[ccp4bb] AW: [ccp4bb] JLigand distorts molecules

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, 1

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

> > > I use the exact same input using ccp4 6.1.13 and > Refmac 5.5 and all is good. I am forced to use the > > > old ccp4 and refmac to publish. Rf 17 R 15. > > > thanks > > > > > > -- > > > Kenneth A. Satyshur, M.S.,Ph.D. > > > Associate Scientist > > > University of Wisconsin > > > Madison, Wisconsin 53706 > > > 608-215-5207 > > > > - -- > > - -- > > Dr Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > > > -BEGIN PGP SIGNATURE- > > Version: GnuPG v1.4.10 (GNU/Linux) > > Comment: Using GnuPG with Mozilla - > http://enigmail.mozdev.org/ > > > > > iD8DBQFOqluhUxlJ7aRr7hoRAjadAJ9Df2hbWjixDCdS3Z4DB7mm4ubRIACeOw6X > > 6JkjyzRUdxqjH/9b/oftBjE= > > =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

Re: [ccp4bb] data processing problem with ice rings

> how should I do to > process the dataset properly? Any suggestion about this > super ice rings? > Thanks! > > Tiantian > > -- > Shanghai Institute of Materia Medica, Chinese Academy of > Sciences > Address: Room 101, 646 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

[ccp4bb] AW: [ccp4bb] changing residue numbering in Coot

uot;X", press [Shift]&[Ctrl], go the the last "X" 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-Universit

Re: [ccp4bb] How to create a link-record

ped 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

[ccp4bb] AW: [ccp4bb] Calculating shape complementarity (sc) parameter using CCP4

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:

[ccp4bb] AW: [ccp4bb] Detergent/lipid crystal diffraction pattern?

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 crysta

[ccp4bb] AW: [ccp4bb] Can procheck or other tools report bad geometry for ligand?

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

[ccp4bb] AW: [ccp4bb] coot

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:

[ccp4bb] AW: [ccp4bb] SC

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

[ccp4bb] AW: [ccp4bb] bruker smart and mosflm

>>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

[ccp4bb] AW: [ccp4bb] Format conversion of Shelx coordinate file

"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 motto/

[ccp4bb] NAD cif in Jligand

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 fi

Re: [ccp4bb] Understanding Conformational Differences

0208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-kell...@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

[ccp4bb] AW: [ccp4bb] is my crystal twinned or not?

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 ano