Re: [COOT] (transparent) sphere

Hi Bernhard, both sound like good enough approximations to me. How would I do the dotted surface? Can I adjust the radius? -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 24 Sep 2009, Bernhard Lohkamp wrote: You currently

Re: [COOT] make-and-draw-map fails to read a difference map

output, which is auto-read-make-and-draw-maps. Works fine and I don't need to specify column names. Still, shouldn't make-and-draw-map work too? -- Coot verendus est -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc

Re: [COOT] Save Coordinates (as) ...

-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 *** -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [COOT] Save Coordinates (as) ...

output file name is not the same as the input file name. Paul. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

[COOT] atoms used for SSM rmsd

Dear all, which atoms are used for the calculation of an SSM superposition in coot? I suppose they are only the C-alpha atoms but would like to have a confirmation. Ta, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [COOT] Output maps

and suggestions, -Andy Torelli -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [COOT] Get Monomer issues under OSX.

-- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax:   (+46) 08-327626 email: bernhard.lohk...@ki.se -- -- Tim Gruene Institut

Re: [COOT] map level sig figs in display window

e/A^3 changes after three wheel increments. this lag varies with settings in Preferences-Maps and Display Manager-Properties, yet the sigfigs do not change. not a big deal, just wondering. -bryan (also from wretched web mail) -- -- Tim Gruene Institut fuer anorganische Chemie

[COOT] display angles in radiant

Hello, how can I make coot display measured angles in radiant instead of degree? Ta, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature

[COOT] latest builds

, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [COOT] latest builds

? I think it's used by libcurl. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- -- Tim Gruene Institut

Re: [COOT] latest builds

sorry, 'though' of course, not tough. It's late, bedtime for reality.. On Thu, Nov 25, 2010 at 01:33:36AM +0100, Tim Gruene wrote: ta (tough odd), ta, Tim On Wed, Nov 24, 2010 at 12:24:56PM -0500, Ben Eisenbraun wrote: Hello Tim, Could anyone point out which version centos mean

Re: [COOT] centering at xyz

-revision-3237 crashed before it presented a scripting window. Steven -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, December 06, 2010 9:44 AM To: COOT@JISCMAIL.AC.UK Subject

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

link, which I've tried between the libldap in my /usr/lib and coot. This did not help. Do I need to install some packages,or is the trouble somewhere else? Kind regards Robert -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

-- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report Robert -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A

Re: [COOT] coot from source: glib-config

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 No, I did not, and doing so fixed the problem. Thanks a lot, Tim On 09/12/2011 10:11 AM, Justin Lecher wrote: On 9/12/11 9:58 AM, Tim Gruene wrote: Dear all, Configuring coot 0.7-pre-1 from source on both Debian testing and Debian stable seems

Re: [COOT] Running Coot on Ubuntu 11.04 Natty

from your debugger if you break on the gdk_x_error() function.) Any help would be appreciated. Thanks Evan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux

Re: [COOT] joining two molecule

do I use coot to join these two domian structures to get one model of my own structure - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG

[COOT] colour by sequence similarity

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, is there a way in coot to colour a molecule according to the match of sequence similarity after an alignment/ superposition with another structure? I would find this really useful. Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische

[COOT] SUMMARY: colour by sequence similarity

out to be utterly useful, especially in combination with prosmart by Rob Nicholls to generate external restraints for refmac5. Cheers, Tim - Original Message Subject: colour by sequence similarity Date: Wed, 28 Sep 2011 11:05:37 +0200 From: Tim Gruene t...@shelx.uni-ac.gwdg.de

[COOT] Coot for suse 10.1

the system be updated? Thanks for all advice/ comments, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

[COOT] display part of PDB file as bonds

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, is it possible to display only one part of a molecule (i.e. one chain) as bonds and the rest as C_alphas, without splitting the PDB file into two and loading them separately? Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische

Re: [COOT] rotamer outlier reduction by coot

reduction by Coot? I am looking forward to getting your reply. Dialing - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [COOT] rotamer outlier reduction by coot

Echols wrote: On Mon, Dec 5, 2011 at 3:17 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: could you first explain why you display hydrogens in coot? Usually hydrogens are used in refinement in riding (calculated) positions and not saved to the PDB file, so there should not be any for coot

Re: [COOT] OS X isn't going to take throw() for getop() in r3716

, char* const*, const char*) throw ()’ Not using throw(), made this file compile cleanly. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D

Re: [COOT] coot and Blob electron density map gap

large to be explained by ions. I am looking forward to getting a reply from you how you process it if you meet this situation. Cheers, Dialing - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [COOT] reordering of atoms

have a simple fix for reordering atoms? I appreciate it! - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [COOT] optimal Hardware for coot

: - is shutter-stereo supported (with need for quadro gpu for synchronisation)? - is polarisation stereo supported (resulting in lower vertical resolution)? thanks for your help Chuck - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

[COOT] Introducing mrprep

happy to improve the program if I can. Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [COOT] Coot nucleic acid issue

. Best Longfei - -- - -- 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: [COOT] Coot 0.6.2 libraries in Ubuntu 12.04

= not found libgtkglext-x11-1.0.so.0 = not found libgdkglext-x11-1.0.so.0 = not found libgsl.so.0 = not found libgslcblas.so.0 = not found libldap-2.2.so.7 = not found libssl.so.4 = not found libcrypto.so.4 = not found Where can i get them? Thank you all - -- - -- Dr Tim Gruene Institut

Re: [COOT] partial double conformers

, 3 and 4 for methinonine in coot, they are pretty much the same except for CE. It seems reasonable that only CE should be modeled in alternative positions. Cheers, Ed On Wed, 2012-06-06 at 23:23 +0200, Tim Gruene wrote: Dear Ed, what resolution do your data have which make you

[COOT] package list for coot on Debian

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/ iD8DBQFQPHG4UxlJ7aRr7hoRAkuDAKDkWjII2G5Lu3C/Mtu3qqaGAljz0wCgzZAm

Re: [COOT] out of the list

, Tim On 09/04/2012 01:56 PM, Camilo Perez wrote: I'm receiving messages from this list and I don't want them anymore, please take me out of the list. Thanks Camilo - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [COOT] No updates at http://lmb.bioch.ox.ac.uk/coot/devel/build-info.html

should be around somewhere, I guess. Any pointers? Thanks, Leon - -- 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

[COOT] fractional coordinates

the symmetry operators to e.g. an atom? Related to this, does coot already have a function which places an atom to the symmetry equivalent position which is closest to the current centre (point of rotation)? Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

[COOT] merging fragment to molecule

? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ7t5rUxlJ7aRr7hoRAoiFAJ9cpmJtk

Re: [COOT] Problem with Coot Density Fit Analysis with PHENIX map coefficients

127 2781-901 OEIRAS Portugal - -- - -- 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: [COOT] favorite linux flavor, or as most of you would say, flavour ;)

, no problem, but I thought I may branch out if others think there are better flavors out there. Thanks so much Dave Roberts - -- - -- 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

[COOT] python script not working in coot

found within the coot installation and those which are system installed (and thus make the code work when called as 'python test.py'). I appreciate any comment, including ways how to create such a table view in a different (more stable/ reliable) way. Best, Tim - -- - -- Dr Tim Gruene Institut fuer

Re: [COOT] Building subversion coot on Ubuntu 12.10 64 bit

- -- - -- 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/ iD8DBQFRAPtPUxlJ7aRr7hoRAjNAAJ0SfzYMIKxSFapdp8mx/+vE0KG

Re: [COOT] Acetylated N-terminus, what's the current state of affairs

, Apply. Then I would do a sphere refine. Would it be better to ask at CCP4? :-( Paul. -- - -- 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: [COOT] Coot graphical performance

in windows with this processor and now have to boot to Win7 to model build with COOT and then back to Linux to refine and analyse. It is getting tedious. Paul - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

[COOT] rev 4630

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Paul, revision 4630 passed testing and is available for download both for Debian squeeze and Debian wheezy. Thanks a lot for the quick fix, Tim - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [COOT] Slow COOT on Debian Wheezy

fluently. This is worse when using the space bar to chase the chain residue by residue. My bet is that this might have something to do with the new version of gnome or kernel, since I have similar problems under Ubuntu 12.04. Thank you so much! Regards, Chen - -- Dr Tim Gruene Institut fuer

Re: [COOT] coot in Ubuntu can't merge molecules

'--'merge molecules'. Have anyone met this before? Thanks. Regards, Yahui - -- 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: [COOT] coot rev4630 builds (and runs) but fails test?

variable COOT_TEST_DATA_DIR. Then build your coot. Paul. - -- 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

[COOT] how to change colour for difference maps

by the Edit- Map Colour only affects the positive density. Is there a way / command to set the colour of both positive and negative level? Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [COOT] how to change colour for difference maps

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I need to correct myself- changing the colour from the menu does affect both levels. I am 100% sure it wouldn't until I wrote this email ;-) Auto-solved, Tim On 05/16/2013 03:49 PM, Tim Gruene wrote: Hello, for neutron maps from non

Re: [COOT] occupancy edit in Residue Info not working?

in a ligand that Phaser zeroed out, using Apply occupancy to all atoms in residue, and nothing happened. r4549, Mac, from Bill Scott's page. thanks, Nat - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [COOT] Wrong Leucine rotamer in Coot 0.7

, the resulting Chi angles are Chi1=-65, Chi2=51. Could you please check this? Best regards, Dirk. - -- 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: [COOT] Debian package of coot

no answer. So I would like to know if you are reading these issues, if not where should I report and attach my patches to have a chance to see them integrated into the coot repository. thanks Frederic Picca [1] http://code.google.com/p/coot/issues/list - -- - -- Dr Tim Gruene Institut

Re: [COOT] Debian package of coot

- at least in my opinion ;-) Cheers, Tim On 07/03/2013 01:04 PM, Paul Emsley wrote: On 07/03/2013 10:54 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Frederic Picca, in case it helps packaging, you find the tar-files of coot both for jessie and wheezy on my web

Re: [COOT] faster coot?

on speeding up coot? Thanks, F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [COOT] two amino acids at the same position

~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 cell 510.206.4418 desk 510.495.2697 beamline 510.495.2134 ~ - -- Dr Tim

Re: [COOT] two amino acids at the same position

On 11/07/2013 11:11 AM, David Shin wrote: True for fitting + coot, but (if the case is moderate resolution/redundancy) how about refinement and data/parameter ratio, after fitting remerge the 95%? On Wed, Nov 6, 2013 at 7:29 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Scott

Re: [COOT] large asymmetric units

: /Applications/ccp4-6.4.0/bin/../coot.app/Contents/coot/bin/guile: No such file or directory What should I look for in a higher end machine? More system memory? Video memory? All of the above? Thanks F -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [COOT] Script to align and mutate multiple chains at once.

! Cheers, Oliver. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature

Re: [COOT] anaglyph stereo: a very inexprensive 3D solution

Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

[COOT] phi/psi angles

Hello all, is it possible to get a listing of all phi/psi angles in the peptide? When I click on the Ramachandran plot they are printed to the console - how to I get the entire list non-interactively? Cheers, Tim -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [COOT] Coot renumbering chains when merging - bug?

/ -- End of COOT Digest - 13 Mar 2014 to 14 Mar 2014 (#2014-40) ** -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital

Re: [COOT] Urgent information regarding Yahoo Email

, but can no longer post to the list. If you wish to post please unsubscribed the Yahoo account resubscribe using a different email provider. Best wishes, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP

Re: [COOT] Deuterium

, Katherine -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature

Re: [COOT] Map selected for scrolling on Auto Open MTZ

but it is a bit annoying... Thanks, Huw - -- - -- 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/ iD8DBQFTmYj

Re: [COOT] delete alternative conformation

Hi Andreas, thanks a lot to you and those who told me off-list. Best, Tim On 07/08/2014 11:24 AM, Andreas Förster wrote: Select Delete - Residue/Monomer from the Model/Fit/Refine and click on the conformation you'd like to remove. Andreas On 08/07/2014 9:49, Tim Gruene wrote

[COOT] coot read-only switch

one of such kind. Regards, Tim -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature

Re: [COOT] Sekvence Alignmutate

), it mutates all the residues, including those which remains same. That cause displacement of correctly placed residues. Best regards, Jan -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital

Re: [COOT] pdb info - where?

the console window? Maps you can find using Display Manager - Properties I don't recall if there is a way to similarly see model info of the top of my head. Paul. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc

Re: [COOT] coot file names with spaces not readable in ccp4

06:54 PM, Kenneth A. Satyshur wrote: Such as Pointer Atoms-coot-1.pdb should be Pointer-Atoms-coot-1.pdb. When using linux. kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 -- Dr Tim Gruene Institut fuer

Re: [COOT] Reordering chains in a pdb file

, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. -- Dr Tim Gruene Institut fuer anorganische

Re: [COOT] wincoot 8.1 - empty menus?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You used the W-word ;-) Cheers, Tim On 01/09/2015 12:00 PM, Frank von Delft wrote: Hi, I installed wincoot 8.1 but most of the Extensions sub-menus are empty... is it something I said? Screenshot below. Frank - -- - -- Dr Tim Gruene

Re: [COOT] Setting MTZ resolution limits on the fly?

progressively higher resolution data, for example). I realize that using a positive B-factor in sharpening achieves a similar effect, but the map doesn't look nearly as good. Best, Oliver. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [COOT] coot validation keywords

scroll wheel to which map ? doesn't show me anything. What's the problem ? What I have to do ? - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFU

Re: [COOT] Ligand density fit scores

138648 DID: +65 6407 0640 Fax: +65 6407 0640 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1

Re: [COOT] CentOS 6 Screenshot

Any help, comments ideas would be appreciated. Thanks, Douglas Bailey NCI-Frederick 1050 Boyles Street Frederick, Maryland 21702 Ph: 301-846-5328 Fax: 301-846-6322 baile...@mail.nih.gov -- Dr Tim Gruene Institut fuer anorganische

Re: [COOT] PyMOL v. Coot map 'level'

will be lower - and thus seem to be noisier (perhaps). I suppose that if you want comparable levels from the same map/mtz file then you should use absolute levels, not rmsd. What does PyMOL's 1.0 mean in electrons/A^3? Regards, Paul. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [COOT] PyMOL v. Coot map 'level'

crystallography notes :-) Thanks, Emily. Regards, Paul. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1

Re: [COOT] Dragged refinement fails with riding hydrogens

of reciprocal space refinement, but this does not seem like the optimal way to be doing things. Cheers, Oliver. -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital

Re: [COOT] Dragged refinement fails with riding hydrogens

Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Wednesday, May 27, 2015 12:16 PM To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Dragged refinement fails with riding hydrogens Hi Oliver, unless these are neutron data, you could simply remove the hydrogen atoms from

Re: [COOT] CHO H-bonds.

and specifically what value is it using for CH...O H-bonds? And of course I'd like to know whether this will affect my percentile ranking in the clashscore from the PDB validation! Cheers -- Ian - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [COOT] model with most likely rotamers

im On Monday 06 February 2017 11:05:44 AM Paul Emsley wrote: > On 06/02/2017 08:45, Tim Gruene wrote: > > I would like to create an artificial PDB model (starting from an existing > > one) where every side chain is replaced with the most likely rotamer. I > > do not care abou

[COOT] model with most likely rotamers

regards, Tim -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.

Re: [COOT] Caps lock feature

> > -- > Jan Stransky, PhD student > Institute of Biotechnology, CAS > Laboratory of structure and function of biomolecules > Prumyslova 595 > Vestec > Czech Republic > > +420325873759 -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Bio

[COOT] colour coding map values on molecular surface

. Is this possible with Coot? Best wishes, Tim -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A

Re: [COOT] Coot-0.8.7 slow in Debian

5 second. > > I also have wincoot-0.8 in Windows that installed on this laptop. The > wincoot works very well. Is there any suggestion to solve my problem? > Thank you, > > Phong -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI pho

Re: [COOT] correct protonation state in His side chain

m>>: > > Dear All, > > > > Can I correct protonation state in His side chain in Coot? -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/104 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.

Re: [COOT] what's the difference between ccp4's coot and a normal coot?

--- To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A ###

Re: [COOT] problems opening mrc file

.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 > > #### > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 -- -- Tim Gruene Head of the Centre fo

Re: [COOT] error fetching coordinates from RCSB

arch Center > Department of Chemistry and Biochemistry, City College of New York > Biochemistry and Chemistry PhD Programs, CUNY Graduate Center > *dke...@gc.cuny.edu<mailto:dke...@gc.cuny.edu> <mailto:dke...@gc.cuny.edu> > (NOT @asrc)* | https://keedylab.org<https://ke

Re: [COOT] Coot installation in Ubuntu

; _ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1> =1 > > > ##

[COOT] building coot fails with gcc-10

anyone know how to remove -Werror from the compile flags for building coot? Cheers, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [COOT] Nature this week

=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty o

Re: [COOT] Feature suggestion: Check/Delete Waters, toggle hydrogens on/off

click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a > mailing list hosted by www.jiscmail.ac.uk, terms & condition

[COOT] build-it: dynamic libs missing in archive

in https://homepage.univie.ac.at/tim.gruene/coot_deb/bookworm/ Cheers, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

[COOT] script for quantitative blobology

in summing the positive and the negative values individually. Thanks a lot! Best, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [COOT] Build-it cannot find self-build guile

eg-dev mesa-common-dev libgtk2.0-dev > >> libgnomecanvas2-dev gfortran libtinfo-dev > > These are in the build-it script. > > > Paul. > > ############ > > To unsubscribe from the COOT list, click the fol

Re: [COOT] fcf import from Shelxl2018 fails

ile -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the COOT list, click the following link: ht

Re: [COOT] Coot-1 missing ssm

`/home/sabine/progs/coot-1': > configure: error: ssm not found > > Thanks a lot! > > Sabine > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [COOT] Build coot-1.0.02 on CentOS7

ww.jiscmail.ac.uk/COOT, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 G

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