Re: [ccp4bb] Stand-alone programs

2017-12-22 Thread Paul Emsley

On 22/12/2017 16:51, Carter, Charlie wrote:

This is a strange question, even from me.

I’ve an undergraduate working on a project that requires superimposing large 
numbers of pdb files. I would like to have him use lsqkab but he is rather 
unsophisticated in a computational sense. He is already using various other 
programs, e.g. Pymol, which he has had to download and install. I’d like to 
avoid having him install and then learn to set up and use the entire ccp4 suite 
if he will not need any of the programs except lsqkab. Further, I feel that 
lsqkab brings functionality to the table that is superior to that in Pymol.

Is there any way to short cut the full CCP4 installation and provide him with a 
functioning lsqkab module based on my ccp4 installation? In a bit more detail, 
is there any way to load the necessary dynamic libraries so that lsqkab will 
work with input pdb files?




Yes.

cd $CCP4_MASTER
tar cvzf ~/just-lsqkab-bits.tar.gz bin/lsqkab lib/libccpf* lib/libccp4* 
lib/libmmdb2.* \
lib/data/syminfo.lib include/environ.def include/default.def

Then (having transferred just-lsqkab-bits.tar.gz as needed)

(just once)

cd some/where/for/extraction/on/student/machine

tar xf just-lsqkab-bits.tar.gz

(every time lsqkab is to be used)

setenv CCP4 /absolutify/some/where/for/extraction/on/student/machine
setenv CCP4_SCR ~/scratch # or wherever, create as needed
setenv CINCL $CCP4/include
setenv CLIBD $CCP4/lib/data

(tada!)

bin/lsqkab XYZIN .. (etc)

Your student can add /absolutify/some/where/for/extraction/on/student/machine/bin to your student's path, of 
course.


Wishing you well,

Paul.

(I'd do superpositions in Coot (which also brings extra functionality to the 
table), it goes without saying :-))


[ccp4bb] Stand-alone programs

2017-12-22 Thread Carter, Charlie
This is a strange question, even from me.

I’ve an undergraduate working on a project that requires superimposing large 
numbers of pdb files. I would like to have him use lsqkab but he is rather 
unsophisticated in a computational sense. He is already using various other 
programs, e.g. Pymol, which he has had to download and install. I’d like to 
avoid having him install and then learn to set up and use the entire ccp4 suite 
if he will not need any of the programs except lsqkab. Further, I feel that 
lsqkab brings functionality to the table that is superior to that in Pymol.

Is there any way to short cut the full CCP4 installation and provide him with a 
functioning lsqkab module based on my ccp4 installation? In a bit more detail, 
is there any way to load the necessary dynamic libraries so that lsqkab will 
work with input pdb files?

Thanks,

Charlie





[ccp4bb] Announcement: Instruct/CIISB Fragment Screening course in Vestec (Prague area) on April 5 and 6 (arrival on April 4, departure on April 7)

2017-12-22 Thread Vellieux Frédéric
Dear all,

Just before the end of the year break, before the festive season:

The Centre of Molecular Structure (IBT, Biocev, Vestec, Prague area, Czech 
Republic, one the the two Instruct CZ and CIISB sites) is organising a course 
on April 5 and 6, 2018 (arrival in Vestec on April 4, departure on April 7).

Title: Instruct / CIISB course on fragment screening using crystallography 
laboratory equipment.

The course has two parts: half a day devoted to lectures on April 5 morning, in 
the Biocev auditorium - no registration is needed, everyone is welcome to 
attend the presentations and lectures given by:
Jan Dohnalek (IBT Biocev Vestec)
Andreas Heine (IPC Marburg)
Bohdan Schneider (IBT Biocev Vestec)
Tomas Koval (IBT Biocev Vestec)
Petr Pompach (CMS IBT Biocev Vestec)
Manfred Weiss (Bessy II)
Sameer Velankar (to be confirmed, or another speaker from EBI)
John Darby (Chemistry, U. of York)

The remaining part of the workshop (three half days, April 5 afternoon, April 6 
morning and April 6 afternoon) consist of a "workshop", hands on sessions for 
16 registered participants. This part will be dealing with

-  The initial pre-screening using biophysical methods (Tatsiana 
Charnavets, CMS)

-  Dispensing target protein crystals to a fragment library (Jiri 
Pavlicek, CMS)

-  In situ testing of crystal diffraction, data collection and 
evaluation of the results (Jiri Pavlicek, CMS)

Due to generous Instruct funding, there will be no registration fees for the 16 
registered participants (hands-on sessions), all costs will be covered from the 
first night (April 4 to April 5) in hotel u Krbu in Vestec (ca. 15 minutes walk 
from the Biocev) to the departure from the hotel on April 7 after breakfast. 
For those accepted, of course you are most welcome to arrive earlier and / or 
depart from the Prague area later in order to discover / visit one of Europe's 
most beautiful cities, Prague. There are numerous hotels and "BnB" style 
accomodation available. This isn't part of the course and must be arranged by 
yourselves. Registered participants (and also the people wanting to attend the 
lectures only) must cover the cost of travelling to the venue.

Again, everyone is welcome for the lectures on April 5 morning, in the Biocev 
auditorium

All information (including Course poster) and details can be found on:
http://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/

The deadline for submission of applications is February 9, 2018. Applications 
from laboratories located abroad are especially welcome.

Can you forward this information to anyone you think would be interested ? 
Thanks.

I wish you all a very good festive season.

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786

-

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