Re: [ccp4bb] question about CCP4 scripts

2013-05-09 Thread Tim Gruene
test script for the program unique - this will use this # program to generate a reflection list containing null values. # set -e unique hklout ${CCP4_SCR}/unique_out.mtz eof labout F=F SIGF=SIGF symmetry p43212 resolution 1.6 cell 78.1 78.1 55.2 90.0 90.0 90.0 eof - -- Dr Tim Gruene

Re: [ccp4bb] reference for true multiplicity?

2013-05-14 Thread Tim Gruene
tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx - -- - -- 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] DNA version converter

2013-05-22 Thread Tim Gruene
file unchanged. - -- 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/ iD8DBQFRnGG4UxlJ7aRr7hoRAsnXAKC

Re: [ccp4bb] DNA version converter

2013-05-22 Thread Tim Gruene
is specific to a particular pdb file (it would be indeed strange if the conversion tool from a major software package would fail in general sense). Ed. On Wed, 2013-05-22 at 08:12 +0200, Tim Gruene wrote: Hi Ed, # pdbvconv -p udo.pdb -o udov.pdb # pdbvconv -p udov.pdb -o udovv.pdb

Re: [ccp4bb] DNA version converter

2013-05-22 Thread Tim Gruene
a question I did not ask. If you are interested in specifics, the problem was that some other program made residue names left-justified. Cheers, Ed. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Negative FoFc around ligand

2013-05-24 Thread Tim Gruene
is unrealistic. But the density comes up around these at around 0.7 sigma. Overall completeness is 99.9% Rmerge 7.5% What else I need to check in the data. Kindly provide some suggestions. Thanking you Regards Kavya - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D

Re: [ccp4bb] Negative FoFc around ligand

2013-05-25 Thread Tim Gruene
. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. - -- 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] Negative FoFc around ligand

2013-05-25 Thread Tim Gruene
, and is believed to be clean. - -- 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] Microseeding technique advice

2013-05-30 Thread Tim Gruene
eventually disolve leading to an unsuccesfull screen? Also how is the seedstock supposed to look under the microscope, clear? Thanks for your help DLadakis - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

2013-05-30 Thread Tim Gruene
a lot. Best, Donghui - -- 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/ iD8DBQFRp3/cUxlJ7aRr7hoRAkV

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

2013-05-31 Thread Tim Gruene
checked for secondary structure elements. Ciao, S -- Sebastiano On 30/mag/2013, at 18:35, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Donghui, did you actually check this stretch IS a beta-strand, given how distorted it looks? I am asking because in my experience people tend

Re: [ccp4bb] MAX IV Life Science Director position

2013-06-03 Thread Tim Gruene
/node/307 Lund University, Box 124, 221 00 Lund, Sweden - -- - -- 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] Helix forming proteins crystallizing as rings

2013-06-05 Thread Tim Gruene
) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 - -- - -- 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] Extracting .pdb info with python

2013-06-06 Thread Tim Gruene
, Grant - -- - -- 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] Td ions in refmac

2013-06-07 Thread Tim Gruene
/ The University of St Andrews is a charity registered in Scotland : No SC013532k - -- 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] Td ions in refmac

2013-06-07 Thread Tim Gruene
a known structure) I have previously experimented with Tim's (works). I am searching for anyone who knew a simple way to restrain metal ion geometry in remfac based on angles at metal. best Jim On 7 Jun 2013, at 10:14, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote

Re: [ccp4bb] pdbset

2013-06-11 Thread Tim Gruene
here? Swastik Phulera - -- - -- 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] Fwd: [ccp4bb] pdbset

2013-06-11 Thread Tim Gruene
, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

2013-06-11 Thread Tim Gruene
shelxl, Also getting rid of Ansiou at first would lead me to an additional step of placing them in their right place later on (is there a short cut that I may take). On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Swastik Phulera, unless you need

Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Tim Gruene
that Rmerg increases with redundancy, is it acceptable to report Rmerg (or Rsym) at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution bin of these crystals? I appreciate any comments. -A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen

Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Tim Gruene
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/ iD8DBQFRufFfUxlJ7aRr7hoRAk5UAKCHC1IpbdXmQE/5e1eRD+SON+jarQCg0b3m

Re: [ccp4bb] Concerns about statistics

2013-06-14 Thread Tim Gruene
, is it acceptable to report Rmerg (or Rsym) at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution bin of these crystals? I appreciate any comments. -A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

Re: [ccp4bb] Definition of diffractometer

2013-06-19 Thread Tim Gruene
diffraction, and that seems to be view of the wikipedia article of that name. eab - -- 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] Definition of diffractometer

2013-06-19 Thread Tim Gruene
. Then the volume of that pizza is equal to pi*z*z*a ! ** - -- 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] Hydrogens from Shelxl

2013-06-20 Thread Tim Gruene
not save the H atoms. Is any one here aware of a way to save Hydrogen atoms correctly such that the prepared pdb file could be successfully submitted to PDB with the Hydrogens intact. Swastik - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] ctruncate bug?

2013-06-20 Thread Tim Gruene
). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved.

2013-06-21 Thread Tim Gruene
operator: k,h,-l Suggests Twinning factor (0.5-H):0.393 Suggests Twinning factor (0.5-H):0.433 operator -k,-h,-l Suggests Twinning factor (0.5-H):0.110 Suggests Twinning factor (0.5-H):0.133 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] query regarding RMSD calculation

2013-06-23 Thread Tim Gruene
'conformation' or 'state'? Thanking all, regards, ansuman - -- 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] Alternating positive and negative density

2013-06-24 Thread Tim Gruene
, especially if anyone has seen anything like this? Thanks a lot, Peter Randolph - -- 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] Refinement against frames

2013-06-24 Thread Tim Gruene
in the surrounding background mask? Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

2013-06-24 Thread Tim Gruene
? thanks, Kay - -- - -- 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] Rfree is 20%,why still green and red density?

2013-06-26 Thread Tim Gruene
. I wonder if anyone met this problem before? Any suggestion is welcome. Best, Jiang Yan - -- - -- 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] Rfree is 20%,why still green and red density?

2013-06-26 Thread Tim Gruene
this proportionality, ~1000 reflections are sufficient to obtain a better than 1% precision for an overall R-free in the 20-30% range, i.e. 'a few hundred' is still not too bad. Best, BR - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] R too low?

2013-06-26 Thread Tim Gruene
of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 or 520 621 4168 s...@email.arizona.edu http://www.cbc.arizona.edu/xray or http://www.cbc.arizona.edu/facilities/x-ray_diffraction - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] cluster Ta6Br12 in phaser

2013-06-27 Thread Tim Gruene
using phaser from ccp4-6.3.0 distributed by sbgrid. Any help will be much appreciated, Kevin Jude - -- - -- 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

[ccp4bb] beta-tester knuspr plugin for coot

2013-06-28 Thread Tim Gruene
in the density). Kind regards, Tim Gruene - -- - -- 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] CNS download Info

2013-07-02 Thread Tim Gruene
Brunger to get the downlad information throguh my official id. Yet I am not getting any response. Could any one help? Thanks in advance Syed - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] XDS not picking spots correctly, please help!

2013-07-05 Thread Tim Gruene
, MI 48824 - -- - -- 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] HKL2000 sigma cutoff

2013-07-07 Thread Tim Gruene
these negative reflections. Is there a setting in HKL2000 that I can change or do I need to switch to a different program. Ursula - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] fw: hey

2013-07-29 Thread Tim Gruene
Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Twin or underestimation of symmetry

2013-07-30 Thread Tim Gruene
I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14

Re: [ccp4bb] X-rays gas scattering picture needed

2013-08-01 Thread Tim Gruene
. Or by any gas for that matter. I have tried Google images without much luck. Can anyone either kindly donate, or point me to, an image of X-rays scattered by a gas? Thanks! Pietro PS of course a picture of X-ray scattering by a liquid would also be very welcome - -- Dr Tim

[ccp4bb] mmCIF as working format?

2013-08-05 Thread Tim Gruene
indespensable to scientists, rather than scientifically needed. Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] mmCIF as working format?

2013-08-05 Thread Tim Gruene
with it even though I have objections to most of the replies to the thread I opened (except for the file size). Best, Tim P.S.: I would hold that bet against you, but I don't think this is the right place to discuss this. On 08/05/2013 03:35 PM, Ian Clifton wrote: On 05/08/13 09:03, Tim Gruene wrote

Re: [ccp4bb] mmCIF as working format?

2013-08-08 Thread Tim Gruene
about does not know any programming language at all, and the next student might require an API in scheme, ruby, java, C#++-3.141, fortran-123, ... - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] mmCIF as working format?

2013-08-08 Thread Tim Gruene
that we can implement them all (by tomorrow)! Cheers, Paul On Aug 8, 2013, at 12:17 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: On 08/07/2013 11:54 PM, Nat Echols wrote: PLEASE tell the developers what you need to get your job done; we can't read minds. -Nat Dear Nat

Re: [ccp4bb] TLS refinement and ANISOU records

2013-08-09 Thread Tim Gruene
Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using

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

2013-08-14 Thread Tim Gruene
? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG

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

2013-08-20 Thread Tim Gruene
' issue (e.g. http://dx.doi.org/10.1107/S0909049599006366 for an overview or http://dx.doi.org/10.1107/S0108767387098763 for the treatment of harmonics). As far as I understand, certain scaling programs take the lambda/2 contribution of monochromators into account. Regards, Tim Gruene On 08/20

Re: [ccp4bb] structural search for homologs in pdb?

2013-08-22 Thread Tim Gruene
/2013 05:14 PM, Gloria Borgstahl wrote: We have a protein sequence that probably contains OB folds. What is the best way to search for the top structural homologs to this sequence in the pdb? G - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

2013-08-23 Thread Tim Gruene
set me in the right direction. --paul - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Twinabs-cell_now

2013-08-24 Thread Tim Gruene
, 2013 at 02:29:54PM -0400, Mahesh Lingaraju wrote: hello everyone Can anyone point to me where i could obtain the programs twinabs, cell_now ? i cannot seem to locate them by simple googling. Thanks mahesh -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] Negative IOBS in XDS

2013-08-27 Thread Tim Gruene
1550.9 1935.5 19.0 0.32158 95 23 -93.63 0 0-7 -4.436E+01 4.495E+02 1547.5 2011.5 54.7 0.37469 100 -11 -85.79 Does this mean the process is wrong? Anything I can do in this case? Best, Niu -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D

[ccp4bb] 'table 1'

2013-08-28 Thread Tim Gruene
on how we think, so language should be kept from too much degradation. All the best, Tim -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Average B-factor

2013-09-02 Thread Tim Gruene
my crystal-data table. So, I want to calculate Average B-factor for protein atoms and water. Can anyone please tell me which CCP4 program that I have to use to calculate average B-factor. Thanks in advance Dhana - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] x-ray diffraction data analysis (XDS)

2013-09-02 Thread Tim Gruene
. 2013/9/1 Kay Diederichs kay.diederi...@uni-konstanz.de I forgot: you should be using FRIEDEL'S_LAW=TRUE - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14

Re: [ccp4bb] Fo simulators?

2013-09-04 Thread Tim Gruene
- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSJwv0UxlJ7aRr7hoRAik1AJ9dwCNkO3pZ4dnHNI15m

Re: [ccp4bb] spot streaking !

2013-09-19 Thread Tim Gruene
. thanx in advance rakesh - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Keeping sequence alignments in register

2013-09-21 Thread Tim Gruene
- not a local program) that accepts wildcards so I can keep the numbering in the resulting alignment in register with the PDB? I've Googled round, and I'm surprised that I can't find this addressed anywhere. Thanks! - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] tNCS: indexing and EP problems

2013-09-23 Thread Tim Gruene
the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] tNCS: indexing and EP problems

2013-09-24 Thread Tim Gruene
to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: Dear Nicolas, shelxd

Re: [ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Tim Gruene
they are present in the toplogy diagrma ? or the reviewer will raise the issue? hope you are able to understand what i mean to say. Please suggest me - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

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

2013-10-02 Thread Tim Gruene
wrong or in the wrong order or my application of linear algebra was mistaken. Any ideas out there? Thanking you in advance, Wolfram Tempel - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG

Re: [ccp4bb] Writing .xplor or CCP4 maps from raw data

2013-10-08 Thread Tim Gruene
of functions that might be able to help me with this? Best wishes, Anthony - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla

Re: [ccp4bb] Rfree stuck

2013-10-12 Thread Tim Gruene
(97.21) are favored region. Can you please suggest, what can be done to reduce the Rfree? Thanking you in advance. DCB - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux

Re: [ccp4bb] Tool to compute F/FP from F(+) / F(-)

2013-10-25 Thread Tim Gruene
, Rojan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

2013-10-29 Thread Tim Gruene
error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Comparison of Water Positions across PDBs

2013-10-30 Thread Tim Gruene
, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Tim Gruene
structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] SA-omit map

2013-11-04 Thread Tim Gruene
dengzq1987 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] convert orientation matrix format

2013-11-05 Thread Tim Gruene
one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- - -- 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] convert orientation matrix format

2013-11-05 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry for the misleading example for the maxima code: you have to create a matrix from a,b,c (X: matrix(a,b,c)) and left-multiply it with the matrix bb in order to make the coordinate transformation. Best, Tim On 11/05/2013 03:58 PM, Tim Gruene

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

2013-11-06 Thread Tim Gruene
control to enhance weak reflections and bug fixes. • truncate (Mac): Fixed harvesting option of old truncate. • Molrep: New interface. • Update (all): Increased maximum waiting time for background update check in ccp4i. Andrey Lebedev - -- - -- Dr Tim Gruene Institut fuer anorganische

Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

2013-11-06 Thread Tim Gruene
Tel. +39 0649910556 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSewyuUxlJ7aRr7hoRAnP

Re: [ccp4bb] switching space group

2013-11-06 Thread Tim Gruene
a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie - -- Dr Tim Gruene Institut

Re: [ccp4bb] convert orientation matrix format

2013-11-06 Thread Tim Gruene
the same axis in both matrices? as well as the rotation axis and the third axis? How can I convert one into the other one? Thank you very much in advance. Best wishes, Almudena. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

2013-11-07 Thread Tim Gruene
no subtraction, anytime. Furthermore, in Tim's example you could end up with negative sigmas.. HTH, Jens On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote: Dear Fulvio, with simple error propagation, the error would be sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Tim Gruene
optimal procedure I should follow? Really thanks for any advice and suggestions! Zhihong - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG

Re: [ccp4bb] Align linux version

2013-11-10 Thread Tim Gruene
) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene On 11/10/2013 01:30 PM, Mintu Chandra wrote: Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards

[ccp4bb] ccp4 man-pages

2013-11-15 Thread Tim Gruene
find them utterly handy, much faster than locating the html-documentation through a web-browser and they probably do not take up much space. So I hope to get some votes for redistributing the man-pages through the ccp4bb. Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] ccp4 man-pages

2013-11-15 Thread Tim Gruene
:48, Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote: Dear all, I am sorry about this 'double' post, but I had no reply on ccp4bb-dev within about three weeks. I wonder if I was the only one using the ccp4 man-pages. They were available until ccp4-6.3

Re: [ccp4bb] shelx anamalous data

2013-11-17 Thread Tim Gruene
. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

Re: [ccp4bb] Fix cell dimensions

2013-11-19 Thread Tim Gruene
there is a option to input cell parameters, but sometimes the program would not follow the input values and switch back to the one it thinks best. Any suggestions will be appreciated. Thanks! Best, Niu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key

Re: [ccp4bb] 100% Rmerge in high resolution shell

2013-11-19 Thread Tim Gruene
Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.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

Re: [ccp4bb] About protein precipitation problem during dialysis

2013-11-20 Thread Tim Gruene
to avoid precipitation. Thanks Dhana - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] the f' and f'' of heavy cluster

2013-11-21 Thread Tim Gruene
with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] How accurate are refined group-occupancies?

2013-11-22 Thread Tim Gruene
between 20 and 30% or even higher, but I would be very happy if someone could come with a more scientific way, however crude, to get an estimate of this error. Best regards, Herman - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] The 10% Gap between R-factor and R-free

2013-11-26 Thread Tim Gruene
, Beatrice Vallone ESRF User Organization Committee - -- - -- 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 Icedove - http://www.enigmail.net

Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex

2013-12-02 Thread Tim Gruene
-metal complex? I am looking forward to getting your reply. Cheers, Acoot - -- - -- 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 Icedove

Re: [ccp4bb] Off topic: Problem in reproducing crystal screen

2013-12-06 Thread Tim Gruene
to overcome the problem insolubility of PEG MME in the buffer mix? I have not faced such problems with other conditions which I prepare in house and have PEG in them. Further, it's not possible for me to use the original screen all the time. Thanks a lot! Regards -- Dr Tim Gruene

Re: [ccp4bb] scala discrepancy between versions

2013-12-10 Thread Tim Gruene
Times: User: 0.0s System:0.0s Elapsed: 0:00 Our current workaround is to use the last, not the latest, release of CCP4. Any help is appreciated, Jens -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] small crystals

2013-12-10 Thread Tim Gruene
always get the same tiny crystals. I think I might try microseeding but I haven't tried that yet. Any suggestions or tricks would be welcome Careina. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP

Re: [ccp4bb] Rfree problem

2013-12-10 Thread Tim Gruene
refinement the Rwork is going down. However, the Rfree is stuck and is not going down with refinement. I have already solved the structure without the co-factor bound. This structure is with the co-factor bound. Can anyone suggest the reason for the Rfree getting stuck? Thanks -- Dr Tim Gruene

Re: [ccp4bb] small crystals

2013-12-10 Thread Tim Gruene
, and much more time available. But that's in few years. Leo On Dec 10, 2013, at 10:01 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Careina, you can also apply for beamtime at PETRA-III. You get away with the same size crystals but only require a nano liter drop rather than a few ml

Re: [ccp4bb] coot error on a Scientific Linux box (32 bit)

2013-12-10 Thread Tim Gruene
a crash report - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFSpzDQUxlJ7aRr7hoRAgO

Re: [ccp4bb] ccp4 version in sharp

2013-12-11 Thread Tim Gruene
to change the ccp4 version for sharp without reinstall sharp? Thank you. Best Regards, lisa - -- - -- 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] Heavy atom sites

2013-12-16 Thread Tim Gruene
and anomalous occupancy and phasing power from my data. What's the best software to do this? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature

Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate

2013-12-17 Thread Tim Gruene
--- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

2013-12-17 Thread Tim Gruene
. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

2013-12-17 Thread Tim Gruene
on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Chang, this is hardly a matter of configuration

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