Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Randy, > On 23 Feb 2024, at 11:49, Randy John Read wrote: > > Why would we want to impose an arbitrary restriction on users for this > relatively common scenario. If the user has the unmerged data this can be imported into CCP4i2 via the data reduction task and merged in P1. How would you

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > so strictly it is possible and correct - if experimentally unlikely - to > have the situation we are discussing here occur. I believe this is only technically possible bec

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

Hi Graeme, > On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > Processing a data set in lower than necessary symmetry e.g. tetragonal as > monoclinic you _cannot_ import the merged MTZ file into i2 because it is > impossible

Re: [ccp4bb] To Trim or Not to To Trim

> On 17 Mar 2023, at 08:57, Manfred S. Weiss > wrote: > > In my view, the best approach is to build the side chains in their > most plausible conformation, or maybe in 2 or 3 or 5 different > conformations, and let the ADPs refine freely. One point I don’t think has been mentioned so far in thi

Re: [ccp4bb] To Trim or Not to To Trim

> On 17 Mar 2023, at 15:01, Guillaume Gaullier > wrote: > > CryoEM papers often show a map in a main figure, and as a reader I think it > is very nice to show me the map that convinced you of some finding before > showing me your interpretation of this map. Surely a key difference is that cry

Re: [ccp4bb] Rmeas in DIALS?

Hi Graeme, > On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) > wrote: > > Total observations 1432839600 559 > Total unique 418512397 494 > Assuming spacegroup: P 41 21 2 > Other likely alternatives are: > P 43

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi Gerard, > On 22 Feb 2021, at 19:38, Gerard Bricogne wrote: > > Did you perhaps deposit only part of the data you collected for the > remote wavelength? For example, only one of several orientations that you > might have collected in order to try and fill the cusp? data_r2xgfsf in the 2xgf-s

Re: [ccp4bb] CCP4i2 Export and Deposition task

Hi, > On 26 Nov 2020, at 17:59, Nikolas wrote: > I have tried to look for the tutorial but both the icon and the input page > illustrated are different from the ones I can see in the software. I have now updated the CCP4i2 documentation at https://ccp4i2.gitlab.io/rstdocs/index.html to reflec

Re: [ccp4bb] CCP4i2 Export and Deposition task

Hi, > On 26 Nov 2020, at 17:59, Nikolas wrote: > > I am trying to prepare and export the files for a structure solved in CCP4i2 > but so far the only tasks available are the "Prepare and validate" and "Merge > experimental data .." tasks. Yes the first of these "Prepare and validate files for

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Best protocols to advance a low resolution twin

Hi Randy, > On 14 Sep 2020, at 18:52, Randy Read wrote: > > Thanks for pointing that out. I guess I hadn’t presumed to brand myself as > an expert! I’ll have to find out now what else I’ve been missing... Surely you should identify yourself as developer and have access to all the options!

Re: [ccp4bb] CCP4i2 Text size

> On 2 Apr 2020, at 14:51, Horrell, Sam (DLSLtd,RAL,LSCI) > wrote: > > . I’ve changed the setting you suggested but it hasn’t changed much. Apologies that didn't work. I was testing on a VM running on a Mac connected to a UHD display and there it did change the resolution that CCP4i2 was drawi

Re: [ccp4bb] CCP4i2 Text size

Hi Sam, > On 2 Apr 2020, at 11:32, Horrell, Sam (DLSLtd,RAL,LSCI) > wrote: > > If anyone has any other suggestions it would be greatly appreciated. What settings do you have for Windows display scaling? From your screenshot it appears that the Windows task bar and window title bar are drawn

Re: [ccp4bb] Refmac5 question

> On 4 Feb 2020, at 09:24, Joern Krausze wrote: > > These hydrogen atoms were present in the input file with their occupancies > matching that of the residues they are attached to. What happens with make hydrogen YES? That should keep all hydrogens present in the input file (http://www.ccp4.

Re: [ccp4bb] Coot in i2

> On 5 Jun 2019, at 20:40, Paul Emsley wrote: > > Ctrl-S will do Quick save as, saving your state files and any unsaved models > with file-name increments. That should put your mind to rest about unsaved > changes. Also, investigate the coot-backup directory - coot should be saving > models

Re: [ccp4bb] Some ccp4i2 menu options seem missing.

Hi, > On 24 Apr 2019, at 22:42, Jonathan Cooper > <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: > > Any clues much appreciated, otherwise I'm back to the old gui. The linux one looks like a job that has been run. If you got to the task menu and click on Refinement - REFMAC5 does the n

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson wrote: > > I've just compiled Coot on the same Mac using Fink, and the dialogue for this > version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the > same residue. From a quick look at the Fink coot.info it appears to get the mono

Re: [ccp4bb] workable data from PDB sf-cif

> On 15 Jun 2015, at 20:00, Donald Damian Raymond wrote: > > Hi, > > I've written a bash script that does just what you want. and potentially deletes a lot of files it didn’t create... #cleanup rm temp* "$cif_file" 2> /dev/null Huw

Re: [ccp4bb] XDS INP

Hi, Also the IXDREF.LP files from yesterday and today suggest that you are having problems with 2 different datasets. Is that correct? IDXREF from yesterday had: NAME_TEMPLATE_OF_DATA_FRAMES=/home/lu/Documents/StructurePro/images/luzk/Hg6/hg6_L1_1_? OSCILLATION_RANGE=0.5000 X-RAY_WAVELE

Re: [ccp4bb] XDS INP

On 12 May 2015, at 13:09, luzuok wrote: > STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 11.13 Is the oscillation range and rotation axis direction correct in your XDS.INP file? Huw

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On 15 Sep 2014, at 15:24, Andrew Leslie wrote: > This would suggest that the standard dictionary that Molprobity uses has > changed, but I cannot find any reference to this on the Molprobity pages. > > I would be very grateful if anyone can throw some light on

[ccp4bb] ctruncate bug?

Hi I seem to be getting a lot of outliers rejected by Phaser with data processed with the latest ctruncate which are not present when data is processed with the older version (or old truncate) - has something been changed in the code that would cause this? With CCP4 6.4: ctruncate

Re: [ccp4bb] Puzzling Structure

On 15 Apr 2013, at 17:19, Michel Fodje wrote: > I imagine somebody accidentally deleted a space between P 21 21 2 and 18 and > tried to fix it by adding it back, between 1 and 8. As this has now been mentioned twice in this discussion it should probably be noted for the archives that the la

Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?

All works fine. You'll need to install XQuartz (Apple are no longer supplying their own X11 builds) but that's just a couple of clicks in the box that pops up the first time you run an program that needs X. The (on by default) versioning auto save is a PITA if you ever use textedit to edit sc

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

Hi Ronan, On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote: > Well spotted! We originally gave structure factors to SHELXE in our testing > as for most of our test cases we only had F/SIGF available. We were advised > to change to intensities but somehow in the released version the "-f"

[ccp4bb] Ample, shelxe-beta and F to I conversion confusion

Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contai

Re: [ccp4bb] How to start my XDS journey after HKL2000?

> ORGX=1016.0 ORGY=1066.8 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 Have you checked the beam centre? It's usually the first thing to check when indexing doesn't give you the expected result. Huw

Re: [ccp4bb] CCP4superpose_only superpose interesting residues

On 25 Oct 2012, at 00:45, Zhijie Li wrote: > This is especially useful when the program does not give you options on > residue ranges (for example, COOT SSM superpose). It does but you need to use the function superpose-with-atom-selection from the scripting interface.

Re: [ccp4bb] loop building with ARP/wARP - REFMAC/gfortran problem? and work-around

On 25 Aug 2011, at 14:12, Gregory Bowman wrote: > When I try to run ARP/wARP classic for loop building, I get the following > message in the logfile: > > QUITTING ... ARP/wARP module stopped with an error message: > REFMAC I get the same error running auto_tracing.sh from ARP/wARP 7.2. (CCP4 6

Re: [ccp4bb] COOT library

everything downstream will work. Hopefully someday this mess will be a distant memory! Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] COOT library

real-space refinement. The versions of Phaser and Coot would be useful too! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] COOT library

he old dictionary (The OS X fink one definitely does because coot.info downloads http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz) and that breaks refinement for nucleic acid. Hope that helps, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] The Good and the Bad crystal contact?

ffinity protein-protein interaction. Meenan NA, Sharma A, Fleishman SJ, Macdonald CJ, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C. Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10080-5. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

[ccp4bb] REFMAC and REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

I've split this off from the too many clashes thread as it's not directly related. I was under the impression that the default in refmac was to add riding hydrogens but some investigation suggests this may be only appear to be the case. If the default option in the CCP4i GUI for refmac with

Re: [ccp4bb] ARP/wARP 7.1; ccp 6.1.13 and Mac OSX 10.6 (64bit fink)

my home directory (and change permissions). Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds h.t.jenk...@leeds.ac.uk

Re: [ccp4bb] fail to install ccp4i task for arp warp

works and once installed ARP/wARP and 64bit CCP4 work together fine. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

only a suggestion. Yes that's exactly what I was using before I found that paper! I think I'll stick with it. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

3 -13.281846 1.4794188 -10.456101 So it's only when I have 3 groups for the same nucleotide. I'll send the files in a minute. > It does sound like that's what they did in the Nat. Struct. Biol. but > they seem to have deposited the pre-TLS coordinates from CNS, so hard to > tell. I noticed that too - I'm not sure if that's not that the PDB removed/didn't accept the TLS info though - the header for the Howlin et al. RNase A TLS groups for rigid sidechains structure (3RN3) also has no TLS information in. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

On 15 Jul 2010, at 16:24, Tim Gruene wrote: > > what happens when you remove the period '.' in the residue range description, > i.e., replace >RANGE 'B 3.' 'B 3.' P > with >RANGE 'B 3' 'B 3' P No difference

[ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] common protein crystallization contaminants

er D, Blangy S, Cambillau C, Sciara G. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] Entering mosflm keywords in imosflm 1.0.4

Hi again, I have just remembered what the magic keystroke combination was. I assume there is a reason this feature is undocumented so I'd better not post it Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

[ccp4bb] Entering mosflm keywords in imosflm 1.0.4

For expert users, iMosflm now has the option of specifying ipmosflm keywords for the very specialised options that are only rarely used and are not yet included in the iMosflm GUI explicitly." but not the details of how to do it! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Struc

[ccp4bb] arp_solvent ignores FreeR flag when run from ccp4i

x27;s the gui that's not writing the command script for ARP/wARP properly. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds

Re: [ccp4bb] Alterate conformers destroyed by Refmac!

s it might now be easier to work out where ifort is breaking things! Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology Room 8.53 Garstang Building University of Leeds Leeds, LS2 9JT +44(0)113 343 4269 h.t.jenk...@leeds.ac.uk

Re: [ccp4bb] Alterate conformers destroyed by Refmac!

ities : 422 Number of planar groups : 495 I hope this helps... Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds Leeds, LS2 9JT

Re: [ccp4bb] Low Bfactor values for waters after TLS

O ATOM 20 C SER A 3 51.877 -52.639 35.480 1.00 2.00 C I'd be happy to send the data for this structure to the developers if it would help in identify the source of the problem. Cheers, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular B