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

[Edward A. Berry]

There seems to be a list of the 7.0 programs (and documentation!) still 
available:
http://www.ccp4.ac.uk/html/FUNCTION.html
I hope this is not going away!
eab

On 07/07/2020 12:09 PM, Tim Gruene wrote:

Dear Kelvin,

the command 'ls $CBIN' lists the majority of CCP4 programs on your
system. This probably even works under Windows 10, since the powershell
acts like a linux/unix shell.

Best regards,
Tim

On Tue, 7 Jul 2020 16:00:18 +
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 are how they are now.

Cheers
Christian

On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin
mailto:kelvin@epfl.ch>> wrote: Hi Christian,

I was in particular looking for the fft program (I couldn’t find that
using the method you described) just to convert an mtz into a .map.
Before in version 7.0 I could just browse all programs, now it seems
like I cannot do that (other than using the filter, and some seem to
be missing)

At the end I just used mtz2map in phenix.

--
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 06.07.20, 13:34, "Christian Roth"
mailto:christianroth...@gmail.com>> wrote:

Hi Kelvin,
not quite sure if I understand you correctly,  but if you press the
Task Manager button you get on the right sight a list of topics
(import data, Molecular Replacemnt etc.) each point can be open up
like a file tree to see all programs or pipelines available. You can
search with the search field (Filter) on top for specific program
names. Does that help?

Cheers
Christian

On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin
mailto:kelvin@epfl.ch>> wrote: Hello,

I am looking for a way to find the list of programs accessible using
the new 7.1 CCP4I2 interface? Is this still possible or do I have to
revert back to version 7.0?

Best regards,

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




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

[Eleanor Dodson]

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 <
>> 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
>>>
>>>
>>> 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 <+41%2021%2069%C2%A030267>
>>>

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

[Dominika Borek]

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 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 [1] 
> 
> 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 [2] 
> 
> If unreachable: +41 21 69 34494 [2] 
> 
> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" 
>  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  
> 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  
> 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 

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

[Eleanor Dodson]

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 <
> 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
>>
>>
>> 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 <+41%2021%2069%C2%A030267>
>>
>> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>>
>>
>>
>>
>>
>> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" <
>> CCP4BB@JISCMAIL.AC.UK on behalf of christianroth...@gmail.com> wrote:
>>
>>
>>
>> yes Eleanor is right. command line still works.[image: :-)]
>>
>> fft is also in 7.1 distribution.
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson 
>> 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 
>> 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 are how they are now.
>>
>>
>>
>> Cheers
>>
>> Christian
>>
>>
>>
>> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:
>>
>> Hi Christian,
>>
>>
>>
>> I was in particular looking for the fft program (I couldn’t find that
>> using the method you described) just to convert an mtz into a .map. Before
>> in version 7.0 I could just browse all programs, now 

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

[Christian Roth]

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
>
>
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" <
> CCP4BB@JISCMAIL.AC.UK on behalf of christianroth...@gmail.com> wrote:
>
>
>
> yes Eleanor is right. command line still works.[image: :-)]
>
> fft is also in 7.1 distribution.
>
>
>
>
>
>
>
> On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson 
> 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 
> 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 are how they are now.
>
>
>
> Cheers
>
> Christian
>
>
>
> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:
>
> Hi Christian,
>
>
>
> I was in particular looking for the fft program (I couldn’t find that
> using the method you described) just to convert an mtz into a .map. Before
> in version 7.0 I could just browse all programs, now it seems like I cannot
> do that (other than using the filter, and some seem to be missing)
>
>
>
> At the end I just used mtz2map in phenix.
>
>
>
> --
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 06.07.20, 13:34, "Christian Roth"  wrote:

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

[Oganesyan, Vaheh]

… 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 
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 are how they are now.

Cheers
Christian

On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:
Hi Christian,

I was in particular looking for the fft program (I couldn’t find that using the 
method you described) just to convert an mtz into a .map. Before in version 7.0 
I could just browse all programs, now it seems like I cannot do that (other 
than using the filter, and some seem to be missing)

At the end I just used mtz2map in phenix.

--
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 06.07.20, 13:34, "Christian Roth" 
mailto:christianroth...@gmail.com>> wrote:

Hi Kelvin,
not quite sure if I understand you correctly,  but if you press the Task 
Manager button you get on the right sight a list of topics (import data, 
Molecular Replacemnt etc.) each point can be open up like a file tree to see 
all programs or pipelines available. You can search with the search field 
(Filter) on top for specific program names.
Does that help?

Cheers
Christian

On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:
Hello,

I am looking for a way to find the list of programs accessible using the new 
7.1 CCP4I2 interface? Is this still possible or do I have to revert back to 
version 7.0?

Best regards,

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




To unsubscribe from the 

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

[Eleanor Dodson]

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
>
>
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" <
> CCP4BB@JISCMAIL.AC.UK on behalf of christianroth...@gmail.com> wrote:
>
>
>
> yes Eleanor is right. command line still works.[image: :-)]
>
> fft is also in 7.1 distribution.
>
>
>
>
>
>
>
> On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson 
> 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 
> 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 are how they are now.
>
>
>
> Cheers
>
> Christian
>
>
>
> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:
>
> Hi Christian,
>
>
>
> I was in particular looking for the fft program (I couldn’t find that
> using the method you described) just to convert an mtz into a .map. Before
> in version 7.0 I could just browse all programs, now it seems like I cannot
> do that (other than using the filter, and some seem to be missing)
>
>
>
> At the end I just used mtz2map in phenix.
>
>
>
> --
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 06.07.20, 13:34, "Christian Roth"  wrote:
>
>
>
> Hi Kelvin,
>
> not quite sure if I understand you correctly,  but if you press the Task
> Manager button you get on the right sight a list of topics (import data,
> Molecular Replacemnt etc.) each point can be open up like a file tree to
> see all programs or pipelines available. You can search with the search
> field (Filter) on top for specific program names.
>
> Does that help?
>
>
>
> Cheers
>
> Christian
>
>
>
> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:
>
> Hello,
>
>
>
> I am looking for a way to find the list of programs accessible using the
> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert
> back to version 7.0?
>
>
>
> Best regards,
>
>
>
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> 

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

[Palm, Gottfried]

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 [1]
Phone: +41 21 69 30267 [2]



If unreachable: +41 21 69 34494 [2]




 



 

  

On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" 
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  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  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 are how they are now.


 

 


 

Cheers


 

Christian





 

  

On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:




   

 Hi Christian,



  



 I was in particular looking for the fft program (I couldn’t find
that using the method you described) just to convert an mtz into a
.map. Before in version 7.0 I could just browse all programs, now it
seems like I cannot do that (other than using the filter, and some
seem to be missing)



  



 At the end I just used mtz2map in phenix.



  

 

 -- 
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 [1]
Phone: +41 21 69 30267 [2]



 If unreachable: +41 21 69 34494 [2]




  



  

  

 On 06.07.20, 13:34, "Christian Roth"  wrote:



 

  


  

 Hi Kelvin,


 

 not quite sure if I understand you correctly,  but if you press the
Task Manager button you get on the right sight a list of topics
(import data, Molecular Replacemnt etc.) each point can be open up
like a file tree to see all programs or pipelines available. You can
search with the search field (Filter) on top for specific program
names.


 

 Does that help?


 

  


 

 Cheers


 

 Christian





  

  

 On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:




   

 Hello,



  



 I am looking for a way to find the list of programs accessible using
the new 7.1 CCP4I2 interface? Is this still possible or do I have to
revert back to version 7.0?



  



 Best regards,



  



 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 [1]
Phone: +41 21 69 30267 [2]



 If unreachable: +41 21 69 34494 [2]



  





  

  
-
 



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 



 


 


 

 
-
 


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 





Links:
--
[1] mailto:kelvin@epfl.ch
[2] tel:+41%2021%2069%C2%A030267

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

[Tim Gruene]

Dear Kelvin,

the command 'ls $CBIN' lists the majority of CCP4 programs on your
system. This probably even works under Windows 10, since the powershell
acts like a linux/unix shell.

Best regards,
Tim

On Tue, 7 Jul 2020 16:00:18 +
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 are how they are now.
> 
> Cheers
> Christian
> 
> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin
> mailto:kelvin@epfl.ch>> wrote: Hi Christian,
> 
> I was in particular looking for the fft program (I couldn’t find that
> using the method you described) just to convert an mtz into a .map.
> Before in version 7.0 I could just browse all programs, now it seems
> like I cannot do that (other than using the filter, and some seem to
> be missing)
> 
> At the end I just used mtz2map in phenix.
> 
> --
> 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 06.07.20, 13:34, "Christian Roth"
> mailto:christianroth...@gmail.com>> wrote:
> 
> Hi Kelvin,
> not quite sure if I understand you correctly,  but if you press the
> Task Manager button you get on the right sight a list of topics
> (import data, Molecular Replacemnt etc.) each point can be open up
> like a file tree to see all programs or pipelines available. You can
> search with the search field (Filter) on top for specific program
> names. Does that help?
> 
> Cheers
> Christian
> 
> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin
> mailto:kelvin@epfl.ch>> wrote: Hello,
> 
> I am looking for a way to find the list of programs accessible using
> the new 7.1 CCP4I2 interface? Is this still possible or do I have to
> revert back to version 7.0?
> 
> Best regards,
> 
> 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
> 
> 
> 
> 
> 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
> 
> 
> 
> 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
> 
> This 

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

[Lau Kelvin]

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 are how they are now.

Cheers
Christian

On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:
Hi Christian,

I was in particular looking for the fft program (I couldn’t find that using the 
method you described) just to convert an mtz into a .map. Before in version 7.0 
I could just browse all programs, now it seems like I cannot do that (other 
than using the filter, and some seem to be missing)

At the end I just used mtz2map in phenix.

--
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 06.07.20, 13:34, "Christian Roth" 
mailto:christianroth...@gmail.com>> wrote:

Hi Kelvin,
not quite sure if I understand you correctly,  but if you press the Task 
Manager button you get on the right sight a list of topics (import data, 
Molecular Replacemnt etc.) each point can be open up like a file tree to see 
all programs or pipelines available. You can search with the search field 
(Filter) on top for specific program names.
Does that help?

Cheers
Christian

On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:
Hello,

I am looking for a way to find the list of programs accessible using the new 
7.1 CCP4I2 interface? Is this still possible or do I have to revert back to 
version 7.0?

Best regards,

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




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Re: [ccp4bb] Protein expression (codon bias)

[00000c2488af9525-dmarc-request]

I did crystallise a protein expressed in M. smegmatis a while ago (early 90's)! The cloning was done by Ying Zhang:https://www.jhsph.edu/faculty/directory/profile/786/ying-zhangIt might be worth dropping him a line. That's all I can suggest, sorry!!Good luck.Jon CooperOn 7 Jul 2020 10:07, Matthew Snee  wrote:

Hi all




I'm designing genes for _expression_ in M. smegmatis (safe host for Mtb proteins), but its not possible (or advisable due to the GC content) to optimise for

mycobacterial _expression_.




Would anyone with experience be able to tell me if its fine to stick with the E. coli codon optimisation, or if there is an advantage going with b. subtilis (or another G+ organism that is in Thermo's list).




Best wishes




Matthew.



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

[Christian Roth]

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 
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 
> 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 are how they are now.
>>
>> Cheers
>> Christian
>>
>> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:
>>
>>> Hi Christian,
>>>
>>>
>>>
>>> I was in particular looking for the fft program (I couldn’t find that
>>> using the method you described) just to convert an mtz into a .map. Before
>>> in version 7.0 I could just browse all programs, now it seems like I cannot
>>> do that (other than using the filter, and some seem to be missing)
>>>
>>>
>>>
>>> At the end I just used mtz2map in phenix.
>>>
>>>
>>>
>>> --
>>> 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 <+41%2021%2069%C2%A030267>
>>>
>>> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>>>
>>>
>>>
>>>
>>>
>>> On 06.07.20, 13:34, "Christian Roth"  wrote:
>>>
>>>
>>>
>>> Hi Kelvin,
>>>
>>> not quite sure if I understand you correctly,  but if you press the Task
>>> Manager button you get on the right sight a list of topics (import data,
>>> Molecular Replacemnt etc.) each point can be open up like a file tree to
>>> see all programs or pipelines available. You can search with the search
>>> field (Filter) on top for specific program names.
>>>
>>> Does that help?
>>>
>>>
>>>
>>> Cheers
>>>
>>> Christian
>>>
>>>
>>>
>>> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:
>>>
>>> Hello,
>>>
>>>
>>>
>>> I am looking for a way to find the list of programs accessible using the
>>> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert
>>> back to version 7.0?
>>>
>>>
>>>
>>> Best regards,
>>>
>>>
>>>
>>> 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 <+41%2021%2069%C2%A030267>
>>>
>>> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> 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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Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Eleanor Dodson]

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 
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 are how they are now.
>
> Cheers
> Christian
>
> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:
>
>> Hi Christian,
>>
>>
>>
>> I was in particular looking for the fft program (I couldn’t find that
>> using the method you described) just to convert an mtz into a .map. Before
>> in version 7.0 I could just browse all programs, now it seems like I cannot
>> do that (other than using the filter, and some seem to be missing)
>>
>>
>>
>> At the end I just used mtz2map in phenix.
>>
>>
>>
>> --
>> 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 <+41%2021%2069%C2%A030267>
>>
>> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>>
>>
>>
>>
>>
>> On 06.07.20, 13:34, "Christian Roth"  wrote:
>>
>>
>>
>> Hi Kelvin,
>>
>> not quite sure if I understand you correctly,  but if you press the Task
>> Manager button you get on the right sight a list of topics (import data,
>> Molecular Replacemnt etc.) each point can be open up like a file tree to
>> see all programs or pipelines available. You can search with the search
>> field (Filter) on top for specific program names.
>>
>> Does that help?
>>
>>
>>
>> Cheers
>>
>> Christian
>>
>>
>>
>> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:
>>
>> Hello,
>>
>>
>>
>> I am looking for a way to find the list of programs accessible using the
>> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert
>> back to version 7.0?
>>
>>
>>
>> Best regards,
>>
>>
>>
>> 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 <+41%2021%2069%C2%A030267>
>>
>> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>>
>>
>>
>>
>> --
>>
>> 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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Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Christian Roth]

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 are how they are now.

Cheers
Christian

On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin  wrote:

> Hi Christian,
>
>
>
> I was in particular looking for the fft program (I couldn’t find that
> using the method you described) just to convert an mtz into a .map. Before
> in version 7.0 I could just browse all programs, now it seems like I cannot
> do that (other than using the filter, and some seem to be missing)
>
>
>
> At the end I just used mtz2map in phenix.
>
>
>
> --
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 06.07.20, 13:34, "Christian Roth"  wrote:
>
>
>
> Hi Kelvin,
>
> not quite sure if I understand you correctly,  but if you press the Task
> Manager button you get on the right sight a list of topics (import data,
> Molecular Replacemnt etc.) each point can be open up like a file tree to
> see all programs or pipelines available. You can search with the search
> field (Filter) on top for specific program names.
>
> Does that help?
>
>
>
> Cheers
>
> Christian
>
>
>
> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:
>
> Hello,
>
>
>
> I am looking for a way to find the list of programs accessible using the
> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert
> back to version 7.0?
>
>
>
> Best regards,
>
>
>
> 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 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
> --
>
> 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] Accessing full list of programs in CCP4I2

[Lau Kelvin]

Hi Christian,

I was in particular looking for the fft program (I couldn’t find that using the 
method you described) just to convert an mtz into a .map. Before in version 7.0 
I could just browse all programs, now it seems like I cannot do that (other 
than using the filter, and some seem to be missing)

At the end I just used mtz2map in phenix.

--
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 06.07.20, 13:34, "Christian Roth" 
mailto:christianroth...@gmail.com>> wrote:

Hi Kelvin,
not quite sure if I understand you correctly,  but if you press the Task 
Manager button you get on the right sight a list of topics (import data, 
Molecular Replacemnt etc.) each point can be open up like a file tree to see 
all programs or pipelines available. You can search with the search field 
(Filter) on top for specific program names.
Does that help?

Cheers
Christian

On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin 
mailto:kelvin@epfl.ch>> wrote:
Hello,

I am looking for a way to find the list of programs accessible using the new 
7.1 CCP4I2 interface? Is this still possible or do I have to revert back to 
version 7.0?

Best regards,

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




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Re: [ccp4bb] cavities volume calculations

[vincent Chaptal]

Dear nathalie,

from the top of my head, I use FLOOD from Upsala software factory: The 
program fills in water molecules in the cavity; you can specify a radius 
and start from a point in the pdb, like a side chain atom or you can put 
a dummy water molecule in the middle of your cavity and start flooding 
from there.
I recommend inspecting the flooding result as it might find every little 
crack, which might not be what you want, or fill in other unwanted 
spaces. This flood pdb can be easily edited in Pymol to remove selected 
atoms and get the volume that you want.
To measure this volume, well... I don't remember exactly, but I think 
VOIDOO can give you this result. Others might be able to chip in too.


Best of luck.
Vincent

Le 07/07/2020 à 10:21, Nathalie Colloc'h a écrit :


thanks joana,

it is true that you can give a set of coordinates to Caver, but to my 
knowledge, Caver look for tunnels only.


It does not seem to compute the volume of surface pockets or internal 
cavities.


best

nathalie


Le 06/07/2020 à 15:46, Joana Pereira a écrit :


Hi Nathalie,

I think Caver tools can do that: https://caver.cz/index.php?sid=133

Best wishes
Joana

On 6. Jul 2020, at 15:39, Nathalie Colloc'h > wrote:


Hi everybody,

I am aware of programs which compute the volume of cavities and pockets.

However, I am looking for a program which can compute the volume 
around a given point (given by its coordinates), and return also the 
information about if it is an open surface pocket or an internal cavity.


Thanks a lot

Nathalie


--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
coll...@cyceron.fr 
http://www.istct.cyceron.fr/



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--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
coll...@cyceron.fr
http://www.istct.cyceron.fr/




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--

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab


MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

http://mmsb.cnrs.fr/en/





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Re: [ccp4bb] cavities volume calculations

[Flavio Di Pisa]

Dear Nathalie,

try CASTp ( http://sts.bioe.uic.edu/castp/index.html?2cpk  )

Cheers,
Flavio.

Il giorno lun 6 lug 2020 alle ore 15:41 Nathalie Colloc'h <
coll...@cyceron.fr> ha scritto:

> Hi everybody,
>
> I am aware of programs which compute the volume of cavities and pockets.
>
> However, I am looking for a program which can compute the volume around
> a given point (given by its coordinates), and return also the
> information about if it is an open surface pocket or an internal cavity.
>
> Thanks a lot
>
> Nathalie
>
>
> --
> Dr. Nathalie Colloc'h
> équipe CERVOxy
> ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
> Centre Cyceron
> bd Becquerel
> 14074 Caen cedex
> France
> 33.2.31.47.01.32
> coll...@cyceron.fr
> http://www.istct.cyceron.fr/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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[ccp4bb] Protein expression (codon bias)

[Matthew Snee]

Hi all

I'm designing genes for expression in M. smegmatis (safe host for Mtb 
proteins), but its not possible (or advisable due to the GC content) to 
optimise for
mycobacterial expression.

Would anyone with experience be able to tell me if its fine to stick with the 
E. coli codon optimisation, or if there is an advantage going with b. subtilis 
(or another G+ organism that is in Thermo's list).

Best wishes

Matthew.



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Re: [ccp4bb] cavities volume calculations

[Nathalie Colloc'h]

thanks joana,

it is true that you can give a set of coordinates to Caver, but to my 
knowledge, Caver look for tunnels only.


It does not seem to compute the volume of surface pockets or internal 
cavities.


best

nathalie


Le 06/07/2020 à 15:46, Joana Pereira a écrit :


Hi Nathalie,

I think Caver tools can do that: https://caver.cz/index.php?sid=133

Best wishes
Joana

On 6. Jul 2020, at 15:39, Nathalie Colloc'h > wrote:


Hi everybody,

I am aware of programs which compute the volume of cavities and pockets.

However, I am looking for a program which can compute the volume 
around a given point (given by its coordinates), and return also the 
information about if it is an open surface pocket or an internal cavity.


Thanks a lot

Nathalie


--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
coll...@cyceron.fr 
http://www.istct.cyceron.fr/



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--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
coll...@cyceron.fr
http://www.istct.cyceron.fr/




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Re: [ccp4bb] Twin law definition in REFMAC5

[Petrus Zwart]

On Mon, Jul 6, 2020 at 10:33 PM Petr Kolenko 
wrote:

> Dear Eleanor,
> The unit cell parameters are 117.385  155.506  155.611  90.00  90.00
> 90.00, as you expected. The twin law was recognized using phenix.xtriage.
> If I refine the structure using phenix.refine with no twin law and the
> Rwork/free values were 28/33. With the twin law "-h,l,k" the R values are
> 22/28. Moreover, many weird features of the electron density map
> disappeared. But I used phenix.refine only as a proof, because I refined
> the structure using REFMAC5 from the beginning and I do not want to change
> the refinement program during the structure refinement.
>


you break my heart 

:-)




> Thank you for your response,
> Petr
>
> 
> From: Eleanor Dodson 
> Sent: Tuesday, July 7, 2020 7:08:44 AM
> To: Petr Kolenko
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Twin law definition in REFMAC5
>
> Is that twin law possible? Presumably the cell lengths for b and c are
> close but you are swapping a 2fold axis along c for a 21 axis along b?
> Eleanor
>
> On Tue, 7 Jul 2020 at 05:36, Petr Kolenko  > wrote:
> Dear colleagues,
> I have a crystal with space group P21212 and merohedral twinning according
> to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5
> recognizes a different twin law and does not refine the structure properly.
> Is there a way to tell REFMAC5 the proper twin law? I tried to find the
> information in the documentation, but I failed. This is an older project
> running under i, not i2.
> Best regards,
> Petr
>
> 
>
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-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
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