From gtzotzos at me.com Fri Jul 1 09:05:14 2011 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 01 Jul 2011 18:05:14 +0200 Subject: [Chimera-users] Coordinates Message-ID: Hi everybody, Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong. Many thanks and best regards George From meng at cgl.ucsf.edu Fri Jul 1 09:30:04 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 1 Jul 2011 09:30:04 -0700 Subject: [Chimera-users] Coordinates In-Reply-To: References: Message-ID: <57A885F9-87AD-47F9-9FB2-F0A9F1B7BD07@cgl.ucsf.edu> Hi George, There are at least a couple of possibilities. (A) the command "measure inertia" -- the mass-weighted center of the specified atoms will be reported in the Reply Log along with other stuff. You can specify any set of atoms. It creates an ellipsoid by default but there is an option to turn that off. For example: measure inertia :47.a (residue 47 in chain A) measure inertia protein showEllipsoid false (B) if you want to show a sphere at the centroid, the command "define centroid" -- again, any set of atoms can be specified, and the center is reported in the Reply Log. In this case, mass weighting is an option, default false (thus giving center of geometry). For example: define centroid mass true radius 1.5 color cyan :47.a I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 1, 2011, at 9:05 AM, George Tzotzos wrote: > Hi everybody, > Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong. > Many thanks and best regards > George From meng at cgl.ucsf.edu Fri Jul 1 09:50:32 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 1 Jul 2011 09:50:32 -0700 Subject: [Chimera-users] Coordinates In-Reply-To: <57A885F9-87AD-47F9-9FB2-F0A9F1B7BD07@cgl.ucsf.edu> References: <57A885F9-87AD-47F9-9FB2-F0A9F1B7BD07@cgl.ucsf.edu> Message-ID: <5C3C9BC0-73A2-4B53-938E-B9B74CFB438D@cgl.ucsf.edu> On second thought, better stick with "define centroid" (method B) for now, as experiments suggest that method A is giving the transformed coordinates, i.e. different answers after you rotate or translate the structure. Elaine On Jul 1, 2011, at 9:30 AM, Elaine Meng wrote: > Hi George, > There are at least a couple of possibilities. > > (A) the command "measure inertia" -- the mass-weighted center of the specified atoms will be reported in the Reply Log along with other stuff. You can specify any set of atoms. It creates an ellipsoid by default but there is an option to turn that off. For example: > > measure inertia :47.a > (residue 47 in chain A) > measure inertia protein showEllipsoid false > > > > > (B) if you want to show a sphere at the centroid, the command "define centroid" -- again, any set of atoms can be specified, and the center is reported in the Reply Log. In this case, mass weighting is an option, default false (thus giving center of geometry). For example: > > define centroid mass true radius 1.5 color cyan :47.a > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jul 1, 2011, at 9:05 AM, George Tzotzos wrote: > >> Hi everybody, >> Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong. >> Many thanks and best regards >> George > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From ybaime at gmail.com Mon Jul 4 04:52:28 2011 From: ybaime at gmail.com (=?UTF-8?B?15nXldeb15HXkw==?=) Date: Mon, 4 Jul 2011 14:52:28 +0300 Subject: [Chimera-users] System requirements Message-ID: Hi I'm looking into upgrading my computer and I was wondering whether Chimera runs properly on Windows7 and with a NVIDIA GT430 1GB graphic card. Thank you Yocheved -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Jul 4 18:17:01 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 04 Jul 2011 18:17:01 -0700 Subject: [Chimera-users] System requirements In-Reply-To: References: Message-ID: <4E12660D.8030208@cgl.ucsf.edu> On 7/4/2011 4:52 AM, ????? wrote: > I'm looking into upgrading my computer and I was wondering whether > Chimera runs properly on Windows7 and with a NVIDIA GT430 1GB graphic > card. Yes, it will work, no problem. The problem systems for Chimera are computers that just have Intel motherboard graphics, but current Intel graphics drivers are *much* better *if* they are available (and they are still underpowered graphically). Other problem systems are laptop systems, because, historically, the graphics drivers are rarely updated with bug fixes -- many newer systems let you update the driver with ones from the graphics vendor (e.g., AMD/ATI or NVIDIA). Enjoy your new system, Greg From Branham at ukzn.ac.za Sat Jul 2 01:46:52 2011 From: Branham at ukzn.ac.za (Mickey Branham) Date: Sat, 02 Jul 2011 10:46:52 +0200 Subject: [Chimera-users] Drug-Metal Complexation Modeling Message-ID: <4E0EF71C0200008500034A67@dbngwia1.ukzn.ac.za> Thanks Elaine, Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. Don't know if this seems interesting but any comments from you would be appreciated. Thanks again for your response. Cheers Mickey >>> Elaine Meng 06/23/11 6:23 PM >>> Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer > Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jul 5 09:25:37 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 5 Jul 2011 09:25:37 -0700 Subject: [Chimera-users] Drug-Metal Complexation Modeling In-Reply-To: <4E0EF71C0200008500034A67@dbngwia1.ukzn.ac.za> References: <4E0EF71C0200008500034A67@dbngwia1.ukzn.ac.za> Message-ID: <68CD598B-EED4-42A7-A5A8-C66A8BE9A935@cgl.ucsf.edu> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > Thanks Elaine, > Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. > > So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. > > We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. > > Don't know if this seems interesting but any comments from you would be appreciated. > > Thanks again for your response. > > Cheers > Mickey From sludtke at bcm.edu Tue Jul 5 12:43:21 2011 From: sludtke at bcm.edu (Steven Ludtke) Date: Tue, 5 Jul 2011 14:43:21 -0500 Subject: [Chimera-users] Problem with multiple monitors and NVidia 3D Vision - any suggestions ? Message-ID: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't go into stereo mode. Here are the relevant lines from the Xorg log file: [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 [ 9016.284] (==) NVIDIA(0): RGB weight 888 [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 [ 9018.466] (==) NVIDIA(1): RGB weight 888 [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision [ 9019.116] (II) NVIDIA(GPU-1): stereo. [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA [ 9021.570] (II) NVIDIA(1): stereo controller [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, it raises an error :^( Here are the relevant xorg.conf sections: Section "ServerLayout" Identifier "Layout0" Screen 0 "Screen0" 0 0 Screen 1 "Screen1" 2560 0 InputDevice "Keyboard0" "CoreKeyboard" InputDevice "Mouse0" "CorePointer" Option "Xinerama" "1" Option "XineramaStereoFlipping" "0" EndSection Section "Device" Identifier "Device0" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Tesla C2070" BusID "PCI:131:0:0" EndSection Section "Device" Identifier "Device1" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Quadro 4000" BusID "PCI:2:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor "Monitor0" DefaultDepth 24 Option "TwinViewXineramaInfoOrder" "DFP-2" Option "TwinView" "0" Option "metamodes" "nvidia-auto-select +0+0" SubSection "Display" Depth 24 EndSubSection EndSection Section "Screen" # Removed Option "metamodes" "nvidia-auto-select +0+0" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "1920x1080_120 +0+0" Option "Stereo" "10" SubSection "Display" Depth 24 EndSubSection EndSection Section "Extensions" Option "Composite" "Disable" EndSection Anyone else have a Stereo configuration with dual monitors working ? cheers ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke at bcm.edu stevel at alumni.caltech.edu From gregc at cgl.ucsf.edu Tue Jul 5 15:35:53 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 05 Jul 2011 15:35:53 -0700 Subject: [Chimera-users] Problem with multiple monitors and NVidia 3D Vision - any suggestions ? In-Reply-To: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> References: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> Message-ID: <4E1391C9.3030003@cgl.ucsf.edu> Looking at the NVIDIA driver's release notes it says for Xinerama: "... the X.Org X server bases the visuals of the logical Xinerama X screen on the visuals of physical X screen 0." So if you physically switched your display connections, so the stereo capable monitor is first, it might work. A low level way to see if stereo visuals are available is to use the glxinfo program and look for y's in the st/ro column -- that's the same information chimera uses to see if stereo is available. Good luck, Greg On 07/05/2011 12:43 PM, Steven Ludtke wrote: > Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 > video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have > one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but > if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode > (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even > when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't > go into stereo mode. Here are the relevant lines from the Xorg log file: > > [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > [ 9016.284] (==) NVIDIA(0): RGB weight 888 > [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor > [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" > [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" > [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" > [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D > [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. > [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 > [ 9018.466] (==) NVIDIA(1): RGB weight 888 > [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor > [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) > [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" > [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" > [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" > [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested > [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision > [ 9019.116] (II) NVIDIA(GPU-1): stereo. > [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) > [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes > [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 > [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA > [ 9021.570] (II) NVIDIA(1): stereo controller > [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" > > So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, > it raises an error :^( > > Here are the relevant xorg.conf sections: > Section "ServerLayout" > Identifier "Layout0" > Screen 0 "Screen0" 0 0 > Screen 1 "Screen1" 2560 0 > InputDevice "Keyboard0" "CoreKeyboard" > InputDevice "Mouse0" "CorePointer" > Option "Xinerama" "1" > Option "XineramaStereoFlipping" "0" > EndSection > > Section "Device" > Identifier "Device0" > Driver "nvidia" > VendorName "NVIDIA Corporation" > BoardName "Tesla C2070" > BusID "PCI:131:0:0" > EndSection > > Section "Device" > Identifier "Device1" > Driver "nvidia" > VendorName "NVIDIA Corporation" > BoardName "Quadro 4000" > BusID "PCI:2:0:0" > EndSection > > Section "Screen" > Identifier "Screen0" > Device "Device0" > Monitor "Monitor0" > DefaultDepth 24 > Option "TwinViewXineramaInfoOrder" "DFP-2" > Option "TwinView" "0" > Option "metamodes" "nvidia-auto-select +0+0" > SubSection "Display" > Depth 24 > EndSubSection > EndSection > > Section "Screen" > # Removed Option "metamodes" "nvidia-auto-select +0+0" > Identifier "Screen1" > Device "Device1" > Monitor "Monitor1" > DefaultDepth 24 > Option "TwinView" "0" > Option "metamodes" "1920x1080_120 +0+0" > Option "Stereo" "10" > SubSection "Display" > Depth 24 > EndSubSection > EndSection > > Section "Extensions" > Option "Composite" "Disable" > EndSection > > > Anyone else have a Stereo configuration with dual monitors working ? > > cheers > > ---------------------------------------------------------------------------- > Steven Ludtke, Ph.D. > Associate Professor > Co-Director National Center For Macromolecular Imaging > Dept of Biochemistry and Mol. Biol. > Baylor College of Medicine > sludtke at bcm.edu > stevel at alumni.caltech.edu > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Tue Jul 5 16:25:45 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 5 Jul 2011 16:25:45 -0700 Subject: [Chimera-users] Not Responding In-Reply-To: <5EFA30BE-D4B3-43B7-9D68-BCA5868D6B4B@cgl.ucsf.edu> References: <1309458987.40276.YahooMailRC@web111015.mail.gq1.yahoo.com> <5EFA30BE-D4B3-43B7-9D68-BCA5868D6B4B@cgl.ucsf.edu> Message-ID: <22447E30-4E5C-497B-9ADB-C06573135FA2@cgl.ucsf.edu> On Jun 30, 2011, at 4:05 PM, Eric Pettersen wrote: > Hi Chad, > My first inclination would be to think that the culprit is > Chimera's ring-finding code, but the fact your input files work > while your output files don't is perplexing. Once you pointed out that neither actually works I was less perplexed. :-) > I don't think I can really help unless you send me some files to > work with (one input and one output would be good). My inclination was close but not quite it. The ring finding code was fine but the code that assigns atom types to fused planar ring system was a little too optimistic about how big a fused ring system it could handle. I have dropped it's maximum size limit and now your files open quickly. The change will be in tomorrow's daily build (1.6 build). --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From menetret at gmail.com Wed Jul 6 04:33:03 2011 From: menetret at gmail.com (Jean-Francois Menetret) Date: Wed, 6 Jul 2011 13:33:03 +0200 Subject: [Chimera-users] movie script Message-ID: Hello, I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? Thank you J-F -------------- next part -------------- An HTML attachment was scrubbed... URL: From sludtke at bcm.edu Wed Jul 6 05:52:17 2011 From: sludtke at bcm.edu (Steven Ludtke) Date: Wed, 6 Jul 2011 07:52:17 -0500 Subject: [Chimera-users] Problem with multiple monitors and NVidia 3D Vision - any suggestions ? In-Reply-To: <4E1391C9.3030003@cgl.ucsf.edu> References: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> <4E1391C9.3030003@cgl.ucsf.edu> Message-ID: <4DBADB89-B4CC-45E3-B8DE-52889F11D560@bcm.edu> Thanks for the suggestion Greg. Unfortunately, still no-go. I've tried every combination of ordering, device assignment, etc. Changing the ordering of the devices DOES change that glxinfo now reports the Quadro card as the renderer instead of the Tesla, but still doesn't list any available stereo visuals, unless I completely disable the second display. Unless I'm willing to kill everything I'm running and restart the X-server every time I want to use stereo, I'm stuck :^( ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke at bcm.edu stevel at alumni.caltech.edu On Jul 5, 2011, at 5:35 PM, Greg Couch wrote: > Looking at the NVIDIA driver's release notes it says for Xinerama: "... > the X.Org X server bases the visuals of the logical Xinerama X screen on > the visuals of physical X screen 0." So if you physically switched your > display connections, so the stereo capable monitor is first, it might > work. A low level way to see if stereo visuals are available is to use > the glxinfo program and look for y's in the st/ro column -- that's the > same information chimera uses to see if stereo is available. > > Good luck, > > Greg > > On 07/05/2011 12:43 PM, Steven Ludtke wrote: >> Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 >> video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have >> one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but >> if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode >> (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even >> when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't >> go into stereo mode. Here are the relevant lines from the Xorg log file: >> >> [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 >> [ 9016.284] (==) NVIDIA(0): RGB weight 888 >> [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor >> [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) >> [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" >> [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" >> [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" >> [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D >> [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. >> [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 >> [ 9018.466] (==) NVIDIA(1): RGB weight 888 >> [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor >> [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) >> [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" >> [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" >> [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" >> [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested >> [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision >> [ 9019.116] (II) NVIDIA(GPU-1): stereo. >> [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) >> [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes >> [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 >> [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA >> [ 9021.570] (II) NVIDIA(1): stereo controller >> [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" >> >> So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, >> it raises an error :^( >> >> Here are the relevant xorg.conf sections: >> Section "ServerLayout" >> Identifier "Layout0" >> Screen 0 "Screen0" 0 0 >> Screen 1 "Screen1" 2560 0 >> InputDevice "Keyboard0" "CoreKeyboard" >> InputDevice "Mouse0" "CorePointer" >> Option "Xinerama" "1" >> Option "XineramaStereoFlipping" "0" >> EndSection >> >> Section "Device" >> Identifier "Device0" >> Driver "nvidia" >> VendorName "NVIDIA Corporation" >> BoardName "Tesla C2070" >> BusID "PCI:131:0:0" >> EndSection >> >> Section "Device" >> Identifier "Device1" >> Driver "nvidia" >> VendorName "NVIDIA Corporation" >> BoardName "Quadro 4000" >> BusID "PCI:2:0:0" >> EndSection >> >> Section "Screen" >> Identifier "Screen0" >> Device "Device0" >> Monitor "Monitor0" >> DefaultDepth 24 >> Option "TwinViewXineramaInfoOrder" "DFP-2" >> Option "TwinView" "0" >> Option "metamodes" "nvidia-auto-select +0+0" >> SubSection "Display" >> Depth 24 >> EndSubSection >> EndSection >> >> Section "Screen" >> # Removed Option "metamodes" "nvidia-auto-select +0+0" >> Identifier "Screen1" >> Device "Device1" >> Monitor "Monitor1" >> DefaultDepth 24 >> Option "TwinView" "0" >> Option "metamodes" "1920x1080_120 +0+0" >> Option "Stereo" "10" >> SubSection "Display" >> Depth 24 >> EndSubSection >> EndSection >> >> Section "Extensions" >> Option "Composite" "Disable" >> EndSection >> >> >> Anyone else have a Stereo configuration with dual monitors working ? >> >> cheers >> >> ---------------------------------------------------------------------------- >> Steven Ludtke, Ph.D. >> Associate Professor >> Co-Director National Center For Macromolecular Imaging >> Dept of Biochemistry and Mol. Biol. >> Baylor College of Medicine >> sludtke at bcm.edu >> stevel at alumni.caltech.edu >> >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Wed Jul 6 10:10:06 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 6 Jul 2011 10:10:06 -0700 Subject: [Chimera-users] movie script In-Reply-To: References: Message-ID: <9CEB8266-5E87-4326-B607-217CAC8B2148@cgl.ucsf.edu> Hi J-F, My "trmovie" script example includes morphing between two conformations. All you have to do to see the movie content is open the script file (named *.com or *.cmd) in Chimera -- it includes opening the structures, superimposing and rotating them, calculating the morph, playing the morph, etc. The movie-recording commands are commented out so you can just see the content without taking the time to record the actual movie, but the resulting movie is in our Image Gallery, called "ball-and-socket motion." Example movie content scripts: Image Gallery: HOWEVER, that example does not rotate while showing the morph. I attached a slightly modified version that does rotation at the same time as playing back the morph trajectory. The only change is insertion of "roll y 1" before the commands that play the trajectory, and further down, appending ";wait" followed by "freeze" to stop that roll. Again, to see this example movie content, all you would have to do is open the attached script file (plain text but name it ending with .com or .cmd) in Chimera -- the movie-recording commands are commented out. There is some other movie stuff you might find interesting, like labels that fade in and out. In your own case, you would probably not include opening the files and calculating the morph in your script. You would probably do that ahead of time, possibly using the Morph Conformations graphical interface (under Tools... Structure Comparison), and then save the session. Then your script would simply act on that session to do the stuff you wanted in your movie, such playing the pre-existing morph trajectory, rotating, etc. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: trmovie2.txt URL: -------------- next part -------------- On Jul 6, 2011, at 4:33 AM, Jean-Francois Menetret wrote: > Hello, > I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? > Thank you > J-F From ice_pek at yahoo.com.hk Wed Jul 6 00:58:33 2011 From: ice_pek at yahoo.com.hk (Flora Ieong) Date: Wed, 6 Jul 2011 15:58:33 +0800 (HKT) Subject: [Chimera-users] Chimera function Message-ID: <1309939113.23623.YahooMailNeo@web19301.mail.hk2.yahoo.com> To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera? 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong -------------- next part -------------- An HTML attachment was scrubbed... URL: From Branham at ukzn.ac.za Wed Jul 6 07:50:49 2011 From: Branham at ukzn.ac.za (Mickey Branham) Date: Wed, 06 Jul 2011 16:50:49 +0200 Subject: [Chimera-users] Drug-Metal Complexation Modeling Message-ID: <4E1492690200008500034E44@dbngwia1.ukzn.ac.za> Thanks Elaine, I did check out the CCL website; a great resource. Mickey >>> Elaine Meng 07/05/11 6:25 PM >>> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > Thanks Elaine, > Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. > > So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. > > We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. > > Don't know if this seems interesting but any comments from you would be appreciated. > > Thanks again for your response. > > Cheers > Mickey Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Jul 6 11:08:32 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 6 Jul 2011 11:08:32 -0700 Subject: [Chimera-users] Chimera function In-Reply-To: <1309939113.23623.YahooMailNeo@web19301.mail.hk2.yahoo.com> References: <1309939113.23623.YahooMailNeo@web19301.mail.hk2.yahoo.com> Message-ID: <8B0D6591-147C-425E-9270-62CE0D32743F@cgl.ucsf.edu> Dear Pek Leong, There is nothing specific for building glycans. However, if you already had separate structures of the glycan part and the protein, you could use Build Structure (under Tools... Structure Editing), the Join Models tab to attach them. This will simply attach the structures -- it will not predict reasonable conformations. Some possible sources of the glycan part would be some other PDB structure (you could just delete the parts you don't want) or if it is in the PubChem compound database, fetching by CID # into Chimera (for example, command: open pubchem:4582185 ) I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 6, 2011, at 12:58 AM, Flora Ieong wrote: > To whom it may concern, > I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. > Sincerely, > Pek Ieong From meng at cgl.ucsf.edu Thu Jul 7 08:51:21 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 7 Jul 2011 08:51:21 -0700 Subject: [Chimera-users] Regarding adding plane surfaces.... In-Reply-To: References: Message-ID: <0A926C60-F877-47D1-982F-85856660B367@cgl.ucsf.edu> On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > Hi Elaine, > > I have three objects in the chimera image. > All these objects are in different planes. > How to add surfaces to each of these so that they can be shown to lie in diff planes? > I have attached a typical image herewith. > > Regards, > Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. Please send Chimera questions to chimera-users at cgl.ucsf.edu instead of directly to me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: mit.bmp Type: image/bmp Size: 589878 bytes Desc: not available URL: -------------- next part -------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: mitside.bmp Type: image/bmp Size: 589878 bytes Desc: not available URL: From ice_pek at yahoo.com.hk Thu Jul 7 04:01:56 2011 From: ice_pek at yahoo.com.hk (Flora Ieong) Date: Thu, 7 Jul 2011 19:01:56 +0800 (HKT) Subject: [Chimera-users] =?utf-8?b?5Zue6KaG77iwICBDaGltZXJhIGZ1bmN0aW9u?= In-Reply-To: <8B0D6591-147C-425E-9270-62CE0D32743F@cgl.ucsf.edu> References: <1309939113.23623.YahooMailNeo@web19301.mail.hk2.yahoo.com> <8B0D6591-147C-425E-9270-62CE0D32743F@cgl.ucsf.edu> Message-ID: <1310036516.52208.YahooMailNeo@web19302.mail.hk2.yahoo.com> Thank You. The information is very helpful ________________________________ ?? Elaine Meng ???? Flora Ieong ??(CC)? "chimera-users at cgl.ucsf.edu" ????? 2011?07?6? (??) 11:08 AM ??? Re: [Chimera-users] Chimera function Dear Pek Leong, There is nothing specific for building glycans.? However, if you already had separate structures of the glycan part and the protein, you could use Build Structure (under Tools... Structure Editing), the Join Models tab to attach them.? This will simply attach the structures -- it will not predict reasonable conformations. Some possible sources of the glycan part would be some other PDB structure (you could just delete the parts you don't want) or if it is in the PubChem compound database, fetching by CID # into Chimera (for example, command: open pubchem:4582185 ) I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 6, 2011, at 12:58 AM, Flora Ieong wrote: > To whom it may concern, > I am a chimera user and am currently doing a glycan research using Chimera? 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. > Sincerely, > Pek Ieong -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Jul 7 09:56:16 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 07 Jul 2011 09:56:16 -0700 Subject: [Chimera-users] Regarding adding plane surfaces.... In-Reply-To: <0A926C60-F877-47D1-982F-85856660B367@cgl.ucsf.edu> References: <0A926C60-F877-47D1-982F-85856660B367@cgl.ucsf.edu> Message-ID: <4E15E530.9050303@sonic.net> Hi Chinmaya, You can use the "shape rectangle" command to make planes. In the attached image I made the two planes with shape rect width 100 height 100 slab .1 color .7,.7,.7,.2 center 0,0,-50 coord #0 shape rect width 100 height 100 slab .1 color .7,.7,.7,.2 center 0,0,50 coord #0 Since I wanted the planes aligned with volume #0 I specified the "coord #0" option. Tom > On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > >> Hi Elaine, >> >> I have three objects in the chimera image. >> All these objects are in different planes. >> How to add surfaces to each of these so that they can be shown to lie in diff planes? >> I have attached a typical image herewith. >> >> Regards, >> Chinmaya > Hi Chinmaya, > There is a tool to define planes from sets of atoms, but I don't know if you have atoms. > > The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). > > > > > I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. > > > > The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. > > > > Please send Chimera questions to chimera-users at cgl.ucsf.edu instead of directly to me. Thanks, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: planes.jpg Type: image/jpeg Size: 23811 bytes Desc: not available URL: From gregc at cgl.ucsf.edu Thu Jul 7 16:27:49 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 07 Jul 2011 16:27:49 -0700 Subject: [Chimera-users] Problem with multiple monitors and NVidia 3D Vision - any suggestions ? In-Reply-To: <4DBADB89-B4CC-45E3-B8DE-52889F11D560@bcm.edu> References: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> <4E1391C9.3030003@cgl.ucsf.edu> <4DBADB89-B4CC-45E3-B8DE-52889F11D560@bcm.edu> Message-ID: <4E1640F5.40206@cgl.ucsf.edu> So next step would be to file a bug with NVIDIA so it can fixed in a newer driver. See http://www.nvidia.com/page/support.html, for the Linux support forums and the bug report link. -- Greg On 07/06/2011 05:52 AM, Steven Ludtke wrote: > Thanks for the suggestion Greg. Unfortunately, still no-go. I've tried every combination of ordering, > device assignment, etc. Changing the ordering of the devices DOES change that glxinfo now reports the > Quadro card as the renderer instead of the Tesla, but still doesn't list any available stereo visuals, > unless I completely disable the second display. Unless I'm willing to kill everything I'm running and > restart the X-server every time I want to use stereo, I'm stuck :^( > > ---------------------------------------------------------------------------- > Steven Ludtke, Ph.D. > Associate Professor > Co-Director National Center For Macromolecular Imaging > Dept of Biochemistry and Mol. Biol. > Baylor College of Medicine > sludtke at bcm.edu > stevel at alumni.caltech.edu > > > > > On Jul 5, 2011, at 5:35 PM, Greg Couch wrote: > >> Looking at the NVIDIA driver's release notes it says for Xinerama: "... >> the X.Org X server bases the visuals of the logical Xinerama X screen on >> the visuals of physical X screen 0." So if you physically switched your >> display connections, so the stereo capable monitor is first, it might >> work. A low level way to see if stereo visuals are available is to use >> the glxinfo program and look for y's in the st/ro column -- that's the >> same information chimera uses to see if stereo is available. >> >> Good luck, >> >> Greg >> >> On 07/05/2011 12:43 PM, Steven Ludtke wrote: >>> Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 >>> video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have >>> one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but >>> if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode >>> (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even >>> when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't >>> go into stereo mode. Here are the relevant lines from the Xorg log file: >>> >>> [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 >>> [ 9016.284] (==) NVIDIA(0): RGB weight 888 >>> [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor >>> [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) >>> [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" >>> [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" >>> [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" >>> [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D >>> [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. >>> [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 >>> [ 9018.466] (==) NVIDIA(1): RGB weight 888 >>> [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor >>> [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) >>> [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" >>> [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" >>> [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" >>> [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested >>> [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision >>> [ 9019.116] (II) NVIDIA(GPU-1): stereo. >>> [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) >>> [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes >>> [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 >>> [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA >>> [ 9021.570] (II) NVIDIA(1): stereo controller >>> [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" >>> >>> So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, >>> it raises an error :^( >>> >>> Here are the relevant xorg.conf sections: >>> Section "ServerLayout" >>> Identifier "Layout0" >>> Screen 0 "Screen0" 0 0 >>> Screen 1 "Screen1" 2560 0 >>> InputDevice "Keyboard0" "CoreKeyboard" >>> InputDevice "Mouse0" "CorePointer" >>> Option "Xinerama" "1" >>> Option "XineramaStereoFlipping" "0" >>> EndSection >>> >>> Section "Device" >>> Identifier "Device0" >>> Driver "nvidia" >>> VendorName "NVIDIA Corporation" >>> BoardName "Tesla C2070" >>> BusID "PCI:131:0:0" >>> EndSection >>> >>> Section "Device" >>> Identifier "Device1" >>> Driver "nvidia" >>> VendorName "NVIDIA Corporation" >>> BoardName "Quadro 4000" >>> BusID "PCI:2:0:0" >>> EndSection >>> >>> Section "Screen" >>> Identifier "Screen0" >>> Device "Device0" >>> Monitor "Monitor0" >>> DefaultDepth 24 >>> Option "TwinViewXineramaInfoOrder" "DFP-2" >>> Option "TwinView" "0" >>> Option "metamodes" "nvidia-auto-select +0+0" >>> SubSection "Display" >>> Depth 24 >>> EndSubSection >>> EndSection >>> >>> Section "Screen" >>> # Removed Option "metamodes" "nvidia-auto-select +0+0" >>> Identifier "Screen1" >>> Device "Device1" >>> Monitor "Monitor1" >>> DefaultDepth 24 >>> Option "TwinView" "0" >>> Option "metamodes" "1920x1080_120 +0+0" >>> Option "Stereo" "10" >>> SubSection "Display" >>> Depth 24 >>> EndSubSection >>> EndSection >>> >>> Section "Extensions" >>> Option "Composite" "Disable" >>> EndSection >>> >>> >>> Anyone else have a Stereo configuration with dual monitors working ? >>> >>> cheers >>> >>> ---------------------------------------------------------------------------- >>> Steven Ludtke, Ph.D. >>> Associate Professor >>> Co-Director National Center For Macromolecular Imaging >>> Dept of Biochemistry and Mol. Biol. >>> Baylor College of Medicine >>> sludtke at bcm.edu >>> stevel at alumni.caltech.edu >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From sludtke at bcm.edu Thu Jul 7 20:43:41 2011 From: sludtke at bcm.edu (Steven Ludtke) Date: Thu, 7 Jul 2011 22:43:41 -0500 Subject: [Chimera-users] Problem with multiple monitors and NVidia 3D Vision - any suggestions ? In-Reply-To: <4E1640F5.40206@cgl.ucsf.edu> References: <35F27665-0621-4217-9320-12B28D481D9E@bcm.edu> <4E1391C9.3030003@cgl.ucsf.edu> <4DBADB89-B4CC-45E3-B8DE-52889F11D560@bcm.edu> <4E1640F5.40206@cgl.ucsf.edu> Message-ID: <6D3697AE-29C4-4E1D-937A-FE25402B4DC4@bcm.edu> Thanks Greg. After your first reply I did actually try the Nvidia linux support forum, and got a reply from someone from Nvidia saying that the Xinerama specs say that the GLX will only report capabilities available on all displays. I am going to get a dual-link capable display-port adapter for the Quadro so I can run it in TwinView instead of Xinerama. The Nvidia guy was reasonably certain that that would work where Xinerama wouldn't. Worth a try... I will report the results here after I give it a try for posterity. ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do Co-Director National Center For Macromolecular Imaging ARE Baylor College of Medicine The converse sludtke at bcm.edu -or- stevel at alumni.caltech.edu also applies http://ncmi.bcm.edu/~stevel On Jul 7, 2011, at 6:27 PM, Greg Couch wrote: > So next step would be to file a bug with NVIDIA so it can fixed in a > newer driver. See http://www.nvidia.com/page/support.html, for the > Linux support forums and the bug report link. > > -- Greg > > On 07/06/2011 05:52 AM, Steven Ludtke wrote: >> Thanks for the suggestion Greg. Unfortunately, still no-go. I've tried every combination of ordering, >> device assignment, etc. Changing the ordering of the devices DOES change that glxinfo now reports the >> Quadro card as the renderer instead of the Tesla, but still doesn't list any available stereo visuals, >> unless I completely disable the second display. Unless I'm willing to kill everything I'm running and >> restart the X-server every time I want to use stereo, I'm stuck :^( >> >> ---------------------------------------------------------------------------- >> Steven Ludtke, Ph.D. >> Associate Professor >> Co-Director National Center For Macromolecular Imaging >> Dept of Biochemistry and Mol. Biol. >> Baylor College of Medicine >> sludtke at bcm.edu >> stevel at alumni.caltech.edu >> >> >> >> >> On Jul 5, 2011, at 5:35 PM, Greg Couch wrote: >> >>> Looking at the NVIDIA driver's release notes it says for Xinerama: "... >>> the X.Org X server bases the visuals of the logical Xinerama X screen on >>> the visuals of physical X screen 0." So if you physically switched your >>> display connections, so the stereo capable monitor is first, it might >>> work. A low level way to see if stereo visuals are available is to use >>> the glxinfo program and look for y's in the st/ro column -- that's the >>> same information chimera uses to see if stereo is available. >>> >>> Good luck, >>> >>> Greg >>> >>> On 07/05/2011 12:43 PM, Steven Ludtke wrote: >>>> Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 >>>> video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have >>>> one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but >>>> if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode >>>> (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even >>>> when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't >>>> go into stereo mode. Here are the relevant lines from the Xorg log file: >>>> >>>> [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 >>>> [ 9016.284] (==) NVIDIA(0): RGB weight 888 >>>> [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor >>>> [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) >>>> [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" >>>> [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" >>>> [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" >>>> [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D >>>> [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. >>>> [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 >>>> [ 9018.466] (==) NVIDIA(1): RGB weight 888 >>>> [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor >>>> [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) >>>> [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" >>>> [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" >>>> [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" >>>> [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested >>>> [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision >>>> [ 9019.116] (II) NVIDIA(GPU-1): stereo. >>>> [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) >>>> [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes >>>> [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 >>>> [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA >>>> [ 9021.570] (II) NVIDIA(1): stereo controller >>>> [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" >>>> >>>> So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, >>>> it raises an error :^( >>>> >>>> Here are the relevant xorg.conf sections: >>>> Section "ServerLayout" >>>> Identifier "Layout0" >>>> Screen 0 "Screen0" 0 0 >>>> Screen 1 "Screen1" 2560 0 >>>> InputDevice "Keyboard0" "CoreKeyboard" >>>> InputDevice "Mouse0" "CorePointer" >>>> Option "Xinerama" "1" >>>> Option "XineramaStereoFlipping" "0" >>>> EndSection >>>> >>>> Section "Device" >>>> Identifier "Device0" >>>> Driver "nvidia" >>>> VendorName "NVIDIA Corporation" >>>> BoardName "Tesla C2070" >>>> BusID "PCI:131:0:0" >>>> EndSection >>>> >>>> Section "Device" >>>> Identifier "Device1" >>>> Driver "nvidia" >>>> VendorName "NVIDIA Corporation" >>>> BoardName "Quadro 4000" >>>> BusID "PCI:2:0:0" >>>> EndSection >>>> >>>> Section "Screen" >>>> Identifier "Screen0" >>>> Device "Device0" >>>> Monitor "Monitor0" >>>> DefaultDepth 24 >>>> Option "TwinViewXineramaInfoOrder" "DFP-2" >>>> Option "TwinView" "0" >>>> Option "metamodes" "nvidia-auto-select +0+0" >>>> SubSection "Display" >>>> Depth 24 >>>> EndSubSection >>>> EndSection >>>> >>>> Section "Screen" >>>> # Removed Option "metamodes" "nvidia-auto-select +0+0" >>>> Identifier "Screen1" >>>> Device "Device1" >>>> Monitor "Monitor1" >>>> DefaultDepth 24 >>>> Option "TwinView" "0" >>>> Option "metamodes" "1920x1080_120 +0+0" >>>> Option "Stereo" "10" >>>> SubSection "Display" >>>> Depth 24 >>>> EndSubSection >>>> EndSection >>>> >>>> Section "Extensions" >>>> Option "Composite" "Disable" >>>> EndSection >>>> >>>> >>>> Anyone else have a Stereo configuration with dual monitors working ? >>>> >>>> cheers >>>> >>>> ---------------------------------------------------------------------------- >>>> Steven Ludtke, Ph.D. >>>> Associate Professor >>>> Co-Director National Center For Macromolecular Imaging >>>> Dept of Biochemistry and Mol. Biol. >>>> Baylor College of Medicine >>>> sludtke at bcm.edu >>>> stevel at alumni.caltech.edu >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From vincent.zoete at gmail.com Thu Jul 7 22:27:22 2011 From: vincent.zoete at gmail.com (Vincent Zoete) Date: Fri, 8 Jul 2011 05:27:22 +0000 (UTC) Subject: [Chimera-users] =?utf-8?q?Invitation_=C3=A0_se_connecter_sur_Link?= =?utf-8?q?edIn?= Message-ID: <1956604462.324579.1310102842899.JavaMail.app@ela4-bed35.prod> LinkedIn ------------ J'aimerais vous inviter ? rejoindre mon r?seau professionnel en ligne, sur le site LinkedIn. Vincent Vincent Zoete Associate group leader chez Swiss Institute of Bioinformatics R?gion de Gen?ve, Suisse Veuillez confirmer que vous connaissez Vincent Zoete https://www.linkedin.com/e/vxh6i1-gpupen7z-1e/isd/3469346511/KWdfhuHl/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: From githae at rostlab.org Fri Jul 8 06:12:40 2011 From: githae at rostlab.org (Dedan Githae) Date: Fri, 8 Jul 2011 15:12:40 +0200 Subject: [Chimera-users] distance between 2 residues Message-ID: <2831401A-7E7B-4978-B733-8419A3176147@rostlab.org> how is the problem solved in chimera? i want to measure distance between 2 residues From meng at cgl.ucsf.edu Fri Jul 8 10:41:28 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 8 Jul 2011 10:41:28 -0700 Subject: [Chimera-users] distance between 2 residues In-Reply-To: <2831401A-7E7B-4978-B733-8419A3176147@rostlab.org> References: <2831401A-7E7B-4978-B733-8419A3176147@rostlab.org> Message-ID: <704F70F2-7F78-47AF-AFF0-41FED388C26E@cgl.ucsf.edu> Hi Dedan, There are many different ways to specify two atoms and measure the distance between them. The GUI way is to Ctrl-click to select one atom, Shift-Ctrl-doubleclick to both select the second atom and get a popup menu that includes the choice to "Show Distance." There's also a Distances tool and the command "distance." Three ways to measure a distance are given here: It is also done in tutorials, for example here: In general, you can use menu "Help... Search Documentation" to find subjects of interest. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 8, 2011, at 6:12 AM, Dedan Githae wrote: > how is the problem solved in chimera? i want to measure distance between 2 residues From jlawton at eastern.edu Sat Jul 9 15:55:17 2011 From: jlawton at eastern.edu (Jeff Lawton) Date: Sat, 09 Jul 2011 18:55:17 -0400 Subject: [Chimera-users] Tear-off menus in Chimera 1.5.3 for Mac OS X Message-ID: Hi, I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and it seems that the "tear off" feature of the menus is not available, though I was previously able to do that when running the X window version of Chimera. Is there a way to use the menu "tear off" feature in the native aqua version? Thanks! Jeff -- Associate Professor of Biochemistry Department of Chemistry Eastern University 1300 Eagle Road St. Davids, PA 19087 (610) 341-1545 From meng at cgl.ucsf.edu Sat Jul 9 16:42:20 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 9 Jul 2011 16:42:20 -0700 Subject: [Chimera-users] Tear-off menus in Chimera 1.5.3 for Mac OS X In-Reply-To: References: Message-ID: <65A4F259-A526-4AB2-93C8-3992C0BD6E71@cgl.ucsf.edu> Hi Jeff, Sorry, tear-off menus are not available in the native aqua version of Chimera (regardless of Chimera version number or Mac OS X version number). For Mac, only the X windows version has this feature. Because the "Actions... Color" menu was one of the most useful to tear off, to provide a similar behavior in all Chimera versions we have implemented a separate Color Actions dialog (opened by choosing "Actions... Color... all options"). No global solution to allow tearing off menus in the native Mac version has been found, however. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 9, 2011, at 3:55 PM, Jeff Lawton wrote: > Hi, > I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and > it seems that the "tear off" feature of the menus is not available, though I > was previously able to do that when running the X window version of Chimera. > Is there a way to use the menu "tear off" feature in the native aqua > version? > Thanks! > Jeff From a_bigley at neo.tamu.edu Mon Jul 11 08:11:04 2011 From: a_bigley at neo.tamu.edu (Bigley, Andrew) Date: Mon, 11 Jul 2011 10:11:04 -0500 (CDT) Subject: [Chimera-users] 3D chimera Message-ID: <627417219.5807571310397064159.JavaMail.root@neo-mail-3> Dear Chimera Developers, The recent advances in 3D technology is affording some unique opportunities to people interested. I have recently seen advertisements for new glasses free 3D smart phones. Can you adapt chimera for such a platform and hence convert a smart phone into a portable 3D protein viewer that would allow manipulation of the view through typical touch screen commands? Andrew N. Bigley, Ph.D. From githae at rostlab.org Mon Jul 11 09:23:52 2011 From: githae at rostlab.org (Dedan Githae) Date: Mon, 11 Jul 2011 18:23:52 +0200 Subject: [Chimera-users] distance between 2 residues In-Reply-To: <704F70F2-7F78-47AF-AFF0-41FED388C26E@cgl.ucsf.edu> References: <2831401A-7E7B-4978-B733-8419A3176147@rostlab.org> <704F70F2-7F78-47AF-AFF0-41FED388C26E@cgl.ucsf.edu> Message-ID: <914928A5-A6F1-45FD-A961-9775D6F2D851@rostlab.org> Hi Elaine; Thanks, it worked :) Cheers On Jul 8, 2011, at 7:41 PM, Elaine Meng wrote: > Hi Dedan, > There are many different ways to specify two atoms and measure the distance between them. > > The GUI way is to Ctrl-click to select one atom, Shift-Ctrl-doubleclick to both select the second atom and get a popup menu that includes the choice to "Show Distance." There's also a Distances tool and the command "distance." > > Three ways to measure a distance are given here: > > > It is also done in tutorials, for example here: > > > In general, you can use menu "Help... Search Documentation" to find subjects of interest. I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jul 8, 2011, at 6:12 AM, Dedan Githae wrote: > >> how is the problem solved in chimera? i want to measure distance between 2 residues From goddard at sonic.net Mon Jul 11 11:54:51 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 11 Jul 2011 11:54:51 -0700 Subject: [Chimera-users] Tear-off menus in Chimera 1.5.3 for Mac OS X In-Reply-To: <65A4F259-A526-4AB2-93C8-3992C0BD6E71@cgl.ucsf.edu> References: <65A4F259-A526-4AB2-93C8-3992C0BD6E71@cgl.ucsf.edu> Message-ID: <4E1B46FB.10707@sonic.net> Hi Jeff, The Tk window toolkit Chimera uses does not support tear-off menus with Mac native windows. So it is not possible for Chimera to provide them. I submitted a Tk bug report about this Mac Tk limitation in January 2010, and the main Mac Tk developer Daniel Steffens commented: "these are deliberately not supported, they were always a horrible hack in the Carbon port, and do not fit in with the Aqua L&F. "Won't fix" as far as I'm concerned, but if someone else wants to provide an implementation, I won't strongly oppose its inclusion." http://sourceforge.net/tracker/index.php?func=detail&aid=2935311&group_id=12997&atid=112997 There currently is no active Mac Tk developer and another Tk bug triager Kevin Walzer closed this bug report so it is not likely Mac Tk will ever support tearoffs. Tom > Hi Jeff, > Sorry, tear-off menus are not available in the native aqua version of Chimera (regardless of Chimera version number or Mac OS X version number). For Mac, only the X windows version has this feature. > > Because the "Actions... Color" menu was one of the most useful to tear off, to provide a similar behavior in all Chimera versions we have implemented a separate Color Actions dialog (opened by choosing "Actions... Color... all options"). No global solution to allow tearing off menus in the native Mac version has been found, however. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jul 9, 2011, at 3:55 PM, Jeff Lawton wrote: > >> Hi, >> I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and >> it seems that the "tear off" feature of the menus is not available, though I >> was previously able to do that when running the X window version of Chimera. >> Is there a way to use the menu "tear off" feature in the native aqua >> version? >> Thanks! >> Jeff > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Jul 11 12:35:14 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 11 Jul 2011 12:35:14 -0700 Subject: [Chimera-users] Curved helical filaments In-Reply-To: <1310261766.8698.YahooMailClassic@web95609.mail.in.yahoo.com> References: <1310261766.8698.YahooMailClassic@web95609.mail.in.yahoo.com> Message-ID: <4E1B5072.2030502@sonic.net> Hi Andy, The "vop unbend" command can straighten the density from a curved filament. The tricky part is you need a center-line path. You could define that by placing 3 markers. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#unbend Bending a straight filament map to follow a curve is not available. This is the inverse of the vop unbend operation. You can do a fake version of this by making a helical curve around the straight density map and then using vop unbend. That won't center the filament on the helical path, but it will create something similar by straightening the helix which I think will twist the density. Tom > Hi Tom- > > Not sure if there is an option for this - > > 1. can we bend an electron density map of a filament/tube by an small > angle ? > > 2. Can we generate an helix using a density map of a filament. > An example will be that of the bacterial flagella - it has the local > helical arrangement of the flagellin molecule and then thAT > ARRANGEMENT extends over several micrometers like a "sinusoidal wave" > with different helical arrangement to the filament axis. > > Best > Andy > > > Dr. Anindito Sen (Ph.D) > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Jul 11 14:57:03 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 11 Jul 2011 14:57:03 -0700 Subject: [Chimera-users] 3D chimera In-Reply-To: <627417219.5807571310397064159.JavaMail.root@neo-mail-3> References: <627417219.5807571310397064159.JavaMail.root@neo-mail-3> Message-ID: <4E1B71AF.1080509@cgl.ucsf.edu> On 07/11/2011 08:11 AM, Bigley, Andrew wrote: > The recent advances in 3D technology is affording some unique opportunities to people interested. I have recently seen advertisements for new glasses free 3D smart phones. Can you adapt chimera for such a platform and hence convert a smart phone into a portable 3D protein viewer that would allow manipulation of the view through typical touch screen commands? We are interested, but in something more than just a molecular viewer. But that might be a good first step.... From bshaanan at exchange.bgu.ac.il Wed Jul 13 08:19:05 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Wed, 13 Jul 2011 15:19:05 +0000 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il> Hi I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It?s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don?t always contain the full set of displayed coordinates (I?ve done this several times on different structures and it seems particularly but not just on pdb?s with aniso card). I?m attaching the session whose coordinates I saved + the saved coordinates (I hope that?s OK with the BB policy). Please help me figure out the problem. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail:bshaanan at bgu.ac.il Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2ez9_ThDP-MAP_waters.py Type: application/octet-stream Size: 1984441 bytes Desc: 2ez9_ThDP-MAP_waters.py URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2ez9_ThDP-MAP_displayed.pdb Type: application/octet-stream Size: 59413 bytes Desc: 2ez9_ThDP-MAP_displayed.pdb URL: From meng at cgl.ucsf.edu Wed Jul 13 10:37:49 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Jul 2011 10:37:49 -0700 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il> Message-ID: <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> Hi Boaz, I believe the saved PDB file includes all the selected and displayed atoms in their correct locations from your session, but the bonds are messed up. That is a bug and the main problem. selected and displayed in session: 2 models, 52 residues, 377 atoms, 361 bonds contents of PDB file: 2 models 52 residues, 377 atoms, 381 bonds (and some of those bonds are wrong) Also contributing to the confusion is that the default initial display tries to simplify structures to ribbons and does not show all the atoms. To see all the atoms, hide ribbon, display all atoms/bonds (for example, commands: ~ribb; disp ). If I simply remove all the CONECT records from the PDB file, it is fine (file no-conect.pdb is attached). You just need to display all atoms as mentioned above. It is OK to attach files to a chimera-users message as you did, but usually the better way to report problems to the developers is to use "Help... Report a Bug" in the Chimera menu, which will automatically include information about your computer and what version you are using. It also allows attaching data and including your email address if you wish a response. One of will file this problem soon and include you on the notification list. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 13, 2011, at 8:19 AM, Boaz Shaanan wrote: > Hi > I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It?s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don?t always contain the full set of displayed coordinates (I?ve done this several times on different structures and it seems particularly but not just on pdb?s with aniso card). I?m attaching the session whose coordinates I saved + the saved coordinates (I hope that?s OK with the BB policy). Please help me figure out the problem. > Thanks, > Boaz > > <2ez9_ThDP-MAP_waters.py><2ez9_ThDP-MAP_displayed.pdb> -------------- next part -------------- A non-text attachment was scrubbed... Name: no-conect.pdb Type: chemical/x-pdb Size: 51169 bytes Desc: not available URL: -------------- next part -------------- From bshaanan at exchange.bgu.ac.il Wed Jul 13 11:35:08 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Wed, 13 Jul 2011 18:35:08 +0000 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one In-Reply-To: <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il>, <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E93F9F@hawk3.auth.ad.bgu.ac.il> Hi Elaine, Thanks a lot for your prompt reply and suggestions. I'll try them soon and report if I still have problems. I did try to edit the saved-pdb file but edited out the secondary structure (sheet, helix) cards rather than the connect cards. Thanks for pointing this out. As for hiding ribbons and showing all atoms: I think I tried something like that but it didn't bring back all the atoms. I'll try again with the new file. Next time I'll use the 'report but' button. Thanks again, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Wednesday, July 13, 2011 8:37 PM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] saving coordinates from a session and re-opening them in another one Hi Boaz, I believe the saved PDB file includes all the selected and displayed atoms in their correct locations from your session, but the bonds are messed up. That is a bug and the main problem. selected and displayed in session: 2 models, 52 residues, 377 atoms, 361 bonds contents of PDB file: 2 models 52 residues, 377 atoms, 381 bonds (and some of those bonds are wrong) Also contributing to the confusion is that the default initial display tries to simplify structures to ribbons and does not show all the atoms. To see all the atoms, hide ribbon, display all atoms/bonds (for example, commands: ~ribb; disp ). If I simply remove all the CONECT records from the PDB file, it is fine (file no-conect.pdb is attached). You just need to display all atoms as mentioned above. It is OK to attach files to a chimera-users message as you did, but usually the better way to report problems to the developers is to use "Help... Report a Bug" in the Chimera menu, which will automatically include information about your computer and what version you are using. It also allows attaching data and including your email address if you wish a response. One of will file this problem soon and include you on the notification list. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 13, 2011, at 8:19 AM, Boaz Shaanan wrote: > Hi > I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It?s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don?t always contain the full set of displayed coordinates (I?ve done this several times on different structures and it seems particularly but not just on pdb?s with aniso card). I?m attaching the session whose coordinates I saved + the saved coordinates (I hope that?s OK with the BB policy). Please help me figure out the problem. > Thanks, > Boaz > > <2ez9_ThDP-MAP_waters.py><2ez9_ThDP-MAP_displayed.pdb> From efratklig at gmail.com Wed Jul 13 11:43:26 2011 From: efratklig at gmail.com (Efrat Kligun) Date: Wed, 13 Jul 2011 21:43:26 +0300 Subject: [Chimera-users] DMS output format Message-ID: Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Jul 13 12:02:40 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Jul 2011 12:02:40 -0700 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF19E93F9F@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il>, <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> <4B2A491F685D1E4FBBF985E193095AAF19E93F9F@hawk3.auth.ad.bgu.ac.il> Message-ID: <49A86361-2A9C-4E89-92EB-A1B4A1A429C4@cgl.ucsf.edu> Hi Boaz, You're welcome! I'm pretty sure the PDB file you sent had all the atoms: first I used Selection Inspector to see how many atoms were selected in your session, then I opened the PDB file and selected only its contents, same number of atoms. Just wanted to reassure you 8-) Also another thing I forgot to mention is that "displayed" can include things that are not visible because they are off to the side or beyond the front/back clipping planes. After I opened your PDB I moved the clipping planes to show all of its atoms (also could be done with the command "focus"). Best regards and sorry about the confusing display! Elaine On Jul 13, 2011, at 11:35 AM, Boaz Shaanan wrote: > Hi Elaine, > > Thanks a lot for your prompt reply and suggestions. I'll try them soon and report if I still have problems. I did try to edit the saved-pdb file but edited out the secondary structure (sheet, helix) cards rather than the connect cards. Thanks for pointing this out. As for hiding ribbons and showing all atoms: I think I tried something like that but it didn't bring back all the atoms. I'll try again with the new file. Next time I'll use the 'report but' button. > > Thanks again, > > Boaz From conrad at cgl.ucsf.edu Wed Jul 13 12:03:36 2011 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 13 Jul 2011 12:03:36 -0700 Subject: [Chimera-users] DMS output format In-Reply-To: References: Message-ID: <4E1DEC08.7020403@cgl.ucsf.edu> DMS documentation may be found at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html. The (brief) section on the file format says: The output consists of a series of atom and surface point records, with the same format for the first six fields. Each atom is followed by the surface points (if any) which belong to it. These first six fields are in the following format: residue name, sequence number, atom name, x coordinate, y coordinate, z coordinate. For an atom record, the seventh field is "A." For a surface point record, the seventh field begins with an "S," followed by a "C," "R," or "S" according to whether the point is part of contact, reentrant, or saddle surface (saddle is a type of reentrant surface where the probe is in contact with exactly two atoms). This is followed by a digit used for depicting different density levels. The eighth field is the molecular surface area associated with the point in square angstroms. If -n is specified, the next three fields are the unit normal vector pointing outward from the surface. Hope this helps. Conrad On Wed Jul 13 11:43:26 2011, Efrat Kligun wrote: > Hello, > > I am a Phd student at the Technion, I use the program- DMS and I would > like to know what is the numeration of the columns of the first six > fields in the output format of the dms. > > Thanks in advance, > Efrat > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From bshaanan at exchange.bgu.ac.il Wed Jul 13 13:41:32 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Wed, 13 Jul 2011 20:41:32 +0000 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one In-Reply-To: <49A86361-2A9C-4E89-92EB-A1B4A1A429C4@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il>, <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> <4B2A491F685D1E4FBBF985E193095AAF19E93F9F@hawk3.auth.ad.bgu.ac.il>, <49A86361-2A9C-4E89-92EB-A1B4A1A429C4@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E943DA@hawk3.auth.ad.bgu.ac.il> Hi Elaine, Thanks for the extra information and for your help on that issue overall. I'll try all your recommendations first thing tomorrow. Best regards, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Wednesday, July 13, 2011 10:02 PM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] saving coordinates from a session and re-opening them in another one Hi Boaz, You're welcome! I'm pretty sure the PDB file you sent had all the atoms: first I used Selection Inspector to see how many atoms were selected in your session, then I opened the PDB file and selected only its contents, same number of atoms. Just wanted to reassure you 8-) Also another thing I forgot to mention is that "displayed" can include things that are not visible because they are off to the side or beyond the front/back clipping planes. After I opened your PDB I moved the clipping planes to show all of its atoms (also could be done with the command "focus"). Best regards and sorry about the confusing display! Elaine On Jul 13, 2011, at 11:35 AM, Boaz Shaanan wrote: > Hi Elaine, > > Thanks a lot for your prompt reply and suggestions. I'll try them soon and report if I still have problems. I did try to edit the saved-pdb file but edited out the secondary structure (sheet, helix) cards rather than the connect cards. Thanks for pointing this out. As for hiding ribbons and showing all atoms: I think I tried something like that but it didn't bring back all the atoms. I'll try again with the new file. Next time I'll use the 'report but' button. > > Thanks again, > > Boaz From gdfriedland at lbl.gov Wed Jul 13 15:32:34 2011 From: gdfriedland at lbl.gov (Greg Friedland) Date: Wed, 13 Jul 2011 15:32:34 -0700 Subject: [Chimera-users] Listing hydrogen bond geometries Message-ID: <2724DE73-0B31-4C84-8292-F0B20620E43D@lbl.gov> Hello, I would like to list the hydrogen bond geometries between two models. I have found the feature to do this in the FindHBond panel but it only lists the distances not the angles. This information appears to be used in identifying the hydrogen bonds however, so is it possible to extract this information as well? If not, can you suggest another tool that could do this? Thanks, Greg From meng at cgl.ucsf.edu Wed Jul 13 16:51:07 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Jul 2011 16:51:07 -0700 Subject: [Chimera-users] Listing hydrogen bond geometries In-Reply-To: <2724DE73-0B31-4C84-8292-F0B20620E43D@lbl.gov> References: <2724DE73-0B31-4C84-8292-F0B20620E43D@lbl.gov> Message-ID: <6F68C3F6-6D50-4EC2-B0F1-A8E042985A55@cgl.ucsf.edu> Hi Greg, You can measure angles with the angle command or Angles/Torsions (under Tools... Structure Analysis). However, as for automatically extruding the relevant angles for hydrogen bonds... It can become quite hairy because several different angles are examined per possible H-bond depending on the donor and acceptor types, as detailed in the figures and tables of Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22 Maybe you meant only the D-H-A angle if your structure has hydrogens, which would be a more tractable data dump. Is that what you wanted? Let us know, someone may be able to provide the needed python or tips toward writing that code. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 13, 2011, at 3:32 PM, Greg Friedland wrote: > Hello, > I would like to list the hydrogen bond geometries between two models. I have found the feature to do this in the FindHBond panel but it only lists the distances not the angles. This information appears to be used in identifying the hydrogen bonds however, so is it possible to extract this information as well? If not, can you suggest another tool that could do this? > Thanks, > Greg From a.pandurangan at mail.cryst.bbk.ac.uk Thu Jul 14 08:52:23 2011 From: a.pandurangan at mail.cryst.bbk.ac.uk (Arun Prasad Pandurangan) Date: Thu, 14 Jul 2011 16:52:23 +0100 Subject: [Chimera-users] Query regarding Ksdssp assignment Message-ID: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> Dear Users and Developers, I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera? Looking forward for the advices. Thank you. with best regards, Arun Prasad From bshaanan at exchange.bgu.ac.il Thu Jul 14 07:45:46 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Thu, 14 Jul 2011 14:45:46 +0000 Subject: [Chimera-users] saving coordinates from a session and re-opening them in another one In-Reply-To: <49A86361-2A9C-4E89-92EB-A1B4A1A429C4@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF19E91EE7@hawk3.auth.ad.bgu.ac.il>, <0114B5ED-5516-4CCE-A1D9-1DA660016896@cgl.ucsf.edu> <4B2A491F685D1E4FBBF985E193095AAF19E93F9F@hawk3.auth.ad.bgu.ac.il>, <49A86361-2A9C-4E89-92EB-A1B4A1A429C4@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E945B2@hawk3.auth.ad.bgu.ac.il> Hi Elaine, Things worked just the way you described. I'm happy. Thanks a lot for your help. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Wednesday, July 13, 2011 10:02 PM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] saving coordinates from a session and re-opening them in another one Hi Boaz, You're welcome! I'm pretty sure the PDB file you sent had all the atoms: first I used Selection Inspector to see how many atoms were selected in your session, then I opened the PDB file and selected only its contents, same number of atoms. Just wanted to reassure you 8-) Also another thing I forgot to mention is that "displayed" can include things that are not visible because they are off to the side or beyond the front/back clipping planes. After I opened your PDB I moved the clipping planes to show all of its atoms (also could be done with the command "focus"). Best regards and sorry about the confusing display! Elaine On Jul 13, 2011, at 11:35 AM, Boaz Shaanan wrote: > Hi Elaine, > > Thanks a lot for your prompt reply and suggestions. I'll try them soon and report if I still have problems. I did try to edit the saved-pdb file but edited out the secondary structure (sheet, helix) cards rather than the connect cards. Thanks for pointing this out. As for hiding ribbons and showing all atoms: I think I tried something like that but it didn't bring back all the atoms. I'll try again with the new file. Next time I'll use the 'report but' button. > > Thanks again, > > Boaz From efratk at techunix.technion.ac.il Thu Jul 14 11:15:00 2011 From: efratk at techunix.technion.ac.il (efratk at techunix.technion.ac.il) Date: Thu, 14 Jul 2011 21:15:00 +0300 Subject: [Chimera-users] (no subject) Message-ID: <1310667300.4e1f32248db7c@webmail.technion.ac.il> Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat From efratk at techunix.technion.ac.il Thu Jul 14 11:16:11 2011 From: efratk at techunix.technion.ac.il (efratk at techunix.technion.ac.il) Date: Thu, 14 Jul 2011 21:16:11 +0300 Subject: [Chimera-users] (no subject) Message-ID: <1310667371.4e1f326be9c41@webmail.technion.ac.il> Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat From meng at cgl.ucsf.edu Thu Jul 14 12:10:00 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 14 Jul 2011 12:10:00 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <1310667371.4e1f326be9c41@webmail.technion.ac.il> References: <1310667371.4e1f326be9c41@webmail.technion.ac.il> Message-ID: <1C44304B-B424-4AC6-A8C7-84EB5924A4F7@cgl.ucsf.edu> Hello, This was answered yesterday: Please don't send the same question several times -- thanks, Elaine On Jul 14, 2011, at 11:16 AM, efratk at techunix.technion.ac.il wrote: > > Hello, > > I am a Phd student at the Technion, I use the program- DMS and I would like to > know what is the numeration of the columns of the first six fields in the > output format of the dms. > > Thanks in advance, > Efrat From efratk at techunix.technion.ac.il Thu Jul 14 13:21:16 2011 From: efratk at techunix.technion.ac.il (efratk at techunix.technion.ac.il) Date: Thu, 14 Jul 2011 23:21:16 +0300 Subject: [Chimera-users] (no subject) In-Reply-To: <1C44304B-B424-4AC6-A8C7-84EB5924A4F7@cgl.ucsf.edu> References: <1310667371.4e1f326be9c41@webmail.technion.ac.il> <1C44304B-B424-4AC6-A8C7-84EB5924A4F7@cgl.ucsf.edu> Message-ID: <1310674876.4e1f4fbc69388@webmail.technion.ac.il> Hello, There was a problem with my mail server and I wasn't sure the mail was sent OK. Sorry for that. Regarding your answer: What I want to know is in which column number each field (in the DMS output format) starts and in which column number it ends. Thanks in advance, Efrat Quoting Elaine Meng : > Hello, > This was answered yesterday: > > > > Please don't send the same question several times -- thanks, > Elaine > > On Jul 14, 2011, at 11:16 AM, efratk at techunix.technion.ac.il wrote: > > > > > Hello, > > > > I am a Phd student at the Technion, I use the program- DMS and I would like > to > > know what is the numeration of the columns of the first six fields in the > > output format of the dms. > > > > Thanks in advance, > > Efrat > > From meng at cgl.ucsf.edu Thu Jul 14 13:29:47 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 14 Jul 2011 13:29:47 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <1310674876.4e1f4fbc69388@webmail.technion.ac.il> References: <1310667371.4e1f326be9c41@webmail.technion.ac.il> <1C44304B-B424-4AC6-A8C7-84EB5924A4F7@cgl.ucsf.edu> <1310674876.4e1f4fbc69388@webmail.technion.ac.il> Message-ID: <9E1B0D68-7908-4C06-A49E-978BEE35B931@cgl.ucsf.edu> Hi Efrat, Just open the dms file in a text-editor and count the columns. (I'm not a programmer and don't know where in the code to look for the output format statement. Also, counting is not that hard!) Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 14, 2011, at 1:21 PM, efratk at techunix.technion.ac.il wrote: > Hello, > There was a problem with my mail server and I wasn't sure the mail was sent OK. > Sorry for that. > Regarding your answer: What I want to know is in which column number each field > (in the DMS output format) starts and in which column number it ends. > > Thanks in advance, > Efrat > > Quoting Elaine Meng : > >> Hello, >> This was answered yesterday: >> >> >> >> Please don't send the same question several times -- thanks, >> Elaine >> >> On Jul 14, 2011, at 11:16 AM, efratk at techunix.technion.ac.il wrote: >> >>> >>> Hello, >>> >>> I am a Phd student at the Technion, I use the program- DMS and I would like >> to >>> know what is the numeration of the columns of the first six fields in the >>> output format of the dms. >>> >>> Thanks in advance, >>> Efrat >> >> > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Thu Jul 14 13:43:09 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 14 Jul 2011 13:43:09 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <9E1B0D68-7908-4C06-A49E-978BEE35B931@cgl.ucsf.edu> References: <1310667371.4e1f326be9c41@webmail.technion.ac.il> <1C44304B-B424-4AC6-A8C7-84EB5924A4F7@cgl.ucsf.edu> <1310674876.4e1f4fbc69388@webmail.technion.ac.il> <9E1B0D68-7908-4C06-A49E-978BEE35B931@cgl.ucsf.edu> Message-ID: <0FE168AB-FF98-45F7-9990-461401182DB0@cgl.ucsf.edu> Hi Efrat, If you know how to read Python code, the Chimera code that writes DMS files is in /share/WriteDMS/__init__.py (on Mac: Chimera.app/Contents/Resources/share/WriteDMS/__init__.py). The code is relatively short (about a page). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 14, 2011, at 1:29 PM, Elaine Meng wrote: > Hi Efrat, > Just open the dms file in a text-editor and count the columns. (I'm > not a programmer and don't know where in the code to look for the > output format statement. Also, counting is not that hard!) > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jul 14, 2011, at 1:21 PM, efratk at techunix.technion.ac.il wrote: > >> Hello, >> There was a problem with my mail server and I wasn't sure the mail >> was sent OK. >> Sorry for that. >> Regarding your answer: What I want to know is in which column >> number each field >> (in the DMS output format) starts and in which column number it ends. >> >> Thanks in advance, >> Efrat >> >> Quoting Elaine Meng : >> >>> Hello, >>> This was answered yesterday: >>> >>> >> > >>> >>> Please don't send the same question several times -- thanks, >>> Elaine >>> >>> On Jul 14, 2011, at 11:16 AM, efratk at techunix.technion.ac.il wrote: >>> >>>> >>>> Hello, >>>> >>>> I am a Phd student at the Technion, I use the program- DMS and I >>>> would like >>> to >>>> know what is the numeration of the columns of the first six >>>> fields in the >>>> output format of the dms. >>>> >>>> Thanks in advance, >>>> Efrat >>> >>> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 14 15:30:04 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 14 Jul 2011 15:30:04 -0700 Subject: [Chimera-users] Query regarding Ksdssp assignment In-Reply-To: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> References: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> Message-ID: On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote: > Dear Users and Developers, > > I would like to know whether its possible to retrieve the full > secondary > structural assignment using Ksdssp within Chimera. For instance, I > would > like to know all the strands that belong to a beta sheet. If I am > right, > running Ksdssp from Chimera only gives details of the strand (using > isStrand) and helix (using isHelix) assignment and not about sheet > information. Using the full output of an another program DSSP, I am > able > deduce which strands belongs to which sheets. I would like to know > whether similar kind of detailed output is available from Ksdssp as > well. If so how to retrieve those information within Chimera? Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature- request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jul 14 15:40:52 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 14 Jul 2011 15:40:52 -0700 Subject: [Chimera-users] Query regarding Ksdssp assignment In-Reply-To: References: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> Message-ID: <132C4994-61C9-4AFB-8F8D-4FB2DEC81617@cgl.ucsf.edu> Hi Arun, A related possibility is to use the FindHBond tool (or command) in Chimera. Then you would get a "visual" of which strands are tied together with H-bonds into sheets. This H-bond detection tool is completely separate from ksdssp and uses different criteria. The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file. However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets. Criteria: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 14, 2011, at 3:30 PM, Eric Pettersen wrote: > On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote: > >> Dear Users and Developers, >> >> I would like to know whether its possible to retrieve the full secondary >> structural assignment using Ksdssp within Chimera. For instance, I would >> like to know all the strands that belong to a beta sheet. If I am right, >> running Ksdssp from Chimera only gives details of the strand (using >> isStrand) and helix (using isHelix) assignment and not about sheet >> information. Using the full output of an another program DSSP, I am able >> deduce which strands belongs to which sheets. I would like to know >> whether similar kind of detailed output is available from Ksdssp as >> well. If so how to retrieve those information within Chimera? > > Hi Arun, > The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature-request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it. > > --Eric From pett at cgl.ucsf.edu Thu Jul 14 17:34:22 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 14 Jul 2011 17:34:22 -0700 Subject: [Chimera-users] Listing hydrogen bond geometries In-Reply-To: <6F68C3F6-6D50-4EC2-B0F1-A8E042985A55@cgl.ucsf.edu> References: <2724DE73-0B31-4C84-8292-F0B20620E43D@lbl.gov> <6F68C3F6-6D50-4EC2-B0F1-A8E042985A55@cgl.ucsf.edu> Message-ID: Did he reply to you as to whether he just wanted D-H-A angles or the whole tamale? --E On Jul 13, 2011, at 4:51 PM, Elaine Meng wrote: > Hi Greg, > You can measure angles with the angle command or Angles/Torsions > (under Tools... Structure Analysis). > > > > > However, as for automatically extruding the relevant angles for > hydrogen bonds... > It can become quite hairy because several different angles are > examined per possible H-bond depending on the donor and acceptor > types, as detailed in the figures and tables of > > Three-dimensional hydrogen-bond geometry and probability information > from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. > 1996 Dec;10(6):607-22 > > > > > Maybe you meant only the D-H-A angle if your structure has > hydrogens, which would be a more tractable data dump. Is that what > you wanted? Let us know, someone may be able to provide the needed > python or tips toward writing that code. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jul 13, 2011, at 3:32 PM, Greg Friedland wrote: > >> Hello, >> I would like to list the hydrogen bond geometries between two >> models. I have found the feature to do this in the FindHBond panel >> but it only lists the distances not the angles. This information >> appears to be used in identifying the hydrogen bonds however, so is >> it possible to extract this information as well? If not, can you >> suggest another tool that could do this? >> Thanks, >> Greg > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon Jul 18 14:29:03 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 18 Jul 2011 14:29:03 -0700 Subject: [Chimera-users] Listing hydrogen bond geometries In-Reply-To: <78932A75-8E64-426B-B99D-68C9534B74C1@lbl.gov> References: <2724DE73-0B31-4C84-8292-F0B20620E43D@lbl.gov> <6F68C3F6-6D50-4EC2-B0F1-A8E042985A55@cgl.ucsf.edu> <76D4AEAD-3BCE-4965-8E66-01DE689F8950@cgl.ucsf.edu> <78932A75-8E64-426B-B99D-68C9534B74C1@lbl.gov> Message-ID: <118016A3-5540-4C42-A350-63DDF09C4B94@cgl.ucsf.edu> Hi Greg, For FindHBond, Chimera "imagines" the possible locations of hydrogens given the atom types (element, hybridization state) of the heavy atoms. "When there are no explicit hydrogens on a potential donor atom, FindHBond will use the donor atom type to infer their presence. For functional groups where the hydrogen positions are well-determined by the positions of the nonhydrogen atoms, the H-bonds detected in the presence and absence of explicit hydrogen atoms should be virtually identical. For functional groups where the hydrogen position is not well-determined (such as rotatable hydroxyls), the presence of an explicit hydrogen atom will limit the detected H-bonds to those appropriate for the observed position, instead of all of its possible positions." If you want explicit hydrogens, you could use Chimera's AddH tool (under Tools... Structure Editing) or addh command. By default, it will look at the surroundings and try to place hydrogens to make hydrogen bonds. However, it does not exhaustively optimize the H-bonding network of the whole structure. The goal is to determine reasonable positions based on immediate surroundings in a fairly short time. However, if you add explicit hydrogens and then use FindHBond, there will be fewer possibilities listed, as explained above. For the next level of computational intensity in adding hydrogens, we recommend the "Reduce" program from the Richardson lab. From the bottom of the AddH page, "When a more intensive approach is desired, the program Reduce (developed by the Richardson Laboratory) is a good alternative. Reduce places hydrogens to optimize local H-bonding networks and avoid steric overlaps, while flipping certain sidechains 180 degrees as deemed appropriate to fulfill these criteria. Asparagine and glutamine sidechains may be flipped to switch their terminal N and O atoms, and the imidazole ring of histidine may be flipped to switch N and C identities. The protonation state of histidine is adjusted based on the local environment. Reduce is available free at http://kinemage.biochem.duke.edu: ? for on-line use as part of the MolProbity service, on a file uploaded or chosen by PDB code (individual sidechain flips can be accepted or rejected) ? for download (from the Software section) to run on most platforms and is described in: Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Word JM, Lovell SC, Richardson JS, Richardson DC. J Mol Biol. 1999 Jan 29;285(4):1735-47. " I hope this helps, Elaine On Jul 18, 2011, at 2:16 PM, Greg Friedland wrote: > Hi Elain, > Thanks very much for you response and sorry for the delay in getting back to you. > > I am trying to determine the potential hydrogen bonding potential (i.e. the ability to form these bonds) from hydrogen-less structures (they are from the PDB). I have been trying to model in the hydrogens but it is not trivial since there are many hydroxyls, which can rotate about their dihedrals. (if you have suggestions on how to model these hydrogens it'd be great to know about them). > > So until I can get a good model with the hydrogens attached I am wondering how Chimera is able to determine potential hbonds from heavy atom positions only. Any insight you can provide would be appreciated. > > Cheers, > Greg From damien.lariviere at fourmentinguilbert.org Wed Jul 20 03:50:22 2011 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Wed, 20 Jul 2011 12:50:22 +0200 Subject: [Chimera-users] problem with a script calculating distance between residues Message-ID: <4E26B2EE.6070608@fourmentinguilbert.org> Dear all, The script below has been validated for me by the Chimera team sometimes ago. In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb. What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem? Many thanks for your help Damien from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C at CB :297.A at CB") rc("distance :246.C at CB :297.B at CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i) -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: dockSL0009.pdb URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: dockSL0010.pdb URL: From michael.sierk at email.stvincent.edu Wed Jul 20 09:43:52 2011 From: michael.sierk at email.stvincent.edu (Sierk, Michael) Date: Wed, 20 Jul 2011 12:43:52 -0400 Subject: [Chimera-users] Structure -> Match in a script Message-ID: <349EA18F-8C33-4CCE-BBCD-9605B4D22264@email.stvincent.edu> All - I would like to write a command file that will automatically read in two structures and a corresponding alignment file, then perform the superposition (and coloring, etc.). I can read in the pdb and pir files using the command line, and I can do the superposition in the Multalign Viewer using Structure->Match, but I cannot figure out how to do the superposition based on the sequence using the command line. I think if there was a way to select the residues that are aligned in the sequence alignment I could use the "match" command, but I don't see a way to do that. Is there an attribute analogous to mavPercentConserved that corresponds to "aligned"? Or is there an automatically generated region based on the sequence alignment? Thanks, Mike Sierk +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Michael Sierk Email: michael.sierkemailstvincentedu Assistant Professor of Bioinformatics Phone: (724) 805-2367 Saint Vincent College Office: Physics 205 ----------------------------------------------------------------------------------------------------------------------------------------- "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From pett at cgl.ucsf.edu Wed Jul 20 11:29:29 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 20 Jul 2011 11:29:29 -0700 Subject: [Chimera-users] Structure -> Match in a script In-Reply-To: <349EA18F-8C33-4CCE-BBCD-9605B4D22264@email.stvincent.edu> References: <349EA18F-8C33-4CCE-BBCD-9605B4D22264@email.stvincent.edu> Message-ID: <44264C23-9226-44D2-A1F6-C715EF12F386@cgl.ucsf.edu> On Jul 20, 2011, at 9:43 AM, Sierk, Michael wrote: > All - > > I would like to write a command file that will automatically read in > two structures and a corresponding alignment file, then perform the > superposition (and coloring, etc.). I can read in the pdb and pir > files using the command line, and I can do the superposition in the > Multalign Viewer using Structure->Match, but I cannot figure out how > to do the superposition based on the sequence using the command > line. I think if there was a way to select the residues that are > aligned in the sequence alignment I could use the "match" command, > but I don't see a way to do that. Is there an attribute analogous > to mavPercentConserved that corresponds to "aligned"? Or is there > an automatically generated region based on the sequence alignment? There are no command equivalents to Multalign Viewer menu items unfortunately. However, using a Python script you can cheat your way around that by locating the Multalign Viewer Python object and invoking its match method. I've attached a script that will invoke match on the newest Multalign Viewer instance open in Chimera. If you want to employ iteration in the matching, change this line of the script: mav.match(associatedStructures[0], associatedStructures[1:]) to: mav.match(associatedStructures[0], associatedStructures[1:], iterate=True, iterateCutoff=2.0) You can execute the Python script in the middle of your Chimera script by simply using the "open" command to open it, e.g. "open ~/mavMatch.py" --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mavMatch.py Type: text/x-python-script Size: 605 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Jul 20 14:27:14 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 20 Jul 2011 14:27:14 -0700 Subject: [Chimera-users] problem with a script calculating distance between residues In-Reply-To: <4E26B2EE.6070608@fourmentinguilbert.org> References: <4E26B2EE.6070608@fourmentinguilbert.org> Message-ID: <4E274832.3020206@cgl.ucsf.edu> This is the first I've heard of this problem. You could try upgrading Chimera to verison 1.5.3, but I would be surprised if that helped. To learn more about where chimera is hanging, I'd recommend installing the Process Explorer program from http://technet.microsoft.com and the Windows SDK. Process Explorer is like the Task Manager, but lets you see partially inside the process, and the Windows SDK includes a debugger. The chimera binaries do not include debugging symbols, so the debugger is of limited utility, but you never know. Also, if you use Chimera's Help / Report a Bug dialog to submit this bug, it will tell us about your system configuration, and we might spot something you could easily fix. Bonne chance, Greg On 07/20/2011 03:50 AM, Damien Larivi?re wrote: > Dear all, > > The script below has been validated for me by the Chimera team > sometimes ago. > > In fact this script does not work each time I run it: When reaching > the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... > Chimera can remained fixed on the current PDB file as if it faces > problem to open it. I'm forced to close Chimera which does not respond > anymore. The exit code is 805306369. I attached dockSL0009.pdb and > dockSL0010.pdb. > > What can I do to report this bug (which may be due to something > external to Chimera; my Chimera version is 1.5.2 Build 32411; my > plateform is Windows 7 64 bits) since I have to brutally stop Chimera, > and know more about this problem? > > Many thanks for your help > > Damien > > from chimera import runCommand as rc > #from chimera.tkgui import saveReplyLog > for i in range(1, 101): > rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex > run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) > rc("distance :246.C at CB :297.A at CB") > rc("distance :246.C at CB :297.B at CB") > rc("close all") > #rc("saveReplyLog('replyLog%04d.txt')" % i) > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Jul 20 14:32:12 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 20 Jul 2011 14:32:12 -0700 Subject: [Chimera-users] problem with a script calculating distance between residues In-Reply-To: <4E274832.3020206@cgl.ucsf.edu> References: <4E26B2EE.6070608@fourmentinguilbert.org> <4E274832.3020206@cgl.ucsf.edu> Message-ID: I don't have anything great to add, but you should check to make sure it isn't anything obvious. When Chimera hangs like this, is it using a very large amount of memory (use the Task Manager to see how much memory)? Is the disk it's writing to filling up? --Eric On Jul 20, 2011, at 2:27 PM, Greg Couch wrote: > This is the first I've heard of this problem. You could try > upgrading Chimera to verison 1.5.3, but I would be surprised if that > helped. To learn more about where chimera is hanging, I'd recommend > installing the Process Explorer program from http://technet.microsoft.com > and the Windows SDK. Process Explorer is like the Task Manager, > but lets you see partially inside the process, and the Windows SDK > includes a debugger. The chimera binaries do not include debugging > symbols, so the debugger is of limited utility, but you never know. > Also, if you use Chimera's Help / Report a Bug dialog to submit this > bug, it will tell us about your system configuration, and we might > spot something you could easily fix. > > Bonne chance, > > Greg > > On 07/20/2011 03:50 AM, Damien Larivi?re wrote: >> >> Dear all, >> >> The script below has been validated for me by the Chimera team >> sometimes ago. >> >> In fact this script does not work each time I run it: When reaching >> the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... >> Chimera can remained fixed on the current PDB file as if it faces >> problem to open it. I'm forced to close Chimera which does not >> respond anymore. The exit code is 805306369. I attached >> dockSL0009.pdb and dockSL0010.pdb. >> >> What can I do to report this bug (which may be due to something >> external to Chimera; my Chimera version is 1.5.2 Build 32411; my >> plateform is Windows 7 64 bits) since I have to brutally stop >> Chimera, and know more about this problem? >> >> Many thanks for your help >> >> Damien >> >> from chimera import runCommand as rc >> #from chimera.tkgui import saveReplyLog >> for i in range(1, 101): >> rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex >> run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) >> rc("distance :246.C at CB :297.A at CB") >> rc("distance :246.C at CB :297.B at CB") >> rc("close all") >> #rc("saveReplyLog('replyLog%04d.txt')" % i) >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Jul 20 17:19:02 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 20 Jul 2011 17:19:02 -0700 Subject: [Chimera-users] Structure -> Match in a script In-Reply-To: <508ECDAC-317F-49EF-9342-817FE5337D0E@email.stvincent.edu> References: <349EA18F-8C33-4CCE-BBCD-9605B4D22264@email.stvincent.edu> <44264C23-9226-44D2-A1F6-C715EF12F386@cgl.ucsf.edu> <508ECDAC-317F-49EF-9342-817FE5337D0E@email.stvincent.edu> Message-ID: <96A7056B-539B-4819-B1B5-A72E188A81B2@cgl.ucsf.edu> On Jul 20, 2011, at 2:09 PM, Sierk, Michael wrote: > Eric, > > Thanks for the script! It works but I have a couple of issues still: > > 1) The second sequence in the alignment is not automatically being > associated with the second structure. (It looks like the first > sequence/structure association is done automatically, but not the > second.) I can do it manually with Structure->Associations (with > zero mismatches), and then the script works. Is there a way to > create the second association via either the Chimera command line or > using python? Is that association supposed to occur automatically > as well? AFAIK the second sequence should associate. If you send me the alignment and the structures (or tell me their PDB codes if they're standard PDB entries) I can investigate (send them off-list!). > 2) What I am trying to do is load in two molecules and 3 different > sequence alignments of the two molecules. In my Chimera script I > make 2 copies of the 2nd molecule (using "combine") and color them > differently. I would like to then do the Structure->Match process > for each of the 3 alignments. Does the "findMAV" function in the > mavMatch.py script return all instances of MAVs or just one? I know > the titles so could I perform 3 different mav.match statements, one > for each MAV instance? Well, this is a more complicated scenario than what the script I wrote really handles -- since you have multiple MAV instances and only want certain open structures to associate with each instance despite the fact that those structures are identical. So it needs two scripts! Here's the approach: In your Chimera script: 1) Open the three alignments. 2) Open the first Python script (no-auto-assoc.py) to turn off auto- association in the MAV instances. 3) Open your two structures, "reference" structure first (more specifically, in a lower model number than the matching structures) 4) Make the two copies, or just open the second structure two more times. 5) Run the second Python script (assoc-and-match.py) to associate the reference structure with the first sequence in all the alignments, and one copy of the matching structure with the second sequence in each alignment, and then match them. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: no-auto-assoc.py Type: text/x-python-script Size: 453 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: assoc-and-match.py Type: text/x-python-script Size: 778 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From veli-pekka.kestila at helsinki.fi Fri Jul 22 01:45:38 2011 From: veli-pekka.kestila at helsinki.fi (=?ISO-8859-1?Q?Veli-Pekka_Kestil=E4?=) Date: Fri, 22 Jul 2011 11:45:38 +0300 Subject: [Chimera-users] Chimera 1.5.3, nvidia quadro 4000 and stereo Message-ID: <4E2938B2.1040009@helsinki.fi> Hello, I found following problem when trying to use Chimera 1.5.3 with stereo in Nvidia Quadro 4000. When starting the chimera in windows I will get error: Error Initializing OpenGL: Couldn't configure togl widget When stating in OpenGL debug mode it starts without any problem. Nvidia driver is 275.65 and everything works in linux without problem. In Manage 3D settings I have put on Stereo Enable. Greetings, Veli-Pekka Kestil? -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila at helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3 From sabujp at gmail.com Fri Jul 22 05:15:03 2011 From: sabujp at gmail.com (Sabuj Pattanayek) Date: Fri, 22 Jul 2011 07:15:03 -0500 Subject: [Chimera-users] Chimera 1.5.3, nvidia quadro 4000 and stereo In-Reply-To: <4E2938B2.1040009@helsinki.fi> References: <4E2938B2.1040009@helsinki.fi> Message-ID: I've seen the same issue with generic active stereo or 3d vision + stereo enabled in the 3d section of the nvidia control panel + 64 bit chimera. For some reason 32 bit chimera seemed to work ok. 2011/7/22 Veli-Pekka Kestil? : > > Hello, > > I found following problem when trying to use Chimera 1.5.3 with stereo > in Nvidia Quadro 4000. When starting the chimera in windows I will get > error: > > Error Initializing OpenGL: Couldn't configure togl widget > > When stating in OpenGL debug mode it starts without any problem. > Nvidia driver is 275.65 and everything works in linux without problem. > > In Manage 3D settings I have put on Stereo Enable. > > Greetings, > Veli-Pekka Kestil? > > -- > University of Helsinki / Institute of Biotechnology / > veli-pekka.kestila at helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From v.james at cryst.bbk.ac.uk Thu Jul 21 04:44:02 2011 From: v.james at cryst.bbk.ac.uk (Victoria James) Date: Thu, 21 Jul 2011 12:44:02 +0100 Subject: [Chimera-users] Chimera for Mac OSX Lion Message-ID: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> Hi there! I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? If not, will you be releasing another build soon that will be able to? Many thanks and kind regards Victoria From goddard at sonic.net Fri Jul 22 10:48:37 2011 From: goddard at sonic.net (Tom Goddard) Date: Fri, 22 Jul 2011 10:48:37 -0700 Subject: [Chimera-users] Chimera for Mac OSX Lion In-Reply-To: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> References: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> Message-ID: <4E29B7F5.1090409@sonic.net> We have not tested Chimera on Mac OS Lion (10.7) yet, but should have results by early next week. If anyone has already tried it, please post if it is working. Tom > Hi there! > > I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? > If not, will you be releasing another build soon that will be able to? > > Many thanks and kind regards > > Victoria > From klexa at umich.edu Fri Jul 22 11:06:26 2011 From: klexa at umich.edu (Katrina Lexa) Date: Fri, 22 Jul 2011 14:06:26 -0400 Subject: [Chimera-users] Chimera for Mac OSX Lion In-Reply-To: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> References: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> Message-ID: <56940504-A458-4B8A-8F14-FC04A6301C57@umich.edu> I've been using it all day on Lion without any trouble. If you use Mapman or Moe though - those don't work with Lion FYI On Jul 21, 2011, at 7:44 AM, Victoria James wrote: > Hi there! > > I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? > If not, will you be releasing another build soon that will be able to? > > Many thanks and kind regards > > Victoria > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From crisrod at chem.ubc.ca Fri Jul 22 10:53:41 2011 From: crisrod at chem.ubc.ca (=?iso-8859-1?Q?Cristina_Rodr=EDguez?=) Date: Fri, 22 Jul 2011 10:53:41 -0700 Subject: [Chimera-users] Chimera for Mac OSX Lion In-Reply-To: <4E29B7F5.1090409@sonic.net> References: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> <4E29B7F5.1090409@sonic.net> Message-ID: Hi there!!!!!!!! I have tested Chimera on Mac OS Lion and it is working - So far so good!!!!! Cheers, Cristina ------------ Dr. Cristina Rodr?guez-Rodr?guez Department of Chemistry University of British Columbia Lab D419 - 2036 Main Mall Vancouver, BC Canada V6T 2A3 Email: crisrod at chem.ubc.ca On 22/07/2011, at 10:48, Tom Goddard wrote: > We have not tested Chimera on Mac OS Lion (10.7) yet, but should have > results by early next week. If anyone has already tried it, please post > if it is working. > > Tom > >> Hi there! >> >> I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? >> If not, will you be releasing another build soon that will be able to? >> >> Many thanks and kind regards >> >> Victoria >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From bshaanan at exchange.bgu.ac.il Fri Jul 22 15:15:48 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Fri, 22 Jul 2011 22:15:48 +0000 Subject: [Chimera-users] castp .poc file is not opened for restored session? Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E9E992@hawk3.auth.ad.bgu.ac.il> An HTML attachment was scrubbed... URL: From bshaanan at exchange.bgu.ac.il Fri Jul 22 15:26:53 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Fri, 22 Jul 2011 22:26:53 +0000 Subject: [Chimera-users] castp .poc file is not opened in restored session (plain text version) Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il> Hi, I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be? Cheers, Boaz P.S. sent again in plain text format since it seems the previous html version has been mangled up Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From pett at cgl.ucsf.edu Fri Jul 22 15:58:09 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 22 Jul 2011 15:58:09 -0700 Subject: [Chimera-users] castp .poc file is not opened in restored session (plain text version) In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il> Message-ID: On Jul 22, 2011, at 3:26 PM, Boaz Shaanan wrote: > Hi, > > I save a session in which I used castp .poc file (very nice > indeed!). However, after saving the session, the restored session > does not open the .poc file. Is that how it's supposed to be? Hi Boaz, CASTp session support has been added relatively recently, and therefore is only available in the 1.6 daily build -- not in the 1.5.3 release. Now, if the 1.6 version doesn't restore the .poc file, please let me know! :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From raj_sss at yahoo.com Fri Jul 22 16:58:10 2011 From: raj_sss at yahoo.com (S. Shunmugasundararaj) Date: Fri, 22 Jul 2011 16:58:10 -0700 (PDT) Subject: [Chimera-users] Chimera for Mac OSX Lion In-Reply-To: <4E29B7F5.1090409@sonic.net> References: <32025726-4704-4A89-A8B1-7A1009BD2B81@cryst.bbk.ac.uk> <4E29B7F5.1090409@sonic.net> Message-ID: <1311379090.58864.YahooMailNeo@web33805.mail.mud.yahoo.com> It is working. ________________________________ From: Tom Goddard To: Victoria James Cc: chimera-users at cgl.ucsf.edu Sent: Friday, July 22, 2011 1:48 PM Subject: Re: [Chimera-users] Chimera for Mac OSX Lion We have not tested Chimera on Mac OS Lion (10.7) yet, but should have results by early next week.? If anyone has already tried it, please post if it is working. ? ? Tom > Hi there! > > I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? > If not, will you be releasing another build soon that will be able to? > > Many thanks and kind regards > > Victoria > _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Fri Jul 22 22:30:07 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Sat, 23 Jul 2011 07:30:07 +0200 Subject: [Chimera-users] gtx-470 GeForce cards Message-ID: With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems in running movie with "define centroid". In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T (six cores)/ Debian amd64 wheezy, on running movie to get the trace of the centroid, the X server hangs and the keyboard is no more sensed. I have to restart the computer from a ssh-linked desktop. In both cases chimera 1.5.3. Chimera was started as the only application, just after booting the OS (I am saying that because, to run molecular dynamics, I have first to command # nvidia-smi -L # nvidia-smi -pm 1 Any experience to this regard? thanks francesco pietra From a.pandurangan at mail.cryst.bbk.ac.uk Sun Jul 24 04:56:40 2011 From: a.pandurangan at mail.cryst.bbk.ac.uk (Arun Prasad Pandurangan) Date: Sun, 24 Jul 2011 12:56:40 +0100 Subject: [Chimera-users] Query regarding Ksdssp assignment In-Reply-To: References: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> Message-ID: <4E2C0878.7080705@mail.cryst.bbk.ac.uk> Dear Eric and Elaine, Thank you for adding the new implementation of ksdssp into the recent daily build. The new -v switch works fine and I am able to read the details of the secondary structural assignments from the reply log. For each residue, the reply log gives details about the helix and strand (ladder) assignment but not about the sheet information (i.e. to know which group of strands make up a sheet). I would like to know whether its possible to add a sheet label along with the strand assignment letter 'E' for each strand residues so that it will aid the identification of all the strands that belong to a sheet? Or to make things simple is it possible to add a sheet summary along with the helix and ladder summary in the reply log? That would be very helpful in annotating seconday structural assignments. I thank Elaine, for your alternative suggestions using FindHBond tool. Thank you. with kind regards, Arun Prasad Eric Pettersen wrote: > On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote: > >> Dear Users and Developers, >> >> I would like to know whether its possible to retrieve the full secondary >> structural assignment using Ksdssp within Chimera. For instance, I would >> like to know all the strands that belong to a beta sheet. If I am right, >> running Ksdssp from Chimera only gives details of the strand (using >> isStrand) and helix (using isHelix) assignment and not about sheet >> information. Using the full output of an another program DSSP, I am able >> deduce which strands belongs to which sheets. I would like to know >> whether similar kind of detailed output is available from Ksdssp as >> well. If so how to retrieve those information within Chimera? > > Hi Arun, > The short answer is no. The C++ function that does the computation > does have the ability to output the same kind of summary information > that the KSDSSP program itself outputs, but due to some shortcomings > in Chimera's Python/C++ API interface when the function was written > there is currently no way to communicate that information up to the > Python layer for display. However, between when the function was > written and now we have improved that API interface and with some work > it would now be possible to pass the information up and show it. That > doesn't really help you a lot right now, but I will open a > feature-request ticket in Chimera's Trac database with you on the > recipient list so that you will be notified when we've had time to > implement it. It may take awhile before we get to it. > > --Eric > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > Hi Arun, > A related possibility is to use the FindHBond tool (or command) in Chimera. Then you would get a "visual" of which strands are tied together with H-bonds into sheets. This H-bond detection tool is completely separate from ksdssp and uses different criteria. The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file. However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets. > > > > > Criteria: > > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco From bshaanan at exchange.bgu.ac.il Sun Jul 24 15:54:29 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sun, 24 Jul 2011 22:54:29 +0000 Subject: [Chimera-users] castp .poc file is not opened in restored session (plain text version) In-Reply-To: References: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il>, Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19EA13B5@hawk3.auth.ad.bgu.ac.il> An HTML attachment was scrubbed... URL: From mucugianganga at gmail.com Sun Jul 24 05:03:20 2011 From: mucugianganga at gmail.com (ALEXANDER MUCHUGIA) Date: Sun, 24 Jul 2011 14:03:20 +0200 Subject: [Chimera-users] creating multimeric units Message-ID: Hi, My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease. It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it. Regards. Alexander. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jul 25 09:48:06 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Jul 2011 09:48:06 -0700 Subject: [Chimera-users] creating multimeric units In-Reply-To: References: Message-ID: <6B14C3BE-D8DF-4C07-AA02-8D28C1AC82DC@cgl.ucsf.edu> Hi Alexander, It depends on the information in the PDB file: there may be various matrices in the header that describe how to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX). If information of one of those types is present and describes the dimer, you can make the dimer in Chimera with Multiscale Models or Unit Cell (both are under Tools... Higher-Order Structure) or the command "sym" If the structure is in the PDB but symmetry information is not included in the file, you could try using Chimera's File... Fetch by ID, PQS option (predicted quaternary structure database) or getting the biological unit directly from the PDB website. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 24, 2011, at 5:03 AM, ALEXANDER MUCHUGIA wrote: > Hi, > My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease. > It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it. > > Regards. > > Alexander. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From gdfriedland at lbl.gov Mon Jul 25 12:59:15 2011 From: gdfriedland at lbl.gov (Greg Friedland) Date: Mon, 25 Jul 2011 12:59:15 -0700 Subject: [Chimera-users] Display of bond between CA's Message-ID: <48D5A26B-B249-4104-B78B-14949A19DD2E@lbl.gov> Hi, I'm trying to prepare an image from a structure in which I'd like to hide the backbone atoms except the CAs. When I do this for two neighboring residues however a long bond is drawn between the CAs. How can I hide this without hiding the CAs? Thanks, Greg From pett at cgl.ucsf.edu Mon Jul 25 14:03:45 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 25 Jul 2011 14:03:45 -0700 Subject: [Chimera-users] Display of bond between CA's In-Reply-To: <48D5A26B-B249-4104-B78B-14949A19DD2E@lbl.gov> References: <48D5A26B-B249-4104-B78B-14949A19DD2E@lbl.gov> Message-ID: <591F0659-ECDB-4B81-8B5D-9D37A7583F0B@cgl.ucsf.edu> On Jul 25, 2011, at 12:59 PM, Greg Friedland wrote: > Hi, > I'm trying to prepare an image from a structure in which I'd like to > hide the backbone atoms except the CAs. When I do this for two > neighboring residues however a long bond is drawn between the CAs. > How can I hide this without hiding the CAs? Hi Greg, In the model panel (Favorites->Model Panel) double-click on the model to bring up its attribute inspector, then change "auto-chaining" to "off". Alternatively, you can use the command line (Favorites- >Command Line) and type "setattr m autochain 0". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Jul 25 16:57:44 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 25 Jul 2011 16:57:44 -0700 Subject: [Chimera-users] Query regarding Ksdssp assignment In-Reply-To: <4E2C0878.7080705@mail.cryst.bbk.ac.uk> References: <4E1F10B7.4080208@mail.cryst.bbk.ac.uk> <4E2C0878.7080705@mail.cryst.bbk.ac.uk> Message-ID: <9FE53250-921A-499B-9C89-5B4EB50F2061@cgl.ucsf.edu> Hi Arun, What Chimera returns is pretty much a straight transcription of what its predecessor, Midas, used to return. I agree it would be nice if it returned a succinct representation of the sheets but unfortunately it does not. I will add that to my to-do list but no guarantees as to when I'll be able to get to it. In the interim you can at least use the "Ladder Summary" to deduce the sheets, e.g. in entry 1WWW, chain V, the summary is: Ladder Summary 17.V -> 22.V antiparallel 53.V -> 58.V 27.V -> 29.V antiparallel 35.V -> 37.V 41.V -> 43.V antiparallel 48.V -> 50.V 76.V -> 92.V antiparallel 97.V -> 114.V Since none of the residue ranges overlap, you have four 2-strand sheets. Whereas for chain X: Ladder Summary 287.X -> 290.X antiparallel 303.X -> 306.X 299.X -> 305.X antiparallel 342.X -> 348.X 312.X -> 317.X antiparallel 359.X -> 364.X 328.X -> 332.X antiparallel 344.X -> 348.X 357.X -> 365.X antiparallel 368.X -> 376.X numbers 1, 2, and 4 overlap, and 3 and 5 overlap. Therefore you have a 4-strand sheet and a 3-strand sheet. --Eric On Jul 24, 2011, at 4:56 AM, Arun Prasad Pandurangan wrote: > Dear Eric and Elaine, > > Thank you for adding the new implementation of ksdssp into the > recent daily build. The new -v switch works fine and I am able to > read the details of the secondary structural assignments from the > reply log. For each residue, the reply log gives details about the > helix and strand (ladder) assignment but not about the sheet > information (i.e. to know which group of strands make up a sheet). I > would like to know whether its possible to add a sheet label along > with the strand assignment letter 'E' for each strand residues so > that it will aid the identification of all the strands that belong > to a sheet? Or to make things simple is it possible to add a sheet > summary along with the helix and ladder summary in the reply log? > That would be very helpful in annotating seconday structural > assignments. > > I thank Elaine, for your alternative suggestions using FindHBond tool. > > Thank you. > > with kind regards, > Arun Prasad > > Eric Pettersen wrote: >> On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote: >> >>> Dear Users and Developers, >>> >>> I would like to know whether its possible to retrieve the full >>> secondary >>> structural assignment using Ksdssp within Chimera. For instance, I >>> would >>> like to know all the strands that belong to a beta sheet. If I am >>> right, >>> running Ksdssp from Chimera only gives details of the strand (using >>> isStrand) and helix (using isHelix) assignment and not about sheet >>> information. Using the full output of an another program DSSP, I >>> am able >>> deduce which strands belongs to which sheets. I would like to know >>> whether similar kind of detailed output is available from Ksdssp as >>> well. If so how to retrieve those information within Chimera? >> >> Hi Arun, >> The short answer is no. The C++ function that does the computation >> does have the ability to output the same kind of summary >> information that the KSDSSP program itself outputs, but due to some >> shortcomings in Chimera's Python/C++ API interface when the >> function was written there is currently no way to communicate that >> information up to the Python layer for display. However, between >> when the function was written and now we have improved that API >> interface and with some work it would now be possible to pass the >> information up and show it. That doesn't really help you a lot >> right now, but I will open a feature-request ticket in Chimera's >> Trac database with you on the recipient list so that you will be >> notified when we've had time to implement it. It may take awhile >> before we get to it. >> >> --Eric >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >> >> Hi Arun, >> A related possibility is to use the FindHBond tool (or command) in >> Chimera. Then you would get a "visual" of which strands are tied >> together with H-bonds into sheets. This H-bond detection tool is >> completely separate from ksdssp and uses different criteria. The >> resulting H-bond info (donor and acceptor atoms, distances) can be >> written to a file. However, it would take a fair amount of >> postprocessing effort to combine this with the strand assignments >> to identify the sheets. >> >> > > >> >> >> Criteria: >> > > >> >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. UCSF Computer Graphics >> Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco > From pett at cgl.ucsf.edu Mon Jul 25 18:23:31 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 25 Jul 2011 18:23:31 -0700 Subject: [Chimera-users] castp .poc file is not opened in restored session (plain text version) In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF19EA13B5@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il>, <4B2A491F685D1E4FBBF985E193095AAF19EA13B5@hawk3.auth.ad.bgu.ac.il> Message-ID: <406817A2-985F-4B99-BFEA-9010B8E49B08@cgl.ucsf.edu> On Jul 24, 2011, at 3:54 PM, Boaz Shaanan wrote: > Hi Eric, > > Indeed with the daily built of 1.6 the castp file opens up too when > restoring the session. However, I noted a strange feature in that a > hole from castp is split between two monomers. I used the bug report > mechanism to report this and attached the session file (bug #9775). > I'd appreciate your input on the issue. Hi Boaz, The most reliable way to match the pocket atoms listed in the .poc file to the PDB is by serial number (due to the vagaries of how CASTp formats the .poc file). Your input PDB (and therefore output PDB) has duplicate serial numbers for corresponding atoms in the two chains. If you open your input PDB in Chimera and write out a new PDB, the new one will have unique serial numbers. You can use that with the CASTp server and get results that Chimera can handle. Sorry for the hassle. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From veli-pekka.kestila at helsinki.fi Tue Jul 26 00:59:41 2011 From: veli-pekka.kestila at helsinki.fi (=?ISO-8859-1?Q?Veli-Pekka_Kestil=E4?=) Date: Tue, 26 Jul 2011 10:59:41 +0300 Subject: [Chimera-users] Chimera 1.5.3, nvidia quadro 4000 and stereo In-Reply-To: References: <4E2938B2.1040009@helsinki.fi> Message-ID: <4E2E73ED.3040204@helsinki.fi> On 7/22/11 3:15 PM, Sabuj Pattanayek wrote: > I've seen the same issue with generic active stereo or 3d vision + > stereo enabled in the 3d section of the nvidia control panel + 64 bit > chimera. For some reason 32 bit chimera seemed to work ok. Either using the 32bit version or latest alpha build solved the error. Still stereo doesn't work and just shows double picture, so there is still not working stereo. > 2011/7/22 Veli-Pekka Kestil?: >> >> Hello, >> >> I found following problem when trying to use Chimera 1.5.3 with stereo >> in Nvidia Quadro 4000. When starting the chimera in windows I will get >> error: >> >> Error Initializing OpenGL: Couldn't configure togl widget >> >> When stating in OpenGL debug mode it starts without any problem. >> Nvidia driver is 275.65 and everything works in linux without problem. >> >> In Manage 3D settings I have put on Stereo Enable. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila at helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3 From bshaanan at exchange.bgu.ac.il Tue Jul 26 02:31:18 2011 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Tue, 26 Jul 2011 09:31:18 +0000 Subject: [Chimera-users] castp .poc file is not opened in restored session (plain text version) In-Reply-To: <406817A2-985F-4B99-BFEA-9010B8E49B08@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF19E9E9A1@hawk3.auth.ad.bgu.ac.il>, <4B2A491F685D1E4FBBF985E193095AAF19EA13B5@hawk3.auth.ad.bgu.ac.il>, <406817A2-985F-4B99-BFEA-9010B8E49B08@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF19EA22CD@hawk3.auth.ad.bgu.ac.il> Hi Eric, OK, thanks for letting me know. I read on the castp site that they can't cope with multiple models (a-la NMR) in the pdb so thought that I managed to circumvent the problem by giving different chain ID's to the two chains that I extracted from the pdb1 files and by deleting the model cards. I didn't realize that there is program that looks into the atom serial numbers in the pdb (none of the crystallographic programs that I use does). I'll fix the problem and submit again to the castp site. Thanks a lot for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: Eric Pettersen [pett at cgl.ucsf.edu] Sent: Tuesday, July 26, 2011 4:23 AM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] castp .poc file is not opened in restored session (plain text version) On Jul 24, 2011, at 3:54 PM, Boaz Shaanan wrote: Hi Eric, Indeed with the daily built of 1.6 the castp file opens up too when restoring the session. However, I noted a strange feature in that a hole from castp is split between two monomers. I used the bug report mechanism to report this and attached the session file (bug #9775). I'd appreciate your input on the issue. Hi Boaz, The most reliable way to match the pocket atoms listed in the .poc file to the PDB is by serial number (due to the vagaries of how CASTp formats the .poc file). Your input PDB (and therefore output PDB) has duplicate serial numbers for corresponding atoms in the two chains. If you open your input PDB in Chimera and write out a new PDB, the new one will have unique serial numbers. You can use that with the CASTp server and get results that Chimera can handle. Sorry for the hassle. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu From gregc at cgl.ucsf.edu Tue Jul 26 11:33:49 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 26 Jul 2011 11:33:49 -0700 Subject: [Chimera-users] gtx-470 GeForce cards In-Reply-To: References: Message-ID: <4E2F088D.4020505@cgl.ucsf.edu> Seems like no one has much experience with this. My only suggestion would be to make sure you are using the latest driver available from nvidia.com. I don't know how closely the Debian package repository tracks the NVIDIA drivers, but the Debian-based Ubuntu ones are not updated very frequently. The downside to using NVIDIA's installer is that you will need to reinstall the NVIDIA driver every time you update the Linux kernel. Good luck, Greg On 07/22/2011 10:30 PM, Francesco Pietra wrote: > With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems > in running movie with "define centroid". > > In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T > (six cores)/ Debian amd64 wheezy, on running movie to get the trace > of the centroid, the X server hangs and the keyboard is no more > sensed. I have to restart the computer from a ssh-linked desktop. > > In both cases chimera 1.5.3. Chimera was started as the only > application, just after booting the OS (I am saying that because, to > run molecular dynamics, I have first to command > > # nvidia-smi -L > > # nvidia-smi -pm 1 > > Any experience to this regard? > > thanks > francesco pietra From gregc at cgl.ucsf.edu Tue Jul 26 13:34:02 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 26 Jul 2011 13:34:02 -0700 Subject: [Chimera-users] Chimera 1.5.3, nvidia quadro 4000 and stereo In-Reply-To: <4E2E73ED.3040204@helsinki.fi> References: <4E2938B2.1040009@helsinki.fi> <4E2E73ED.3040204@helsinki.fi> Message-ID: <4E2F24BA.9090801@cgl.ucsf.edu> The error "Error Initializing OpenGL: Couldn't configure togl widget" is because the graphics driver reported that it did not support stereo. So either this is a graphics driver bug or a driver configuration bug. The fact that it doesn't get the error with the 32-bit version of chimera suggests that it is a graphics driver bug and you should report the bug to NVIDIA. On the other hand, the fact that you are getting a double image and stereo still isn't working suggests that the graphics driver is misconfigured. Double-check that the "Stereo - Display mode" setting is correct for your setup. Good luck, Greg On 07/26/2011 12:59 AM, Veli-Pekka Kestil? wrote: > On 7/22/11 3:15 PM, Sabuj Pattanayek wrote: >> I've seen the same issue with generic active stereo or 3d vision + >> stereo enabled in the 3d section of the nvidia control panel + 64 bit >> chimera. For some reason 32 bit chimera seemed to work ok. > Either using the 32bit version or latest alpha build solved the error. > Still stereo doesn't work and just shows double picture, so there is > still not working stereo. > > >> 2011/7/22 Veli-Pekka Kestil?: >>> Hello, >>> >>> I found following problem when trying to use Chimera 1.5.3 with stereo >>> in Nvidia Quadro 4000. When starting the chimera in windows I will get >>> error: >>> >>> Error Initializing OpenGL: Couldn't configure togl widget >>> >>> When stating in OpenGL debug mode it starts without any problem. >>> Nvidia driver is 275.65 and everything works in linux without problem. >>> >>> In Manage 3D settings I have put on Stereo Enable. From veli-pekka.kestila at helsinki.fi Tue Jul 26 23:57:38 2011 From: veli-pekka.kestila at helsinki.fi (=?ISO-8859-1?Q?Veli-Pekka_Kestil=E4?=) Date: Wed, 27 Jul 2011 09:57:38 +0300 Subject: [Chimera-users] Chimera 1.5.3, nvidia quadro 4000 and stereo In-Reply-To: <4E2F24BA.9090801@cgl.ucsf.edu> References: <4E2938B2.1040009@helsinki.fi> <4E2E73ED.3040204@helsinki.fi> <4E2F24BA.9090801@cgl.ucsf.edu> Message-ID: <4E2FB6E2.3040600@helsinki.fi> Thanks for the reply. I finally got it working. Seems that the problem was in monitor settings. Only thing not working is Chimera 1.5.3 (32bit and 64bit) when I start it normally. 2011-07-23 alpha works without problem. And also the current version works when started in OpenGL Debug mode. For posterity the thing which was configured wrong was in Nvidia Control Panel -> Display -> Change Resolution Here in resolution field were "HD, SD" and "PC" selection. When I changed to PC selection things started to work. (The previous set the refresh rate wrong) Greetings, Veli-Pekka On 7/26/11 11:34 PM, Greg Couch wrote: > The error "Error Initializing OpenGL: Couldn't configure togl widget" is > because the graphics driver reported that it did not support stereo. So > either this is a graphics driver bug or a driver configuration bug. The > fact that it doesn't get the error with the 32-bit version of chimera > suggests that it is a graphics driver bug and you should report the bug > to NVIDIA. On the other hand, the fact that you are getting a double > image and stereo still isn't working suggests that the graphics driver > is misconfigured. Double-check that the "Stereo - Display mode" setting > is correct for your setup. > > Good luck, > > Greg > > On 07/26/2011 12:59 AM, Veli-Pekka Kestil? wrote: >> On 7/22/11 3:15 PM, Sabuj Pattanayek wrote: >>> I've seen the same issue with generic active stereo or 3d vision + >>> stereo enabled in the 3d section of the nvidia control panel + 64 bit >>> chimera. For some reason 32 bit chimera seemed to work ok. >> Either using the 32bit version or latest alpha build solved the error. >> Still stereo doesn't work and just shows double picture, so there is >> still not working stereo. >> >> >>> 2011/7/22 Veli-Pekka Kestil?: >>>> Hello, >>>> >>>> I found following problem when trying to use Chimera 1.5.3 with stereo >>>> in Nvidia Quadro 4000. When starting the chimera in windows I will get >>>> error: >>>> >>>> Error Initializing OpenGL: Couldn't configure togl widget >>>> >>>> When stating in OpenGL debug mode it starts without any problem. >>>> Nvidia driver is 275.65 and everything works in linux without problem. >>>> >>>> In Manage 3D settings I have put on Stereo Enable. > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila at helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3 From biocjh at gmail.com Thu Jul 28 02:05:55 2011 From: biocjh at gmail.com (C.J.) Date: Thu, 28 Jul 2011 17:05:55 +0800 Subject: [Chimera-users] hide a peptide in Chimera Message-ID: Hi,all, I have a pdb file containing several peptides. And I want to hide some of them when visualizing the file in Chimera. Anyone would like to help me to that? I'm appreciated of any suggestions. -- Regards! C.J. From meng at cgl.ucsf.edu Thu Jul 28 08:36:53 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Jul 2011 08:36:53 -0700 Subject: [Chimera-users] hide a peptide in Chimera In-Reply-To: References: Message-ID: Hi C.J., There are many ways to hide specific atoms. For example, (A) use menu "Actions... Atoms/Bonds... hide" after selecting the atoms you want to hide. There are several ways to select atoms, for example (i) Ctrl-click on an atom or bond in the peptide, then up arrow key to expand to whole residue, then whole chain. The selection is shown with green highlighting. (ii) use the "Select" menu, perhaps a particular chain ... or ... (B) use command "~display" with specification of the atoms you want to hide. For example, to hide chain A: ~disp :.a Here is info on command-line atom specification: You may want to take a look at the "getting started" tutorials: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 28, 2011, at 2:05 AM, C.J. wrote: > Hi,all, > I have a pdb file containing several peptides. And I want to hide some > of them when visualizing the file in Chimera. > Anyone would like to help me to that? > I'm appreciated of any suggestions. > -- > Regards! > C.J. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From maciek at wojcikowski.pl Thu Jul 28 03:35:18 2011 From: maciek at wojcikowski.pl (=?ISO-8859-1?Q?Maciek_W=F3jcikowski?=) Date: Thu, 28 Jul 2011 12:35:18 +0200 Subject: [Chimera-users] Hbond in CLI + cacheDA Message-ID: Hello everyone, I'm trying to compute hbonds for quite large molecular database, so i do it in CLI. I've added cacheDA parameter which speeds up whole process at first by 10 times, although after time cache is getting bigger and bigger operations slows down as one can expect, because Chimera is caching every compound. Is there a way to limit the size of a cache, or even better to tell chimera to cache only protein donors and acceptors? ---- Pozdrawiam, | Best regards, Maciek W?jcikowski maciek at wojcikowski.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 28 11:06:07 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Jul 2011 11:06:07 -0700 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: References: Message-ID: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> On Jul 28, 2011, at 3:35 AM, Maciek W?jcikowski wrote: > Hello everyone, > > I'm trying to compute hbonds for quite large molecular database, so > i do it in CLI. I've added cacheDA parameter which speeds up whole > process at first by 10 times, although after time cache is getting > bigger and bigger operations slows down as one can expect, because > Chimera is caching every compound. Is there a way to limit the size > of a cache, or even better to tell chimera to cache only protein > donors and acceptors? Hi Maciek, Are you closing the compound models after you do the H-bond computation? I ask because the caching uses a "weak key dictionary" where the key is the model. What this means is that if the model is closed it should simply disappear from the cache, no fuss no muss. If you are closing the models then either the slowdown is due to something else, or the models aren't being properly removed from the cache. Let me know if your script is closing the models but still having this problem and I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From maciek at wojcikowski.pl Thu Jul 28 11:24:28 2011 From: maciek at wojcikowski.pl (=?ISO-8859-1?Q?Maciek_W=F3jcikowski?=) Date: Thu, 28 Jul 2011 20:24:28 +0200 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> References: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> Message-ID: Hello Eric, My script is quite simple, but I'm not an python expert: #! /usr/bin/env python # -*- coding: utf-8 -*- import os import glob import sys if len(sys.argv) < 2: print 'No directory specified.' sys.exit() path = sys.argv[1] from chimera import runCommand runCommand("open 0 model.mol2") i=0 for files in glob.glob( os.path.join(path, '*.mol2') ): #print path+files runCommand('open 1 %s' % files) if i < 100: cache = " cacheDA true" else: cache = "" i=0 try: runCommand("hbonds intramodel false distSlop 0.8 angleSlop 40" + cache ) except: pass runCommand("close 1") i+=1 I've added the "non-cache" run every 100 iterations, since I've noticed in source code that non-cache hbond check trigers flushCache() and it seams to help. When I previously had all iterations with "cacheDA true" chimera was eating RAM like a beast (up to about 2GB per 100.000 molecules) making the cache searches slow. It would be ideal to have cached only those D+A from the model (protein). Some tech. details: Chimera 1.5.3, Fedora 14, CentOS 6.0, Debian Sid - all have this problem. PS. Is it possible to get the number of donors and acceptors somehow? Or should I add this to the source code? It can be achieved easily since it counts them, but doesn't print such number. Thank you in advance for your help. ---- Pozdrawiam, | Best regards, Maciek W?jcikowski maciek at wojcikowski.pl 2011/7/28 Eric Pettersen > On Jul 28, 2011, at 3:35 AM, Maciek W?jcikowski wrote: > > Hello everyone, > > I'm trying to compute hbonds for quite large molecular database, so i do it > in CLI. I've added cacheDA parameter which speeds up whole process at first > by 10 times, although after time cache is getting bigger and > bigger operations slows down as one can expect, because Chimera is caching > every compound. Is there a way to limit the size of a cache, or even better > to tell chimera to cache only protein donors and acceptors? > > > Hi Maciek, > Are you closing the compound models after you do the H-bond computation? I > ask because the caching uses a "weak key dictionary" where the key is the > model. What this means is that if the model is closed it should simply > disappear from the cache, no fuss no muss. If you *are* closing the > models then either the slowdown is due to something else, or the models > aren't being properly removed from the cache. Let me know if your script is > closing the models but still having this problem and I will investigate. > > --Eric > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 28 13:29:41 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Jul 2011 13:29:41 -0700 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: References: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> Message-ID: <8D149723-3225-40A0-8F0A-8A347064974B@cgl.ucsf.edu> This seems to be a memory leak in Chimera. Using the 1.3 production release (1.3.2577) the weak key dictionary discards entries as they are closed, but with the 1.4 production release (1.4.1) and later the entries accumulate in the dictionary. That means that some code somewhere in Chimera is holding onto a reference to the closed model, preventing it from being destroyed and its memory freed (and its weak- key dictionary references from being deleted). This is why your "flush cache" trick helps some but doesn't completely solve the problem: the closed models aren't freeing up memory like they should. I will be investigating this and will post something here when I've fixed it, but memory leaks are pretty difficult to track down so it might take until sometime next week for me to find/ fix it. --Eric On Jul 28, 2011, at 11:24 AM, Maciek W?jcikowski wrote: > Hello Eric, > > My script is quite simple, but I'm not an python expert: > > #! /usr/bin/env python > # -*- coding: utf-8 -*- > > import os > import glob > import sys > > if len(sys.argv) < 2: > print 'No directory specified.' > sys.exit() > > path = sys.argv[1] > > from chimera import runCommand > runCommand("open 0 model.mol2") > > i=0 > > for files in glob.glob( os.path.join(path, '*.mol2') ): > #print path+files > runCommand('open 1 %s' % files) > if i < 100: > cache = " cacheDA true" > else: > cache = "" > i=0 > try: > runCommand("hbonds intramodel false distSlop 0.8 angleSlop 40" + > cache ) > except: > pass > runCommand("close 1") > i+=1 > > I've added the "non-cache" run every 100 iterations, since I've > noticed in source code that non-cache hbond check trigers > flushCache() and it seams to help. When I previously had all > iterations with "cacheDA true" chimera was eating RAM like a beast > (up to about 2GB per 100.000 molecules) making the cache searches > slow. It would be ideal to have cached only those D+A from the model > (protein). > > Some tech. details: Chimera 1.5.3, Fedora 14, CentOS 6.0, Debian Sid > - all have this problem. > > PS. > Is it possible to get the number of donors and acceptors somehow? Or > should I add this to the source code? It can be achieved easily > since it counts them, but doesn't print such number. > > Thank you in advance for your help. > ---- > Pozdrawiam, | Best regards, > Maciek W?jcikowski > maciek at wojcikowski.pl > > > 2011/7/28 Eric Pettersen > On Jul 28, 2011, at 3:35 AM, Maciek W?jcikowski wrote: > >> Hello everyone, >> >> I'm trying to compute hbonds for quite large molecular database, so >> i do it in CLI. I've added cacheDA parameter which speeds up whole >> process at first by 10 times, although after time cache is getting >> bigger and bigger operations slows down as one can expect, because >> Chimera is caching every compound. Is there a way to limit the size >> of a cache, or even better to tell chimera to cache only protein >> donors and acceptors? > > Hi Maciek, > Are you closing the compound models after you do the H-bond > computation? I ask because the caching uses a "weak key dictionary" > where the key is the model. What this means is that if the model is > closed it should simply disappear from the cache, no fuss no muss. > If you are closing the models then either the slowdown is due to > something else, or the models aren't being properly removed from the > cache. Let me know if your script is closing the models but still > having this problem and I will investigate. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 28 13:46:09 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Jul 2011 13:46:09 -0700 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: <8D149723-3225-40A0-8F0A-8A347064974B@cgl.ucsf.edu> References: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> <8D149723-3225-40A0-8F0A-8A347064974B@cgl.ucsf.edu> Message-ID: Okay, I have a workaround until I get a fix in: in the "New Molecules" category of Preferences, change "smart initial display" from true to false (then run your script, or "Save" your change if you want to run your script in a new Chimera). --Eric On Jul 28, 2011, at 1:29 PM, Eric Pettersen wrote: > This seems to be a memory leak in Chimera. Using the 1.3 production > release (1.3.2577) the weak key dictionary discards entries as they > are closed, but with the 1.4 production release (1.4.1) and later > the entries accumulate in the dictionary. That means that some code > somewhere in Chimera is holding onto a reference to the closed > model, preventing it from being destroyed and its memory freed (and > its weak-key dictionary references from being deleted). > > This is why your "flush cache" trick helps some but doesn't > completely solve the problem: the closed models aren't freeing up > memory like they should. I will be investigating this and will post > something here when I've fixed it, but memory leaks are pretty > difficult to track down so it might take until sometime next week > for me to find/fix it. > > --Eric > > On Jul 28, 2011, at 11:24 AM, Maciek W?jcikowski wrote: > >> Hello Eric, >> >> My script is quite simple, but I'm not an python expert: >> >> #! /usr/bin/env python >> # -*- coding: utf-8 -*- >> >> import os >> import glob >> import sys >> >> if len(sys.argv) < 2: >> print 'No directory specified.' >> sys.exit() >> >> path = sys.argv[1] >> >> from chimera import runCommand >> runCommand("open 0 model.mol2") >> >> i=0 >> >> for files in glob.glob( os.path.join(path, '*.mol2') ): >> #print path+files >> runCommand('open 1 %s' % files) >> if i < 100: >> cache = " cacheDA true" >> else: >> cache = "" >> i=0 >> try: >> runCommand("hbonds intramodel false distSlop 0.8 angleSlop 40" + >> cache ) >> except: >> pass >> runCommand("close 1") >> i+=1 >> >> I've added the "non-cache" run every 100 iterations, since I've >> noticed in source code that non-cache hbond check trigers >> flushCache() and it seams to help. When I previously had all >> iterations with "cacheDA true" chimera was eating RAM like a beast >> (up to about 2GB per 100.000 molecules) making the cache searches >> slow. It would be ideal to have cached only those D+A from the >> model (protein). >> >> Some tech. details: Chimera 1.5.3, Fedora 14, CentOS 6.0, Debian >> Sid - all have this problem. >> >> PS. >> Is it possible to get the number of donors and acceptors somehow? >> Or should I add this to the source code? It can be achieved easily >> since it counts them, but doesn't print such number. >> >> Thank you in advance for your help. >> ---- >> Pozdrawiam, | Best regards, >> Maciek W?jcikowski >> maciek at wojcikowski.pl >> >> >> 2011/7/28 Eric Pettersen >> On Jul 28, 2011, at 3:35 AM, Maciek W?jcikowski wrote: >> >>> Hello everyone, >>> >>> I'm trying to compute hbonds for quite large molecular database, >>> so i do it in CLI. I've added cacheDA parameter which speeds up >>> whole process at first by 10 times, although after time cache is >>> getting bigger and bigger operations slows down as one can expect, >>> because Chimera is caching every compound. Is there a way to limit >>> the size of a cache, or even better to tell chimera to cache only >>> protein donors and acceptors? >> >> Hi Maciek, >> Are you closing the compound models after you do the H-bond >> computation? I ask because the caching uses a "weak key >> dictionary" where the key is the model. What this means is that if >> the model is closed it should simply disappear from the cache, no >> fuss no muss. If you are closing the models then either the >> slowdown is due to something else, or the models aren't being >> properly removed from the cache. Let me know if your script is >> closing the models but still having this problem and I will >> investigate. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 28 14:01:53 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Jul 2011 14:01:53 -0700 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: References: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> Message-ID: <97A18B10-E5F6-4871-9E33-5DA12A55E49C@cgl.ucsf.edu> On Jul 28, 2011, at 11:24 AM, Maciek W?jcikowski wrote: > Is it possible to get the number of donors and acceptors somehow? Or > should I add this to the source code? It can be achieved easily > since it counts them, but doesn't print such number. The fastest way for you to get this is for you to add print statements at the end of the _findAcceptors and _findDonors routines in FindHBond.base. I'll put adding a nice interface for this on my to-do list. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jul 28 17:56:52 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Jul 2011 17:56:52 -0700 Subject: [Chimera-users] Hbond in CLI + cacheDA In-Reply-To: <8D149723-3225-40A0-8F0A-8A347064974B@cgl.ucsf.edu> References: <5643EEFC-4C7D-42E0-B0AA-6EC0553B1502@cgl.ucsf.edu> <8D149723-3225-40A0-8F0A-8A347064974B@cgl.ucsf.edu> Message-ID: Okay, the memory leak is fixed in tonight's daily build. --Eric On Jul 28, 2011, at 1:29 PM, Eric Pettersen wrote: > This seems to be a memory leak in Chimera. Using the 1.3 production > release (1.3.2577) the weak key dictionary discards entries as they > are closed, but with the 1.4 production release (1.4.1) and later > the entries accumulate in the dictionary. That means that some code > somewhere in Chimera is holding onto a reference to the closed > model, preventing it from being destroyed and its memory freed (and > its weak-key dictionary references from being deleted). > > This is why your "flush cache" trick helps some but doesn't > completely solve the problem: the closed models aren't freeing up > memory like they should. I will be investigating this and will post > something here when I've fixed it, but memory leaks are pretty > difficult to track down so it might take until sometime next week > for me to find/fix it. > > --Eric > > On Jul 28, 2011, at 11:24 AM, Maciek W?jcikowski wrote: > >> Hello Eric, >> >> My script is quite simple, but I'm not an python expert: >> >> #! /usr/bin/env python >> # -*- coding: utf-8 -*- >> >> import os >> import glob >> import sys >> >> if len(sys.argv) < 2: >> print 'No directory specified.' >> sys.exit() >> >> path = sys.argv[1] >> >> from chimera import runCommand >> runCommand("open 0 model.mol2") >> >> i=0 >> >> for files in glob.glob( os.path.join(path, '*.mol2') ): >> #print path+files >> runCommand('open 1 %s' % files) >> if i < 100: >> cache = " cacheDA true" >> else: >> cache = "" >> i=0 >> try: >> runCommand("hbonds intramodel false distSlop 0.8 angleSlop 40" + >> cache ) >> except: >> pass >> runCommand("close 1") >> i+=1 >> >> I've added the "non-cache" run every 100 iterations, since I've >> noticed in source code that non-cache hbond check trigers >> flushCache() and it seams to help. When I previously had all >> iterations with "cacheDA true" chimera was eating RAM like a beast >> (up to about 2GB per 100.000 molecules) making the cache searches >> slow. It would be ideal to have cached only those D+A from the >> model (protein). >> >> Some tech. details: Chimera 1.5.3, Fedora 14, CentOS 6.0, Debian >> Sid - all have this problem. >> >> PS. >> Is it possible to get the number of donors and acceptors somehow? >> Or should I add this to the source code? It can be achieved easily >> since it counts them, but doesn't print such number. >> >> Thank you in advance for your help. >> ---- >> Pozdrawiam, | Best regards, >> Maciek W?jcikowski >> maciek at wojcikowski.pl >> >> >> 2011/7/28 Eric Pettersen >> On Jul 28, 2011, at 3:35 AM, Maciek W?jcikowski wrote: >> >>> Hello everyone, >>> >>> I'm trying to compute hbonds for quite large molecular database, >>> so i do it in CLI. I've added cacheDA parameter which speeds up >>> whole process at first by 10 times, although after time cache is >>> getting bigger and bigger operations slows down as one can expect, >>> because Chimera is caching every compound. Is there a way to limit >>> the size of a cache, or even better to tell chimera to cache only >>> protein donors and acceptors? >> >> Hi Maciek, >> Are you closing the compound models after you do the H-bond >> computation? I ask because the caching uses a "weak key >> dictionary" where the key is the model. What this means is that if >> the model is closed it should simply disappear from the cache, no >> fuss no muss. If you are closing the models then either the >> slowdown is due to something else, or the models aren't being >> properly removed from the cache. Let me know if your script is >> closing the models but still having this problem and I will >> investigate. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jul 28 19:39:19 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Jul 2011 19:39:19 -0700 Subject: [Chimera-users] hide a peptide in Chimera In-Reply-To: References: Message-ID: <558ED2E4-CBFB-43CB-BA70-97CC01CA1198@cgl.ucsf.edu> I forgot to mention that if the peptides are shown with ribbons and/or surfaces, those would be handled separately from the atoms and bonds. My previous reply described using "Actions... Atoms/Bonds... hide" or command "~display" for hiding the atoms and bonds. Analagously you could use "Actions... Ribbon... hide" or command "~ribbon" for ribbons, and "Actions... Surface... hide" or command "~surface" for molecular surfaces. Another point is that the most convenient way to specify or select the individual peptides depend on how they are described in the PDB files. They could be different chains, as mentioned in my previous message, or they could be different submodels, as is often the case for NMR structures in the PDB. If they are different submodels, you could simply uncheck the S or Shown boxes in the Model Panel to hide them. The Model Panel is in the Favorites menu. Elaine On Jul 28, 2011, at 8:36 AM, Elaine Meng wrote: > Hi C.J., > There are many ways to hide specific atoms. For example, > > (A) use menu "Actions... Atoms/Bonds... hide" after selecting the atoms you want to hide. > > There are several ways to select atoms, for example > (i) Ctrl-click on an atom or bond in the peptide, then up arrow key to expand to whole residue, then whole chain. The selection is shown with green highlighting. > (ii) use the "Select" menu, perhaps a particular chain > > ... or ... > > (B) use command "~display" with specification of the atoms you want to hide. For example, to hide chain A: > ~disp :.a > > Here is info on command-line atom specification: > > > You may want to take a look at the "getting started" tutorials: > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jul 28, 2011, at 2:05 AM, C.J. wrote: > >> Hi,all, >> I have a pdb file containing several peptides. And I want to hide some >> of them when visualizing the file in Chimera. >> Anyone would like to help me to that? >> I'm appreciated of any suggestions. >> -- >> Regards! >> C.J. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From biocjh at gmail.com Fri Jul 29 05:16:35 2011 From: biocjh at gmail.com (C.J.) Date: Fri, 29 Jul 2011 20:16:35 +0800 Subject: [Chimera-users] hide a peptide in Chimera In-Reply-To: <558ED2E4-CBFB-43CB-BA70-97CC01CA1198@cgl.ucsf.edu> References: <558ED2E4-CBFB-43CB-BA70-97CC01CA1198@cgl.ucsf.edu> Message-ID: thank you. 2011/7/29 Elaine Meng : > I forgot to mention that if the peptides are shown with ribbons and/or surfaces, those would be handled separately from the atoms and bonds. > > My previous reply described using "Actions... Atoms/Bonds... hide" or command "~display" for hiding the atoms and bonds. ?Analagously you could use "Actions... Ribbon... hide" or command "~ribbon" for ribbons, and "Actions... Surface... hide" or command "~surface" for molecular surfaces. > > Another point is that the most convenient way to specify or select the individual peptides depend on how they are described in the PDB files. ?They could be different chains, as mentioned in my previous message, or they could be different submodels, as is often the case for NMR structures in the PDB. ?If they are different submodels, you could simply uncheck the S or Shown boxes in the Model Panel to hide them. ?The Model Panel is in the Favorites menu. > > Elaine > > On Jul 28, 2011, at 8:36 AM, Elaine Meng wrote: > >> Hi C.J., >> There are many ways to hide specific atoms. ?For example, >> >> (A) use menu "Actions... Atoms/Bonds... hide" after selecting the atoms you want to hide. >> >> There are several ways to select atoms, for example >> (i) Ctrl-click on an atom or bond in the peptide, then up arrow key to expand to whole residue, then whole chain. The selection is shown with green highlighting. >> (ii) use the "Select" menu, perhaps a particular chain >> >> ... or ... >> >> (B) use command "~display" with specification of the atoms you want to hide. ?For example, to hide chain A: >> ~disp :.a >> >> Here is info on command-line atom specification: >> >> >> You may want to take a look at the "getting started" tutorials: >> >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Jul 28, 2011, at 2:05 AM, C.J. wrote: >> >>> Hi,all, >>> I have a pdb file containing several peptides. And I want to hide some >>> of them when visualizing the file in Chimera. >>> Anyone would like to help me to that? >>> I'm appreciated of any suggestions. >>> -- >>> Regards! >>> C.J. >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- Regards! C.J. From chiendarret at gmail.com Sun Jul 31 09:57:15 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 31 Jul 2011 18:57:15 +0200 Subject: [Chimera-users] centroid trace problems Message-ID: hello: "centroid" works fine to me in getting the trace of a moving molecule in and out of a protein, using command define centroid radius 0.2 color red :residuename when the residue is unique. In fact, the method has produced extraordinarily illustrative (I am using the words of the referee) in a paper that will appear shortly on Chemistry & Biodiversity. Now I have three diatomic molecules, only one of which is made moving around. In this case define centroid radius 0.2 color red :residuename:residuenumber for the moving residue does not work. What happens is that "red balls" for the specified residue are being accumulated at the place of origin of the residue, while the residue is leaving the protein as a short bar, not a ball. Could that be fixed in the above command? thanks francesco pietra From meng at cgl.ucsf.edu Sun Jul 31 10:14:19 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 31 Jul 2011 10:14:19 -0700 Subject: [Chimera-users] centroid trace problems In-Reply-To: References: Message-ID: <3B6002DA-B656-4440-8BA7-12140B338667@cgl.ucsf.edu> Hi Francesco, I'm glad to hear you like the centroid feature! If you want only a specific residue, use only the residue number. If you use both the name and the number you will get all of the residues with the name, PLUS all of the residues with the number. For example, if there are three histidines HIS 126,152, and 225, :his:225 will specify all three histidines. To specify only HIS 225, use :225 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote: > hello: > "centroid" works fine to me in getting the trace of a moving molecule > in and out of a protein, using command > > define centroid radius 0.2 color red :residuename > > when the residue is unique. In fact, the method has produced > extraordinarily illustrative (I am using the words of the referee) in > a paper that will appear shortly on Chemistry & Biodiversity. Now I > have three diatomic molecules, only one of which is made moving > around. In this case > > define centroid radius 0.2 color red :residuename:residuenumber > > for the moving residue does not work. What happens is that "red balls" > for the specified residue are being accumulated at the place of origin > of the residue, while the residue is leaving the protein as a short > bar, not a ball. Could that be fixed in the above command? > > thanks > francesco pietra From chiendarret at gmail.com Sun Jul 31 22:38:56 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Mon, 1 Aug 2011 07:38:56 +0200 Subject: [Chimera-users] centroid trace problems In-Reply-To: <3B6002DA-B656-4440-8BA7-12140B338667@cgl.ucsf.edu> References: <3B6002DA-B656-4440-8BA7-12140B338667@cgl.ucsf.edu> Message-ID: Hi Elaine: I could not use the residue number. This is a patched couple psf/pdb, where the various parts are bound together to establish chemical bonds within the enzyme active center. The various groups maintain the original residue number, which means that there are various different residue with the same number, and this applies in particular to the residue of my interest.. francesco On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng wrote: > Hi Francesco, > I'm glad to hear you like the centroid feature! > > If you want only a specific residue, use only the residue number. ?If you > use both the name and the number you will get all of the residues with the > name, PLUS all of the residues with the number. ?For example, if there are > three histidines HIS 126,152, and 225, > > :his:225 > > will specify all three histidines. ?To specify only HIS 225, use > > :225 > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. ? ? ? ? ? ? ? ? ? ? ? ? ?meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > ? ? ? ? ? ? ? ? ? ? http://www.cgl.ucsf.edu/home/meng/index.html > > On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote: > >> hello: >> "centroid" works fine to me in getting the trace of a moving molecule >> in and out of a protein, using command >> >> define centroid radius 0.2 color red :residuename >> >> when the residue is unique. In fact, the method has produced >> extraordinarily illustrative (I am using the words of the referee) in >> a paper that will appear shortly on Chemistry & Biodiversity. Now I >> have three diatomic molecules, only one of which is made moving >> around. In this case >> >> define centroid radius 0.2 color red :residuename:residuenumber >> >> for the moving residue does not work. What happens is that "red balls" >> for the specified residue are being accumulated at the place of origin >> of the residue, while the residue is leaving the protein as a short >> bar, not a ball. Could that be fixed in the above command? >> >> thanks >> francesco pietra > > > > From chiendarret at gmail.com Sun Jul 31 22:47:31 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Mon, 1 Aug 2011 07:47:31 +0200 Subject: [Chimera-users] Fwd: centroid trace problems In-Reply-To: References: <3B6002DA-B656-4440-8BA7-12140B338667@cgl.ucsf.edu> Message-ID: Elaine: the sole chance would be to use the ID number, which, of course, is unique even in my case. I had looked around if it were possible. Not found. The residue consists of two ID numbers. francesco ---------- Forwarded message ---------- From: Francesco Pietra Date: Mon, Aug 1, 2011 at 7:38 AM Subject: Re: [Chimera-users] centroid trace problems To: "chimera-users at cgl.ucsf.edu BB" Hi Elaine: I could not use the residue number. This is a patched couple psf/pdb, where the various parts are bound together to establish chemical bonds within the enzyme active center. The various groups maintain the original residue number, which means that there are various different residue with the same number, and this applies in particular to the residue of my interest.. francesco On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng wrote: > Hi Francesco, > I'm glad to hear you like the centroid feature! > > If you want only a specific residue, use only the residue number. ?If you > use both the name and the number you will get all of the residues with the > name, PLUS all of the residues with the number. ?For example, if there are > three histidines HIS 126,152, and 225, > > :his:225 > > will specify all three histidines. ?To specify only HIS 225, use > > :225 > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. ? ? ? ? ? ? ? ? ? ? ? ? ?meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > ? ? ? ? ? ? ? ? ? ? http://www.cgl.ucsf.edu/home/meng/index.html > > On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote: > >> hello: >> "centroid" works fine to me in getting the trace of a moving molecule >> in and out of a protein, using command >> >> define centroid radius 0.2 color red :residuename >> >> when the residue is unique. In fact, the method has produced >> extraordinarily illustrative (I am using the words of the referee) in >> a paper that will appear shortly on Chemistry & Biodiversity. Now I >> have three diatomic molecules, only one of which is made moving >> around. In this case >> >> define centroid radius 0.2 color red :residuename:residuenumber >> >> for the moving residue does not work. What happens is that "red balls" >> for the specified residue are being accumulated at the place of origin >> of the residue, while the residue is leaving the protein as a short >> bar, not a ball. Could that be fixed in the above command? >> >> thanks >> francesco pietra > > > > From pett at cgl.ucsf.edu Sun Jul 31 22:52:03 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Sun, 31 Jul 2011 22:52:03 -0700 Subject: [Chimera-users] centroid trace problems In-Reply-To: References: <3B6002DA-B656-4440-8BA7-12140B338667@cgl.ucsf.edu> Message-ID: <60D08AB0-DBCD-4C02-B443-683F184EB62E@cgl.ucsf.edu> Hi Francesco, In that case there are two things you can do. One is to use the '&' operator to select the residue that is number 225 and named HIS, like so: :his & :225 Or, if you select the residue somehow (say by selecting an atom with the mouse and then using up-arrow to select the residue) you could name the selection with: namesel his225 and after that you can use 'his225' in exactly the same way you were trying to use ':his:225' before. --Eric On Jul 31, 2011, at 10:38 PM, Francesco Pietra wrote: > Hi Elaine: > I could not use the residue number. This is a patched couple psf/pdb, > where the various parts are bound together to establish chemical bonds > within the enzyme active center. The various groups maintain the > original residue number, which means that there are various different > residue with the same number, and this applies in particular to the > residue of my interest.. > > francesco > > On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng > wrote: >> Hi Francesco, >> I'm glad to hear you like the centroid feature! >> >> If you want only a specific residue, use only the residue number. >> If you >> use both the name and the number you will get all of the residues >> with the >> name, PLUS all of the residues with the number. For example, if >> there are >> three histidines HIS 126,152, and 225, >> >> :his:225 >> >> will specify all three histidines. To specify only HIS 225, use >> >> :225 >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote: >> >>> hello: >>> "centroid" works fine to me in getting the trace of a moving >>> molecule >>> in and out of a protein, using command >>> >>> define centroid radius 0.2 color red :residuename >>> >>> when the residue is unique. In fact, the method has produced >>> extraordinarily illustrative (I am using the words of the referee) >>> in >>> a paper that will appear shortly on Chemistry & Biodiversity. Now I >>> have three diatomic molecules, only one of which is made moving >>> around. In this case >>> >>> define centroid radius 0.2 color red :residuename:residuenumber >>> >>> for the moving residue does not work. What happens is that "red >>> balls" >>> for the specified residue are being accumulated at the place of >>> origin >>> of the residue, while the residue is leaving the protein as a short >>> bar, not a ball. Could that be fixed in the above command? >>> >>> thanks >>> francesco pietra >> >> >> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >