[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, 12. Januar 2012 13:44 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] JLigand distorts molecules Hi, You are right. I happen to have 1.0.7 lying around and there 3GP is fine. A bug must have been introduced somewhere on the way between versions. I wonder whether it's only 3GP. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Wolfgang Skala [wolfgang.sk...@sbg.ac.at] Sent: Thursday, January 12, 2012 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] JLigand distorts molecules Dear colleagues, has anyone of you experienced problems regarding regularization in JLigand? When I start the first tutorial and load 3'-GMP (3GP), the double bond to the O6 atom is about twice as long as the remainder of the molecule; the rings are also highly distorted. Similarly, if I modify a ligand, regularization yields a structure that is definitely out of shape. I'm using JLigand 1.0.25 on Ubuntu 11.10 and tried both the current version of OpenJDK and Sun Java JRE 6u30; even compiling the JLigand source on my platform with Sun Java SE 6u30 did not help. Kind regards, Wolfgang Skala -- Structural Biology Group / Department of Molecular Biology University of Salzburg Billrothstraße 11 5020 Salzburg Austria Phone: +43 662 8044 7278 http://www.uni-salzburg.at/xray
Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
, 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
try a frozen xtal ... On Fri, 14 Oct 2011 13:12:12 +0800 ChenTiantian chentiantian2...@gmail.com wrote: Hi there, I am processing a dataset which has bad ice rings (as you can see in the attach png file). I tried both XDS and imosflm, and got similar results, it seems that adding EXCLUDE_RESOLUTION_RANGE cannot get rid of the effects of the ice rings. the following is part of the CORRECT.LP which is the second attached file, you can find more details there. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 4.24 371525537 5545 99.9% 46.9% 52.7% 371502.4850.8%19.4% -28% 0.5135136 3.01 553449002 9840 91.5% 62.7% 65.1% 551161.7668.3%48.1% -28% 0.5207760 2.46 84636 12699 12703 100.0% 67.4% 84.7% 846341.5573.0%54.2% -19% 0.513 12104 2.13 97910 14743 14987 98.4% 254.5%199.3% 979080.16 276.2% 4899.9% -23% 0.473 14037 1.90 110260 16846 16940 99.4% 299.2%303.3% 1102450.06 325.0% -99.9% -17% 0.422 15995 1.74 118354 18629 18744 99.4% 1062.0% 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 1.61 122958 20193 20331 99.3% 967.5% 1571.1% 1228680.10 1059.7% 987.3%-2% 0.402 18348 1.51 125075 21554 21794 98.9% 838.9% 1355.1% 1249330.08 922.6% 1116.9%-1% 0.402 18977 1.42 72057 17042 23233 73.4% 640.8%775.3% 703910.08 732.5% 826.7%-8% 0.425 10003 total 823746 136245144117 94.5% 166.4%166.7% 8215620.40 181.1% 296.7% -15% 0.435 119774 Note that I/SIGMA of each resolution shell is 2.5, so 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
Hi, worth to try moleman - %moleman Choose READ_pdb_file - your_pdbfile.pdb Choose AUTO_chain_segid Choose WRITE_pdb_file - out.pdb Or the tedious NEDIT way Open your pdb.file in nedit, mark ONLY the chain ID column - put your cursor before the first 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-Universität Freiburg Inst. f. Org.Chemie u. Biochemie Raum 911 Albertstrasse 21 79104 Freiburg office: +49 761 2035970
Re: [ccp4bb] How to create a link-record
dear Subhangi, have a look at http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link cheers Stefan On Wed, 22 Jun 2011 14:04:31 +0100 Subhangi Ghosh subhang...@gmail.com wrote: Hello All, I have a covalent link in my structure model that I created using JLigand. I manually 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-Ludwigs-Universität Freiburg Inst.f.Org.Chem.u.Biochem Albertstrasse 21 79104 Freiburg Tel. +49 761 2035970 Fax. +49 761 2036161
[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: D(A-B) D(B-A) D(A-B)+D(B-A)/2 Mean 0.6790.6860.682 Median 0.5810.5800.581 S(A-B) S(B-A) S(A-B)+S(B-A)/2 Mean 0.6340.6290.631 Median 0.6840.6820.683 Shape complementarity statistic Sc =0.683 Logfile attached !! :) cheers Stefan -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Li Chen Gesendet: Mittwoch, 1. Juni 2011 15:18 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Calculating shape complementarity (sc) parameter using CCP4 Dear all, I am trying to use the sc program in CCP4 suite the calculate the shape complementarity parameter, but there is problem with reading the PDB file. Unfortunately the examples webpage is not active anymore so I have no idea how to fix it. I attached the output log as follows: BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: SC version 6.1 : 17/09/07## ### User: li Run date: 30/ 5/2011 Run time: 20:18:39 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Sc (Version 2.0): A program for determining Shape Complementarity Copyright Michael Lawrence, Biomolecular Research Institute 343 Royal Parade Parkville Victoria Australia This program is designed to compute Sc between two molecules. It also allows the normal products to be merged into grasp surface files for display in grasp. ___ FORMATTED OLD file opened on unit 7 BFONT COLOR=#FF!--SUMMARY_BEGIN-- Logical name: SCRADII, Filename: /home/li/NMRsoftwareInstruction/CCP4/ccp4-6.1.13/lib/data/sc_radii.lib !--SUMMARY_END--/FONT/B Number of radii read from sc_radii file: 78 Opening PDB input file with logical name XYZIN Logical name: XYZIN File name: 1XOU.pdb PDB file is being opened on unit 1 for INPUT. MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE RF RO 0.028 -0.000 -0.000 -0.000 35.422 0.000 0.000 -0.000 -0.000 0.014 -0.000 0.0000.000 72.383 0.000 0.000 0.000 -0.000 0.010 -0.0000.000 0.000 95.679 -0.000 -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 UNFORMATTEDSCRATCH file opened on unit 7 BFONT COLOR=#FF!--SUMMARY_BEGIN-- Logical name: SCTEMP, Filename: /tmp/li/sc_dots.09428 !--SUMMARY_END--/FONT/B Number of atoms read from PDB file: 1238 GRASP mode disabled - no Grasp output will be produced Selection commands: --- molecule 1 Molecule 1 molecule 2 Molecule 2 chain A Number of atoms selected in chain A =565 chain B Number of atoms selected in chain B =673 zone A 170 B 24 Number of atoms selected in zone=345 at_excl A 170 N Atom A 170 Nexcluded end Parameter values Dot density :15.00 per square Angstrom Interface separation : 8.00 Angstroms Trim width : 1.50 Angstroms Probe radius : 1.70 Angstroms Weight factor: 0.50 per square Angstrom Selected atoms: --- Number of atoms for first molecule 0 Number of atoms for second molecule 1237 Total number of atoms 1237 Setting up atoms for surfacing: Potential interface atoms 0 Blocked atoms 1237 Atoms in Molecule 10 Atoms in Molecule 2 1237 Output diagnostics from Connolly subroutine MDS: UNFORMATTEDSCRATCH file opened on unit 7 BFONT COLOR=#FF!--SUMMARY_BEGIN-- Logical name: SCDOTS, Filename: /tmp/li/sc_dots.09428 !--SUMMARY_END--/FONT/B Number of surface points: Convex 0 Toroidal0 Concave 0 Total 0 BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: No atoms found in
[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 crystal Cheers Stefan
[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 the CSD would flag up easily issues. MOGUL http://www.ccdc.cam.ac.uk/products/csd_system/mogul/ has been a great tool, which can be easily incorporated into COOT (ouuups). :) Cheers Stefan -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robert Immormino Gesendet: Donnerstag, 10. März 2011 21:56 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand? Hi Halliang, If the ligands are in the pdb het dictionary I think MolProbity will look at bonds and angles...maybe even dihedrals. Cheers, -bob On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
[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@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] coot Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y2, z2, x3, y3, z3], [a, b, c]]) filename=output_pdb+str(i)+'.pdb' save_coordinates (1, filename) I think you can write all the the tranformation matrix out instead of the loop if they differ significantly. Others may have more experience. Best, Joe On Mon, Feb 28, 2011 at 6:32 PM, FREITAG-POHL S. stefanie.freitag-p...@durham.ac.uk wrote: Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Stefanie Freitag-Pohl Durham University Chemistry Dept South Road Durham. DH1 3LE Tel: 0191 3342143 Email: stefanie.freitag-p...@durham.ac.uk
[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 intekhab alam Gesendet: Donnerstag, 11. November 2010 09:14 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] SC I want to calculate the shape comlementarity statitics (SC) of a dimeric protein using CCp4. I am using CCP4 6.1.3 on windows but the SC program is not available in that suite. Which version of CCP4 has that program. Are there any other programs that can calculate that. Thanks -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[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... (more needed surely soon :) ) Cheers Stefan
[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/slogan of coot? I read so often about it on ccp4bb. If there is not one yet, I propose: coot, the crystallographer's swiss knife :'D Regards, F. Tim Gruene wrote: Hello Florian, you can read the .hat-file into coot and save it from there, changing the suggested file-extenstion from .ins to .pdb. In case coot crashes when it reads the .res-file, edit the file and make sure there is only one END-card. Maybe shelxpro would also work. Tim On Mon, Aug 30, 2010 at 05:36:37PM -0400, Florian Schmitzberger wrote: Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602 attachment: mac-gyver-00_thumb.jpg
[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 fine in Refmac. Now I working on a hydroxylated molecule of NAD (NADOH), OH group at C6N of the nicotinamid ring of NAD. what I have done: starting jligand importing the nad_ebi.cif file showing hydrogens changing atom type and name of H6N to O6N of the nad_ebi.cif file change the ligand ID to XAD regularize XAD (ligand regularize XAD) and I am always ending up with a screwed up nicotinamid ring! the C5N carbon atom is moving out of the aromatic ring. I tried to change the bond type to aromatic and/or delocated of the nicotinamid ring but it is always the same result. Am I doing something very bad here? Please could you advice me how to get it right?? It is worse when I start with the original NAD dictionary directly within Jligand ! Please try out for yourself, any help is much appreciated Many thanks for your help Stefan
Re: [ccp4bb] Understanding Conformational Differences
Hi Jacob, please have a look at the program ESCET from Thomas Schneider, which I have used to look at changes in over hundred structures of kinases upon ligand binding. cheers Stefan On Thu, 29 Apr 2010 12:18:38 -0500 Jacob Keller j-kell...@md.northwestern.edu wrote: Dear Crystallographers, I am looking at ~20 unique crystal structures of the same protein in somewhat different conformations, although not radically different, and would like to order them somehow to gain an understanding of how the protein can move. Is there software that does this somewhat automatically? Thanks for your consideration, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 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 another Fab fragment? Speaking from own experiences that is very often the case if you are working on antibody-antigen complexes. Cheers Stefan -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Eleanor Dodson Gesendet: Donnerstag, 23. Juli 2009 14:50 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] is my crystal twinned or not? It seems very likely your crystal is twinned - the moments and cumulative intensity are a good indicator of twinning, especially when there isnt much NCS. But your solution is almost certainly partially correct - the Rfactor is pretty low. It is a good idea to run pointless which gives you the correlation Coefficient for each symmetry operator. see if there is any difference between the different ones.) You could have twinning with either 4-fold or 222 symmetry. the 222 is less likely seeing that would mean the a=b axes are accidently equal. If you decide the symmetry is really PG 4 you need to remerge the data in that point group ( no need to reintegrate - the cell dimensions will still be the same) The most likely solution is that one of your P43212 molecules is corrrect, but it is probably a good idea to run the MR search again. Use your refined antibody molecule as the search model to save work later.. Eleanor Matthew Franklin wrote: Hi all - I'm trying to solve the structure of an antibody-receptor complex, and I've hit a wall which may be due to a twinned crystal form. This crystal has the apparent space group P43212, with cell constants a=64.02 c=274.83. Solvent content analysis using this space group suggests 1 mol/asu, with 47% solvent, which would be fairly consistent with the diffraction limit of about 2.8 A. I've been able to place the antibody using molecular replacement and refine it to R=0.289, Rf=0.338. There is some density for the receptor, which represents about 20% of the mass of the complex, but not clear enough to build into, and all efforts to improve the density or place the receptor by molecular replacement have failed. Well, tough luck, you might say, but I noticed at the very beginning of the process that this crystal form may be a perfect twin. The 4th moment of E graph from Truncate shows nearly all resolution bins with values of 1.4 - 1.6, except in the very topmost few bins where the values rise up to 2. The other moment graphs are likewise at their perfect twin values across the resolution range. The cumulative intensity distribution graph shows the observed values are about 30% lower than the expected values for both acentric and centric reflections. As I understand it, both of these are strong indicators of twinning, and the twin fraction analysis in DETWIN suggests a twin fraction of ~0.5. So what do I do now? I think I'm supposed to reprocess the data in the space group without the twin transformation (which would be P43), then run molecular replacement which should show me solutions for both halves of the twin. However, all I'm seeing is two copies of the antibody in the (P43) asymmetric unit, which don't overlap, and both of which need to be present in the same unit cell in order to form a 3-dimensional lattice. This is exactly what I would expect to see if there were no twinning present. So my question is, is this crystal form twinned or not? Is there some way that the intensity statistics could be misleading me? On the other side, am I doing something wrong with the structure determination if the crystal is twinned? How should I proceed? Thanks for any help anyone can provide. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
