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
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,
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
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
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 mi
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, bu
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
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
>
>
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 S
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,
Kel
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
>
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.
Gr
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 t
… 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 CC
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
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
O
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 w
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 gener
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
19 matches
Mail list logo
