[ccp4bb] (Off-topic) X-mas gift idea for cool scientists?
Hi all, Someone pointed me to this: http://cdn3.spiegel.de/images/image-287176-galleryV9-qokb.jpg Apparently, it is a page from this book: http://www.amazon.co.uk/Science-Ink-Tattoos-Obsessed/dp/1402783604 Personally, if I had to get a tramp stamp, it would obviously be of 1cbs (http://pdbe.org/1cbs) --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let "z" be the radius and "a" the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
[ccp4bb] Script problem
Hi there,
I've got a text file with multiple conformations of a ligand that has been
docked to a protein using autodock, which I am trying to split into separate
pdb files in order to visualise in pymol/coot etc.
Previously I've used the script pasted below, but it is now falling over just
after it creates the pdb file with the error:
expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
Can any of you wizzy programmers give me a hand with getting this to work
again? (it's on a mac just in the normal terminal)
Thanks,
Simon
The script:
#!
grep '^DOCKED' output.dlg | cut -c9- > my_docking.pdbqt
cut -c-66 my_docking.pdbqt > my_docking.pdb
# csh to split pdb files from autodock output.
# edit outputname.
#
set outputname=output
set a=`grep ENDMDL my_docking.pdb | wc -l`
set b=`expr $a - 2`
csplit -k -s -n 3 -f $outputname. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
foreach f ($outputname.[0-9][0-9][0-9])
mv $f $f.pdb
end
Re: [ccp4bb] Script problem
Simon
This appears to be a csh or tcsh script: if so the first line must be
"#!/bin/csh" or "#!/bin/tcsh", otherwise it takes it to be a sh
script.
Cheers
-- Ian
On 2 December 2011 14:45, Simon Kolstoe wrote:
> Hi there,
>
> I've got a text file with multiple conformations of a ligand that has been
> docked to a protein using autodock, which I am trying to split into separate
> pdb files in order to visualise in pymol/coot etc.
>
> Previously I've used the script pasted below, but it is now falling over just
> after it creates the pdb file with the error:
>
> expr: syntax error
> csplit: }: bad repetition count
> ./split_results.com: line 11: syntax error near unexpected token `('
> ./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
>
> Can any of you wizzy programmers give me a hand with getting this to work
> again? (it's on a mac just in the normal terminal)
>
> Thanks,
>
> Simon
>
> The script:
>
> #!
> grep '^DOCKED' output.dlg | cut -c9- > my_docking.pdbqt
> cut -c-66 my_docking.pdbqt > my_docking.pdb
> # csh to split pdb files from autodock output.
> # edit outputname.
> #
> set outputname=output
> set a=`grep ENDMDL my_docking.pdb | wc -l`
> set b=`expr $a - 2`
> csplit -k -s -n 3 -f $outputname. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
> foreach f ($outputname.[0-9][0-9][0-9])
> mv $f $f.pdb
> end
Re: [ccp4bb] Script problem
On 02/12/11 14:45, Simon Kolstoe wrote:
I've got a text file with multiple conformations of a ligand that has been
docked to a protein using autodock, which I am trying to split into separate
pdb files in order to visualise in pymol/coot etc.
Previously I've used the script pasted below, but it is now falling over just
after it creates the pdb file with the error:
expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
This doesn't answer your question.
But I'd just do it in Coot:
(define (split-multi-alt-confs)
(using-active-atom
(let ((alt-confs (residue-alt-confs aa-imol aa-chain-id aa-res-no
aa-ins-code)))
(for-each (lambda (alt-conf)
(let* ((ss (string-append "//*/*/*: ," alt-conf ""))
(imol-new (new-molecule-by-atom-selection aa-imol ss))
(new-name (string-append (strip-extension (molecule-name
aa-imol))
"-alt-conf-" alt-conf)))
(set-molecule-name imol-new new-name)))
(residue-alt-confs aa-imol aa-chain-id aa-res-no aa-ins-code)
Centre on your interesting ligand with multiple alt-confs and then use
scripting -> scheme
(split-multi-alt-confs)
If you want to write out the various pdb files, you can add in a
(write-pdb-file imol-new (string-append (molecule-name imol-new) ".pdb"))
before the set-molecule-name... line.
Paul.
[ccp4bb] Diffraction Data Deposition -> Data Woes in general
All: The recent discussion on the CCP4BB about Diffraction Data Deposition made me think at that at least certain people might be interested in an article in Thursday, Dec. 1, New York Times business section entitled "A Genome Deluge" in the print version: http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html?_r=1&scp=1&sq=Genome%20Deluge&st=Search It makes the woes of crystallography data seem tame by comparison. Steven This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
[ccp4bb] refmac model statistics in cif format
Hello all.
Did anyone encounter the following?
Running refmac 5.6.0117/ccp4-6.2/ccp4i-2.1.0, I hoped to obtain, for
pdb_extract, the appropriate output model statistics. When I did not
find the cif file with a modification date similar to my output
coordinates, I noticed a series of
${project}_${crystalname}_${jobnumber}_${dataset}.refmac.cif files,
with appropriate job numbers, but with identical older creation dates.
They all have the same sizes, and random checksum comparison indicates
that they are in fact identical, corresponding to the oldest refmac
job in the group. This does not happen all the time (with other
projects) under this software configuration. Any ideas out there what
might be going on?
Thank you,
Wolfram Tempel
[ccp4bb] Software for optimizing drug molecules
Dear All I have a protein crystal structure with a bonded drug molecule. Before I proceed to serious and expensive computational approach, is there a free and simple software that I can use to do a little optimization of the drug in order to enhance the bonding affinity, solubility and so on? I would like to have a general idea before going further. Any input will be greatly appreciated. Have a good weekend! Jie Liu PHRI/NJMS/UMDNJ
[ccp4bb] Postdoctoral applications JAEdoc-CSIC in Structural biology of viral fibres
Our research group is looking for applicants with a Ph.D. degree to apply for a 3 year postdoctoral position supported by the CSIC JAEdoc program. The deadline for these applications is January 13th, 2012. Information, in Spanish, about this postdoctoral program can be found at the CSIC web page: https://sede.csic.gob.es/servicios/formacion-y-empleo/convocatorias-personal/-/convocatoria/34736 Our main line of research is Structual Biology of Viral Fibres. We use X-ray crystallography to solve fibre structures and aim to use the structural knowledge in applications. Proposals focussing on bacteriophage fibres or on adenovirus fibres are envisaged. We are looking for postdoctoral fellows with experience in one or more of the following techniques and willingness to learn the others. - construction of bacterial expression vectors - protein purification - protein crystallography - biology of bacteriophages or adenovirus Useful language skills include Unix and English. Recent publications of our lab include: - Bartual SG, Otero JM, Garcia-Doval C, Llamas-Saiz AL, Kahn R, Fox GC, van Raaij MJ. Structure of the bacteriophage T4 long tail fiber receptor-binding tip. Proc Natl Acad Sci USA. 2010 Nov 23;107(47):20287-92. - Guardado-Calvo P, Muñoz EM, Llamas-Saiz AL, Fox GC, Kahn R, Curiel DT, Glasgow JN, van Raaij MJ. Crystallographic structure of porcine adenovirus type 4 fiber head and galectin domains. J Virol. 2010 Oct;84(20):10558-68. If selected, positions will be available before summer 2012. There are no nationality restrictions. Interested individuals should submit their CVs and a specific motivation letter by January 2nd, 2012 to the e-mail address indicated. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/index.php/en/research/macromolecular-structures/structural-biology-of-viral-fibres.html mjvanra...@cnb.csic.es
[ccp4bb] Software for showing crystal packing
Hello everyone, Whats a "good" software for showing crystal packing and unit cell, axes , etc... I know pymol and coot will do it but would love to hear other possibilities/ideas. Cheers,
Re: [ccp4bb] Software for showing crystal packing
Swiss PDB viewer will do this. Also XPAND will fill a unit cell with a symmetry generated PDB. Roger Rowlett On Dec 2, 2011 11:05 PM, "Yuri Pompeu" wrote: > Hello everyone, > Whats a "good" software for showing crystal packing and unit cell, axes , > etc... > I know pymol and coot will do it but would love to hear other > possibilities/ideas. > Cheers, >
