Re: [ccp4bb] Dry shipper in limbo

t; 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&A=1 > > -- > > To unsubscribe from the CCP4BB li

[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] 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&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail

[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

-- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&

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

; Prumyslova 595 > 252 50 Vestec near Prague > Czech Republic > > 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&A=1 >

Re: [ccp4bb] powdery residue on pucks?

gt; > CAUTION: This email 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 me

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

Re: [ccp4bb] map rotation

. I guess I am missing 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 t

[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&A=1

[ccp4bb] Acrimboldo BORGES standard libraries

t this installed. Thanks, 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

[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]

Re: [ccp4bb] Tricky MR problem

h 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 Se

[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

[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

Re: [ccp4bb] Large unit cell, overlaps

most 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,

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

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

to unpack temporary copy of >>>> /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz >>>> >>>> /tmp is not at all full and has plenty of inodes left. >>>> (running the install.sh from the arp_warp_7.1 directory doesn't >>>> ins

[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] xds question: inverse beam, lots of wedges

s to integrate each each wedge separately, but with 24 > wedges per xtal, 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] mosflm in script mode

Hi all, I have been trying to use mosflm in script mode, in a quick-n-dirty effort to pipe some information from labelit.index into a simple data collection strategy. While doing that, I run into the following issue. I have not been able to find a way to read in image information without startin

[ccp4bb] refmac5 and sphericity restraints, 2nd attempt

ill active? Cheers Jan On Mon, Feb 8, 2010 at 6:29 AM, Jan Abendroth wrote: > 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 > wor

[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

Re: [ccp4bb] Arp/wArp error

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

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] xds and cell refinement in cI

nts during integration, unless they're wrong. Cheers, Graeme 2009/10/8 Jan Abendroth : 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 at the value speci

[ccp4bb] xds and cell refinement in cP

. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

[ccp4bb] LINKR in refmac

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

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] ccp4i problem - bad marshal data

> is the machine using, and has it been updated recently. > > Charles 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

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions 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 Abendr

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions 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 Abendr

[ccp4bb] ccp4i problem - bad marshal data

e advanced functions 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 Abendr

[ccp4bb] nad woes

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

Re: [ccp4bb] ccp4i / refmac issue

University of Dundee Dow Street Dundee DD1 5EH Jan Abendroth 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 6.

[ccp4bb] ccp4i / refmac issue

source [file join $env(CCP4I_TOP) src execute.tcl] source [file join $env(CCP4I_TOP) src job_utils..." (file "/usr/local/ccp4-6.1.1/share/ccp4i/bin/ccp4ish.tcl" line 145) invoked from within "source [file join $env(CCP4I_TOP) bin ccp4ish.tcl]" (file "/u

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

re 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 re

[ccp4bb] unit cell flags in mtz files and refmac

79.0610 79.0610 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] 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] refmac 5.5.063 vs. 5.5.066

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

Re: [ccp4bb] iMosflm 1.0.0

aubles to work should get you 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 / Bainb

[ccp4bb] low B factors

, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I could retrain a bit more... Any ideas how to handle this? Basically, my question is: how do I get the overall B factor to realistic numbers? Thanks a lot for any hints Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA

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

[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

[ccp4bb] refmac, twin - really low Rfactors

y low 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 Aben

Re: [ccp4bb] Change reflection file names

is stupid. 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] 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 geomet

[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] 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: -

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 me

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

[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 informati

[ccp4bb] external phases in sharp

Hi all, I am trying to include exteral phase information in a sharp refinement. The phases come from dmmulti. Steps this far: - convert PHI and FOM to HLA and HLB in sftools, - rename PA and PB to HLA and HLB in cad - copy file (xx.extern.mtz) with all F, DANOs and HLA HLB into my datafiles directo

[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 replaceme

Re: [ccp4bb] tricky molecular replacement

gt; 4. If 3 works, multicrystal averaging to improve both crystals > til the map is traceable. > > 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 wit

[ccp4bb] tricky molecular replacement

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 homology model. For the hexagonal crys

[ccp4bb] phaser and rotation function solutions

Hi all, in a rather weak molecular replacement the rotation solution that eventually produces a decent translation search (Z>9 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. S

[ccp4bb] refmac and ramachandran troubles

POSITIVE" problems. Any ideas? Cheers Jan -- Jan Abendroth deCode Biostructures Seattle/Bainbridge Island, WA, USA work: [EMAIL PROTECTED] home: [EMAIL PROTECTED]

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 cas

[ccp4bb] mosflm and APS BM17

Hi all, processing data collected on APS beamline BM17 on a MAR165 detector causes unexpected troubles. Even though the crystals are well-diffracting and the spots are sharp and well-resolved, indexing only works with a certain selection of frames, the refinement the goes totally hairwire. Probalby

[ccp4bb] xds, saturn94 and 2theta

d to be changed? - 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 Abe

[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/ _

Re: [ccp4bb] scala and cell dimensions

heers, 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

[ccp4bb] scala and cell dimensions

ength 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 Str

[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

Re: [ccp4bb] Bio-rad DuoFlow

oo.com/dir/index;_ylc=X3oDMTFvbGNhMGE3BF9TAzM5NjU0NTEwOARfcwMzOTY1NDUxMDMEc2VjA21haWxfdGFnbGluZQRzbGsDbWFpbF90YWcx?link=ask&sid=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

Re: ccp4bb on new site

t of office replies, but I am assured that it is possible. So, please forgive any problems that occur over the next few days/weeks as we try and get everything together. Charles Ballard CCP4 ps - posting to ccp4bb@dl.ac.uk will still work as this address is now an alias. -- Jan Abendroth Univ