From anna.feldman-salit at eml-r.villa-bosch.de Fri Dec 1 02:36:54 2006 From: anna.feldman-salit at eml-r.villa-bosch.de (Anna Feldman-Salit) Date: Fri, 01 Dec 2006 11:36:54 +0100 Subject: [Chimera-users] Uploading several trajectories for MDmovie Message-ID: <457005C6.9090908@eml-r.villa-bosch.de> Dear all, I would like to know if there is any possibility to sequentially upload several trajectories with MDmovie option (or command line) and then to visualize them with "no stop" in between. These trajectories were generated by AMBER with "restart" input files. Such an option happens to be in VMD, but it's more convenient for me to work with Chimera (I have Chimera1.2304). Thanks a lot in advance, Anna From meng at cgl.ucsf.edu Fri Dec 1 12:11:02 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 1 Dec 2006 12:11:02 -0800 Subject: [Chimera-users] inter-surface calculations in Chimera Message-ID: <87cfe793b9b661e254b5f86f8dfef75a@cgl.ucsf.edu> Hi Gali, Eric forwarded your question to me. The Intersurf tool generates a surface between the interacting molecules that is different from the surface of either molecule - it is mainly useful for viewing an interface and showing its properties (for example, with coloring by hydrophobicity or electrostatic potential), but not for measuring the surface area. It is possible to measure volume and surface area in Chimera, but currently it is a long process. We hope to have a simpler process available in the future. I'll describe two different approaches. (1) the simpler and more approximate way to calculate buried surface area and void volume in the complex: approx buried surface area = [(surface area of X) + (surface area of Y) - (surface area of XY)] / 2 approx interface void volume = (volume of XY) - (volume of X) - (volume of Y) The "Measure Volume and Area" tool can be used to calculate the surface areas and volumes. [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/ measurevol.html ] The trick is to first make a surface that encloses both X and Y and measure its values. Then, make surfaces that separately enclose X and Y and measure again. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel command: surfcat complex :.a-d command: surf complex Tools... Surface/Binding Analysis... Measure Volume and Area (measure values for the complex) command: surfcat protein :.a-b command: surf protein (choose the protein surface in Measure Volume and Area, compute again) command: surfcat dna :.c-d command: surf dna (choose the dna surface in Measure Volume and Area, compute again) Finally, use the equations above. All the results can be viewed in the Reply Log (under Favorites). These values are for molecular surfaces (also known as solvent-excluded, where the probe touches), not solvent-accessible (traced by the probe center). For this structure, I calculate approx 530 square angstroms surface area buried, approx 730 cubic angstroms of interface void volume. (2) A more detailed approach can yield different values for the areas buried on X and Y: (surface area of X buried in the XY interface) = (surface area from all atoms of X in surface enclosing XY) - (surface area from all atoms of X in surface enclosing just X) with a similar equation for Y. Currently, the only way to get atomic rather than total surface areas in Chimera is by using the "Area/Volume from Web" tool [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html ] which uses a Web server at NCBI and loads the atomic values into Chimera. Because the MSMS option of the server has problems with nucleic acids, the only choice for your complexes is to calculate solvent-accessible surface areas (not the solvent-excluded surface areas calculated by method (1) above). The main trick is to first send only XY to the server (making sure solvent, ions, etc. are NOT included). Then using Attribute Calculator, [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html ] sum the values for the atoms of X in that combined surface, and likewise get a total for Y. Then, delete everything except X and send it to the server again, getting the total for X alone. Close/reopen the structure, delete everything except Y, and send it to the server to get the total for Y alone. Subtract the value for X (Y) in the complex from the total for X (Y) alone. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein and DNA command: select :.a-b Tools... Structure Analysis... Attribute Calculator calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for A-B (which is the PROTEIN IN THE COMPLEX) (I get approx 7473) command: select :.c-d calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for C-D (which is the DNA IN THE COMPLEX) (I get approx 4502) command: delete :.c-d now only the protein is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein - get the total for PROTEIN ALONE (Favorites... Reply Log) (I get approx 8842) command: close 0 command: open 1cf7 command: select :.c-d command: sel invert command: delete sel now only the DNA is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the DNA - get the total for DNA ALONE (Favorites... Reply Log) (I get approx 5758) Use the equation above to get the buried solvent-accessible surface areas. I calculate approx 1369 square angstroms buried for the protein, approx 1256 square angstroms buried for the DNA. You can't compare these solvent-accessible areas to the solvent-excluded areas calculated by method (1) ... the solvent-accessible values are generally much larger. PHEW! I congratulate everyone who got this far. The written explanation makes it seem longer than actually performing the process. I hope this helps, Elaine On Nov 30, 2006, at 7:35 AM, galig wrote: > Dear Eric, > > I have a small question regarding the calculation of inter-surfaces in > Chimera: > I have several protein/DNA complexes, and I would like to compare > their protein/DNA interfaces. I used Tools-->surface/binding > analysis-->compute interface surface and chose the protein and DNA > chains. the result, if I understand it correct, is per atom. Is there > a place to find the overall number representing the contact surface? > is this a different or similar calculation? > One more thing- how do I calculate the void intermolecular volume > between the chains? > > Thank you and sorry to bother you, > > Gali Golan > Dept. of Inorganic Chemistry > The Hebrew U. of Jerusalem > Jerusalem 91904 Israel > Tel. 972-2-6585610 > Fax 972-2-6585319 > ----- 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 From goddard at cgl.ucsf.edu Fri Dec 1 13:10:45 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 1 Dec 2006 13:10:45 -0800 (PST) Subject: [Chimera-users] inter-surface calculations in Chimera In-Reply-To: <87cfe793b9b661e254b5f86f8dfef75a@cgl.ucsf.edu> (message from Elaine Meng on Fri, 1 Dec 2006 12:11:02 -0800) References: <87cfe793b9b661e254b5f86f8dfef75a@cgl.ucsf.edu> Message-ID: <200612012110.kB1LAjJ01882655@guanine.cgl.ucsf.edu> Hi Elaine, Would be nice to have a single Chimera command like buriedarea :.a-b :.c-d that computes all of the needed surfaces and reports all of the relavent areas without going to the web. I think it is about a day's work to make that. It has been on my list but is not a high enough priority to get any time for the next few months. Tom From hsosa at aecom.yu.edu Sat Dec 2 06:42:46 2006 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Sat, 02 Dec 2006 09:42:46 -0500 Subject: [Chimera-users] Fit models to map Message-ID: <457190E6.3050103@aecom.yu.edu> I wonder how the "Fit models to map" function do the fitting. Does it find the best cross-correlation value between a 3D density calculated from the atomic model and the 3D density map?. What is the maximum displacements and rotations tested around the current position? What is the step size of the rotations/displacements? Thanks Regards Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Mon Dec 4 10:11:04 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 4 Dec 2006 10:11:04 -0800 (PST) Subject: [Chimera-users] Fit models to map In-Reply-To: <457190E6.3050103@aecom.yu.edu> (hsosa@aecom.yu.edu) References: <457190E6.3050103@aecom.yu.edu> Message-ID: <200612041811.kB4IB44a1797448@guanine.cgl.ucsf.edu> Hi Hernando, The details about how fitting models in maps is works are described in the Chimera manual. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodels.html You can display the manual page by pressing the Help button on the Fit Models in Maps dialog. Briefly, it does not compute a density from the atomic model -- that would require you specify a resolution if you wanted a meaningful cross correlation value. It simply looks at interpolated density values at the atom positions and maximizes their sum. It uses gradient descent and typically translates by no more than about the molecule radius and rotates by no more than about 90 degrees. There are no coded limits though. For step sizes and convergence criteria see the manual. A few weeks ago I wrote some code to fit a map in another map and report the correlation coefficient: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/001105.html This will be part of Chimera in the next snapshot releases. It still does not compute a density from a PDB model so you would have to do that with an external program. We will add that capability in the future. Tom From pett at cgl.ucsf.edu Mon Dec 4 14:58:48 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 4 Dec 2006 14:58:48 -0800 Subject: [Chimera-users] Uploading several trajectories for MDmovie In-Reply-To: <457005C6.9090908@eml-r.villa-bosch.de> References: <457005C6.9090908@eml-r.villa-bosch.de> Message-ID: <7F8851B4-E65F-430A-9881-4147935D2D2F@cgl.ucsf.edu> Hi Anna, The short answer is no, Chimera can't do this now. After examining the trajectory code, I think I could add this capability with a moderate amount of effort. Let me know if you want to be a guinea pig. Otherwise, I will add it to my to-do list and it will get in there eventually. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 1, 2006, at 2:36 AM, Anna Feldman-Salit wrote: > Dear all, > > I would like to know if there is any possibility to sequentially > upload > several trajectories with MDmovie option (or command line) and then to > visualize them with "no stop" in between. These trajectories were > generated by AMBER with "restart" input files. > > Such an option happens to be in VMD, but it's more convenient for > me to > work with Chimera (I have Chimera1.2304). > > Thanks a lot in advance, > > Anna > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mshawkey at nature.berkeley.edu Wed Dec 6 14:58:08 2006 From: mshawkey at nature.berkeley.edu (Matthew Shawkey) Date: Wed, 6 Dec 2006 14:58:08 -0800 Subject: [Chimera-users] volume viewer issue Message-ID: Hi, I am using chimera to visualize a stack of EM serial sections. I can load them into Chimera (as MRC file), but when I try to view the stack in the volume viewer w the "solids" option all I see is a white square.. w the mesh and surface options the stack shows up as a grainy image on which it's difficult to see any depth.. any suggestions? THanks, Matt From goddard at cgl.ucsf.edu Wed Dec 6 16:07:47 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 6 Dec 2006 16:07:47 -0800 (PST) Subject: [Chimera-users] volume viewer issue In-Reply-To: (message from Matthew Shawkey on Wed, 6 Dec 2006 14:58:08 -0800) References: Message-ID: <200612070007.kB707lRv1656481@guanine.cgl.ucsf.edu> Hi Matt, Do you see a filled white square or just a white wire outline? Have you tried adjusting the "transfer function" -- that is moving the nodes of the yellow curve on the volume histogram that controls the brightness of voxels as a function of data value? If that doesn't make sense have a look at the Chimera manual page for volume data display, in particular, the "solid display" section: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html Tom From hwwang at lbl.gov Wed Dec 6 18:26:18 2006 From: hwwang at lbl.gov (Hong-Wei Wang) Date: Wed, 6 Dec 2006 18:26:18 -0800 Subject: [Chimera-users] Apply the symmetry to the fitted models in map Message-ID: <005c01c719a7$13e24fe0$29ea2080@nogaleshongwei> Hi, Tom I remember you were showing docking a model into map with high symmetry (you showed the actomyosin filament example). I am wondering how you generate the symmetry in the docking and if the symmetry information is necessary for the correct fitting. Thanks a lot! Hongwei ----------------------------------- Hongwei Wang, Ph D MS 20A-355, LSD, LBNL 1 Cyclotron Rd, Berkeley, CA 94720 510-642-2222 (O) 510-642-8806 (FAX) hwwang at lbl.gov From goddard at cgl.ucsf.edu Wed Dec 6 19:48:02 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 6 Dec 2006 19:48:02 -0800 (PST) Subject: [Chimera-users] Apply the symmetry to the fitted models in map In-Reply-To: <005c01c719a7$13e24fe0$29ea2080@nogaleshongwei> (hwwang@lbl.gov) References: <005c01c719a7$13e24fe0$29ea2080@nogaleshongwei> Message-ID: <200612070348.kB73m2u71598657@guanine.cgl.ucsf.edu> Hi Hongwei, You do not need to use symmetric copies of a molecule when fitting into a symmetric map. Fitting a single asymmetric unit works. I demonstrated fitting one copy of a molecule into a myosin thick filament map while two neighboring symmetrically placed copies move automatically to maintain symmetry. This has no effect on the fitting. It merely lets you see when a fit position causes a steric clash with a symmetrically place copy. The placement for the symmetric copies is described with matrices in the header of the PDB file. Here is a description of this if you want to try it: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcopies Tom From moocow at mindless.com Fri Dec 8 03:15:25 2006 From: moocow at mindless.com (Moo Cow) Date: Fri, 08 Dec 2006 06:15:25 -0500 Subject: [Chimera-users] Read compressed PDB files -question, suggestion Message-ID: <20061208111526.3302D1BF287@ws1-1.us4.outblaze.com> We store the PDB locally, but compressed. Can one persuade chimera to read coordinates from a pipe ? Maybe this could be done at the python level. It might also not be too hard to use the python binding to the zlib library, but I would not know how to do this. I imagine the interest (or not) would not be limited to reading PDB files. many thanks for any suggestions. -- Search for products and services at: http://search.mail.com From goddard at cgl.ucsf.edu Fri Dec 8 08:26:16 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 8 Dec 2006 08:26:16 -0800 (PST) Subject: [Chimera-users] Read compressed PDB files -question, suggestion In-Reply-To: <20061208111526.3302D1BF287@ws1-1.us4.outblaze.com> (moocow@mindless.com) References: <20061208111526.3302D1BF287@ws1-1.us4.outblaze.com> Message-ID: <200612081626.kB8GQG4s2051677@guanine.cgl.ucsf.edu> Hi Moo Cow, You can use the Chimera File / Open... dialog to directly open a gzip PDB file. This was added to Chimera about one year ago. It does not work for all types of files, for instance, compressed volume data is not automatically uncompressed. Tom From pett at cgl.ucsf.edu Fri Dec 8 13:34:35 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 8 Dec 2006 13:34:35 -0800 Subject: [Chimera-users] Read compressed PDB files -question, suggestion In-Reply-To: <200612081626.kB8GQG4s2051677@guanine.cgl.ucsf.edu> References: <20061208111526.3302D1BF287@ws1-1.us4.outblaze.com> <200612081626.kB8GQG4s2051677@guanine.cgl.ucsf.edu> Message-ID: <0BD3EA82-F909-4792-BAC0-ACE752674DD8@cgl.ucsf.edu> You can also open gzipped files with Chimera's "open" command or as an argument as you start Chimera. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 8, 2006, at 8:26 AM, Thomas Goddard wrote: > Hi Moo Cow, > > You can use the Chimera File / Open... dialog to directly open a > gzip > PDB file. This was added to Chimera about one year ago. It does > not work > for all types of files, for instance, compressed volume data is not > automatically uncompressed. > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From moocow at mindless.com Mon Dec 11 03:54:40 2006 From: moocow at mindless.com (Moo Cow) Date: Mon, 11 Dec 2006 06:54:40 -0500 Subject: [Chimera-users] compressed versus gzipped Re: Read compressed PDB files -question, suggestion Message-ID: <20061211115441.48C7D86AE0@cal1-1.us4.outblaze.com> A thousand pardons. You are right. I phrased the question wrongly. Chimera does open gzip'd files ( xx.gz). It does not open compress'd files (xx.Z). > You can also open gzipped files with Chimera's "open" command or as > an argument as you start Chimera. [...] > > You can use the Chimera File / Open... dialog to directly open a gzip > > PDB file. This was added to Chimera about one year ago. It does not work Why, you may ask, would anyone use compress these days ? If you mirror or rsync the protein data bank, they are still distributing files that have been squashed with compress and have a ".Z" extension. gunzip will happily eat and uncompress these files. I do not know how chimera handles compressed files. If it reads from a pipe, it might be nice to persuade it to feed .Z files to gunzip. I think it might be more difficult if chimera uses the python/zlib interface. Many thanks -- Search for products and services at: http://search.mail.com From sette at uniroma2.it Mon Dec 11 04:23:35 2006 From: sette at uniroma2.it (sette at uniroma2.it) Date: Mon, 11 Dec 2006 13:23:35 +0100 Subject: [Chimera-users] Delphi Controller Message-ID: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> Dear all, I have a simple question: does Delphi controller works under unix only or it is possible to work with it under Linux and/or Windows XP? Thanks a lot, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette at uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328 From papai at titus.u-strasbg.fr Mon Dec 11 06:46:32 2006 From: papai at titus.u-strasbg.fr (Gabor Papai) Date: Mon, 11 Dec 2006 15:46:32 +0100 Subject: [Chimera-users] saving with angles Message-ID: <457D6F48.2040508@igbmc.u-strasbg.fr> Dear everybody, Is there a way in Chimera to save density maps when I rotate them with the modified angles? In practice, I use the 'fit map in map' to align two maps in respect to each other and I would like to save them for further analysis with different softwares. Therefore I would like to conserve their position (shift and rotation). Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai at igbmc.u-strasbg.fr From kvaughan at bc.cc.ca.us Mon Dec 11 08:28:15 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Mon, 11 Dec 2006 08:28:15 -0800 Subject: [Chimera-users] Delphi Controller In-Reply-To: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> References: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> Message-ID: <20061211162815.GA7836@hpotter.vaughan.home> On Mon, Dec 11, 2006 at 01:23:35PM +0100, sette at uniroma2.it wrote: > > Dear all, > I have a simple question: > does Delphi controller works under unix only or it is possible to work > with it under Linux and/or Windows XP? It works fine under Linux. Unfortunately (?) I don't try to do much under Windows so I can't address that part... > > Thanks a lot, > Marco Cheers, Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? From goddard at cgl.ucsf.edu Mon Dec 11 10:00:52 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 11 Dec 2006 10:00:52 -0800 (PST) Subject: [Chimera-users] Delphi Controller In-Reply-To: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> (sette@uniroma2.it) References: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> Message-ID: <200612111800.kBBI0qSd2019553@guanine.cgl.ucsf.edu> Hi Marco, I don't think DelphiController works on Windows. Looking at the Chimera code I did not see any changes that would make this work versus a few years ago. Here's my answer when you asked this same question a few years ago: http://www.cgl.ucsf.edu/pipermail/chimera-users/2003-July/000025.html We have been thinking recently about how to make electrostatics calculations in Chimera easier. Ideas include a simple Coulomb calculation, or using APBS which would be included in Chimera. It may be simple to make DelphiController work on Windows since the only obvious problem I saw was in the command used to invoke Delphi. That seems like a simple step to try before we include some other electrostatics calculation. Eric Pettersen is the one who is looking at electrostatics and maybe he can comment further. Tom From meng at cgl.ucsf.edu Mon Dec 11 10:01:56 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 11 Dec 2006 10:01:56 -0800 Subject: [Chimera-users] Delphi Controller In-Reply-To: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> References: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> Message-ID: <054AC2F4-A75E-4F6B-A077-01BAF6ED75D1@cgl.ucsf.edu> Hello, In the DelPhiController description where we said it only works on unix systems, I believe that includes all of the current Chimera platforms (including Linux, Mac OS X, IRIX, etc.) *except* Windows. As Dr. Vaughn said, it should work on your linux system. (As an aside, although DelPhi is distributed for Mac, we have not been able to get the Mac version working; there were several chimera- users messages about this in November.) Best, 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 Dec 11, 2006, at 4:23 AM, sette at uniroma2.it wrote: > > Dear all, > I have a simple question: > does Delphi controller works under unix only or it is possible to work > with it under Linux and/or Windows XP? > > Thanks a lot, > Marco > > > > > Dr.Marco Sette, Ph.D. > > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail: sette at uniroma2.it > Tel.: +39-0672594424 > Fax: +39-0672594328 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Mon Dec 11 10:09:48 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 11 Dec 2006 10:09:48 -0800 (PST) Subject: [Chimera-users] saving with angles In-Reply-To: <457D6F48.2040508@igbmc.u-strasbg.fr> (message from Gabor Papai on Mon, 11 Dec 2006 15:46:32 +0100) References: <457D6F48.2040508@igbmc.u-strasbg.fr> Message-ID: <200612111809.kBBI9mHQ2016895@guanine.cgl.ucsf.edu> Hi Gabor, This question was recently discussed on the Chimera mailing list: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000877.html Currently Chimera cannot write out a rotated map. That would require resampling the map (degrading resolution) because none of the common map formats support specifying a rotation for the grid of data values. A number of people have requested the ability to write out rotated maps even if it requires resampling and it will be added at some point, I'd estimate within 6 months. It is possible to get from Chimera the rotation matrix for a map but that is probably not usable in other software. It would be helpful to know what other software you want to use the rotated map in. If you use the other software for plane by plane display with planes aligned to the data axes then resampling would be the only option. Tom From pett at cgl.ucsf.edu Mon Dec 11 11:51:09 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 11 Dec 2006 11:51:09 -0800 Subject: [Chimera-users] Delphi Controller In-Reply-To: <200612111800.kBBI0qSd2019553@guanine.cgl.ucsf.edu> References: <20061211132335.m3dq2zksg0ksg8gg@webmail.uniroma2.it> <200612111800.kBBI0qSd2019553@guanine.cgl.ucsf.edu> Message-ID: <0E333E85-FF03-406D-A589-CABB0DB55911@cgl.ucsf.edu> On Dec 11, 2006, at 10:00 AM, Thomas Goddard wrote: > We have been thinking recently about how to make electrostatics > calculations in Chimera easier. Ideas include a simple Coulomb > calculation, or using APBS which would be included in Chimera. I am evaluating the speed of a simple Coulombic calculation vs. Poisson-Boltzmann for interactive use. If the PB calculation always takes many minutes for reasonable results then I would probably make the Coulombic calculation available "directly" (i.e. the results made available in that same session as a volume data set or a surface coloring) but allow the PB input (i.e. a PQR file for APBS) to be easily created. Adding these features has become feasible now that Chimera includes charge-assignment capabilities. I'm open to opinions/suggestions about what people would like to see in this regard. > It may be simple to make DelphiController work on Windows since the > only obvious problem I saw was in the command used to invoke Delphi. > That seems like a simple step to try before we include some other > electrostatics calculation. Eric Pettersen is the one who is looking > at electrostatics and maybe he can comment further. Conrad is investigating getting Delphi to work on Windows and will be following up. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From papai at titus.u-strasbg.fr Tue Dec 12 04:40:07 2006 From: papai at titus.u-strasbg.fr (Gabor Papai) Date: Tue, 12 Dec 2006 13:40:07 +0100 Subject: [Chimera-users] saving with angles In-Reply-To: <200612111809.kBBI9mHQ2016895@guanine.cgl.ucsf.edu> References: <457D6F48.2040508@igbmc.u-strasbg.fr> <200612111809.kBBI9mHQ2016895@guanine.cgl.ucsf.edu> Message-ID: <457EA327.3050501@igbmc.u-strasbg.fr> Hi Tom, I am currently exploring sample heterogeneity using tomographic approach on single particles. Because of the tomography I have a missing cone in the angular information, so my structures are distorted in the Z direction. To obtain a reasonable structure I have to average the similar structures and I want to do it in IMAGIC. My thought is to average the projections of several structures in the same direction and rebuild the model. Therefore I need to align the different starting density maps in rotation and translation also. Since this feature is not working very well in IMAGIC I would like to use Chimera, but I need the transformation values (angles and shifts) after the fitting, to apply it on the density maps. It would also help me a lot if you tell me how I can obtain these informations! Thanks in advance! Bye, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai at igbmc.u-strasbg.fr From heiland at indiana.edu Tue Dec 12 05:57:11 2006 From: heiland at indiana.edu (Randy Heiland) Date: Tue, 12 Dec 2006 08:57:11 -0500 Subject: [Chimera-users] SDF format Message-ID: <002101c71df5$6c440aa0$ea90a695@escher> Just wanted to ask about Chimera's support for reading in SDF formatted files, e.g. from PubChem. It seems not to be one of the supported formats. Obviously we can use a converter to get pdb format, but thought I'd ask the experts. Thanks, Randy From anna.feldman-salit at eml-r.villa-bosch.de Tue Dec 12 07:18:25 2006 From: anna.feldman-salit at eml-r.villa-bosch.de (Anna Feldman-Salit) Date: Tue, 12 Dec 2006 16:18:25 +0100 Subject: [Chimera-users] Transparent Ribbon Message-ID: <457EC841.5000406@eml-r.villa-bosch.de> Dear All, From some reason I cannot find the option of making ribbon representation transparent. Can you please give me a hint? Thanks a lot in advance, Anna From goddard at cgl.ucsf.edu Tue Dec 12 09:39:38 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 12 Dec 2006 09:39:38 -0800 (PST) Subject: [Chimera-users] saving with angles In-Reply-To: <457EA327.3050501@igbmc.u-strasbg.fr> (message from Gabor Papai on Tue, 12 Dec 2006 13:40:07 +0100) References: <457D6F48.2040508@igbmc.u-strasbg.fr> <200612111809.kBBI9mHQ2016895@guanine.cgl.ucsf.edu> <457EA327.3050501@igbmc.u-strasbg.fr> Message-ID: <200612121739.kBCHdcsk2017339@guanine.cgl.ucsf.edu> Hi Gabor, Thanks for the details about what you are doing. The Fit Map in Map tool I gave you reports the 3 by 3 rotation matrix and the translation vector to fit one map in another in the Chimera Reply Log which is displayed with menu entry Favorites / Reply Log. Here is an example of the output: Fit map microtubule.mrc <1> in map microtubule.mrc using 11355 points correlation = 0.999, overlap = 3.167e+08 steps = 68, shift = 7.29, angle = 5.69 degrees Transformation of microtubule.mrc <1> (#1) in microtubule.mrc (#0): 0.99999980 -0.00061658 0.00010850 -0.06294723 0.00061658 0.99999981 -0.00002551 -0.03578213 -0.00010849 0.00002558 0.99999999 81.17044268 In this example I just fit a microtubule map to itself shifted along its length. The rotation matrix is the first 3 columns and you see it is approximately the identity matrix. The shift is the last column, 81 angstroms along the z-axis. The third line that reports "shift" and "angle" just indicate how big a move was made from the hand-placed position to the optimal fit -- not the relative orientations of the maps. I don't know if this matrix is usable in IMAGIC. I could easily add the same information in expressed as rotation axis vector and rotation angle. Euler angles is a bit trickier since there are many alternate conventions. By the way, I changed the way correlation is calculated to use the conventional meaning. It is described in the Chimera manual. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html The code I gave you gave higher correlation values using a different definition. The code optimizes overlap, not correlation, so the actual fitting has not changed. I also added an option to only use the data within the contour surface for fitting. The new code is on the web and should work with Chimera 1.2309 https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmapinmap.zip Michael Schmid at Baylor College of Medicine gave an interesting talk on aligning tomograms of carboxysomes in a way that accounts for the missing wedge. I think this paper reports the results (I have not read it). Schmid MF, Paredes AM, Khant HA, Soyer F, Aldrich HC, Chiu W, Shively JM. Structure of Halothiobacillus neapolitanus Carboxysomes by Cryo-electron Tomography. J Mol Biol. 2006 Dec 1;364(3):526-35. Epub 2006 Sep 14. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17028023&query_hl=1&itool=pubmed_docsum I leave today for a workshop in Germany and return Sunday. So I will not be able to offer more help until Monday. Tom From meng at cgl.ucsf.edu Tue Dec 12 10:01:14 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 12 Dec 2006 10:01:14 -0800 Subject: [Chimera-users] Transparent Ribbon In-Reply-To: <457EC841.5000406@eml-r.villa-bosch.de> References: <457EC841.5000406@eml-r.villa-bosch.de> Message-ID: Hi Anna, First make a transparent color, and then use it to color the ribbon. There are a few approaches. (A) Menu way. Transparent colors can be created interactively in the Color Editor (under Tools... Utilities) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html and then Actions... Color... from editor uses that color. You can set the target to ribbons only if you want (Actions... Color... ribbons). (B) Command way. Transparent colors can be created with the command "colordef" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html for example, colordef transred 1 0 0 .3 colordef transblue 0 0 1 .3 and then used with the command "color" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html for example, color transred,r :1-10.a color transblue,r :1-10.b (you could go back and adjust the colors with colordef at this point as needed, and the items will adjust their colors without another "color" statement) The color command can also use the Color Editor color (that color can be indicated with the name "fromeditor" or "colorpanel"). This process differs from making a surface transparent for technical reasons - in a nutshell, a surface patch has a transparency property that is separate from its color, while a ribbon segment does not. 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 Dec 12, 2006, at 7:18 AM, Anna Feldman-Salit wrote: > Dear All, > > From some reason I cannot find the option of making ribbon > representation transparent. > Can you please give me a hint? > > Thanks a lot in advance, > > Anna > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue Dec 12 10:26:42 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 12 Dec 2006 10:26:42 -0800 Subject: [Chimera-users] SDF format In-Reply-To: <002101c71df5$6c440aa0$ea90a695@escher> References: <002101c71df5$6c440aa0$ea90a695@escher> Message-ID: <4A1639B3-9CB7-4AD2-87FE-1BA84B2AF679@cgl.ucsf.edu> Hi Randy, This is somewhat tangential to your main question, but I believe the SDF files from PubChem only contain 2D coordinates, i.e. flat "chemist's diagrams" ... probably not what you really wanted. This conclusion is based on a limited sample of structures I've investigated personally, so it is possible that there are also SDFs with 3D coordinates in there. If you click SDF Display for a PubChem entry, you can see whether the third coordinate column is all zeroes or not. For finding 3D coordinates of small molecules, sites I've found useful in the past are the NCI database browser http://129.43.27.140/ncidb2/ (I usually search by CAS number) and NLM ChemIDPlus http://chem.sis.nlm.nih.gov/chemidplus/ (process is somewhat elaborate... let me know if you want details) 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 Dec 12, 2006, at 5:57 AM, Randy Heiland wrote: > Just wanted to ask about Chimera's support for reading in SDF > formatted > files, e.g. from PubChem. It seems not to be one of the supported > formats. > Obviously we can use a converter to get pdb format, but thought I'd > ask the > experts. > > Thanks, Randy > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Tue Dec 12 11:17:45 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 12 Dec 2006 11:17:45 -0800 Subject: [Chimera-users] SDF format In-Reply-To: <002101c71df5$6c440aa0$ea90a695@escher> References: <002101c71df5$6c440aa0$ea90a695@escher> Message-ID: <0C065502-07ED-47BF-9DF8-ECD9BDFB9B1F@cgl.ucsf.edu> On Dec 12, 2006, at 5:57 AM, Randy Heiland wrote: > Just wanted to ask about Chimera's support for reading in SDF > formatted > files, e.g. from PubChem. It seems not to be one of the supported > formats. > Obviously we can use a converter to get pdb format, but thought I'd > ask the > experts. As per Elaine's mail, SDF does seem to be frequently used for 2D diagrams rather than true 3D positions, so maybe reading SDF wouldn't be all that useful. Nonetheless, if you actually some 3D SDF files, the format is simple enough that adding it wouldn't be terribly difficult. It would probably take me an hour if you provided some example files. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From pett at cgl.ucsf.edu Tue Dec 12 16:51:40 2006 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 12 Dec 2006 16:51:40 -0800 Subject: [Chimera-users] compressed versus gzipped Re: Read compressed PDB files -question, suggestion In-Reply-To: <20061211115441.48C7D86AE0@cal1-1.us4.outblaze.com> References: <20061211115441.48C7D86AE0@cal1-1.us4.outblaze.com> Message-ID: <6C4C3403-31A4-4053-98DC-7B74F0147289@cgl.ucsf.edu> On Dec 11, 2006, at 3:54 AM, Moo Cow wrote: > A thousand pardons. You are right. > I phrased the question wrongly. > > Chimera does open gzip'd files ( xx.gz). > It does not open compress'd files (xx.Z). Right. This is because Python's built-in gzip module can only uncompress '.gz' files and not '.Z' files. Since the gzip/uncompress programs aren't available on all platforms (and since .gz compression is considerably more popular than .Z compression) we hadn't bothered offering .Z decompression. >> You can also open gzipped files with Chimera's "open" command or as >> an argument as you start Chimera. > [...] >>> You can use the Chimera File / Open... dialog to directly open >>> a gzip >>> PDB file. This was added to Chimera about one year ago. It >>> does not work > > Why, you may ask, would anyone use compress these days ? > If you mirror or rsync the protein data bank, they are still > distributing > files that have been squashed with compress and have a ".Z" extension. > gunzip will happily eat and uncompress these files. > > I do not know how chimera handles compressed files. If it reads > from a pipe, > it might be nice to persuade it to feed .Z files to gunzip. > I think it might be more difficult if chimera uses the python/zlib > interface. The underlying C++ code that handles PDB files needs a filename (this limitation is being worked on), so .Z decompression would have to go into a temporary file -- which is another reason we weren't motivated to offer it. Here in our lab, we mirror the uncompressed PDB hierarchy, which obviously works fine with Chimera. It uses more bandwidth (though the biggest hit is when you initially set it up) and disk space, but is easier to work with for tools like 'grep' and custom programs. I've added .Z decompression support to Chimera now. It is only enabled if Chimera can find a 'gzip' executable on your execution path (if it can't, it will say so in the Reply Log). I'll be sending you 3 files in a separate mail that should allow you to use your compressed PDB mirror. You will have to edit the pdbDir file to point to the mirror location as mentioned here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html . --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From daniilz at bgnet.bgsu.edu Tue Dec 12 14:19:06 2006 From: daniilz at bgnet.bgsu.edu (Daniil Zaitsev) Date: Tue, 12 Dec 2006 17:19:06 -0500 Subject: [Chimera-users] Benchmark results Message-ID: <1165961946-23856.044.5-smmsdV2.1.2@smtp.bgsu.edu> hi - here is benchmark result for new version of Chimera. Original benchmark progress log file is attached. Graphics NVidia GeForce Go 7200 Processor Intel Core Duo T2050 Clock (MHz) 533 OS Type Windows Surface 990 Mesh 368 Contour 148 Solid 173 Recolor 87 Notes Laptop Test Date 12/06 Chimera Version 2304 Machine HP Pavilion dv2000t Graphics Memory (Mb) 128 Main Memory (Mb) 1024 OS Version XP Home Driver Version 8.4.6.4 From goddard at cgl.ucsf.edu Tue Dec 19 12:33:52 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 19 Dec 2006 12:33:52 -0800 (PST) Subject: [Chimera-users] Benchmark results In-Reply-To: <1165961946-23856.044.5-smmsdV2.1.2@smtp.bgsu.edu> (daniilz@bgnet.bgsu.edu) References: <1165961946-23856.044.5-smmsdV2.1.2@smtp.bgsu.edu> Message-ID: <200612192033.kBJKXqFf2016412@guanine.cgl.ucsf.edu> Hi Daniil, The Chimera surface benchmark you report (990) looks too high to be correct. Probably indicates some OpenGL optimization is circumventing the Chimera timing code -- basically a bug in our Benchmark tool. Could you do the following consistency check. Show the Benchmark dialog (menu entry Tools / Utilities / Benchmark), enter 400 in the "Show standard model, size N" entry field, press the Surface button *below* that entry field. That will show a white cube on your screen. Then click the "Monitor actual frame rate" button. Send me the frame rate it reports. You could also try just running the surface benchmark a few times by pressing the surface button under "Run volume benchmark" and see if it gives a consistent number (to within 5 or 10%). Thanks, Tom From goddard at cgl.ucsf.edu Fri Dec 22 09:08:54 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 22 Dec 2006 09:08:54 -0800 (PST) Subject: [Chimera-users] Flickering graphics In-Reply-To: <6ada93190612220742s5aaa721cn5e57b936b497b19a@mail.gmail.com> (mayaluru@gmail.com) References: <6ada93190612220742s5aaa721cn5e57b936b497b19a@mail.gmail.com> Message-ID: <200612221708.kBMH8s8P1901926@guanine.cgl.ucsf.edu> Hi Murali, What kind of flickering do you see when moving maps in Chimera? Does the surface appear shattered? One nvidia graphics driver bug I have seen causes the surface to appear broken into many triangles instead of smooth while it is moved. Or is it tearing that you see? That is when the top half of the screen momentarily shows one position for the map but the bottom shows a different one. That happens because you are moving the model and the redraw is not synchronized to the vertical refresh of the display. That is a graphics driver setting problem. Or does flicker mean it appears like every other frame is black? Every possibility I can think of points to a graphics driver problem, not a Chimera problem. You can check on Linux what graphics driver you are using with the glxinfo command: % glxinfo ... OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.5.2 NVIDIA 66.29 ... The OpenGL renderer and version lines tell you the driver. If it says "Mesa" this means you have no driver installed and it is using software rendering (no hardware acceleration). Usually a new Linux system does not have a graphics driver installed by default so you have to get the driver from the NVidia web site. http://www.nvidia.com/content/drivers/drivers.asp The latest Nvidia GeForce driver version is 9746. The first step to try to fix your problem is update to the newest driver. Tom > Date: Fri, 22 Dec 2006 09:42:43 -0600 > From: "Murali Ayaluru" > To: goddard at cgl.ucsf.edu > Subject: flickerings in model > > Hi, > > Greetings! > > I am using Chimera (chimera-1.2304-linux.exe) in Linux (FC-6) environment. > Basically I use this > for visualizing the structures generated from EM. While moving the model > (either vertical or horizontal) and also while rendering the volumes, I saw > lot of flickering in the model. Is there some parameter I have to change > to fix this problem? The graphic card we use is nVidia GeForce 7300 LE. I > don't have much experience in linux OS. Any suggestions to fix the problem > will be highly appreciated. > > Thanks and have a nice day. > > Regards, > Murali From goddard at cgl.ucsf.edu Fri Dec 29 14:33:13 2006 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 29 Dec 2006 14:33:13 -0800 (PST) Subject: [Chimera-users] chimera and my ATI card In-Reply-To: <20061229075929.21E271DB02@handler9.mail.rice.edu> (triffo@rice.edu) References: <20061229075929.21E271DB02@handler9.mail.rice.edu> Message-ID: <200612292233.kBTMXDbM1731460@guanine.cgl.ucsf.edu> Hi Jeff, The system crash on your laptop indicates it is a graphics driver problem. Unfortunately these are very common -- maybe 1 in 20 driver version / graphics card combinations have Chimera crashing or system crashing bugs. I intend to make a web page that includes all the bad combinations we have encountered -- hopefully I'll get to it in January. The reason Chimera is particularly susceptible to these bugs is that it uses many capabilities of the OpenGL 3-d graphics library -- some that are seldom used by video games and other 3-d applications. There are only 4 practical solutions: 1) update the driver, 2) use an older driver, 3) set driver options to use less OpenGL acceleration, or 4) use a different machine. I use solution 2 on my home machine with an Nvidia Quadro driver that is a dozen versions behind the current one and over a year old. New drivers come out fairly often for both Nvidia and ATI cards and usually do not offer better performance -- only a new set of bugs (old ones fixed, new ones introduced). If you could send us a Chimera bug report by starting Chimera and use menu entry Help / Report a Bug this will send us your graphics driver version so we can include it on our bad drivers page. And if you find another driver version that works I would of course like to know which version. Sorry to offer so little help on this. Tom From: Jeff To: "'Thomas Goddard'" Subject: chimera and my ATI card Date: Thu, 28 Dec 2006 23:59:26 -0800 hi Tom, on my laptop (IBM T43p), chimera is crashing the machine. I have the latest release installed in WinXP (as of 12/21), and a fairly recent release (within 2006) installed on Linux (also on same machine, different drive). this occurs with both really small volumes (100 cubed) and larger ones (600x400x100 or so), doing common tasks like rotating a surface rendering. in XP, it froze with a required reboot; with Linux, I got the screen that I have attached. the GPU is an 'ATI MOBILITY FireGL V3200', which was one of the GPUs you could get on a 'workstation laptop' back in June '05. I am pretty sure the drivers are current (within '06) and I use the ATI proprietary drivers in both XP and Linux - there is a standard ATI driver package that you download and then it just installs the proper version for your card. On an older laptop (prior to '05) I had similar issues with crashing, also on an ATI card, but different generation (was a Dell purchased in feb. '02). on my desktop workstation with an NVidia card, it works fine, although sometimes surfaces get rendered in the wrong place (something in background looks more in foreground, etc) - but I don't have problems with chimera getting killed (or killing the OS). any thoughts on having it run on my laptop? this machine is the only one I have access to outside of the lab, and was originally bought for this purpose (reconstructions and processing). thanks, -jeff From kvaughan at bc.cc.ca.us Sat Dec 30 08:16:34 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Sat, 30 Dec 2006 08:16:34 -0800 Subject: [Chimera-users] command line zone selection? Message-ID: <200612300816.34842.kvaughan@bc.cc.ca.us> I'm putting together a demo for my students this next semester, and was hoping to be able to do a zone selection about the ligand. Is this possible with the command line? I haven't been able to pull out a reference for such, yet. Certainly I could pull together the list of residues myself, but thought it'd be nice to have the command available. Some students might like to create a demo file for their reports, and this would become a pivotal tool for a subset of those. If not directly available, then a wishlist addition, perhaps? Something like: zonesel [within|beyond] [+/- angstroms] [atom-spec] where the sign of the angstrom value denotes whether to include (+) or exclude (-) the atoms in atom-spec. Cheers, Kenward Vaughan -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? From meng at cgl.ucsf.edu Sat Dec 30 10:08:05 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 30 Dec 2006 10:08:05 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: <200612300816.34842.kvaughan@bc.cc.ca.us> References: <200612300816.34842.kvaughan@bc.cc.ca.us> Message-ID: <4dfe8875b1721ff0f0f114d63f4a31ee@cgl.ucsf.edu> Hi Kenward, There *is* a command-line way to specify atoms/residues in a zone defined by other atoms. It might have been hard to find since it's not a separate command, but instead an atom specification that can be used with many commands. The general form is command atom-spec zaN" could be used for all atoms farther away than N angstroms. Using "z" or "zr" instead of "za" gives a residue-based cutoff - you would always get whole residues even if only parts of them fall in the zone. The "command" can be "select" or many other things (color, display, etc.). Here are a couple more examples: rlabel ions z<4 (label residues within 4 angstroms of any ions) disp #0 & #2 z<5 (display residues in model 0 that are within 5 angstroms of any atoms in model 2). The description in the manual (click the "zones" link): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html It can be confusing, so feel free to write back if you have problems generating the command needed in your particular situation! Best, 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 Dec 30, 2006, at 8:16 AM, Kenward Vaughan wrote: > I'm putting together a demo for my students this next semester, and > was hoping > to be able to do a zone selection about the ligand. Is this possible > with the > command line? I haven't been able to pull out a reference for such, > yet. > > Certainly I could pull together the list of residues myself, but > thought it'd > be nice to have the command available. Some students might like to > create a > demo file for their reports, and this would become a pivotal tool for a > subset of those. > > If not directly available, then a wishlist addition, perhaps? > Something like: > > zonesel [within|beyond] [+/- angstroms] [atom-spec] > > where the sign of the angstrom value denotes whether to include (+) or > exclude > (-) the atoms in atom-spec. > > Cheers, > > > Kenward Vaughan > -- > .'^~;,_ > Dr. Kenward Vaughan `:,'~~~~~ > Professor of Chemistry \;:/ > Bakersfield College |,;| > 1801 Panorama Drive / ', \ > Bakersfield, CA 93305 / o O \ > http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) > ---========--- > ???$$MM$$??? > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From gregc at cgl.ucsf.edu Sat Dec 30 10:09:49 2006 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Sat, 30 Dec 2006 10:09:49 -0800 (PST) Subject: [Chimera-users] command line zone selection? In-Reply-To: <200612300816.34842.kvaughan@bc.cc.ca.us> References: <200612300816.34842.kvaughan@bc.cc.ca.us> Message-ID: On Sat, 30 Dec 2006, Kenward Vaughan wrote: > I'm putting together a demo for my students this next semester, and was hoping > to be able to do a zone selection about the ligand. Is this possible with the > command line? I haven't been able to pull out a reference for such, yet. > > Certainly I could pull together the list of residues myself, but thought it'd > be nice to have the command available. Some students might like to create a > demo file for their reports, and this would become a pivotal tool for a > subset of those. > > If not directly available, then a wishlist addition, perhaps? Something like: > > zonesel [within|beyond] [+/- angstroms] [atom-spec] > > where the sign of the angstrom value denotes whether to include (+) or exclude > (-) the atoms in atom-spec. Take a look at the Atom Specification documentation in the subsection on Zones. So: display ligand z<5 Will display all of the residues that are less than 5 angstroms from the ligand. - Greg From kvaughan at bc.cc.ca.us Sat Dec 30 10:43:59 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Sat, 30 Dec 2006 10:43:59 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: References: <200612300816.34842.kvaughan@bc.cc.ca.us> Message-ID: <200612301044.00073.kvaughan@bc.cc.ca.us> On Saturday 30 December 2006 10:09, you wrote: > On Sat, 30 Dec 2006, Kenward Vaughan wrote: > > I'm putting together a demo for my students this next semester, and > > was hoping to be able to do a zone selection about the ligand. Is > > this possible with the command line? I haven't been able to pull > > out a reference for such, yet. > > > > Certainly I could pull together the list of residues myself, but > > thought it'd be nice to have the command available. Some students > > might like to create a demo file for their reports, and this would > > become a pivotal tool for a subset of those. > > > > If not directly available, then a wishlist addition, perhaps? > > Something like: > > > > zonesel [within|beyond] [+/- angstroms] [atom-spec] > > > > where the sign of the angstrom value denotes whether to include (+) > > or exclude (-) the atoms in atom-spec. > > Take a look at the Atom Specification documentation in the subsection > on Zones. So: > > display ligand z<5 > > Will display all of the residues that are less than 5 angstroms from > the ligand. > > - Greg Ah. That was too easy! I obviously didn't go deep enough into that section. :( Many thanks, Greg! Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? From kvaughan at bc.cc.ca.us Sat Dec 30 12:30:09 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Sat, 30 Dec 2006 12:30:09 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: <4dfe8875b1721ff0f0f114d63f4a31ee@cgl.ucsf.edu> References: <200612300816.34842.kvaughan@bc.cc.ca.us> <4dfe8875b1721ff0f0f114d63f4a31ee@cgl.ucsf.edu> Message-ID: <200612301230.09310.kvaughan@bc.cc.ca.us> On Saturday 30 December 2006 10:08, you wrote: > Hi Kenward, > There *is* a command-line way to specify atoms/residues in a zone > defined by other atoms. It might have been hard to find since it's > not a separate command, but instead an atom specification that can be > used with many commands. > > The general form is > command atom-spec za It can be confusing, so feel free to write back if you have problems > generating the command needed in your particular situation! > Best, > Elaine Thank you so much, Elaine and Greg. I appreciate the fact that y'all are up and running even today (things are different at a community college :). In my demo, I've found that rotating a model about to create a specific view in one panel, followed in the next panel by either changing the atom representation or recoloring the atoms, causes a resetting of the view to the opening orientation. Is this a known issue? Kenward ps. BTW, can a selected group of atoms be named at the command line? Another question I can't seem to find an answer to... :( -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? From meng at cgl.ucsf.edu Sat Dec 30 14:29:25 2006 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 30 Dec 2006 14:29:25 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: <200612301230.09310.kvaughan@bc.cc.ca.us> References: <200612300816.34842.kvaughan@bc.cc.ca.us> <4dfe8875b1721ff0f0f114d63f4a31ee@cgl.ucsf.edu> <200612301230.09310.kvaughan@bc.cc.ca.us> Message-ID: Hi Kenward, Just changing the color or representation should not reset the orientation *achieved by commands* (more explanation below) at the end of the previous panel. There are examples in the demos that come with Chimera (Tools... Demos) - e.g. in the hormone-receptor demo, the position does not reset to the original when switching from panel 2 to panel 3 (FSH undisplayed, leucines in FSH receptor displayed). I also tried playing this demo up to panel 2, opening the demo in the editor (from the Demo dialog, File... Open in Editor), unchecking the roll commands in panel 3, and then clicking Execute to test whether having some movement suppresses a reset bug. However, there was still no reset between panels 2 and 3. I'm using version 1.2304. Note that any rotations/translations performed *manually* will not be incorporated into a panel, only the ones expressed as commands. If you rotated/translated manually, there will be a resetting to the orientation without those manual movements before the next set of commands are applied. Perhaps that is what happened. That is the tricky thing about Demos: everything must be done with commands, and it can take a fair amount of effort to get the orientations you want. Actually, the resetting to the orientation achieved purely by commands is at least partly a feature rather than a bug, because it allows demo viewers to change the view manually within a panel however they desire without disrupting the views the demo creator intended to be visited during the course of the demo. Hope that makes sense... It may be instructive to open the existing demos in the editor as mentioned above, if you haven't tried that already. If the problem persists, let me know what version of Chimera you're using. Also, if you want you could send me your demo file and any associated data files and I could take a more in-depth look next week. About specifying a bunch of atoms over and over, you can name a selection and then use the selection's name. See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#namesel However, a selection can only be named using the menu currently, so for Demos a different approach is required. In similar situations, I bypass selection entirely and instead alias that set of atoms (using the same specifications that you would have used to select the atoms) and then use the resulting alias in subsequent commands. For example: Command: alias key #0:17.a,138.a,190.a #1:38.b,158.b,221.b #2:86.a,247.a,342.a Command: rep sphere key Command: focus key Command: color byatom key The alias statement can include all kinds of specifications - zones, categories such as "ligand," combination operators & | ~ , etc. Man page for "alias": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html Technically we aren't working today. However, I like to check my mail every day and will occasionally answer mail from devoted Chimera users! 8-) 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 Dec 30, 2006, at 12:30 PM, Kenward Vaughan wrote: > In my demo, I've found that rotating a model about to create a specific > view in one panel, followed in the next panel by either changing the > atom representation or recoloring the atoms, causes a resetting of the > view to the opening orientation. Is this a known issue? > > > Kenward > > ps. BTW, can a selected group of atoms be named at the command line? > Another question I can't seem to find an answer to... :( > -- > .'^~;,_ > Dr. Kenward Vaughan `:,'~~~~~ > Professor of Chemistry \;:/ > Bakersfield College |,;| > 1801 Panorama Drive / ', \ > Bakersfield, CA 93305 / o O \ > http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) > ---========--- > ???$$MM$$??? > From sabuj.pattanayek at vanderbilt.edu Sat Dec 30 14:53:10 2006 From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek) Date: Sat, 30 Dec 2006 16:53:10 -0600 Subject: [Chimera-users] how to change the color and thickness of the unit cell outline Message-ID: <4596EDD6.8090503@vanderbilt.edu> Hi, How do I change the color and thickness of the unit cell outline? Thanks, Sabuj From kvaughan at bc.cc.ca.us Sat Dec 30 19:11:31 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Sat, 30 Dec 2006 19:11:31 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: References: <200612300816.34842.kvaughan@bc.cc.ca.us> <200612301230.09310.kvaughan@bc.cc.ca.us> Message-ID: <200612301911.32120.kvaughan@bc.cc.ca.us> On Saturday 30 December 2006 14:29, Elaine Meng wrote: > Hi Kenward, > Just changing the color or representation should not reset the > orientation *achieved by commands* (more explanation below) at the > end of the previous panel. There are examples in the demos that come > with Chimera (Tools... Demos) - e.g. in the hormone-receptor demo, > the position does not reset to the original when switching from panel > 2 to panel 3 (FSH undisplayed, leucines in FSH receptor displayed). I > also tried playing this demo up to panel 2, opening the demo in the > editor (from the Demo dialog, File... Open in Editor), unchecking the > roll commands in panel 3, and then clicking Execute to test whether > having some movement suppresses a reset bug. However, there was still > no reset between panels 2 and 3. I'm using version 1.2304. ... > If the problem persists, let me know what version of Chimera you're > using. Also, if you want you could send me your demo file and any > associated data files and I could take a more in-depth look next > week. I have uncovered the "problem." In one panel, I might have the following: roll y 1 22 ; roll x -0.8182 22 and in the following panel: repre stick ; color byatom This causes the view in the second panel to revert to what existed prior to the first. **This happens regardless of how long one waits before moving forward from one panel to the next. It is independent of any manual manipulation as well.** If the first line is terminated with a wait: roll y 1 22 ; roll x -0.8182 22 ; wait then the view generated by the rolls is maintained. I took the COX inhibitor demo and tested this with several lines in there as well (7-10, IIRC). The results matched what I see with my own. I've attached two small jpg's which show the effect of removing the wait found in panel 9. I had understood from the help files that "wait" insured following commands were not processed until molecular motion had stopped. I had not included it in my lines since I knew that it wouldn't be needed (the rolls were the only commands processed before control was relinquished back to the user). Apparently the "wait" is required to properly set the coordinates for the next panel. > About specifying a bunch of atoms over and over, you can name a > selection and then use the selection's name. See > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#namesel > > However, a selection can only be named using the menu currently, so > for Demos a different approach is required. In similar situations, I > bypass selection entirely and instead alias that set of atoms (using > the same specifications that you would have used to select the atoms) ... It's definitely a good start! Thanks! > Technically we aren't working today. However, I like to check my > mail every day and will occasionally answer mail from devoted Chimera > users! 8-) > > I hope this helps, > Elaine Happy New Year! :-) Kenward > On Dec 30, 2006, at 12:30 PM, Kenward Vaughan wrote: > > In my demo, I've found that rotating a model about to create a > > specific view in one panel, followed in the next panel by either > > changing the atom representation or recoloring the atoms, causes a > > resetting of the view to the opening orientation. Is this a known > > issue? > > > > > > Kenward > > > > ps. BTW, can a selected group of atoms be named at the command > > line? Another question I can't seem to find an answer to... :( -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? -------------- next part -------------- A non-text attachment was scrubbed... Name: imageNoWait.jpg Type: image/jpeg Size: 2638 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: imageWait.jpg Type: image/jpeg Size: 2842 bytes Desc: not available URL: From kvaughan at bc.cc.ca.us Sat Dec 30 19:14:02 2006 From: kvaughan at bc.cc.ca.us (Kenward Vaughan) Date: Sat, 30 Dec 2006 19:14:02 -0800 Subject: [Chimera-users] command line zone selection? In-Reply-To: References: <200612300816.34842.kvaughan@bc.cc.ca.us> <200612301230.09310.kvaughan@bc.cc.ca.us> Message-ID: <200612301914.02817.kvaughan@bc.cc.ca.us> On Saturday 30 December 2006 14:29, Elaine Meng wrote: > Hi Kenward, > Just changing the color or representation should not reset the > orientation *achieved by commands* (more explanation below) at the > end of the previous panel. There are examples in the demos that come > with Chimera (Tools... Demos) - e.g. in the hormone-receptor demo, > the position does not reset to the original when switching from panel > 2 to panel 3 (FSH undisplayed, leucines in FSH receptor displayed). I > also tried playing this demo up to panel 2, opening the demo in the > editor (from the Demo dialog, File... Open in Editor), unchecking the > roll commands in panel 3, and then clicking Execute to test whether > having some movement suppresses a reset bug. However, there was still > no reset between panels 2 and 3. I'm using version 1.2304. ... > If the problem persists, let me know what version of Chimera you're > using. Also, if you want you could send me your demo file and any > associated data files and I could take a more in-depth look next > week. I have uncovered the "problem." In one panel, I might have the following: roll y 1 22 ; roll x -0.8182 22 and in the following panel: repre stick ; color byatom This causes the view in the second panel to revert to what existed prior to the first. **This happens regardless of how long one waits before moving forward from one panel to the next. It is independent of any manual manipulation as well.** If the first line is terminated with a wait: roll y 1 22 ; roll x -0.8182 22 ; wait then the view generated by the rolls is maintained. I took the COX inhibitor demo and tested this with several lines in there as well (7-10, IIRC). The results matched what I see with my own. I've attached two small jpg's which show the effect of removing the wait found in panel 9. I had understood from the help files that "wait" insured following commands were not processed until molecular motion had stopped. I had not included it in my lines since I knew that it wouldn't be needed (the rolls were the only commands processed before control was relinquished back to the user). Apparently the "wait" is required to properly set the coordinates for the next panel. > About specifying a bunch of atoms over and over, you can name a > selection and then use the selection's name. See > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#namesel > > However, a selection can only be named using the menu currently, so > for Demos a different approach is required. In similar situations, I > bypass selection entirely and instead alias that set of atoms (using > the same specifications that you would have used to select the atoms) ... It's definitely a good start! Thanks! > Technically we aren't working today. However, I like to check my > mail every day and will occasionally answer mail from devoted Chimera > users! 8-) > > I hope this helps, > Elaine Happy New Year! :-) Kenward > On Dec 30, 2006, at 12:30 PM, Kenward Vaughan wrote: > > In my demo, I've found that rotating a model about to create a > > specific view in one panel, followed in the next panel by either > > changing the atom representation or recoloring the atoms, causes a > > resetting of the view to the opening orientation. Is this a known > > issue? > > > > > > Kenward > > > > ps. BTW, can a selected group of atoms be named at the command > > line? Another question I can't seem to find an answer to... :( -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$??? -------------- next part -------------- A non-text attachment was scrubbed... Name: imageNoWait.jpg Type: image/jpeg Size: 2638 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: imageWait.jpg Type: image/jpeg Size: 2842 bytes Desc: not available URL: