[COOT] Coot graphical performance
I am attempting to use coot0.7 installed using the yum archive on Fedora 18 and a computer with intel HD graphics 4000 driver. When coot starts initially, the rotation and translation is nearly at the speed that I am used to with Fedora 16 install. If I do not translate, the rotation speed remains good. If I do translate, the rotation speed drops off by about 50 %. At drops off more after each translation and eventually is so slow that it is unusable. I do not think that it is a graphics issue as pymol does not have any speed problems even with surfaces exhibited. Does anyone have a suggestion as to what I am doing wrong in the coot install? Thank you very much for any help you can give me. Paul
Re: [COOT] Add other solvent molecules setting
Just for completeness, there is actually an extra function for this: (define *additional-solvent-ligands* '()) which can be added to the .coot file. B On 14/02/2013 17:10, Debreczeni, Judit wrote: Yes, it can be added to the .coot file like this: (append! *solvent-ligand-list* (list "TRS")) or like this for multiple molecules: (append! *solvent-ligand-list* (list "TRS" "XXX" "YYY")) -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ulrich Gohlke Sent: 14 February 2013 10:48 To: COOT@JISCMAIL.AC.UK Subject: [COOT] Add other solvent molecules setting Dear crystalleagues, in Extensions -> Modelling -> Add Other Solvent Molecules..., is there a way to add common compounds such as TRS to the pre-selected molecules permanently, i.e. one doesn't have to "Add a new Residue Type" every time Coot is started? Can this be added to the .coot file or something? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc- berlin.de/en/research/research_teams/macromolecular_structure_and_inter action/ -- *** 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
Re: [COOT] Add other solvent molecules setting
Yes, it can be added to the .coot file like this: (append! *solvent-ligand-list* (list "TRS")) or like this for multiple molecules: (append! *solvent-ligand-list* (list "TRS" "XXX" "YYY")) > -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ulrich Gohlke > Sent: 14 February 2013 10:48 > To: COOT@JISCMAIL.AC.UK > Subject: [COOT] Add other solvent molecules setting > > Dear crystalleagues, > > in Extensions -> Modelling -> Add Other Solvent Molecules..., is there > a way to add common compounds such as TRS to the pre-selected molecules > permanently, i.e. one doesn't have to "Add a new Residue Type" every > time Coot is started? Can this be added to the .coot file or something? > > Cheers, > > Uli > > --- > > > dr ulrich gohlke > > staff scientist - macromolecular structure and interaction > > max-delbrück-center for molecular medicine (mdc) > > +49 30 9406 - 2725 (w) > > +49 30 9406 - 2548 (fax) > > ulrich.goh...@mdc-berlin.de > > http://www.mdc- > berlin.de/en/research/research_teams/macromolecular_structure_and_inter > action/
[COOT] Add other solvent molecules setting
Dear crystalleagues, in Extensions -> Modelling -> Add Other Solvent Molecules..., is there a way to add common compounds such as TRS to the pre-selected molecules permanently, i.e. one doesn't have to "Add a new Residue Type" every time Coot is started? Can this be added to the .coot file or something? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
