Re: [ccp4bb] effective iodide conc. for SAD data

! Cheers, Jan -- Jan Abendroth Emerald Bio Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote: Dear All, I have very thin crystals but diffracting. I was not able

Re: [ccp4bb] Large unit cell, overlaps

valuable in several cases. Good luck. Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On Jul 16, 2012, at 8:28 PM, Jason Busby wrote: Hi, The autoindexing

[ccp4bb] refmac5, SIGF/SIGIMEAN labels

NONE0.1 2270.0 0 100.00 267.05 267.05 47.42 2.40 F FC_ALL_LS 17 NONE0.0 360.0 0 100.00 180.30 180.30 47.42 2.40 P PHIC_ALL_LS -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work

[ccp4bb] Phaser and space groups

the two lines mentioned above with SPACEGROUP P41 This is a bit inconvenient though. Any ideas what is going wrong with the standard way? Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http

Re: [ccp4bb] Tricky MR problem

. With the great software packages available nowadays, you can have an initial structure within minutes after finishing the data set. For a recent review of this old technique see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836 Best wishes, Jan -- Jan Abendroth Emerald BioStructures / SSGCID Seattle

Re: [ccp4bb] Bio-rad DuoFlow

=X3oDMTFvbGNhMGE3BF9TAzM5NjU0NTEwOARfcwMzOTY1NDUxMDMEc2VjA21haWxfdGFnbGluZQRzbGsDbWFpbF90YWcx?link=asksid=396545367 -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002

[ccp4bb] mosflm getbox error

-- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002

[ccp4bb] scala and cell dimensions

error0.000 Angle error 0.00 Cell constraints: Scala: *** Error in batch cell dimensions *** -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742

Re: [ccp4bb] scala and cell dimensions

, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jan Abendroth Sent: 29 May 2007 19:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] scala and cell dimensions Hi mosflm experts, last week's problem with mosflm solved, another one appearing

[ccp4bb] MSGPP cocktails for fragment crystallography

posted on behalf of Christophe Verlinde, MSGPP, University of Washington, Seattle Replies only to him, please. MSGPP: The recipes for our cocktails for fragment crystallography designed to aid in drug design are now available. More info is at this URL: faculty.washington.edu/verlinde/

[ccp4bb] xds, saturn94 and 2theta

? - I also tried to use only a few or plenty of images for indexing. I know there are other programs for processing data, however, there are good reasons why I'd like to get this data set integrated with xds. Any ideas would be greatly appreciated! Cheers Jan -- Jan Abendroth University

Re: [ccp4bb] mosflm and APS BM17

Hi all, thanks a lot for all the responses! As anticipated, the solution is rather simple - the origin of the beam: denzo refines to: x=82.6 y=80.3 mosflm reads from header: x=80.0 y=84.0 - bad indexing etc mosflm works with: x=82.6 y=80.3 No swapping of x and y between denzo and mosflm in this

[ccp4bb] phaser and rotation function solutions

Hi all, in a rather weak molecular replacement the rotation solution that eventually produces a decent translation search (Z9 with a couple of clashes) is way down in the list of rotation function peaks. Sometimes this solution is included in the translation function, in similar runs it is not.

Re: [ccp4bb] tricky molecular replacement

. Jan Abendroth wrote: Hi all, I have a tricky molecular replacement case. One protein in two different crystal forms: hexagonal with 1 mol/asu, triclinic with 2 mol/asu (based on packing and self rotation). No experimental phases are available this far, however, there is a distant

[ccp4bb] tricky molecular replacement III

Hi all, thanks to several tremendously helpful replies I got the molecular replacement, which I bugged the ccp4bb with during the last weeks, under control. Thanks for all the input, I'll send out a summary soon. One question remains, though: With an improved search model, the molecular

[ccp4bb] ciftr troubles - now with logfile

... meant to include this logfile in my previous post: -Jan /sw/xtal/ciftr/ciftr-v2.053-prod-bin-darwin/bin/CIFTr -i output.cif Translating a mmCIF file [1] output.cif to PDB file output.cif.pdb Warning skipping item _computing.pdbx_density_modification is NOT in dictionary. Warning skipping item

[ccp4bb] ciftr troubles

Hi all, has anyone sorted out how to get ciftr running? pdb_extract nicely bundles the information from the pdb header and additional information from the supplementary file (data_template.text, for instance) and writes it into the a cif file. CIFTr, however, does not re-translate lots of

Re: [ccp4bb] Tough Low-Res MR

Hi all, just to second previous statements: Phaser has done wonders for me in a few tough cases, also at low resolution: Eg. various 6-10AA data sets with highly homologous search models. Or a rather bad search model: 1.8AA rmsd over ~50% of the residues. Often up to a point where the solution was

Re: [ccp4bb] Finding NCS operator from one heavy atom site?

Hi Partha, ncs6d did really great things to me a while ago. Similar case as yours, only one Met site in each of the 4 monomers, pretty horrible maps. I was amazed how ncs6d could sort its way through the maps and find the ncs operators. As a simple approach I just took a spherical map around the

[ccp4bb] ccp4mg and speed

Hi all, ... tried on the ccp4mg bb before ... ccp4mg is such a nice program, yet it is so slow in my hands. An average sized map calculated from a mtz file takes about 30s to display, while coot displays both 2FoFc and FoFc maps in about 5s. Is there anything I can do to speed things up? I use: -

[ccp4bb] monomer library sketcher troubles

Hi all, our library sketcher all of a sudden started acting up after working just fine. - read in or draw a structure works fine, - Create library description - a message pops up: Error running Libcheck program see /tmp/jabendroth/7547_tmp Sorry - this means we can not list the monomers in the

[ccp4bb] sketcher and nitrogen in rings

Hi experts, whenever create a ligand description with the sketcher that contains a saturated ring with nitrogens (piperidine, piperazine, etc) it flattens the nitrogens a la sp2 and consequently does weird things to the ring puckering. One can artificially protonate the nitrogen to get a sp3

Re: [ccp4bb] Change reflection file names

. Anyone can give me a very simple UNIX shell file to finish the job quickly? Thank you! Yanming -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

[ccp4bb] refmac, twin - really low Rfactors

for a 1.9AA structure. As expected, the maps from the twin treatment are a bit nicer that for the non-twinned treatment. Any reasons for concerns or just a very rigid structure that refines really well or refmac handling twinning really nicely? Thanks for any input Jan -- Jan Abendroth

[ccp4bb] xds and Saturn troubles

: !!! ERROR !!! ILLEGAL RAXIS_COMPRESSION_RATIO Any ideas what this might be? Thanks a lot Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] xds and Saturn troubles

Hi all, thanks a lot for all the replies! Using the very current version of XDS fixed all the problems, really nice data, structure solved, yet another one for SSGCID. re input file: attached the XDS.INP file that worked for the Saturn 944+ detector. Thanks again! Jan 2008/9/4 Jan Abendroth

Re: [ccp4bb] iMosflm 1.0.0

up and running. Unix/Linux/Mac OS X users are unaffected. Thanks to the CCP4 team for pointing this out and apologies to all Windows users. Luke http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is

Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066

/ That should fix the problem (please let us know if it does not) Pavol. -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

[ccp4bb] unit cell flags in mtz files and refmac

311.7950 90. 90. 90. 1.0 -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] unit cell flags in mtz files and refmac

mtz. IF there was one dataset in mtz then there was no problem Please have a look: www.ysbl.york.ac.uk/refmac/latest_refmac.html Garib On 26 Feb 2009, at 21:52, Jan Abendroth wrote: Hi all, I am trying to follow good practices and keep my set of free reflections between data sets, eg

Re: [ccp4bb] ccp4i / refmac issue

University of Dundee Dow Street Dundee DD1 5EH Jan Abendroth jan.abendr...@gmail.com 03/06/09 6:40 AM Hi all, I keep on getting the following error message when I try to start a refmac job through ccp4i with ccp4 version

[ccp4bb] nad woes

the * nomenclature. Cheers Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

[ccp4bb] mosflm in script mode

PROFILE OVERLOAD PARTIALS RASTER 19 19 9 4 4 SEPARATION 1.80 1.80 CLOSE REFINEMENT RESID 7.5 REFINEMENT INCLUDE PARTIALS RESID 10.0 #High s/n scanner adsc strategy auto stats on go end exit eof -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home

Re: [ccp4bb] xds question: inverse beam, lots of wedges

, this is starting to look a little tedious. Cheers, Pat -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

[ccp4bb] pdb_extact and refmac5.6

/mmcif_pdbx_2.items) in get_lines_from_file pdb_extract version-3.010, as downloaded form the rcsb webpage also chokes on the refmac5 logfile with a segmentation fault. Any ideas how to treat the new refmac log files in pdb_extract? Thanks a lot. Jan -- Jan Abendroth Emerald Biostructures

Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?

? Thanks! Jonathan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

[ccp4bb] ccp4i problem - bad marshal data

may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendroth deCODE

[ccp4bb] ccp4i problem - bad marshal data

may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendroth deCODE

Re: [ccp4bb] ccp4i problem - bad marshal data

Ballard CCP4 -- *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Jan Abendroth *Sent:* 02 June 2009 22:56 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] ccp4i problem - bad marshal data Hi all, we a one weird problem with one of our

[ccp4bb] LINKR in refmac

will be created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home

[ccp4bb] LINKR in refmac

will be created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home

Re: [ccp4bb] xds and cell refinement in cI

integration, unless they're wrong. Cheers, Graeme 2009/10/8 Jan Abendroth jan.abendr...@gmail.com: Hi all, I am running into a strange behaviour fo xds for a primitive cubic data set. Neither in the INTEGRATE nor in the CORRECT step the cell parameters are refined and stay exactly

Re: [ccp4bb] sulfur sad phasing

be appropriate to maximize anomalous scattering to position chlorides, calcium, sulfate in already phased structures? Thanks in advance, Matthias -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] Arp/wArp error

welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr -- -- Jan

[ccp4bb] refmac5 and spericity restraints

Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

[ccp4bb] refmac5 and sphericity restraints, 2nd attempt

Jan On Mon, Feb 8, 2010 at 6:29 AM, Jan Abendroth jan.abendr...@gmail.comwrote: Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http

[ccp4bb] Speaker opportunity at ACA 2018, session: Current state of instrumentation, automation, status and future

com> Jan Abendroth, Beryllium Discovery, jabendr...@be4.com<mailto:jabendr...@be4.com> Thanks and best wishes, Matt Clifton Jan Abendroth JAN ABENDROTH, Dr. Core Leader, CrystalCore P 206-780-8925 F 206-780-8547 Seattle | Boston | USA | be4.com [cid:image001.png@01D350FE.EE91E390]

[ccp4bb] Acrimboldo BORGES standard libraries

-- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

[ccp4bb] map rotation

12 5.510 -57.243 eof -- Jan Abendroth Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] map rotation

110.24328.112 ! to rotate map by B to A > rotation > > TRANS -42.212 5.510 -57.243 > > end > > > > > > On Mon, 25 Mar 2019 at 04:58, Jan Abendroth > wrote: > >> Hi all, >> thanks for the feedback. Suggestions like coot or pymol won't work

Re: [ccp4bb] map rotation

ng something in maprot. Any input would be appreciated. This is public data, so I would be happy to share the data. Cheers, Jan On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth wrote: > Hi all, > this should be easy, scripting the rotation of a map. > Purpose for this is: Superimpo

Re: [ccp4bb] powdery residue on pucks?

mail originated from outside UTSW. Please be cautious of > links or attachments, and validate the sender's email address before > replying. > > > > -- > > UT Southwestern > > Medical Center > > The future of medicine, today. > > ---

[ccp4bb] diffdump in CCP4 7.1

Hi all, It looks as if the utility ‘diffdump’ is no longer part of the standard linux CCP4 7.1 distribution. It has been a very handy tool for preparing XDS input files. Does anyone know if there is an equivalent script in CCP4 7.1? Thanks, Jan -- Jan Abendroth UCB BioSciences Seattle

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

; Tel. +420 325 873 758 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protect

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

h.D > Institute of Biotechnology > Academy of Sciences of the Czech Republic > Biocev > Prumyslova 595 > 252 50 Vestec near Prague > Czech Republic > > Tel. +420 325 873 758 > > -- > > To unsubscribe from the CCP4BB list, click the following link: &

Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditi

[ccp4bb] coot 0.9.8.1 and phenix mtz files

*mydata*.mtz will only open up the PDB but ont the mtz file. The latter can be opened via the Load menu. - The Coot window launched from the phenix gui does not displany the pdb or the map. Any pointers would be appreciated. Thanks! Jan -- Jan Abendroth UCB BioSciences Seattle

Re: [ccp4bb] Dry shipper in limbo

> Phone: (650) 723-6431 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- > > To unsubscribe from the CCP4BB list