[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.

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

. -- Forwarded message -- From: Randy J. Read rj...@cam.ac.uk Date: Wed, Oct 2, 2013 at 1:07 PM Subject: Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel wtem...@gmail.com Cc: CCP4BB@JISCMAIL.AC.UK CCP4BB@jiscmail.ac.uk I suspect the problem is that sftools hasn't been

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

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

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

transfered free flags. I just do not know how to accomplish that transfer. W. -- Forwarded message -- From: Tim Gruene t...@shelx.uni-ac.gwdg.de Date: Wed, Oct 2, 2013 at 4:13 PM Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel wtem...@gmail.com

[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] 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

Re: [ccp4bb] merging of reflection with identical indices

( 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 wrong in this respect Phil On 10 Jun 2014, at 17:23, wtempel wtem...@gmail.com wrote

[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 saving

[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 (ac by a hair) and (ii) 59,125,61,118. There is a

[ccp4bb] Refmac: ADP is non-positive

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

[ccp4bb] Refmac: ADP is non-positive

, respectively. Could refmac just be taking exception to the missing N atom? -- Forwarded message -- From: Ethan Merritt merr...@u.washington.edu Date: Tue, Jul 24, 2012 at 11:27 AM Subject: Re: [ccp4bb] Refmac: ADP is non-positive To: wtempel wtem...@gmail.com Cc: CCP4BB@jiscmail.ac.uk

[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

[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: COLLECT.LP LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM DEGREES) CHARACTER

[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

[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

[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] 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

[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] 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%; I/sigma 3 2.61-2.55A: Rsym=39.6%, I/sigma 10 50.00-6.13: Rsym=6.4% Some mild anisotropy in the resolution limits is

[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

[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 obsolete)

[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

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

Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 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 specify

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

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 *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https

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

*** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply

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 http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html#data_from_denzo. By default, HKL2000 (scalepack) will have output *merged* intensities, but merging is inherently

[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 exists,

Re: [ccp4bb] Rfree below Rwork

[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 concerns refinement of a structure with 6-fold NCS (local automatic restraints in REFMAC) against 2.8 A data

[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

[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

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

[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] AIMLESS unmerged MTZ output

symmetry operators in the > order they are stored in the MTZ file > Phil > > Sent from my iPhone > > > On 22 Jun 2017, at 17:04, wtempel <wtem...@gmail.com> wrote: > > > > Hello all, > > > > Are the following statements regarding AIMLESS unmerged mtz output &

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=COOT===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.

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

[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

[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

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

[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

[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

[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