Re: [ccp4bb] AI and cis-peptides

UBED1=CCP4BB&A=1 Links: -- [1] http://www-structmed.cimr.cam.ac.uk -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +

Re: [ccp4bb] About the A in AI

click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Links: -- [1] http://www.hofkristallamt.org/ -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133

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

cmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cg

Re: [ccp4bb] Tools for structure-based multiple sequence alignment

-- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/ Adjunct Lect

Re: [ccp4bb] Map superposition!

P4BB&A=1 -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/

Re: [ccp4bb] Regarding Patents

implicitly - the push for a change in which IP is handled in Universities. Let's see which way it goes but I remain hopeful with best wishes Pietro = Dr. Pietro Roversi As of July 2018 I shall take up a two-year LISCB and Leicester-Wellcome Trust

Re: [ccp4bb] Incorrect Structure in the PDB

that all is done in good faith but sometimes on-trust policy + absence of a "court" to appeal to in case of misconduct are a rather insufficient combination when it comes to PDB depositions/withdrawals. with best wishes, Pietro best regards, Sanchayita Sen PDBe Depositions Se

[ccp4bb] I am struggling to compile fasta36

ld returned 1 exit status make: *** [fasta36] Error 1 Googling for this -lz ld flag does not seem to hit anything immediately relevant in the top pages. Please help! Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks R

Re: [ccp4bb] Selenomethionine crystals

ystal went up into the beam. Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.

Re: [ccp4bb] Phasing with Many Monomers/AU

intramolecular heavy-atom Patterson vectors. Has anyone ever had such data and tried that strategy? Is it implemented in any of the currently available difference Patterson-solvers/heavy atom finders? Ciao! Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department

[ccp4bb] in summary

:-) Thank you all contributors to the thread! Regards Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulleti

[ccp4bb] Dependency of theta on n/d in Bragg's law

1,2,3 ...) All textbooks I know on the argument neglect to mention this and in fact only n=1 is ever considered. Does anybody know a book where this trivial issue is discussed? Thanks! Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobi

Re: [ccp4bb] Rmerge of the last shell is zero

HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100% OUCH Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From

[ccp4bb] X-rays gas scattering picture needed

Dear all, together with two fellow crystallographers, I am writing a pamphlet to introduce schoolchildren to X-ray crystallography. For the introductory chapter, we would need a picture of X-rays scattered by air. Or by any gas for that matter. I have tried Google images without much luck. Can

[ccp4bb] 2D-bar code scanner to read Hampton pins barcodes

Dear all, I am looking into a 2D-bar code scanner to read Hampton pins barcodes. Something we can plug directly to any computer running Windows, Mac or Linux, via a supplied USB cable, and feed the barcodes into Excel. Does anybody know a cheaper alternative to the FOCUS MS-1690-38? Grazie, ciao

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Dear all, just to add that Clemens Vonrhein already a few years ago has implemented a procedure similar to the one Simon describes, to automatically fill the cavities in the macromolecule before computing the mask for the solvent, thus avoiding placing solvent where the core of the protein is,

[ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++

Dear all, How do I set up a Refmac dictionary to constrain octahedrally coordinated Ca++? Refmac5 seems to detect the potential bond between the Ca++ and the ligands: INFO: link is found (not be used) dist= 2.229 ideal_dist= 2.320 ch:AA res: 263 GLU at:O .->ch:Ag

[ccp4bb] Molecular replacement with merohedarlly twinned data

)? Thanks! Ciao Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

Re: [ccp4bb] DM and MR

ging in dm in the high-resolution form. Admittedly this extra crystal form has 90% solvent! So if possible at all use dmmulti and multi-crystal averaging. I hope this helps! Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Patho

Re: [ccp4bb] Se oxidation

therein. Regards Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

[ccp4bb] http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

actions at a dimer interface (polar, ie hydrogen bonds and salt > bridges, and non polar). > > Thanks in advance for your replies. > > Best regards, > > Fred. -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Patholo

Re: [ccp4bb] phased MR

density - after that your maps can be improved with dmmulti cross-crystal averaging. Good luck! Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044

[ccp4bb] CCP4-ecalc crashes

INPUT") I think the keyword is correct in the manual and wrong in the error message. Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

Re: [ccp4bb] is it Ok to freeze

ietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

Re: [ccp4bb] Crystals grown directly on loop?

> *** > 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: [EMAIL PR

[ccp4bb] sfall in "MODE ATMMAP RESMOD" mode misreads PDB coordinates

if so how did they solve it? I would rather avoid digging into the code if I can! Best regards Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385

Re: [ccp4bb] DM - NCS averaging after phaser molecular replacement run-confused about coefficients

Dear Hari, you also might want to specify, on the dm input LABOUT card, the FCDM=FCDM and PHICDM=PHICDM coefficients, that output Fourier coefficients avoiding the recombination with the initial phases, and will allow you to inspect the truly-solvent-flattened, truly-averaged dm

Re: [ccp4bb] Placing an EM map in a large P1 box

Hi Larry, here is how I'd do it: mapmask MAPIN MAPOUT << EOF SYMMETRY 1 XYZLIM CELL PAD 0.0 END EOF Good luck with it! Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385

[ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2

o keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385

Re: [ccp4bb] Question about strange MR solution

Dear Michele, I think your MR solution is on a different allowed origin - that's all Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385

Re: [ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?

Hello Sun, Roman Hillig and I refined a mixture of ADP+PO4 and ATP in the active site of ARL2 - it is enough to exclude all contacts of the superposing ligands and let the occupancies refine. The protocol we followed is described in: Hanzal-Bayer M, Renault L, Roversi P, Witti

[ccp4bb] How to override the use of NCS in Molrep?

! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385

[ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

used in a Molecular Replacement rotation search? Our search model is an elongated object and we are searching in a cell with a=205 b=100 c=21 Angstrom ... ;-) Ciao Pietro -- Pietro Roversi Sir William Dunn