Re: [ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

Hi Kyle DynDom gives you the angle of the relative domain movement, which I also find a good quantitative measure. http://dyndom.cmp.uea.ac.uk/dyndom/runDyndom.jsp Best Sabine On 12/11/2021 15:13, Edwin Pozharski wrote: https://pymolwiki.org/index.php/Rms_cur

[ccp4bb] cell discrepancies and stuck refinement using different XDS-versions

nd it..) Cheers Sabine -- ---------- Dr. Sabine Schneider Research Group Leader Technical University of Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 85748 Garching Germany Tel.: +49 (0) 89 289 13759 Fax: +49 (0) 89 289 13363 http://www.biochemie.ch

Re: [ccp4bb] Problem with lattice disorder / tNCS / whatever - SOLVED!

Hello everyone, Maybe of interest/help to others: The solution of my problem is a totally unexpected structural change of 2 out of 4 protein molecules in the asu! The straight forward solution was additionally obscured through the presence of tNCS. What I did: - placed as many molecules as po

Re: [ccp4bb] Problem with lattice disorder / tNCS / whatever ?!

9 192.7 110.0 90.0 90.0 108.1 ------ Dr. Sabine Schneider Research Group Leader Technical University of Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 85748 Garching Germany Tel.: +49 (0) 89 289 13336 Fax: +49 (0) 89 289 13

Re: [ccp4bb] Problem with lattice disorder / tNCS / whatever ?!

in IDXREF.LP clean in this respect? Best, Kay On Wed, 16 Nov 2016 17:26:59 +0100, Sabine Schneider wrote: Hello everybody, I got a problem with solving and refining a structure of a small protein of 20kDa, where we just swapped two residue at the surface by mutation (AF vs FA). For the FA v

[ccp4bb] Problem with lattice disorder / tNCS / whatever ?!

Hello everybody, I got a problem with solving and refining a structure of a small protein of 20kDa, where we just swapped two residue at the surface by mutation (AF vs FA). For the FA variant we got three crystal forms, where we had no problem whatsoever with MR and refinement - P6522 cell

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

Hello Wei, is the modified base defined as DNA in the cif? (see below) Is the O3* or O3'? You need the latter. And check whether there are three hydrogens on the O3. You need to either remove one from the cif file manually, or name them according to a normal DNA base. (In the latter case, by ma

[ccp4bb] 3D Monitors

Hello everyone, I know there already has been discussion about 3D monitors on the Coot/CCP4bb. However since there are a few more out there now and I am currently thinking about buying one, I thought to get a few opinions from crystallographers would be nice! Especially if there are people hap

Re: [ccp4bb] Stabilization of crystals and ligand exchange

highest possible ligand concentration, since in many cases, although the ligand should bind in theory, in practise it is quite a different story. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sabine Schneider Sent: Wednesday

[ccp4bb] Stabilization of crystals and ligand exchange

Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotr

Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand

Hi Yu, A few things which caused this happened to me with other non-standart nucleotides: - the hydrogen of the 3'O of the BrdU is defined as 3'OH in the cif file - order of the atoms in the pdb file ie compare the position of the 3'OH with the standard dNTP in the PDB - is the 3BrdU defined as '

Re: [ccp4bb] idiffdisp fails from CCP4 gui in ccp4-6.2.0

2 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sabine Schneider [sabine.schnei...@mytum.de] Sent: Tuesday, August 09, 2011 3:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] idiffdisp fails from CCP4 gui in ccp4-6.

[ccp4bb] idiffdisp fails from CCP4 gui in ccp4-6.2.0

age.so.0.0.0 Anyone an idea what's going on, or how I can fix that problem? Thanks for your help! Sabine -- ------ Dr. Sabine Schneider Technische Universität Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 D-85747 Garching Ger

[ccp4bb] script for pdbset to apply repetitive rotation and translation

Hello, I want to apply to a small structure a rotation and translation (i.e 10A translation and 10dg rotation), write out the coordinates and apply the same rotation/translation to the new coordinates and repeat this lets say 100 times. I guess the program of choice would be pdbset but I am

Re: [ccp4bb] Freezing under oil

SPAM protection. Sign up now. <https://signup.live.com/signup.aspx?id=60969> -- ------ Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77752 Fax: +49

[ccp4bb] Twin refinement - selecting FreeR

-- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/

[ccp4bb] imosflm fails on suse

since I thought ie shar might get upset). I also installed CCP4 6.1 on a different suse linux-box (where there hadn't been CCP4 on it before) and it worked just fine? I got Tkl/tk version 8.4 installed. Any ideas? Thanks a lot for your help! Sabine -- --

[ccp4bb] Summary - crystals grown from high ammonium sulphate

(Yevgeniy Kalinin and Robert Thorne, Acta Cryst. (2005). D61, 1528–1532.) - be quick Sabine >Sabine Schneider wrote: >Hi everyone, > >We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and

[ccp4bb] Crystals grown from high ammonium sulphate

--- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/

[ccp4bb] difference in data processed with xscale and scala

Hello everyone, I am puzzled about differences I see when I refine the very same structure against data processed with xscale or scala. I got data to 2.55A from a protein-ligand complex. The data were processed with xds/xscale (1) or xds/scala (2) Free R was imported from a previously solved

[ccp4bb] overlapping DNA in prt-DNA complex structure

Hello everyone, I am working on the structure of a protein-DNA complex with 2 mol/ASU. Data are to 2.8A and the symmetry appears to be orthorhombic (P212121; a=42.280 b=113.340 c=134.670) I solved the structure by moleculare replacement using the coordinates of the protein in phaser. I got r

Re: [ccp4bb] xds to mtz using pointless

.linux (eg) Otherwise if you send me the file I'll investigate Phil On 20 Feb 2008, at 09:39, Sabine Schneider wrote: Hi everyone, I have a fine sliced dataset consisting of 720 frames (0.25dg / frame). I processed them with Xds and used Pointless to convert it to mtz for putting

[ccp4bb] xds to mtz using pointless

Hi everyone, I have a fine sliced dataset consisting of 720 frames (0.25dg / frame). I processed them with Xds and used Pointless to convert it to mtz for putting it in Scala. Spacegroup is P212121 and the resolution ~3.2. After ~200 frames the Rmerge goes up crazy and after 560 it is OK again

[ccp4bb] dictionary for DNA in Coot/Refmac

Hi everyone, I am working on Protein-DNA complex and am struggling to generate a dictionary with the right bonds/restraints for a the ds DNA of 15nt length with 1nt overhang and a lesion. How do I link the nucleotides together and set the right restraints in the bit with the lesion? Tried to