Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

2021-08-31 Thread Dirk Kostrewa
=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *** Dirk Kostrewa Ge

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-27 Thread Dirk Kostrewa
olicyandsecurity/ -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@g

Re: [ccp4bb] Omit maps in phenix and ccp4

2021-04-07 Thread Dirk Kostrewa
ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-S

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

2020-12-03 Thread Dirk Kostrewa
terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <http

Re: [ccp4bb] [xds] how to specify measuring angle

2020-10-09 Thread Dirk Kostrewa
. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-11 Thread Dirk Kostrewa
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 & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ***

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-11 Thread Dirk Kostrewa
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 & conditions are ava

Re: [ccp4bb] Help With Setting up a Stereo view system_walkthrough

2020-08-03 Thread Dirk Kostrewa
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, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 --

Re: [ccp4bb] Help With Setting up a Stereo view system

2020-07-31 Thread Dirk Kostrewa
mail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

2020-07-01 Thread Dirk Kostrewa
se, and solve structures much more easily. How often you count a reflection is up to you; I don't see what you gain by this. best, Kay Am 01.07.20 um 11:42 schrieb Dirk Kostrewa: Dear Gerard and Kay, yes, you are both right - I have totally forgotten radiation damage! And correcting for this r

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

2020-07-01 Thread Dirk Kostrewa
eflections measurements is problematic for the same reason that Heraclitus wrote (something like) "You cannot step twice into the same river". With best wishes, Gerard. -- On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote: Dear Herman, I think, your MPR prop

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

2020-07-01 Thread Dirk Kostrewa
Kl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=J0zDXf_fmFuuuSdL_f3Rux6-Dkg9g4Myb2J6inlBYOY=Ib310E3JW-V0qyXGEQchrvA7HBHF9JKxtpRbxK4HkMo=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.ex

Re: [ccp4bb] Space group/Unit cell

2020-05-22 Thread Dirk Kostrewa
To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry

Re: [ccp4bb] nVidia 3D Vision2 glasses

2020-01-15 Thread Dirk Kostrewa
4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-7684

Re: [ccp4bb] nVidia 3D Vision2 glasses

2020-01-09 Thread Dirk Kostrewa
<https://nvidia.custhelp.com/app/answers/detail/a_id/4845/~/3d-vision-end-of-life---faq> on the Nvidia site. Best regards, Dirk Kostrewa. On 1/9/20 10:37 AM, Barone, Matthias wrote: Hi Patricia All modern graphics cards still support 3D vision, but you are correct that nvidia is addr

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2019-01-08 Thread Dirk Kostrewa
### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Max

[ccp4bb] Fwd: Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2019-01-07 Thread Dirk Kostrewa
cp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation Date: Mon, 7 Jan 2019 14:12:05 +0100 From: Dirk Kostrewa Reply-To: dirk.kostr...@lmu.de To: CCP4BB@JISCMAIL.AC.UK Lieber Kay, ich wünsche Dir ein Frohes und Gesundes Neues Jahr! Ich staune auch, dass es anschei

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2019-01-07 Thread Dirk Kostrewa
following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phon

[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa <ko

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
to:CCP4BB@JISCMAIL.AC.UK> *Onderwerp: *Re: [ccp4bb] Calculation of generalised R-factor? I'd be interested as well. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Tuesday, December 20, 2016 8:47 AM To: CCP4BB@JISCMAIL.A

[ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
t reported by the usual refinement programs. Is there a program that reads an mtz file with Fo and refined Fc and just calculates RG? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-M

Re: [ccp4bb] AW: [ccp4bb] Rfree below Rwork

2015-07-02 Thread Dirk Kostrewa
or otherwise using them for any purpose. Thank you for your cooperation. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49

Re: [ccp4bb] [SUSPECTED SPAM] Re: [ccp4bb] nVidia quadro Update for Linux

2015-04-07 Thread Dirk Kostrewa
, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. -- -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [ccp4bb] Bulk solvent

2015-01-12 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Bulk solvent

2015-01-12 Thread Dirk Kostrewa
Dear Bernhard, further thinking about the Babinet scaling effects, I have to correct my conclusion in the last sentence: On 12.01.2015 14:21, Dirk Kostrewa wrote: If, however, the unmodelled part is less well ordered (which is the more common case), it's contribution will mainly affect

Re: [ccp4bb] Bulk solvent

2015-01-09 Thread Dirk Kostrewa
of possibly important difference density peaks in narrow regions. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone

Re: [ccp4bb] twin or untwinned

2014-07-03 Thread Dirk Kostrewa
! Yamei Yu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] twin or untwinned

2014-07-03 Thread Dirk Kostrewa
really not happen. Cheers, Tim On 07/03/2014 01:42 PM, Dirk Kostrewa wrote: ... and please check, whether phenix.xtriage recognized the input data as intensities or as amplitudes. In case of doubt, convert the intensives first into an mtz file with Fs instead of Is and run phenix.xtriage

Re: [ccp4bb] twinning fun

2014-01-28 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-09-02 Thread Dirk Kostrewa
*From:* Dirk Kostrewa kostr...@genzentrum.lmu.de *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Friday, 30 August 2013, 15:36 *Subject:* Re: [ccp4bb] Fractional coordinate shift with two-character chain names? Hi Martyn, excellent - this worked! Many thanks

[ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Dirk Kostrewa
. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Dirk Kostrewa
: pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb eof translate * frac 0 0.2 0 end eof I just tried it on a little example, and it works for me. Cheers Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: 30 August 2013 14:41

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

2013-07-31 Thread Dirk Kostrewa
too... F. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] Concerns about statistics

2013-06-14 Thread Dirk Kostrewa
. -A -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

[ccp4bb] Single-Gaussian Atomic Scattering Factors?

2012-11-28 Thread Dirk Kostrewa
regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

[ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread Dirk Kostrewa
. o CHANGE: Dotted surfaces now are coloured by atom type and are at atomic radii rather than 1A. o CHANGE: map transformation no longer has symmetry overwrite problems. -- *** Dirk Kostrewa Gene Center Munich Department

Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?

2012-10-01 Thread Dirk Kostrewa
of Coot package, which is something completely doable in principle, in which case it can deliver fixes for current release. Eugene On 1 Oct 2012, at 09:46, Dirk Kostrewa wrote: Dear CCP4 developers, this question might be interesting for many CCP4/Coot users: will the Coot release 0.7 and future

Re: [ccp4bb] Which Coot for Scientific Linux 6.3

2012-09-20 Thread Dirk Kostrewa
rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 tel:%2B33%20438789605 Fax: +33 438785494 tel:%2B33%20438785494 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians

Re: [ccp4bb] CNS installation

2012-07-12 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] bulk solvent treatment inside protein cavities

2012-04-17 Thread Dirk Kostrewa
, - Allister Crow -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] proper or improper ncs?

2012-02-21 Thread Dirk Kostrewa
University of Colorado at Boulder -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] Freezing crystal

2012-02-07 Thread Dirk Kostrewa
, and Robert E Thorne: Hyperquenching for protein cryocrystallography, J. Appl. Crystallogr., 39, 805-811 (2006) -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377

Re: [ccp4bb] NMR review

2012-01-12 Thread Dirk Kostrewa
weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89

Re: [ccp4bb] NMR review

2012-01-12 Thread Dirk Kostrewa
out of phase imply incoherent scattering? I though it means inelastic Compton scattering? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Thursday, January 12, 2012 1:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR

Re: [ccp4bb] NMR review

2012-01-12 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Sub-angstrom resolution

2012-01-11 Thread Dirk Kostrewa
structure factors? For a larger unit cell (assuming a similar solvent content), I would then expect larger structure factors. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität

Re: [ccp4bb] Distinguish NH4 from Na?

2011-11-17 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] [PyMOL] Putting a protein molecule into a grid and traversing through the grid

2011-10-28 Thread Dirk Kostrewa
)cube? As in, can pymol be used to tell me which residues are lying in which (smaller) cube and so on? Can all this be done in a single pymol window/script? please let me know. Thanks -Anasuya -- *** Dirk Kostrewa Gene Center Munich, A5.07

Re: [ccp4bb] Linux vs MacOS for crystallographic software

2011-09-29 Thread Dirk Kostrewa
? ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 -- *** Dirk Kostrewa Gene Center

Re: [ccp4bb] question regarding secondary-structure restraints

2011-09-26 Thread Dirk Kostrewa
structures and other hydrophilic interactions to some reasonable geometry, even at very low resolution. Best regards, Dirk. Am 26.09.11 16:17, schrieb Nat Echols: On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de wrote: when I

Re: [ccp4bb] Protein structure solved by computer gamers (and phaser)!

2011-09-19 Thread Dirk Kostrewa
solved by protein folding game players The paper (Nature SB): http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf The game: http://fold.it/portal/ -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig

[ccp4bb] PIR - was Re: [ccp4bb] Another paper structure retracted

2011-08-12 Thread Dirk Kostrewa
Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig

Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0

2011-07-19 Thread Dirk Kostrewa
be set during packaging unfortunately. Cheers Clemens -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax

[ccp4bb] Lattice sampling and resolution - a seeming paradox?

2011-04-15 Thread Dirk Kostrewa
. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?

2011-04-15 Thread Dirk Kostrewa
to the von Laue condition, S*a = h. In fact the sampling of the molecular transform has nothing to do with h, it's sampled at points separated by a* = 1/a in the 1-D case. Cheers -- Ian On Fri, Apr 15, 2011 at 12:20 PM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Dear colleagues, I just stumbled

Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?

2011-04-15 Thread Dirk Kostrewa
Dear colleagues of the CCP4BB, many thanks for all your replies - I really got lost in the trees (or wood?) and you helped me out with all your kind responses! I should really leave for the weekend ... Have a nice weekend, too! Best regards, Dirk. Am 15.04.11 13:20, schrieb Dirk Kostrewa

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Dirk Kostrewa
://skuld.bmsc.washington.edu/DarkMatter -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] Density sharpening with Truncate?

2011-02-28 Thread Dirk Kostrewa
be thought of as sharpening the data anyway. Best wishes, Randy Read On 28 Feb 2011, at 09:02, Dirk Kostrewa wrote: Dear CCP4ers, I really would sharpen the structure factors, not only the electron density maps. The simple reason is: if sharpening emphasizes enough information at higher resolution

Re: [ccp4bb] strange density

2011-02-24 Thread Dirk Kostrewa
: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu mailto:rrowl...@colgate.edu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377

[ccp4bb] Postdoc position at the Gene Center Munich

2011-02-21 Thread Dirk Kostrewa
Dear CCP4ers, on behalf of Patrick Cramer, I send a Postdoc position offer, given below. Please, do not respond to me, but to the e-mail addresses given in the job description. Best regards, Dirk Kostrewa. *** Applications are invited

[ccp4bb] PDB deposition ADIT without frames?

2011-02-15 Thread Dirk Kostrewa
the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen

Re: [ccp4bb] PDB deposition ADIT without frames?

2011-02-15 Thread Dirk Kostrewa
Dirk Kostrewa: Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump

[ccp4bb] Counting of geometrical restraints?

2011-01-31 Thread Dirk Kostrewa
in macromolecular least-squares refinement, Acta Cryst., D54, 547-557 (1998) -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845

Re: [ccp4bb] Merging data to increase multiplicity

2011-01-28 Thread Dirk Kostrewa
Trincão, PhDCQFB@FCT-UNL 2829-516 Caparica, Portugal It's very hard to make predictions... especially about the future - Niels Bohr -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [ccp4bb] High Rmerge with thin frames

2010-11-05 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW

[ccp4bb] Off-Topic: CNS MAXLEV error

2010-11-05 Thread Dirk Kostrewa
: MAXLEV exceeded Does anyone could point me to a direction what that means? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich

Re: [ccp4bb] Against Method (R)

2010-10-29 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E

Re: [ccp4bb] Against Method (R)

2010-10-29 Thread Dirk Kostrewa
be performed in reciprocal space. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 29 Oct 2010, Dirk Kostrewa wrote: Hi Robbie, yes

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

2010-10-28 Thread Dirk Kostrewa
-windedness. Regards, Tim -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail

Re: [ccp4bb] Fill map/mask with dummy atoms?

2010-10-18 Thread Dirk Kostrewa
programs, em2dam and vol2pdb, to convert low resolution maps into dummy atoms. Now, I have plenty of options to play with! Best regards, Dirk. Am 13.10.10 13:49, schrieb Dirk Kostrewa: ... maybe, to clarifiy my question a little bit: I want to fill an essentially flat cryo-EM-map with dummy atoms

Re: [ccp4bb] Question regarding S-SAD

2010-10-18 Thread Dirk Kostrewa
Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians

[ccp4bb] Fill map/mask with dummy atoms?

2010-10-13 Thread Dirk Kostrewa
Dear CCP4ers, is there a program around that allows to fill an input map or mask with dummy atoms? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München

[ccp4bb] Fwd: [ccp4bb] Fill map/mask with dummy atoms?

2010-10-13 Thread Dirk Kostrewa
, Dirk. Am 13.10.10 13:00, schrieb Dirk Kostrewa: Dear CCP4ers, is there a program around that allows to fill an input map or mask with dummy atoms? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [ccp4bb] Difference map

2010-09-29 Thread Dirk Kostrewa
missing from the calculation. kindly help me out. Thanks and regards Intekhab alam -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

2010-09-21 Thread Dirk Kostrewa
20, 2010 at 9:20 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Hi Ian, Am 19.09.10 15:25, schrieb Ian Tickle: Hi Florian, Tight NCS restraints or NCS constraints (they are essentially the same thing in effect if not in implementation) both reduce the effective parameter count on a 1

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

2010-09-20 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

2010-09-17 Thread Dirk Kostrewa
. Then, there will be no problems, as far as I can see. Best regards, Dirk -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

2010-09-16 Thread Dirk Kostrewa
. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW

Re: [ccp4bb] Molecular replacement question

2010-09-14 Thread Dirk Kostrewa
70.99 110.9 2.75 Sol_RF 3063.23 -44.73 180.00 135.27 -126.47 44.73 108.9 2.70 Cheers, Paul Holland -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München

Re: [ccp4bb] Practical MR advice

2010-09-01 Thread Dirk Kostrewa
13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu mailto:rrowl...@mail.colgate.edu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München

Re: [ccp4bb] which software can calculate binding energy

2010-07-23 Thread Dirk Kostrewa
anyone introduce me a software? Any help would be greatly appreciated. Best Min -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone

Re: [ccp4bb] differences Rfactor calculations

2010-07-14 Thread Dirk Kostrewa
you. Cheers, Ariel -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

2010-07-13 Thread Dirk Kostrewa
! ERROR --- While opening map file Is there a way to re-write the header to be compatible with CCP4? --James -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str

Re: [ccp4bb] Question about R/Rfree value difference

2010-07-09 Thread Dirk Kostrewa
it is significantly higher. Could any one suggest me to reduce the Rfree value more? or is it good to submit the data in the PDB database with this 12% difference? Thanks for the suggestions. Sincerely, Sampath N -- *** Dirk Kostrewa Gene Center

Re: [ccp4bb] R values are higher in SF-CHECK

2010-07-06 Thread Dirk Kostrewa
C Cheers Rakesh Graduate student Purdue University -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax

Re: [ccp4bb] Wilson B and Mean B factors

2010-07-01 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] problem with coot

2010-06-30 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] measure of anamolous signal

2010-06-29 Thread Dirk Kostrewa
be ~ 30%, and SIGANO should be ~ 1.2. However, these indicators might not be realistic (see references above) and therefore should be taken with a grain of salt. Good luck, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [ccp4bb] Snow leopard + NVidia quadro FX4500

2010-06-15 Thread Dirk Kostrewa
, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue, Box 295 New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department

Re: [ccp4bb] sigma cutoff for fitting waters in model

2010-04-21 Thread Dirk Kostrewa
density level. Is this true or did I misunderstand something? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone

Re: [ccp4bb] Hydrogen Bond Restraints

2010-04-14 Thread Dirk Kostrewa
luck, Dirk. [1] Nature 462, 323-330 (2009) Am 14.04.10 15:41, schrieb Bradley Hintze: I am looking for published examples where hydrogen bond restraints were helpful in refinement. Can anyone point me to some papers? -- *** Dirk

Re: [ccp4bb] How to show electron density map for my ligand in pymol, which is bound in the active site..??/

2010-04-13 Thread Dirk Kostrewa
to the map file.. thank u Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University

Re: [ccp4bb] Phasing statistics

2010-04-12 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Phenix version 1.6.1 released

2010-03-31 Thread Dirk Kostrewa
-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax

Re: [ccp4bb] self rotation education

2010-03-19 Thread Dirk Kostrewa
- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians

Re: [ccp4bb] self rotation education

2010-03-19 Thread Dirk Kostrewa
- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig

Re: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials

2010-02-26 Thread Dirk Kostrewa
-- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

[ccp4bb] Research Scientist / Postdoc Position at the Gene Center, University of Munich

2010-02-25 Thread Dirk Kostrewa
Dear CCP4ers, on behalf of Patrick Cramer, I would like to draw your attention to the following open position at the Gene Center, University of Munich. Please, do not reply directly to me, but to the e-mail addresses given at the end of this job offer. Best regards, Dirk Kostrewa

Re: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials

2010-02-25 Thread Dirk Kostrewa
verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E

Re: [ccp4bb] anomalous difference fourier maps

2010-02-19 Thread Dirk Kostrewa
in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- *** Dirk Kostrewa Gene Center, A 5.07

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