[COOT] more suggestions - sorry
1) The check on GLN and ASN and HIS? for likely hydrogen bonding is very useful. Do you think it would be worth extending this to THR? 2) The Ramachandran plot includes residues with zero occupancy - it woyuld help if they were flaggeed somehow differently.. Eleanor
Re: [COOT] more suggestions - sorry
Dear Eleanor, Eleanor Dodson wrote: 1) The check on GLN and ASN and HIS? for likely hydrogen bonding is very useful. Do you think it would be worth extending this to THR? HIS is not part of the ASN/GLN check. And indeed the ASN/GLN check works by B-factor analysis, not hydrogen bonding. For hydrogen bond checking, I use reduce. (Once can also use What_check, but the support for that is not so good). I do not think the algorithm in Coot is suitable to extend to THR. 2) The Ramachandran plot includes residues with zero occupancy - it would help if they were flagged somehow differently.. I see. Thank you. This is duly noted (along with your prior request to show the Ramachandran plot of only a selection of residues). Paul.
Re: [COOT] merge water chains
> From: Christian Roth > >> Hi all, >> >> I am not sure but If I remember correctly Bernhard mentioned on the >> last CCP4 >> study weekend in Nottingham that Coot is able to merge the >> different water >> chains, generated through repeated refinement runs, in one. If this >> function >> exist, how can I use it? >> >> Thanks in advance for your help. Bernhard Lohkamp wrote: Since I supposedly mentioned this (and I have made a script)... there is a python function to do so: use merge_solvent_chains(imol) or merge_water_chains(imol) alternatively you have to do it by hand, i.e. using Calculate->Change Chain ID (use residue range). B P.S. no corresponding scheme function there yet. As of revision 1980, there is a scheme version. Both this and the python version renumber the waters as they merge them. Paul.
Re: [COOT] problems of version 0.6
Maia Cherney wrote: The general torsion function is not as good as the torsion in old X-fit. Are you or have you ever been a member of the von Delft Pressure Group? In x-fit you click on two atoms of a single bond and you can rotate the rest of the molecule around that bond. This bond can be in the middle of the main chain etc. It's a very useful function, if you need to rotate a polypeptide around a single bond. Are you planning to do a similar thing? Yes - we intend to have that before version 1.0. Paul.
[COOT] Extended draft paper submission: BCBGC-09 call for papers
Extended draft paper submission: BCBGC-09 call for papers This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: · International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) · International Conference on Automation, Robotics and Control Systems (ARCS-09) · International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) · International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) · International Conference on Information Security and Privacy (ISP-09) · International Conference on Recent Advances in Information Technology and Applications (RAITA-09) · International Conference on Software Engineering Theory and Practice (SETP-09) · International Conference on Theory and Applications of Computational Science (TACS-09) · International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely John Edward Publicity committee
Re: [COOT] problems of version 0.6
Paul, Bernhard, Thank you for your reply. I am using version: 0.6-pre-1 (revision 1950) [with guile 1.6.8 embedded]. I will upgrade it with gtk2 in the name. Thank you for working on the torsion thing. Well, now help me with key-bindings, please. I need one or two buttons on the mouse for map dragging. Pymol and x-fit use the middle button for translation. It confuses me all the time, when I work in coot after working in pymol. Do you have any unused two-button combinations on the mouse? If it's not possible to touch the mouse buttons in the key-bindings, please help me to program arrow key for translation. Could you give me a script for that, I can't write it myself. Maia Paul Emsley wrote: Maia Cherney wrote: The general torsion function is not as good as the torsion in old X-fit. Are you or have you ever been a member of the von Delft Pressure Group? In x-fit you click on two atoms of a single bond and you can rotate the rest of the molecule around that bond. This bond can be in the middle of the main chain etc. It's a very useful function, if you need to rotate a polypeptide around a single bond. Are you planning to do a similar thing? Yes - we intend to have that before version 1.0. Paul.
Re: [COOT] RSR exploding RNA
For anyone that is interested, it appears as if the Refmac monomer library has the hydrogen on the 2' hydroxyl of RNA backbone named as HO2*, different from pdb v2.3 nomenclature which has it listed as 2HO*. Simply editing my PDB to reflect the Refmac library name makes the hydrogen behave normally in coot. -Chris On May 6, 2009, at 6:06 AM, Paul Emsley wrote: CK wrote: I think perhaps I should clarify what I've been doing. I've been refining my structure using phenix.refine and had reached a fairly satisfactory point with suitably low R-factors (21/25) and very reasonable RMSDs for bonds and angles. At this point I ran my structure through the molprobity server to take a closer look at geometry and clashes. OK, so that's the issue, right there. Molprobity is a modern program - using PDB v3 atom names. Coot uses the Refmac dictionary, i.e. version 2.3 names. Coot does not recognise the new atom names e.g. C1' (in Ar) or HB3 (in ARG) and so pushes them out with non- bonded contact restraints. If you want to use the output of molprobity with coot/Refmac dictionary, then you will need to downgrade the molprobity output file. Yes, this needs to be fixed - upgrading and validating the new dictionary is a substantial task. For the record, Coot ignores the occupancy of the atoms when refining. Adding hydrogens to a model should do reasonable (if not good) things no matter the resolution of the data. As going through the entire clash list by hand can be very tedious I wanted to see if adding hydrogens in the riding positions and refining again would help alleviate some of the clashes, which it did. Yes, it should. Paul.
[COOT] error loading pixmap file
Hi, I just upgraded coot to 0.6 (pre-1 revision 1941) on my Intel MacOS X (10.4.11). It launches, but gives a long list of errors, couldn't find any workaround following Bill Scott's page, coot's FAQ, etc. The errors start right away starting with : " ** (coot-real:2487): WARNING **: Error loading pixmap file: /usr/local/xtal/coot /share/coot/pixmaps/display-manager.png " ...and then a bunch of " Error loading icon: Couldn't recognize the image file format for file '/usr/loca l/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' ... " Also a few of these at the end : " (coot-real:2487): Gtk-WARNING **: Error loading icon: Couldn't recognize the ima ge file format for file '/usr/local/xtal/coot/share/themes/Glossy_P/gtk-2.0/stoc k_zoom_fit_width.png ..." It still works, but the windows, buttons and general appearance are really looking quite bad (or even absent); annoyingly enough, each molecule being loaded again triggers a long list of warnings of the kind: " ** (coot-real:2487): WARNING **: Pixbuf theme: Cannot load pixmap file /usr/loca l/xtal/coot/share/themes/Glossy_P/gtk-2.0/button_round.png: Couldn't recognize t he image file format for file '/usr/local/xtal/coot/share/themes/Glossy_P/gtk-2. 0/button_round.png' ** (coot-real:2487): WARNING **: Invalid borders specified for theme pixmap: /usr/local/xtal/coot/share/themes/Glossy_P/gtk-2.0/button_round.png, borders don't fit within the image " Any help will be very much appreciated!!
