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
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.
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But there are some common sense oversights in all software, and it is often easier to find an outdated procedure to get round the difficulties than to influence the developers to alter their code.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
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..
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
... and how all these changes being justified?
From: CCP4 bulletin board <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..
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.
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
....yes Eleanor is right. command line still works.![:-)]()
fft is also in 7.1 distribution.
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..
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.
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.
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.
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.
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