Re: [COOT] low res real-space refinement

+1 > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa > Sent: Thursday, April 14, 2011 5:37 AM > To: COOT@JISCMAIL.AC.UK > Subject: Re: [COOT] low res real-space refinement > > Another idea, that

Re: [COOT] coot hardware stereo wrong hand

Hi Jim, two ways I can think of to solve this. 1) from the driver side, see if the MAC comes with 'nvidia-settings'. If it does under 'OpenGL' settings should be an entry for 'Exchange Stereo Eyes'. 2) from within coot one can manipulate the stereo angle: (set-hardware-stereo-angle-factor f) Tr

Re: [COOT] Centos Linux stereo images suddenly reverse rotation direction

Chris, this is a hardware problem. The older NVIDIA cards together with the stereographics emitter used to do that. The only fix I know is to upgrade the card to a later model. I have not seen this with a FX3800 using 120Hz LCDs and NVIDIA 3D vision. HTH Carsten > -Original Messa

Re: [COOT] merge chains?

Mirek, coot's merging algorithm is a bit over-cautious in these cases. Try using "Calculate->Change Chain ID" and define the residue ranges for the merge, that should help. HTH Carsten > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [m

Re: [COOT] Failure to mount /home/emsley delays coot startup

MAIL.AC.UK > Subject: Re: [COOT] Failure to mount /home/emsley delays coot startup > > On Wed, Jun 23, 2010 at 06:03:22PM +0100, Paul Emsley wrote: > > On 23/06/10 13:26, Schubert, Carsten [PRDUS] wrote: > > >Is there any way to get rid of these references in the pre-compil

[COOT] Failure to mount /home/emsley delays coot startup

Hi, I wonder if anyone has a solution to this problem. We are starting to run coot (0.6.2 pre) on SuSe Enterprise 10.x edition machines. The load times per session are approx 2 minutes, before coot is up and running. Loading with the older RedHat EL 4 machines is almost instantaneous from the same

[COOT] Hydrogens lost upon mutate of residue or addition of terminal residue

Hi, is there a way to toggle the use of Hydrogens in the mutate and add terminal residue commands? Currently coot (2486) does not seem to allow building of Hydrogens upon changing or adding residues. If that is not currently possible, what are the plans to include that functionality, would be nic

Re: [COOT] rot-trans zone toolbar button not found

Thanks for your comments Paul. I see what we can do about the updates... Cheers, Carsten > -Original Message- > From: Paul Emsley [mailto:paul.ems...@bioch.ox.ac.uk] > Sent: Tuesday, September 29, 2009 11:04 PM > To: Schubert, Carsten [PRDUS]; coot@jiscmail.ac.uk &

[COOT] rot-trans zone toolbar button not found

Hi, On redhat El4 with coot 0.6-2283 (Centos-python-gtk2) the rot-trans button in the toolbar does not show up. Toggling the button in the preferences produces the following warning: *** (coot-real 4220: WARNING **: Widget not found: model_toolbar_rot_trans_toolbutton The button is however prese

[COOT] Check/Delete Waters ... with Hydrogens in model

Hi Paul, would it be possible to have a feature in which Hydrogens present in the model are ignored, when checking for questionable waters in the Check/Delete Waters functionality? Turns out that the default close contact of 2.3A is too inclusive and leads to a lot of questionable or worse deleted

Re: [COOT] regularize zone fits to density?

Probably just the latter (guess on my part) If you need tighter geometry you can decrease the matrix weight under Extensions->Refine->Set Matrix for the real space refinement. The default (60, in 0.6pre) is suitable for good density, set it lower for marginal density. That way you still get good ge

Re: [COOT] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT

nix for this purpose. Schubert, Carsten [PRDUS] wrote: > Hi, > Sorry for the crosspost, but I am not sure were the problem is located: > I noticed that the xplor maps generated by phenix seem to be on a different > scale than the maps generated from the map-coefficients from the same

[COOT] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT

Hi, Sorry for the crosspost, but I am not sure were the problem is located: I noticed that the xplor maps generated by phenix seem to be on a different scale than the maps generated from the map-coefficients from the same refinement run when the maps-coeffs are read into coot. Usually I only rea

Re: [COOT] Stereo projection with Coot

ubject: Re: [COOT] Stereo projection with Coot Schubert, Carsten [PRDUS] wrote: > Yep it does. On linux there may be issues, because the drivers may or may not > support swap-eyes. The problem is that the images are out of sync with the > glasses, or to be more precise, the left image is disp

Re: [COOT] Stereo projection with Coot

Yep it does. On linux there may be issues, because the drivers may or may not support swap-eyes. The problem is that the images are out of sync with the glasses, or to be more precise, the left image is displayed when the right shutter on the glasses is open. That was the case with the version w

[COOT] Enhancement Request: Ability to add residues into an empty slot in a chain

Would it be possible to enhance the "Change Chain ID.." function to allow for insertion of residues into an existing chain if the given resid range is not occupied? For instance I have a single atom already present in the loaded pdb file with chain B and resid 1, otherwise chain B is empty. Afte

Re: [COOT] drawing symmetry

Hi Paul, could you please comment on the precedence of the default settings in either ".coot-preferences/coot-preferences.scm" or its python equivalent. The comments in the file state that the user should feel free to edit the values, but not add/delete entries. This could potentially lead to a

[COOT] problems with setting dialog positions and applying defaults in coot5

Hi, I noticed a couple of issues with 0.5.1-pre-1474. - The following settings for dialog positions seem to be no longer honored by coot, I tried both the python and scheme commands with the same lack of effect: set_model_fit_refine_dialog_position() set_delete_dialog_position() set_rot

Re: [COOT] Fedora 8 binary core dumps - please help

Nat, is probably right. I did not see a "Module" section in your xorg.conf file, which is required. Attached are 2 examples of xorg.conf. One for single screen CRT, the other for a dual head FX Quadro card, which uses 2 monitors. Use them as templates to adapt to your configuration. HTH

Re: [COOT] Problem displaying R3 spacegroup maps in coot

Try to change the SG to H3. Worked for me Carsten > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [mailto:[EMAIL PROTECTED] Behalf Of Watier Yves > Sent: Friday, July 11, 2008 10:45 AM > To: COOT@JISCMAIL.AC.UK > Subject: [COOT] Problem displaying R

Re: [COOT] refining with hydrogens

Joe coot currently does not handle PDB V3 hydrogens. You need to tell reduce to write out old style hydrogens. This should take of this problem. Carsten -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] Behalf Of Joe Batchelor

Re: [COOT] change size of gui

Andreas, try (set-graphics-window-size x y) in the command input. Replace x, y with the desired dimensions. Works in the .coot file, no reason why not interactively (FLW). Cheers, Carsten > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [