Re: [ccp4bb] need suggestions

Regards AFSHAN - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Off-topic: PDB statistics

doing the searches is no good. Does someone have a better way to do this? Thanks much. Raji - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using

Re: [ccp4bb] Refmac error

Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRaCFtUxlJ7aRr7hoRAhTcAKCU7lbVkKNjgOvsapJMD95UkQ1GjQCfQNef

Re: [ccp4bb] 2Theta data set solving problem

. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment

Re: [ccp4bb] CCP4 Update 021

will not have ccp4.setup-sh in $CCP4/bin If this is the case or you does not have this file for any other reasons, please remove the following line . ./ccp4.setup-sh from the file $CCP4/bin/ccp4um Andrey On 5 Apr 2013, at 06:09, Tim Gruene wrote: Dear Andrey, when I click on 'Manage

Re: [ccp4bb] COOT usage for structure comparison

that I pick up one atom and see that this atom belongs to 2q9o, chain a and so on. Thank you in advance, - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment

Re: [ccp4bb] COOT usage for structure comparison

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, I guess your criticism is adequate - I'll stop doing this. My apologies to Eugene. Best, Tim On 04/04/2013 02:43 PM, Ed Pozharski wrote: On 04/04/2013 04:29 AM, Tim Gruene wrote: Dear --, Are we, the ccp4bb community, recently on the hunt

Re: [ccp4bb] High Rmerge and I/sigma values....?

pointless! If these data are from an article you are refereeing please point out that Rmerge should not be published anymore and be replaced by Rmeas (alias Rrim)! Best, Tim Gruene On 03/29/2013 02:19 PM, hamid khan wrote: Dear CCP4BB Members, I am interested in your expert comments/opinions

Re: [ccp4bb] High Rmerge and I/sigma values....?

bytes it takes up in your paper. -James Holton MAD Scientist On Fri, Mar 29, 2013 at 6:48 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Hamid, the statistics for I/sigI and the R-value per resolution shell would shed more light than the overall values. Judging from the Rmerge

Re: [ccp4bb] refinement protein structure

78486435 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

[ccp4bb] Rfree reflections

irrespective of the total number of unique reflections in the data set, or is it 5-10% (as a compromise)? Thanks and regards, Tim -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Rfree reflections

Of Tim Gruene Sent: Tuesday, March 26, 2013 09:33 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rfree reflections Dear all, I recall that the set of Rfree reflections should be 500-1000, rather than 5- 10%, but I cannot find the reference for it (maybe Ian Tickle?). I would

Re: [ccp4bb] Resolution limit of index in XDS

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS Dear Niu, indexing relies on strong reflections only, that is (in very brieft) why INCLUDE_RESOLUTION_RANGE indeed does

Re: [ccp4bb] COOT running slow after upgrading to CENTOS 6.4 from 6.3

? Zhijie - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

...@imbb.forth.gr - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRSjcvUxlJ7aRr7hoRAhZbAKDl++SESOqHcqqDdfA

Re: [ccp4bb] DNA Restraints or Cif file for Phenix refinement

mutate” as compatible with Phenix but still I can’t use phenix.refine to refine this model. So how can I force the phenix.eLBOW to generate the restraints? or is there any other software could be used to generate the cif file? Many thanks, Yurong - -- Dr Tim Gruene Institut fuer

Re: [ccp4bb] Resolution limit of index in XDS

step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Thanks! Niu - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux

Re: [ccp4bb] How to use SHELXE to perform phasing and density modification

10 S HAT10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei - -- - -- Dr Tim Gruene

Re: [ccp4bb] Please recommend linux workstation

? Kind regards, Tim On 03/15/2013 05:34 PM, jie liu wrote: Dear All I am planning to buy a linux workstation for crystallography. It seems that Dell does not offer workstations with linux right now. Any good experience to recommend? Thank you! Jie Liu - -- - -- Dr Tim Gruene Institut

Re: [ccp4bb] Diffraction data with big rotation angle

on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment

Re: [ccp4bb] RNA 3D structure alignment

by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] How to set the contour level to a specific value in COOT?

with COOT, and I want to set the contour level to a specific value, say, 2.0. Since the initial value is not a whole number, I cannot manage it by scrolling the wheel. Can I change this value by scripting or something like that? Thanks in advance. - -- - -- Dr Tim Gruene Institut fuer

Re: [ccp4bb] Best practice for transformed PDB coordinates?

and registration details link at the bottom of the page.. __ - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12

Re: [ccp4bb] statistical or systematic? bias or noise?

as a point of reference. Cheers, Ed. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Child Killed error in SCALA

child killed: kill signal *** #CCP4I TERMINATION STATUS 0 child killed: kill signal #CCP4I TERMINATION TIME 05 Mar 2013 14:28:22 #CCP4I MESSAGE Task failed - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] Child Killed error in SCALA

, Tim On 03/08/2013 12:49 PM, Frank von Delft wrote: (Is it time to change the macabre title of this thread? If I were Phil it'd give me a jolt every time time I read it... what have I wrought!) phx On 08/03/2013 11:35, Tim Gruene wrote: Dear Roger, apart from Francois' suggestion

Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

in advance, Fred. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

. Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] visualizing ds DNA conformation

harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] stereo monitor for DELL T7600

://proteincrystallography.org/ccp4bb/message29933.htmlSyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Any advice will be highly appreciated. Thanks so much in advance! Jl - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] stereo monitor for DELL T7600

...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/3/1 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Jl, the Zalmans are probably compatible with ANY graphics card you can buy in a shop nowadays. The technique they use was invented in the 1920s... Best, Tim On 03

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

source are appreciated. Refmac version is 5.7.0032. Cheers, Ed. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] Rfree flag

- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLyQ2UxlJ7aRr7hoRAsHBAJ43K7f2lcSZwm6fD1pH8

Re: [ccp4bb] SHELX-2013 release and homepage

, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG

Re: [ccp4bb] How to split a dataset with PST?

to the symmetry. Did anyone know how to split the data set in this case? Best regards, Yuan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using

Re: [ccp4bb] the matrix format

-- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux

Re: [ccp4bb] Measure Cell option in imosflm

Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG

Re: [ccp4bb] observed reflections

for the straightforward question. I'm just a bit confused about the observed reflections quoted in tables. What exactly is this and should it include outer shell separately? Best Careina - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] how to update phenix

for valentine's day. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert

. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

Re: [ccp4bb] COOT v. 0.7

. ERROR 20 READ: Attempt to read unknown-type file. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 There was a coordinates read error Any hints on how to circumvent this? Best wishes, Xavier -- - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] need some suggestions for crystallization

. It always amazes me how helpful this group is. Thank you very much. Dave - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla

Re: [ccp4bb] off topic: DSSP

/dssp-2.1.0.tgz from http://swift.cmbi.ru.nl/gv/dssp/ I tried doing make followed by make install. I got error on compiling. Thanks in advance - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] refmac5 vs phenix refine mixed up

, and they provide option to define the flag value to use. Pavel - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] off topic - legacy hardware help needed

, Adam Ralph wrote: You can just connect two machines together with an ethernet cable, no switches or routers. However you need a crossover cable to do this. Most likely you have standard cables only in the lab. Adam - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4

Re: [ccp4bb] refmac5 vs phenix refine mixed up

question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] refmac5 vs phenix refine mixed up

the same input mtz-file you avoid such possibilities and it also points a novice user to what refinement is actually doing. Best, Tim On 01/24/2013 12:03 PM, Qixu Cai wrote: Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Rajesh, first of all, a model is not true

Re: [ccp4bb] Hi clashscore

is not at all reducing and showing a value of 12. Can anybody suggest how to reduce the clashscore. Is there any technique to do it. Or i have to deal with each individual clashes mentioned in the list manually ? Supratim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4

Re: [ccp4bb] R-factors of various kind

in the literature. I like to understand various kind of R-Factors, their mathematical formula, and relations among them. Thank you. Teri - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] Confused with pirate::Refine_HL_coeff::operator() function

on the line 694. Once the iteration (690-718) was terminated on the line 718, f2 could be any value. However, on the line 737, f2 was used again without pointing to any specific Miller indices. Could anybody explain the reason for that, or it's a bug? Best, Jiawei Wang - -- - -- Dr Tim

Re: [ccp4bb] Crystallization buffer pH optimization

, etc. This is useful for crystallization pH optimization, where can I buy or download this info? Alternatives? Thank you very much! Mike - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] ccp4 update

/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen

Re: [ccp4bb] ccp4 update

some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] P212121 and P213

structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

of CORRECT.LP. Please, note that I am not referring to the table output by XSCALE, in which you can change the resolution bins with the keyword RESOLUTION_SHELLS=, but rather the table output by the CORRECT job of XDS. Thanks in advance, ciao, Sebastiano - -- - -- Dr Tim Gruene Institut fuer

Re: [ccp4bb] advices

3.5A in a home source of 1.2 KW sealed tube Angilent equipment. But the data can not be indexed due to one direction has poor diffraction and the crystal quality. Seeking advices on improving the crystal quality. Thank you very much Mike - -- - -- Dr Tim Gruene Institut fuer anorganische

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

3.00 Y ISYM 9 NONE0.0 1.0 0 100.00 0.95 0.95 48.22 3.00 I FreeRflag No. of reflections used in FILE STATISTICS11643 Aren't they supposed to be the exact same number? Thanks, ciao, s On Jan 16, 2013, at 1:12 PM, Tim Gruene t...@shelx.uni

Re: [ccp4bb] a challenge

until a solution is in place. Neither would make an excellent macromolecular crystallographer by necessity. Tassos - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux

Re: [ccp4bb] Convert cbf to png/tiff?

. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu - -- - -- Dr Tim Gruene Institut

Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?

installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG

Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?

On 11/01/2013 16:34, Tim Gruene wrote: Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File

Re: [ccp4bb] adding H to DNA

phenix.ready_set or phenix.reduce. Hydrogens are only added to protein but not to DNA. Any ideas of fixing the problem? Many thanks and best regards sheng - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Does Scala merge anomalous/non-anomalous?

factors? I don't need the anomalous data so I don't need to keep it separate. Thanks. -Yarrow - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using

Re: [ccp4bb] Planar restraints in Refmac

674269 Fax 39-081 674090 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] about coot

-loading ~/.coot file? Thank you very much for your help! Q. Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] Hgen ccp4i gui is broken

(command bound to event) - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] occupancy vs. Bfactors

read on exactly how to correctly fix this problem. Thanks, GM - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] ctruncate/scapepacktomtz : terminate called after throwing an instance of clipper::Message_fatal

TERMINATION TIME 19 Nov 2012 16:50:26 #CCP4I MESSAGE Task failed - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] hkl2000 install

anyone tell me how to do it ? Rui Wang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] vitrification vs freezing

, this will improve their quality, though, comparing my level of French with my level of English ;-) Lovely discussion, Tim On 11/15/2012 09:15 PM, James Stroud wrote: On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote: I have heard this discussion before and reminds me of people claiming strawberries were

Re: [ccp4bb] diffraction protein or salt

: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] seleno methionine labelling of protein

and extraction of phases. Or will be the same for both..? - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] Problems with PDB validation

: +33 438785494 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] model protein for ligand soaking

that can be easily identified in the electron density rather than halide or heavy atom derivatization. Does anybody have a suggestion for a protein/ligand combination that could be used for that and that is commercially available? Thanks! Uli - -- - -- Dr Tim Gruene Institut

Re: [ccp4bb] Assemble Protein-DNA complex

. However, the one I am currently working on seems to be very picky. If you have any suggestion regarding to my problems, I will be thankful. Best regards, - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Weird electron density on the two-fold axis

- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQl5NkUxlJ7aRr7hoRAkUtAKC/6mrt5LdcG9bjZm3rN6UfDzpotQCg7B20

Re: [ccp4bb] Copying R-free flags - possibly daft question.

)1273 677512 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQl6Q

Re: [ccp4bb] Termination of Shelxc/d/e

mentioned problem. For your convenience I have attached the log file of this run. Thanks is advance. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] Termination of Shelxc/d/e

November 2012 20:29, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear, from the lack of any shelxc-related output in the log-file my first guess is you don't have shelxc installed on your system - do you? It is not part of ccp4 and must be installed separately. (http://shelx.uni

Re: [ccp4bb] low-resolution data and SG

low resolution data, I want use this opportunity to learn refmac well. So could you please let me know if my doubt is right regarding SG and how do I troubleshoot. Thanks SDY - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Unusually low B factors with phenix

and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

[ccp4bb]

themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] Orientation of the crystal and it importance in data collection

. With regards B. Vijay - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Modelling Flexible Regions

, or if there are any tips for fitting residues into poor density. Thanks in advance, Rhys Grinter PhD Candidate University of Glasgow - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] Plate crystals

I got the same or nothing. I tried seeding but I had so many crystals without any improvement. Does anyone have better idea than routine optimization method in the lab? Thanks in advance. Jahan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen

Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image

not be protein diffraction. I never saw so strange images like this. Does anyone know what it is? Is it a kind of salt diffraction? Thank you very much Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Only su (root) can get ccp4i to run

: No such file or directory Anyone out there knows what to do in order to solve this problem ? Ta. F.V. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using

Re: [ccp4bb] off topic: PDB data mining

anyone know how to search for structures based on molecular weight. For example, I want to get a list of all the enzymes (molecular weight, say, 10kD), is it possible to manage it? Thank you in advance! - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] Tricky MR problem

is most likely C2221 with two molecules per ASU (giving around 58% solvent). Thanks, Rhys Grinter PhD Candidate University of Glasgow - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] How to output water molecules with Phaser?

clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

of the information contained in this message is prohibited. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Off Topic: help locating CNS data

suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU

Re: [ccp4bb] Series termination effect calculation.

termination errors. It is only map calculation where series termination can become a problem. Thanks to Garib for clearing up that last point for me! -James Holton MAD Scientist On 9/15/2012 3:12 AM, Tim Gruene wrote: Dear Ian, provided that f(s) is given by the formula in the Cromer

Re: [ccp4bb] Series termination effect calculation.

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry, 6e^-/A^3 (or -6e/A^3 for charge density people) this should have said. On 09/20/2012 11:39 AM, Tim Gruene wrote: tg@slartibartfast:~/tmp$ phenix.python run.py 0.001 627.413 -4.01639e+06 303880 0.1 275.984

Re: [ccp4bb] Series termination effect calculation.

: why should the density be 6A^-3 at the centre of a C atom? -- Ian On 20 September 2012 10:39, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: tg@slartibartfast:~/tmp$ phenix.python run.py 0.001 627.413-4.01639e+06 303880 0.1 275.984 275.247 435.678 0.5

Re: [ccp4bb] Series termination effect calculation.

/2012 02:47 PM, Tim Gruene wrote: Because C has 6 electrons and without thermal vibrations (T=0/B=0) I thought you'd catch all six of them with a box of 1A side length. Is this too simple thinking? Tim On 09/20/2012 02:19 PM, Ian Tickle wrote: Tim, I don't follow your argument: why

Re: [ccp4bb] Series termination effect calculation.

Scientist On 9/18/2012 6:32 AM, Tim Gruene wrote: Hello Oliver, when you fit the values from ICA Tab 6.1.1.1 with gnuplot, the values of C and N become much more comparable. c(C) = 0.017 and especially c(N) = 0.025 0!!! for C: Final set of parameters Asymptotic Standard Error

Re: [ccp4bb] Help Please!

GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference. It looks like a serious problem. Did I damage the operating system? Could you please give some advice on how to fix it? I am anxiously waiting for your help! Best regards Jie Liu - -- Dr Tim Gruene Institut

Re: [ccp4bb] Series termination effect calculation.

-FFTs, it is formally insensitive to series termination errors. It is only map calculation where series termination can become a problem. Thanks to Garib for clearing up that last point for me! -James Holton MAD Scientist On 9/15/2012 3:12 AM, Tim Gruene wrote: Dear Ian, provided

Re: [ccp4bb] B-iso vs. B-aniso

-factor refinement significantly improved R-work and R-free, while maintaining a reasonable gap for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts and/or opinions from the community are welcome. Cheers, - -- Dr Tim

<    1   2   3   4   5   6   7   8   9   10   >