Re: [COOT] Atoms
It turns out that Eugine Krissinel is way ahead of me - in mmdb he provides a flag to fix up the missing elements. This is non-optionally done now in 0.5.1-pre-1 and following versions. Paul Charlie Bond wrote: How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz .
Re: [COOT] Atoms
It would seem sensible to do this if the element column is not present (which of course it should be ...) Phil On 3 Oct 2008, at 10:33, Paul Emsley wrote: It turns out that Eugine Krissinel is way ahead of me - in mmdb he provides a flag to fix up the missing elements. This is non-optionally done now in 0.5.1-pre-1 and following versions. Paul Charlie Bond wrote: How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz .
Re: [COOT] where did add alt conf go?
Where can I find the instructions to add/delete buttons onto the toolbar? I particularly need the backbone torsion angle recently. Could somebody share the information? Thanks. -- Jianghai On Aug 2, 2008, at 4:57 AM, Bernhard Lohkamp wrote: As Paul already mentioned in this thread you can add you own buttons to the horizontal toolbar now (pre version with python and gtk2). I made a few pre-defined functions but more will be added in future and can be customized. I recently added an Alt Conf button. Bernhard Dear Paul -- On 26 Jul 2008, at 14:57, Paul Emsley wrote: I recently discovered that on a laptop with 100dpi fonts and a 800- pixel height resolution (not uncommon), then the tool-bar is so long that the GNOME panel obscures the status bar. Not good. I suppose that the Right Thing is to make it runtime configurable. Just a quick thought (I'm sure you're only considering this, but well...): what about adding an option just like your Tips window? What I have in mind is to add a pop-up window when you click on the Model/Fit/Refine button that will ask you which option you'd like to have in your refinement bar. You might put the all list of functions, with pre-selected buttons for the most common ones. The user will then have the possibility to choose what (s)he want according to the most used functions /or the size of the screen. Sorry for the post if you already implemented it or already planed to do it. Just a thought. Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/ *** Dr. Bernhard Lohkamp Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487698 fax: (+46) 08-327626 email: [EMAIL PROTECTED]
Re: [COOT] where did add alt conf go?
To edit the backbone angle: 1.) use the button from the 'old' Model/Fit/Refine dialog 2.) add the following line to the last list in your coot_toolbuttons.py file (in COOTDIR/share/coot/python; e.g. after [Add alt conf, altconf(), Add alternative conformation, add-alt-conf.svg],): [Edit BB, setup_backbone_torsion_edit(1), Edit Backbone Torsion Angle, flip-peptide.svg], N.B. will be an option in the next version... 3.) Edit (or if not there create) coot_toolbuttons.py in $HOME/.coot-preferences/coot_toolbuttons.py and add: coot_toolbar_button(Edit BB, setup_backbone_torsion_edit(1), flip-peptide.svg) The last two points are general to add new functions to the toolbuttons manager. I may include a GUI to add a simple function in the next release if requested. Bernhard *** Dr. Bernhard Lohkamp now University of York, YSBL Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487698 fax: (+46) 08-327626 email: [EMAIL PROTECTED] - Original Message - From: Jianghai Zhu [EMAIL PROTECTED] Date: Friday, October 3, 2008 6:09 pm Subject: Re: [COOT] where did add alt conf go? To: COOT@JISCMAIL.AC.UK Where can I find the instructions to add/delete buttons onto the toolbar? I particularly need the backbone torsion angle recently. Could somebody share the information? Thanks. -- Jianghai On Aug 2, 2008, at 4:57 AM, Bernhard Lohkamp wrote: As Paul already mentioned in this thread you can add you own buttons to the horizontal toolbar now (pre version with python and gtk2). I made a few pre-defined functions but more will be added in future and can be customized. I recently added an Alt Conf button. Bernhard Dear Paul -- On 26 Jul 2008, at 14:57, Paul Emsley wrote: I recently discovered that on a laptop with 100dpi fonts and a 800- pixel height resolution (not uncommon), then the tool-bar is so long that the GNOME panel obscures the status bar. Not good. I suppose that the Right Thing is to make it runtime configurable. Just a quick thought (I'm sure you're only considering this, but well...): what about adding an option just like your Tips window? What I have in mind is to add a pop-up window when you click on the Model/Fit/Refine button that will ask you which option you'd like to have in your refinement bar. You might put the all list of functions, with pre-selected buttons for the most common ones. The user will then have the possibility to choose what (s)he want according to the most used functions /or the size of the screen. Sorry for the post if you already implemented it or already planed to do it. Just a thought. Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/ *** Dr. Bernhard Lohkamp Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487698 fax: (+46) 08-327626 email: [EMAIL PROTECTED]
