmetry coordinates etc) . It is just another way 
to do it. I had the chance and pleasure to work for a while with the 
programmers of some of these programs in one building and such decisions are 
not taken lightly. But one cannot support all programs and write for every 
program interfaces or even keep two interfaces alive. There are just not enough 
people and money to do that. Also most scientific programmers don't get paid to 
keep the things just running. Would it be better to have also programmers to 
keep legacy up to date and write and update GUI's, maybe? But again someone 
needs to pay for that.
Just my 2 cents.

Cheers
Christian


On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
… and how all these changes being justified?

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

Yes - there are things I use all the time which are not part of the CCP4I2 list
pdbset to generate symmetry equivalents  or find the centre of mass etc etc
coordconv to turn orthogonal coordinates to fractional - after all we are 
crystallographers and need to relate models to unit cells..
distang to do a quick check on crystal contacts..
nd there must be more..
Eleanor

On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
mailto:p...@uni-greifswald.de>> wrote:
For occasions like Laus, it would be useful to further on have access to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian explained.
I was for instance looking for translating coordinates as in pdbset, but 
couldn't find a replacement in the ccp4i2 gui.
Greetings
  Gottfried


On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote:
Ah I see! Great I can run it that way

And yes, Eleanor, after I realized that list was gone, I was panicking that 
there are some random things I used to do with those programs would no longer 
be possible. Good to know that the command line versions are still there in the 
7.1 distro.

Best,

Kelvin

--
Kelvin Lau
https://people.epfl.ch/kelvin.lau

Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 30267
If unreachable: +41 21 69 34494


On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
christianroth...@gmail.com> wrote:

yes Eleanor is right. command line still works.[:-)]
fft is also in 7.1 distribution.



On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Oh Lau - how I miss that list!
But if you just run fft online it is still distributed..wombat:Downloads 
eleanor$

fft hklin  mapout 

LABIN 

Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Oganesyan, Vaheh]

Thank you for explanation. There are many small programs in CCP4 that have not 
been updated for years and they still work despite being in unsupported folder. 
By making them inaccessible (or more difficult to access) nobody gets 
easier/cheaper life. Even if there are newer programs that may do the same it 
is not a good reason to forget the old ones. It is like forgetting the history 
and the culture. Then making new discoveries just to find that it is the same 
old “wheel” just a bit more round. It is probably very personal, but I do not 
throw away old edition of Thermodynamics text book when new one is coming out. 
And I’m not a hoarder, do not have OCD or ADHD.

This is already 4 cents together. Sorry to clutter your mailbox.

Vaheh (CCP4 user since 1992)

From: Christian Roth 
Sent: Tuesday, July 7, 2020 12:42 PM
To: Oganesyan, Vaheh 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

I understand that one is used to the programs one is familiar with and Eleanor 
especially is very fond of these things, but there are several things which can 
be done for example in Coot (symmetry coordinates etc) . It is just another way 
to do it. I had the chance and pleasure to work for a while with the 
programmers of some of these programs in one building and such decisions are 
not taken lightly. But one cannot support all programs and write for every 
program interfaces or even keep two interfaces alive. There are just not enough 
people and money to do that. Also most scientific programmers don't get paid to 
keep the things just running. Would it be better to have also programmers to 
keep legacy up to date and write and update GUI's, maybe? But again someone 
needs to pay for that.
Just my 2 cents.

Cheers
Christian


On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
… and how all these changes being justified?

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2

Yes - there are things I use all the time which are not part of the CCP4I2 list
pdbset to generate symmetry equivalents  or find the centre of mass etc etc
coordconv to turn orthogonal coordinates to fractional - after all we are 
crystallographers and need to relate models to unit cells..
distang to do a quick check on crystal contacts..
nd there must be more..
Eleanor

On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried 
mailto:p...@uni-greifswald.de>> wrote:
For occasions like Laus, it would be useful to further on have access to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian explained.
I was for instance looking for translating coordinates as in pdbset, but 
couldn't find a replacement in the ccp4i2 gui.
Greetings
  Gottfried


On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote:
Ah I see! Great I can run it that way

And yes, Eleanor, after I realized that list was gone, I was panicking that 
there are some random things I used to do with those programs would no longer 
be possible. Good to know that the command line versions are still there in the 
7.1 distro.

Best,

Kelvin

--
Kelvin Lau
https://people.epfl.ch/kelvin.lau

Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 30267
If unreachable: +41 21 69 34494


On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
christianroth...@gmail.com> wrote:

yes Eleanor is right. command line still works.[:-)]
fft is also in 7.1 distribution.



On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Oh Lau - how I miss that list!
But if you just run fft online it is still distributed..wombat:Downloads 
eleanor$

fft hklin  mapout 

LABIN FP=  and so on..


On Tue, 7 Jul 2020 at 14:22, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:
Hi Kelvin,
well fft as single program is kind of not longer supported as is not ccp4i. In 
i2 internally, as well in communication with mg or coot, everything is done 
using map coefficients.
Their are two options:
First via i2: Use the unusual map coefficients Task and choose not to compare 
maps, but to generate the map coefficients plus a map (button is in Advanced 
tab) the standard grid parameters can be changed, but are actually optimized 
already.
Second just save the map out of Coot (Export map)

To avoid redundancy, the old fft task was discontinued. i2 works with 
coefficients, which generates smaller files and Coot provides all the functions 
to generate the map and is its own gui.

Hope that explains a bit why things 

Re: [ccp4bb] adding external planar restraint in refmac5

[Paul Emsley]

On 08/07/2020 12:39, Laurent wrote:



I am currently refinining an enzyme structure obtained in the presence 
of a substrate analog : the catalytic serine is acylated and form an 
ester bond with the ligand. I have added a LINK record in the PDB file 
to specify the newly created covalent bond between OG atom of Serine 
and C1 atom of the ligand. I would also like to restraint the ester 
linkage in a plane (atom OG of Ser623 and atoms O1, C1 and CA or 
residue 901, both in chain A)  I am trying to use the external 
restraint keyword in refmac (the documentation clearly indicates the 
syntax in case of a dihedral external restraint and only says that if 
can also be used for planar restraint).


external planar first chain A residue 623 atom OG next chain A residue 
901 atom CA next chain A residue 901 atom C1 next chain A residue 901 
atom O1 value 0 sigma 10


In the refmac logfile there are no error messages, but this specific 
command line is not echoed, although all other are. However, it seems 
to be red [sic] and checked by refmac, as introducing a wrong keyword 
(eternal instead of external) generated an error message. However, the 
ester linkage is not planar in the refined PDB when viewed with coot.



While one can refine a model this way, it is not typically the way to do 
so - we use a dictionary for the link rather than external restraints.




So, is my syntax correct ?



I notice that you don't include a specifier for the insertion code. 
Maybe that's related. Coot should give you an error message if it fails 
to parse the external planar restraints line. If you are using Coot to 
do so, what does it say?



Should I keep the value keyword (as it is likely not used I the case 
of a plane restraint) ?
Sigma is set to 10… As far as I understood, this means that this 
specific plane restraint will be 10 times weaker than the normal plane 
restraint defined in the standard dictionnairy… is that correct ?



I don't think so. 10 means 10A, not 10 rmsd. Such a restraint will 
practically be ignored in the minimization.




Any clues will be more than welcome !



Have a look at my blog for how to add a link between a ligand and a 
protein residue:


https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html

In your case, only the bottom part is relevant - where Coot interacts 
with Acedrg.



Paul





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[ccp4bb] adding external planar restraint in refmac5

[Laurent]

Dear CCP4 users,

I am currently refinining an enzyme structure obtained in the presence of a 
substrate analog : the catalytic serine is acylated and form an ester bond with 
the ligand. I have added a LINK record in the PDB file to specify the newly 
created covalent bond between OG atom of Serine and C1 atom of the ligand. I 
would also like to restraint the ester linkage in a plane (atom OG of Ser623 
and atoms O1, C1 and CA or residue 901, both in chain A)  I am trying to use 
the external restraint keyword in refmac (the documentation clearly indicates 
the syntax in case of a dihedral external restraint and only says that if can 
also be used for planar restraint).

external planar first chain A residue 623 atom OG next chain A residue 901 atom 
CA next chain A residue 901 atom C1 next chain A residue 901 atom O1 value 0 
sigma 10

In the refmac logfile there are no error messages, but this specific command 
line is not echoed, although all other are. However, it seems to be red and 
checked by refmac, as introducing a wrong keyword (eternal instead of external) 
generated an error message. However, the ester linkage is not planar in the 
refined PDB when viewed with coot.
So, is my syntax correct ?
Should I keep the value keyword (as it is likely not used I the case of a plane 
restraint) ?
Sigma is set to 10… As far as I understood, this means that this specific plane 
restraint will be 10 times weaker than the normal plane restraint defined in 
the standard dictionnaire… is that correct ?
Any clues will be more than welcome !

Have a nice day,

Laurent



Laurent Maveyraud 
Prof. University of Toulouse 
www.ipbs.fr | cribligand.ipbs.fr 
IPBS-Toulouse | CNRS-Université Toulouse III-Paul Sabatier  
205 Route de Narbonne, BP 64182, 31077 Toulouse Cedex 4 
+33 5 61 17 54 35 | +33 6 46 04 21 11





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Re: [ccp4bb] Twin law definition in REFMAC5

[Andrey Lebedev]

Dear Petr

Both questions, on twin law and R-factors, are mainly questions about 
definitions and standards.

From Online Dictionary of Crystallography: "The twin law is the SET of twin 
operations mapping two individuals of a twin." 

In your P 21 21 21 example with a=b, the set contains four operations:
2-fold rotations around [110] and [-110], and rotations around [001] by 90 and 
-90 degrees. These operations can be written as k,h,-l; -k,-h,-l; -k,h,l; 
k,-h,l. Four is because there are four operations in 222 point group. All four 
are equivalent twin operations for this particular twin. Any of them can be 
taken as a REPRESENTATIVE of the twin law, but it will be incorrect use of 
terminology to say that one of then IS a twin law.  It is valid to use any of 
them in calculations.

Again, the question about R-factors for data from twinned crystal is a question 
of definition. The standard definitions of R-cryst and R-free are NOT 
applicable to such data. (Let's leave alone the discussion on whether and when 
R-factors are useful statistics).

This is because the definitions of R-cryst and R-free use the notion of  
"observed" structure amplitudes. In case of non-twinned crystal, there is 
French-Wilson procedure (implemented in truncate program), which is a de-facto 
standard (good or bad - different story) for calculating "observed" structure 
amplitudes from "observed" intensities. To calculate the "observed" intensities 
from "twinned" intensities we need yet another standard, e.g. a standard 
de-twining procedure, which does not exist. Moreover, refinement programs do 
not use de-twinning, but, other way round, fit calculated "twinned" intensities 
to "observed" "twinned" intensities. This is robust. But when it goes to 
R-factors, there is range of options.

In Refmac, "twinned" refinement can be conducted against intensities or 
structure amplitudes, however calculated. The former is in theory more robust, 
but it uses definitions of R-factors that results in higher values, especially 
when there are many weak reflections.

For bureaucratic purposes, I may suggest the option of refinement against 
structure amplitudes (obtained e.g. using truncate). That will give lower 
R?factors. Alternatively, refinement against intensities can be followed by 
refmac job with zero cycles using structure amplitudes option.

Andrey

P.S. An important reminder from Garib: output mtz-file from refmac should not 
be used in subsequent refinements as input. It is only for map calculation and 
for internal use in model building pipelines. Please always use mtz-file form 
data reduction program (e.g. aimless) as input for refmac. This comment is 
especially relevant for "twin refinement".



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[ccp4bb] PhD position (or Research Associate) opportunity

[Apirat Chaikuad]

Posted on behalf of Dr. Xinlai Cheng

 

In the Department of Biochemistry, Chemistry and Pharmacy - Institute of
Pharmaceutical Chemistry in the field of Medicinal Chemistry -  Dr. Xinlai
Cheng offers a position starting instantly of a PhD-Student/ Research
Associate (E13 TV-G-U, 50 % part-time).

 

limited up to 31.12.2022 (possible expansion to 31.12.2025). The salary
grade is based on the job characteristics of the collective agreement
applicable to Goethe University (TV-G-U).

 

Link to job webpage -
https://www.uni-frankfurt.de/81647683/Aktueller_Stellenmarkt_vom_08_Juli_202
0.pdf

 

Area of responsibility

 

The work will be done in a multi-disciplinary research environment
encompassing medicinal chemistry, stem cell and chemotherapy. The candidate
will work at the Buchmann Institute for Molecular Life
Sciences/Pharmaceutical Chemistry (Frankfurt am Main). The work will be
performed in close collaboration with other research groups in Frankfurt,
Heidelberg and Jena.

 

We are looking for a PhD-student (graduate student) who is interested to
work on a challenging project at the interface of chemistry, biochemistry
and (stem) cell biology. The aim of our project is to identify new bioactive
compounds and study the mechanism of action for regenerative medicine and
cancer therapy.

 

The candidate will be offered the opportunity to do self-directed research
and develop further scientific qualification.

 

Employment requirements

 

Applicants should have a master degree (or equal) in organic chemistry and
medicinal chemistry. The candidate should have experience in organic
synthesis, and in particular heterocyclic compounds synthesis. Knowledge on
the application of novel synthetic methodologies and PROTAC will be
advantageous. High level knowledge and good communication skills in English
and German are expected.

 

In order to increase the proportion of women in research, we particularly
encourage women to apply for this position. Disabled people will be
considered preferentially in the case of equal aptitude.

 

The planned research will be carried out in an international research
environment at the Life Science Campus Riedberg. Interested candidates are
encouraged to send applications until July, 22th 2020 to the following
e-mail address: Dr. rer.nat.habil.  Xinlai Cheng,
ch...@pharmchem.uni-frankfurt,de, Goethe-Universität, Buchmann Institute for
Molecular Life Sciences; Pharmaceutical Chemistry; Max-von-Laue-Strasse 15.
R. 3.652 ; 60438 Frankfurt am Main.

 

Best,

Dr. Xinlai Cheng




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[ccp4bb] Postdoctoral position in Structural Biology, Cambridge UK

[Janet Deane]

Dear CCP4 community,

I am looking to hire a Postdoctoral Scientist to join our team at the
Cambridge Institute for Medical Research (UK) studying molecular mechanisms
driving neurodegenerative disease. If you are a biochemist/structural
biologist with experience in protein crystallography and/or cryo-EM and
have an interest in studying how human proteins interact with membrane
components apply here:
https://www.jobs.ac.uk/job/CAM118/research-associate-in-structural-biology


-- 
Dr Janet Deane
Wellcome Trust Senior Research Fellow
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Keith Peters Building
Hills Road
Cambridge CB2 0XY
Ph: 01223 762815
je...@cam.ac.uk



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Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Palm, Gottfried]

As a longtime user few comments.
I have also started with writing scripts and have seen a couple of
changes in ccp4. Each time I briefly think "do I have to learn another
script, gui, ...?" but I get used to it and appreciate it, once I can
see the new rationale. Some older procedure are still useful, though.
For one, I simply know how they work and how to read the output, for
another not every option is continued in the follow up format. Do I
wish ccp4 to write a gui for every old program. Certainly not. The
question is probably not, would this be a nice feature to have, but,
where do the programmers spend their time best. If something is really
missing, the discussion in the bulletin board is length enough for the
staff to listen and react. Overall, great thanks to the developers for
their job, even if (or is it because?) most changes have not been
discussed in prior. 

I wouldn't applaud without having a request, I think a doable one.
Please keep the old programs (pdbset, coordconv and co in the bin
directory) and the corresponding manuals
(http://www.ccp4.ac.uk/html/INDEX.html, the fact, that it says CCP4
v7.0 Program Documentation made me fear, that it will go away with
v7.1 and later) as is, even without further development. Old users
will have their scripts for specific purposes, new users won't bother
to learn that, anyway. 

Greetings
  Gottfried








On Tuesday, 07-07-2020 at 21:12 Eleanor Dodson wrote:


I really didnt mean to start this discussion - actually you did, Lau!
I am so grateful to the modern developers who have provided GUIs to
guide our work, and now semi-automated pipelines which mean structures
can be solved routinely and quickly..

 Certainly it is easy enough to bypass fft to generate a map, and
COOT has many many more facilities than the tools I quoted..
But there are some common sense oversights in all software, and it is
often easier to find an outdated procedure to get round the
difficulties than to influence the developers to alter their code.
One example is software which put solutions for heavy atoms, or
molecular replacement distant from the origin . Crystallographically
this is irrelevant but it can lead to problems in visualisation or
building assemblies..
Enough - Eleanor


Cheers anyway 


On Tue, 7 Jul 2020 at 19:36, Dominika Borek  wrote:



 

I remember when I started using ccp4 programs, that frustration of
writing scripts to run programs, and a relief when the first version
of the GUI became available.  I have to say that there is a joy in
knowing that students in 2020 will have to also write scripts to run
unsupported programs (who would guess that fft will be the one of
those?). 



Does CCP4online provide an access to all these programs? I was
hesitant to switch, but it might be the push I needed.



What about discussing these "not taken lightly" decisions on this
forum with, you know, users... Asking couple thousands people with
combined expertise of a few thousands of "X-ray crystallography"
years, should provide deeper insight into needs of community, than
asking programmers around.



D.



On 2020-07-07 12:17 PM, Eleanor Dodson wrote:



 I dont expect anyone to install these in the interface, and indeed if
COOT told you the symmetry operators in a comprehensive way the
distang style searches would be almost redundant .. But sometimes it
helps to have textual information.. clearer andeasier to record than
graphical messages.. E

 




 On Tue, 7 Jul 2020 at 17:42, Christian Roth  wrote:


  I understand that one is used to the programs one is familiar with
and Eleanor especially is very fond of these things, but there are
several things which can be done for example in Coot (symmetry
coordinates etc) . It is just another way to do it. I had the chance
and pleasure to work for a while with the programmers of some of these
programs in one building and such decisions are not taken lightly. But
one cannot support all programs and write for every program interfaces
or even keep two interfaces alive. There are just not enough people
and money to do that. Also most scientific programmers don't get paid
to keep the things just running. Would it be better to have also
programmers to keep legacy up to date and write and update GUI's,
maybe? But again someone needs to pay for that.
Just my 2 cents.
 
Cheers
Christian
 


 On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh  wrote:


   

... and how all these changes being justified?



 



From: CCP4 bulletin board   On Behalf Of Eleanor Dodson
Sent: Tuesday, July 7, 2020 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2



 

 

Yes - there are things I use all the time which are not part of the
CCP4I2 list

 

pdbset to generate symmetry equivalents  or find the centre of mass
etc etc


 

coordconv to turn orthogonal coordinates to fractional - after all we
are crystallographers and need to relate models to unit cells..


 

distang to do a quick check on