not on my machine (Suse11.3)
Jligand (1.0.25) - Load Ligand - type 3GP - the ligand looks totally
normal, incl the C6,O6 double bond.
Cheers
Stefan
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Boaz
Shaanan
Gesendet: Donnerstag, 12.
=
=xRXE
-END PGP SIGNATURE-
Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst.f.Org.Chem.u.Biochem
Albertstrasse 21
79104 Freiburg
Tel. +49 761 2035970
Fax. +49 761 2036161
Songtao Road, Zhangjiang Hi-Tech
Park,
Shanghai, 201203
Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst.f.Org.Chem.u.Biochem
Albertstrasse 21
79104 Freiburg
Tel. +49 761 2035970
Fax. +49 761 2036161
in your chain.
Then perform a replace/Find by selecting only the Selection option ...
done. Repeat for each chain.
Cheers
Stefan
__
Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst. f. Org.Chemie u. Biochemie
Raum 911
Albertstrasse 21
79104 Freiburg
office
typed the link record
in the header information of the pdb file, however when I
refine the structure using this pdb, the output pdb does
not show the link record. Please can anyone help me with
establishing a link record in the pdb?
Thank you very much,
Subhangi
Dr Stefan Gerhardt
Albert
Hi Li Chen,
try
#!/bin/sh -f
sc xyzin 1XOU.pdb eof-sc
Molecule 1
CHAIN A
MOLECULE 2
CHAIN B
end
eof-sc
in a small script lets say sc.com
then run %sc.com |tee sc.log
and you'll get something like this :
Summary of results:
Hi Pius
DS_1.png - protein diffraction !
DSA6E.png - surface ice formation and protein crystal which did not survive
the freezing !!
DSA2F.png - protein crystal which does not diffract, but cryo condition is
right !
Psp4f.png - internal ice formation plus some surface ice also protein
crystal
Dear Roberto,
I believe there are many badly modeled ligands with distorted geometry
deposited in the PDB.
Basically, because they haven't been checked properly beforehand, so I think
running a geometry check of you desired ligand against the PDB.
I think running your modeled geometry against
Hi Zheng
I think, it's much easier to go this way:
Coot - Extensions - NCS - Copy NCS Chain or Copy NCS Residue Range
Cheers
Stefan
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zheng
Zhou
Gesendet: Montag, 28. Februar 2011 12:13
An:
Hi,
you should be able to run SC from the command line or from a short shell
script:
#!/bin/sh -f
sc xyzin FAb-antigen.pdb eof-sc
Molecule 1
CHAIN A
MOLECULE 2
CHAIN B
end
eof-sc
cheers
Stefan
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
I'd have to say, in general the easiest thing to do when confronted with
Mosflm issues is to get in touch with the authors and ask them. We are all
very friendly, approachable people who will do our best to help!
I cannot agree more with this...
Many thanks with all your help provided so far...
Coot MacGyver
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Francois Berenger
Gesendet: Dienstag, 31. August 2010 08:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Format conversion of Shelx coordinate file
Hi,
What is the
Dear all,
I'm trying using Jligand for generating a new ligand describition. Have to
say I'm using it for the first time, but so far it look very nice.
I trying to optimize a new lib file for a modified NAD molecule.
I'm using a nad_ebi.cif file of NAD supplied by Garib a while ago which
works
...@northwestern.edu
***
Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst.f.Org.Chem.u.Biochem
Albertstrasse 21
79104 Freiburg
Tel. +49 761 2035970
Fax. +49 761 2036161
Dear Matt,
as Eleanor pointed out your obtained solution is certainly correct, and for
2.8ang resolution almost as good as it could get.
But could it not just be that the residual density you observed in your
electron density (There is some density for the receptor ) isn't the
receptor but
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