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

-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ******* Dirk

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

scmail.ac.uk/policyandsecurity/ -- *** 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

Re: [ccp4bb] Omit maps in phenix and ccp4

https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians

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

p;A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -

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

Dirk. -- *** 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.l

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

ww.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ****

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

t, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *** D

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

rom the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- ***

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

www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-7684

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

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 t

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

ot; reflections 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

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

-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=J0zDXf_fmFuuuSdL_f3Rux6-Dkg9g4Myb2J6inlBYOY&s=Ib310E3JW-V0qyXGEQchrvA7HBHF9JKxtpRbxK4HkMo&e=> To unsubscribe from the CCP4

Re: [ccp4bb] Space group/Unit cell

hank you, Maria To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *** Dirk Kostrewa Gene Center Munich Departm

Re: [ccp4bb] nVidia 3D Vision2 glasses

scribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany

Re: [ccp4bb] nVidia 3D Vision2 glasses

<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

To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Bioch

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

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

4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Mu

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

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 Reply

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

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@JISCM

[ccp4bb] Calculation of generalised R-factor?

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 Lud

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

smission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- *** Dirk Kostrewa Gene Center Munich,

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

n, 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

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 affec

Re: [ccp4bb] Bulk solvent

s there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando -- *** 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

in 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

Re: [ccp4bb] Free Reflections as Percent and not a Number

hburn, VA 20147 email: kell...@janelia.hhmi.org <mailto:kell...@janelia.hhmi.org> >> *** . >> > > -- -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlRviu4ACgkQU5C0gGfAG12TMwCfTT0Q4yfCCOxJ

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

nes Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu -- *****

Re: [ccp4bb] twin or untwinned

hould 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 o

Re: [ccp4bb] twin or untwinned

! 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] twinning fun

eavy atom derivatives). Thanks for any insights! Bert -- *** 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] Fractional coordinate shift with two-character chain names?

yn Symmons (not Winn) Cambridge ---- *From:* Dirk Kostrewa *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 thank

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

: pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb < -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: 30 August 2013 14:41 To: ccp4bb Subject: [ccp4bb] Fractional coordinate shift with two-character chain names? Dear CCP4ers, I want

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

Best 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...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

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

uster 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...@genzen

Re: [ccp4bb] Concerns about statistics

? Also, I am aware 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 -- ******* Dirk Kost

[ccp4bb] Single-Gaussian Atomic Scattering Factors?

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

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

pdater may be made a part 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

[ccp4bb] Coot Release 0.7 in CCP4 Software Update?

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 of Biochemistry Ludwig-Maximilians-Universität München Feodor

Re: [ccp4bb] Which Coot for Scientific Linux 6.3

x (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 Fax: +33 438785494 -- ******* Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universitä

Re: [ccp4bb] CNS installation

University of Rome, Italy -- ******* 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

thanks in advance for all your help, - 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

Re: [ccp4bb] proper or improper ncs?

s M.Sc. 215 UCB 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:+49-89-2180-7699

Re: [ccp4bb] Freezing crystal

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-81

Re: [ccp4bb] NMR review

2 January 2012 10:33, Dirk Kostrewa wrote: My understanding of coherence is a constant phase relation between waves. Correct. For a perfect crystal all the unit cells are identical so they scatter in phase and this gives rise to the interference effect we see as Bragg spots, as you say arising f

Re: [ccp4bb] NMR review

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

less clear about the weights of NMR restraint 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 Feod

Re: [ccp4bb] Sub-angstrom resolution

cture 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 Mü

Re: [ccp4bb] Distinguish NH4 from Na?

here? JPK -- *** 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.

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

gh the protein molecule, (smaller)cube by (smaller)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 -- *******

Re: [ccp4bb] Linux vs MacOS for crystallographic software

s on a Mac? 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 G

Re: [ccp4bb] question regarding secondary-structure restraints

secondary 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 mailto:kostr...@genzentrum.lmu.de>> wrote: when I pl

Re: [ccp4bb] question regarding secondary-structure restraints

available, is a much better option.) -Nat -- *** 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] Protein structure solved by computer gamers (and phaser)!

viral protease 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 Biochemis

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

iversity Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität

Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0

e correct permissions can only 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

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

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] Lattice sampling and resolution - a seeming paradox?

ccording 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 wrote: Dear colleagues, I just stumbled

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

est 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 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

http://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:

Re: [ccp4bb] Density sharpening with Truncate?

both good, the likelihood target can 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

Re: [ccp4bb] Density sharpening with Truncate?

ith SigmaA-weighted phases (i.e., PHWT label). 3. In Infrequently used options, "Apply B-factor scaling to F1", specify negative B-factor scaling value, usually within -10 to -50. - Dima -- *** Dirk Kostrewa Gene Center Munich,

Re: [ccp4bb] strange density

(315)-228-7245 ofc: (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 Münche

[ccp4bb] Postdoc position at the Gene Center Munich

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

Re: [ccp4bb] PDB deposition ADIT without frames?

hrieb 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

[ccp4bb] PDB deposition ADIT without frames?

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

[ccp4bb] Counting of geometrical restraints?

siduals used 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

Re: [ccp4bb] Merging data to increase multiplicity

José Trincão, PhDCQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr -- ******* Dirk Kostrewa Gene Cente

[ccp4bb] Off-Topic: CNS MAXLEV error

XLEV 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 Mu

Re: [ccp4bb] High Rmerge with thin frames

thanks in advance, Sergei -- ******* 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] Against Method (R)

ut the final refinement should 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

Re: [ccp4bb] Against Method (R)

== > > Bart Hazes (Associate Professor) > Dept. of Medical Microbiology& Immunology > University of Alberta > 1-15 Medical Sciences Building > Edmonton, Alberta > Canada, T6G 2H7 > phone: 1-780-492-0042 > fax: 1-780-492-7521 &

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

way, I hope this helps explain it a bit more, and again: sorry for the long-windedness. Regards, Tim -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-

Re: [ccp4bb] Question regarding S-SAD

ental 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-Maximi

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

pointed to two SAXS 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 cr

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

Best regards, 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, A5.0

[ccp4bb] Fill map/mask with dummy atoms?

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

Re: [ccp4bb] Difference map

thing 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 L

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

r of X-ray data (f) and the number of restraints (r) are being added. However if you consider the test set residual: = f + (m - r + Drest) = f - r + m + Drest this is clearly not the case. All you can say is that the effective number of parameters is reduced by the number of restraints + constr

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

130 Boston, MA 02115, US Tel: 001 617 432 5602 -- *** 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

development of more advanced methods and algorithms, I have my doubts ... *sigh* Cheers, Dirk. Cheers -- Ian On Fri, Sep 17, 2010 at 10:20 AM, Dirk Kostrewa wrote: Hi Pavel, Am 16.09.10 17:56, schrieb Pavel Afonine: Hi Dirk, so, wouldn't be the deposition of the final

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

ates and structure factors. 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-

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

dding riding hydrogens or not. 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 Fax:+49

Re: [ccp4bb] Molecular replacement question

01 -166.63 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-Universit

Re: [ccp4bb] Practical MR advice

ve Hamilton, NY 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-Ma

Re: [ccp4bb] which software can calculate binding energy

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

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

File name: DLP_100.map Cannot send after transport endpoint shutdown ERROR --- While reading map header. Sorry ! ERROR --- While opening map file Is there a way to re-write the header to be compatible with CCP4? --James -- *** Dirk Kostr

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

difference is about 12% in final refinement. I feel 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 -- **

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

0 0 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

Re: [ccp4bb] Wilson B and Mean B factors

-- *** 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

adova 35131, Italy -- *** 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

d 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 Dep

Re: [ccp4bb] Snow leopard + NVidia quadro FX4500

fine in stereo. Thanks, 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

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

t to the same absolute electron 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.

Re: [ccp4bb] Hydrogen Bond Restraints

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..??/

bound in the active site. i uploaded map as .xplor extension 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 -- *** Di

Re: [ccp4bb] Phasing statistics

+31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- ******* 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

under grant P01-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-

Re: [ccp4bb] self rotation education

150 ... as required by your explanation. Also you haven't explained the very clear peaks near theta = 45, phi = 0. 90 ... . I won't be convinced until I see the results from RFCORR! Cheers -- Ian On Fri, Mar 19, 2010 at 9:47 AM, Dirk Kostrewa wrote: ... and here a slightly cle

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