Thread: [Apbs-users] problem in displaying elec pot in surface
Biomolecular electrostatics software
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From: Rute A R da F. <fo...@bi...> - 2007-10-22 10:26:47
Attachments:
vmd-surface-display.jpg
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Hi! I am trying to map the electrostatic potential onto a biomolecular surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a surface totally coloured with the potential, but a black surface with small geometric figures bearing the potential colours (see attached picture). I followed all the steps of the tutorial (using the plugin with APBS) and also tried creating the pot.dx file in standalone APBS and then loading it into the pqr in VMD (since within VMD I was getting an error message about a gamma keyword and thought it could be related). Can anyone give me some hint on what´s happening? Thanks a lot! Best Rute .................................... .Rute A R da Fonseca . . . .Genomics Group . .Department of Biology . .University of Copenhagen . .Universitetsparken 15, Building 10. .DK-2100 Copenhagen Ø . .Denmark . . . .Tel : +45 35 32 12 12 . .Email:fo...@bi... . .................................... .................................... .Rute A R da Fonseca . . . .Genomics Group . .Department of Biology . .University of Copenhagen . .Universitetsparken 15, Building 10. .DK-2100 Copenhagen Ø . .Denmark . . . .Tel : +45 35 32 12 12 . .Email:fo...@bi... . .................................... |
From: Nathan B. <ba...@cc...> - 2007-10-24 19:09:36
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Hello -- > I am trying to map the electrostatic potential onto a biomolecular > surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a > surface totally coloured with the potential, but a black surface with > small geometric figures bearing the potential colours (see attached > picture). I have also seen this using VMD in conjunction with some graphics cards. I'm Cc'ing John Stone, a VMD developer for more information/advice. > I followed all the steps of the tutorial (using the plugin with APBS) > and also tried creating the pot.dx file in standalone APBS and then > loading it into the pqr in VMD (since within VMD I was getting an > error message about a gamma keyword and thought it could be related). > > Can anyone give me some hint on what=B4s happening? I don't think this is user error; it is likely a problem with the graphics drivers. Sorry for the problems, Nathan > Thanks a lot! > > Best > > Rute > > > .................................... > .Rute A R da Fonseca . > . . > .Genomics Group . > .Department of Biology . > .University of Copenhagen . > .Universitetsparken 15, Building 10. > .DK-2100 Copenhagen =D8 . > .Denmark . > . . > .Tel : +45 35 32 12 12 . > .Email:fo...@bi... . > .................................... > > .................................... > .Rute A R da Fonseca . > . . > .Genomics Group . > .Department of Biology . > .University of Copenhagen . > .Universitetsparken 15, Building 10. > .DK-2100 Copenhagen =D8 . > .Denmark . > . . > .Tel : +45 35 32 12 12 . > .Email:fo...@bi... . > .................................... > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > --=20 Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: John S. <jo...@ks...> - 2007-10-24 19:21:43
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Hi, Yes, black dots, geometric patterns, or other strange or unexpected colorings typically indicate a broken graphics driver. Depending on what graphics card/driver you're using, you may be able to upgrade to a newer driver and the problem will go away. For some other graphics chipsets/cards, there's no known solution other than to get a bug-free card. If you tell me more about your system I should be able to give you more specific suggestions. Cheers, John Stone vm...@ks... On Wed, Oct 24, 2007 at 02:09:37PM -0500, Nathan Baker wrote: > Hello -- > > > I am trying to map the electrostatic potential onto a biomolecular > > surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a > > surface totally coloured with the potential, but a black surface with > > small geometric figures bearing the potential colours (see attached > > picture). > > I have also seen this using VMD in conjunction with some graphics > cards. I'm Cc'ing John Stone, a VMD developer for more > information/advice. > > > I followed all the steps of the tutorial (using the plugin with APBS) > > and also tried creating the pot.dx file in standalone APBS and then > > loading it into the pqr in VMD (since within VMD I was getting an > > error message about a gamma keyword and thought it could be related). > > > > Can anyone give me some hint on what´s happening? > > I don't think this is user error; it is likely a problem with the > graphics drivers. > > Sorry for the problems, > > Nathan > > > Thanks a lot! > > > > Best > > > > Rute > > > > > > .................................... > > .Rute A R da Fonseca . > > . . > > .Genomics Group . > > .Department of Biology . > > .University of Copenhagen . > > .Universitetsparken 15, Building 10. > > .DK-2100 Copenhagen Ø . > > .Denmark . > > . . > > .Tel : +45 35 32 12 12 . > > .Email:fo...@bi... . > > .................................... > > > > .................................... > > .Rute A R da Fonseca . > > . . > > .Genomics Group . > > .Department of Biology . > > .University of Copenhagen . > > .Universitetsparken 15, Building 10. > > .DK-2100 Copenhagen Ø . > > .Denmark . > > . . > > .Tel : +45 35 32 12 12 . > > .Email:fo...@bi... . > > .................................... > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: jo...@ks... Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 |
From: Rute F. <fo...@bi...> - 2007-10-25 08:22:22
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Hi, > there's no known solution other than to get a bug-free card. If you tel= l > me more about your system I should be able to give you more specific > suggestions. I'm working on a machine (using Windows Vista) with these characteristics: Intel(R) Core 2 Duo T7250 (2.0GHz; 2MB Cache; FSB800) 2GB SODIMM DDR2 667MHz exp a 4GB Intel 965GM Intel GMA X3100 at=E9 358MB partilhada What is your suggestion? Thanks a lot. :) Best, Rute .................................... .Rute A R da Fonseca . .Genomics Group .Department of Biology .University of Copenhagen .Universitetsparken 15, Building 10 .DK-2100 Copenhagen =D8 .Denmark . .Tel : +45 35 32 12 12 .Email:fo...@bi... .................................... > On 10/24/07, John Stone <jo...@ks...> wrote: > > > > Hi, > > Yes, black dots, geometric patterns, or other strange or unexpected > > colorings typically indicate a broken graphics driver. Depending on wh= at > > graphics card/driver you're using, you may be able to upgrade to a newe= r > > driver and the problem will go away. For some other graphics chipsets/= cards, > > > > Cheers, > > John Stone > > vm...@ks... > > > > > > > > On Wed, Oct 24, 2007 at 02:09:37PM -0500, Nathan Baker wrote: > > > Hello -- > > > > > > > I am trying to map the electrostatic potential onto a biomolecular > > > > surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a > > > > surface totally coloured with the potential, but a black surface wi= th > > > > small geometric figures bearing the potential colours (see attached > > > > picture). > > > > > > I have also seen this using VMD in conjunction with some graphics > > > cards. I'm Cc'ing John Stone, a VMD developer for more > > > information/advice. > > > > > > > I followed all the steps of the tutorial (using the plugin with APB= S) > > > > and also tried creating the pot.dx file in standalone APBS and then > > > > loading it into the pqr in VMD (since within VMD I was getting an > > > > error message about a gamma keyword and thought it could be related= ). > > > > > > > > Can anyone give me some hint on what=B4s happening? > > > > > > I don't think this is user error; it is likely a problem with the > > > graphics drivers. > > > > > > Sorry for the problems, > > > > > > Nathan > > > > > > > Thanks a lot! > > > > > > > > Best > > > > > > > > Rute > > > > > > > > > > > > .................................... > > > > .Rute A R da Fonseca . > > > > . . > > > > .Genomics Group . > > > > .Department of Biology . > > > > .University of Copenhagen . > > > > .Universitetsparken 15, Building 10. > > > > .DK-2100 Copenhagen =D8 . > > > > .Denmark . > > > > . . > > > > .Tel : +45 35 32 12 12 . > > > > .Email:fo...@bi... . > > > > .................................... > > > > > > > > .................................... > > > > .Rute A R da Fonseca . > > > > . . > > > > .Genomics Group . > > > > .Department of Biology . > > > > .University of Copenhagen . > > > > .Universitetsparken 15, Building 10. > > > > .DK-2100 Copenhagen =D8 . > > > > .Denmark . > > > > . . > > > > .Tel : +45 35 32 12 12 . > > > > .Email:fo...@bi... . > > > > .................................... > > > > -------------------------------------------------------------------= ------ > > > > This SF.net email is sponsored by: Splunk Inc. > > > > Still grepping through log files to find problems? Stop. > > > > Now Search log events and configuration files using AJAX and a brow= ser. > > > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > > _______________________________________________ > > > > apbs-users mailing list > > > > apb...@li... > > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > > > > > > > > -- > > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > > > Center for Computational Biology, Washington University in St. Louis > > > Web: http://cholla.wustl.edu/ > > > > -- > > NIH Resource for Macromolecular Modeling and Bioinformatics > > Beckman Institute for Advanced Science and Technology > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 > > Email: jo...@ks... Phone: 217-244-3349 > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 > > > |
From: John S. <jo...@ks...> - 2007-10-25 20:28:28
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Hi, Since you have one of the newer Intel chips, it is possible that a driver upgrade may fix your problem. (for many older Intel chips, the only solution wass to buy a better video card, e.g. from NVIDIA or AMD/ATI). The Intel graphics drivers are available from their web site here: http://downloadcenter.intel.com/Default.aspx?lang=eng# You'll have to identify which (there are are several) 965 based graphics product you're using, and download the latest Vista driver. If that still does not correct your problem, my suggestion would be to first file a bug report with Intel. Then I'd consider whether you are willing to wait for them to fix it, or whether you'd rather buy a better video card and move on (i.e. assuming this isn't a laptop). I'm personally of the opinion that lost research time is far more important than the cost of a video card, so if I were in your position I'd probably consider upgrading the video card to something that's more appropriate for your needs. The Intel chips are a good for things like business/office apps, but historically they have been slow and have had limited functionality in terms of scientific visualization, games, and other intensive 3-D apps. Cheers, John Stone vm...@ks... On Thu, Oct 25, 2007 at 10:11:45AM +0200, Rute Fonseca wrote: > Hi, > > > there's no known solution other than to get a bug-free card. If you tell > > me more about your system I should be able to give you more specific > > suggestions. > > I'm working on a machine (using Windows Vista) with these characteristics: > > Intel(R) Core 2 Duo T7250 (2.0GHz; 2MB Cache; FSB800) > 2GB SODIMM DDR2 667MHz exp a 4GB > Intel 965GM > Intel GMA X3100 até 358MB partilhada > > What is your suggestion? > > Thanks a lot. :) > > Best, > > Rute > > On 10/24/07, John Stone <jo...@ks...> wrote: > > > > Hi, > > Yes, black dots, geometric patterns, or other strange or unexpected > > colorings typically indicate a broken graphics driver. Depending on what > > graphics card/driver you're using, you may be able to upgrade to a newer > > driver and the problem will go away. For some other graphics chipsets/cards, > > > > Cheers, > > John Stone > > vm...@ks... > > > > > > > > On Wed, Oct 24, 2007 at 02:09:37PM -0500, Nathan Baker wrote: > > > Hello -- > > > > > > > I am trying to map the electrostatic potential onto a biomolecular > > > > surface using VMD 1.8.6 and APBS 0.5.1. Somehow what I get is not a > > > > surface totally coloured with the potential, but a black surface with > > > > small geometric figures bearing the potential colours (see attached > > > > picture). > > > > > > I have also seen this using VMD in conjunction with some graphics > > > cards. I'm Cc'ing John Stone, a VMD developer for more > > > information/advice. > > > > > > > I followed all the steps of the tutorial (using the plugin with APBS) > > > > and also tried creating the pot.dx file in standalone APBS and then > > > > loading it into the pqr in VMD (since within VMD I was getting an > > > > error message about a gamma keyword and thought it could be related). > > > > > > > > Can anyone give me some hint on what´s happening? > > > > > > I don't think this is user error; it is likely a problem with the > > > graphics drivers. > > > > > > Sorry for the problems, > > > > > > Nathan > > > > > > > Thanks a lot! > > > > > > > > Best > > > > > > > > Rute > > > > > > > > > > > > .................................... > > > > .Rute A R da Fonseca . > > > > . . > > > > .Genomics Group . > > > > .Department of Biology . > > > > .University of Copenhagen . > > > > .Universitetsparken 15, Building 10. > > > > .DK-2100 Copenhagen Ø . > > > > .Denmark . > > > > . . > > > > .Tel : +45 35 32 12 12 . > > > > .Email:fo...@bi... . > > > > .................................... > > > > > > > > .................................... > > > > .Rute A R da Fonseca . > > > > . . > > > > .Genomics Group . > > > > .Department of Biology . > > > > .University of Copenhagen . > > > > .Universitetsparken 15, Building 10. > > > > .DK-2100 Copenhagen Ø . > > > > .Denmark . > > > > . . > > > > .Tel : +45 35 32 12 12 . > > > > .Email:fo...@bi... . > > > > .................................... > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by: Splunk Inc. > > > > Still grepping through log files to find problems? Stop. > > > > Now Search log events and configuration files using AJAX and a browser. > > > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > > _______________________________________________ > > > > apbs-users mailing list > > > > apb...@li... > > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > > > > > > > > -- > > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > > > Center for Computational Biology, Washington University in St. Louis > > > Web: http://cholla.wustl.edu/ > > > > -- > > NIH Resource for Macromolecular Modeling and Bioinformatics > > Beckman Institute for Advanced Science and Technology > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 > > Email: jo...@ks... Phone: 217-244-3349 > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 > > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: jo...@ks... Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 |