[ccp4bb] REFERENCE_DATA_SET in XDS-CORRECT

Hi all, I have a dataset that looks like from (a) primitive hexagonal crystal(s), apparent (from merging stats) point group 32 or may be (twinned?) 3. During CORRECT, I am imposing space group number 143 and specify a REFERENCE_DATA_SET to determine the optimal reindexing operator between two wedge

[ccp4bb] ARP/wARP awk: Command not found.

Hi, auto_tracing.sh “ARP/wARP 8.0 patch 1”, after a few cycles, prints awk: Command not found., and exits a little later with: Data line -- RESOLUTION 20 2.2 Data line -- REMOVE ATOMS 8 CUTSIGMA 1.0 FORCE NEGATIVE MERGE 0.7 Data line -- FIND ATOMS CHAIN Z CUTSIGMA 3.2 RESN DUM T

[ccp4bb] hybrid photon counter in the home lab

Hi, I would value your opinions in this equipment-related question. Allé et al have compared detector types with a molybdemon source for a small molecule application . Are there similar published comparisons for protein crystallography? What benefit

[ccp4bb] wwpdb validation

Hi, did I hear correctly that the wwpdb validation pipeline can be accessed from within ccp4 and/or phenix? If so, how does one access that functionality in either software suite? Many thanks. Wolfram Tempel To unsubscribe f

[ccp4bb] PISA command line

Hi, has anyone of you performed a PISA command line analysis using the version distributed with CCP4 on ubuntu-16.04? My attempt to "-list interfaces" after seemingly successful "-analysis" resulted in a core dump: PISA v.2.1.1 built 05-04-2017 with SSM v.1.4.0, SRS v.1.0.0, MMDB v.2,0.17 Ses

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

Hi Nat, could you be referring to side-by-side stereo in this (computer monitor) use case? http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node97.html W. On Fri, Mar 2, 2018 at 2:41 PM, nathanielclar5 . wrote: > To learn how to cross eyes, just hold you index fingers strait up, ~12-18 > inches

Re: [ccp4bb] coot 0.8.9

Yes. Paul Emsley has responded to our crash report on the COOT message board: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1801&L=COOT&F=&S=&P=5852 On Thu, Jan 25, 2018 at 5:56 PM, L. Doyle wrote: > Hello all, > > I recently update CCP4 to 7.0.050, which updated coot to 0.8.9. Now > whenev

Re: [ccp4bb] Issues with latest XDS (20171218)

I agree that accurate and complete image header information is useful, but not universal. How about a routine similar to dials.discover_better_ experimental_model? W. On Wed, Jan 24, 2018 at 10:12 AM, Engin Özkan wrote: > Dear all, > > I have to agree with all sentiments stated, and I have defin

Re: [ccp4bb] AIMLESS unmerged MTZ output

ey are stored in the MTZ file > Phil > > Sent from my iPhone > > > On 22 Jun 2017, at 17:04, wtempel wrote: > > > > Hello all, > > > > Are the following statements regarding AIMLESS unmerged mtz output > accurate? > > - the H, K, L, M/ISYM column

[ccp4bb] AIMLESS unmerged MTZ output

Hello all, Are the following statements regarding AIMLESS unmerged mtz output accurate? - the H, K, L, M/ISYM columns are sufficient to recover the "original" H K L indices. - a combination of "original" H K L and the BATCH value is unique inside the file. Thank you in advance. Wolfram Tempel

Re: [ccp4bb] ccp4 release 7.0 update 023

Hello, after installing updates 22 and 23 on an Ubuntu-14.04 (x86_64) box, I have yet to successfully “mutate” any amino acid residue in COOT. (setup-mutate 1) is printed to the terminal, followed by a line confirming on which atom I have clicked, but the residue type selection dialog does not appe

[ccp4bb] Nickel coordination

Hello again. How does one prepare restraints for a Ni ion with four ligands: - NE2 atoms from two His residues - N and O from one Gly residue REFMAC nailed down the distance. How do I specify a near square-planar arrangement of the ligands? Thank you, Wolfram Tempel

Re: [ccp4bb] Rfree below Rwork

gt; Cheers, > > Robbie > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * > wtempel > *Sent:* Tuesday, June 30, 2015 18:59 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Rfree below Rwork > > > > Hello, > > my question

[ccp4bb] Rfree below Rwork

Hello, my question concerns refinement of a structure with 6-fold NCS (local automatic restraints in REFMAC) against 2.8 A data. The size of my free set is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to 4.3 % of reflections. A refmac run of 10 cycles of TLS and 10 cycles of

[ccp4bb] refinement restraints for C-terminal amide

Hello, how does one specify C-terminal amidation of a peptide for REFMAC refinement? I intended to prepare link restraints between the C-terminal amino acid residue and a residue "NH2". But JLIGAND reports "Code 'NH2' does not exist in the library". On my system, $CLIB/data/monomers/n/NH2.cif exist

Re: [ccp4bb] obtaining CC1/2 from old log file of hkl 2000

Ansuman, you can calculate arbitrary merging stats, including CC1/2, Rmeas from *unmerged* intensities, with a program like AIMLESS . By default, HKL2000 (scalepack) will have output *merged* intensities, but merging is inherently

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

or a single dataset is that the user can specify the > >> limits of the resolution shells. > >> > >> _Scaling with scala/aimless_ > >> > >> > http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 > >>

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

972-8-647-2992 or 972-8-646-1710* > > > > > > -- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [ > wtem...@gmail.com] > *Sent:* Tuesday, November 11, 2014 9:50 PM > *To:* CCP4BB@JISCMAIL.AC.UK >

[ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Hello all, in a discussion on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specif

Re: [ccp4bb] merging of reflection with identical indices

uld (I hope) do a better job than COMBAT. > > Aimless (& Pointless) assume two reflections are part of the same one if > they have the same "true" hkl (same ISYM) and adjacent batch numbers (and a > few other conditions, e.g. total fraction). Output from COMBAT may be wr

[ccp4bb] merging of reflection with identical indices

Hello all, suppose I extracted H K L Intensity sigma[Intensity] from a file of unmerged intensities, such XDS_ASCII.HKL or scalepack format ('no merge original index'). Batch or rotation angle information would have been omitted, due to a limitation of the output file's format. Should I not sti

[ccp4bb] twin refinement

Dear colleagues, this is a request for comments on the evaluation of crystal structures that resulted from twin refinement. >From http://www.ysbl.york.ac.uk/~garib/refmac/Tutorials/refmac_tutorial.pdf: "Although Rfactors are substantially smaller with twin refinement than without twin refinement

[ccp4bb] determining "best" of alternative indexes with POINTLESS

Hello, using merged scalepack intensities and a reference MTZ file as inputs, I would like to prepare an MTZ of scalepack intensities reindexed so that the intensities optimally correspond to those in the reference MTZ file. Invoking POINTLESS with the CELL, SCAIN, HKLREF keywords results in CCP

[ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

P21 with properly transfered free flags. I just do not know how to accomplish that transfer. W. -- Forwarded message -- From: Tim Gruene Date: Wed, Oct 2, 2013 at 4:13 PM Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel Cc: CCP4BB@jiscmail.ac.uk -

[ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

-- From: Appu kumar Date: Wed, Oct 2, 2013 at 1:29 PM Subject: Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel , CCP4BB How do you suspect that C2221 is 'pseudo' and P21 is 'real'? You can use the reindex programme incorporated in ccp4 suit. Reindex programme

[ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

. -- Forwarded message -- From: Randy J. Read Date: Wed, Oct 2, 2013 at 1:07 PM Subject: Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel Cc: "CCP4BB@JISCMAIL.AC.UK" I suspect the problem is that sftools hasn't been modernised to alter all the cell di

[ccp4bb] expanding reflections from C2221 to P21

Hello, I would like to expand a reflection data set in mtz format from C2221 to P21. The purpose is to obtain consistent R-free flags based on a structure already refined in C2221 for a related data set that I suspect is pseudo-C2221 but "real" P21. Primitive cell dimensions are: 37.6 126.1 40.61

[ccp4bb] peptide planarity restraints for modified residues

Dear CCP4ers/REFMACers, the C-terminal peptide bond of a modified lysyl, M3L, appears less planar than other peptide bonds in the same structure. What is the currently preferred method of restraining such planarity? I have currently not added any link record in the header of my coordinates file. Wo

[ccp4bb] indexing/data reduction

Dear colleagues, we have collected 200 degrees worth of oscillation data on a selenomethionine derivative (1 "non-terminal" methionyl per 120 residues) to 2A resolution. XDS provides the following output: LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) CHARACTER LATTICE

[ccp4bb] scala, cad, free flag

Hello all, please consider the following scenario of converting XDS data to MTZ, preserving the rfree flag from an older MTZ file. 1. POINTLESS with input XDS_ASCII.HKL 2. CCP4I-scaling: scala with 'Copy FreeR from another MTZ' option, implicitly using CAD, cad log attached. I would expect my out

[ccp4bb] Refmac: ADP is non-positive

38, 33A**2, respectively. Could refmac just be taking exception to the missing N atom? -- Forwarded message -- From: Ethan Merritt Date: Tue, Jul 24, 2012 at 11:27 AM Subject: Re: [ccp4bb] Refmac: ADP is non-positive To: wtempel Cc: CCP4BB@jiscmail.ac.uk On Tuesday, 24 July 2012, wte

[ccp4bb] Refmac: ADP is non-positive

CCP4ers, a log file from Refmac_5.7.0027 presents me with this line: Problem with the ADP of the atom N A 3 ADP is non-positive -1.7740907E+35 I did not explicitely refine ADPs or TLS. Should I modify my model when I encounter such a message? If yes, does the message refer to a

[ccp4bb] indexing(?) question in P21 - solved

Hello Phil, I went ahead and explicitly applied that +0.5*a translation. Worked like a charm. My excuse for not trying earlier? Within the project, I have dealt with many additional complex crystals, and have gotten used to simply "hopping crystals", i.e. refine the same structure in the highly iso

[ccp4bb] indexing(?) question in P21

Hello all, I am puzzled by this situation: I have two different crystal of the same protein, in the presence, one in the absence of a ligand. Both structures refine nicely in space group P21. Cell constants (a,b,c,beta) are (i) 61,124,61,119 (a

[ccp4bb] ccp4i project display

Thank you, Zhijie and Hans. I may resort to your fixes once this temporary fix is no longer effective: "System Administration"|"Configure Interface"|->"Maximum length of drop-down menu columns" I still had some space to spare vertically to increase it from 25. The change becomes effective after sav

[ccp4bb] ccp4i project display

Dear colleagues, likely some of you have experienced that with 100s of ccp4i projects, the menu (limited to 25 lines?) exceeds the horizontal limitations of the computer display. Are there any suggestions how to handle this many projects? Added difficulty: I expect that were I to eliminate selected

[ccp4bb] twin refinement in refmac

Dear CCp4ers, A good morning to everyone. Today, I have a structure that I initially refined in space group P6522, 1mol/asu. Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; / > 3 2.61-2.55A: Rsym=39.6%, / > 10 50.00-6.13: Rsym=6.4% Some mild anisotropy in the resolution limits is apparent on the

[ccp4bb] sftools expand

Hello, here is a question about the EXPAND command in SFTOOLS, specifically its effect on a free reflection flag. Do the flag values get copied to newly generated reflections based on symmetry, for example in the case of a P622 -> P6 expansion? many thanks, Wolfram Tempel

[ccp4bb] refmac model statistics in cif format

Hello all. Did anyone encounter the following? Running refmac 5.6.0117/ccp4-6.2/ccp4i-2.1.0, I hoped to obtain, for pdb_extract, the appropriate output model statistics. When I did not find the cif file with a modification date similar to my output coordinates, I noticed a series of ${project}_${cr

[ccp4bb] Follow-up: non-waters among structured solvent atoms

Thank you everyone for your replies. The Nayal & Di Cera (1996) paper may be what I had in mind. I was looking for some estimate of how often water atoms are placed in protein models where they do not belong, and I expected a relatively high percentage. Simply extrapolating from the 0.01% water <->

[ccp4bb] non-waters among structured solvent atoms

Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect "water" a

[ccp4bb] cphasematch

Dear colleagues, here is one cunning plan: to quickly evaluate the anomalous signal of a test data set with a non-interactive script that: 1. solves the structure using SAD 2. does some solvent flattening 3. compares the resulting phases against calculated phases from a refined, isomorphous struc

[ccp4bb] phosphate v sulfate

Dear colleagues, I would like to poll the community on the prevailing practice of distinguishing between phosphate and sulfate in their structures. Suppose all of the following apply: 1) a well contoured tetrahedral density in your model-phased 2Fo-Fc map in the active site of your kinase or GTPase

[ccp4bb] cell constants in MTZ file after transfer of Rfree flag

Dear colleagues, trying to be a responsible citizen, I occasionally activate the "Copy Rfree from another MTZ" button in the {Data Reduction|Import Integrated Data|Import Merged Data} CCP4I task. This appears to have the unintended effect of setting the "relevant/dataset" (as opposed to the "obsole