From dmorgan at ucdavis.edu Thu Dec 1 09:48:07 2005 From: dmorgan at ucdavis.edu (David G. Morgan) Date: Thu, 1 Dec 2005 09:48:07 -0800 Subject: [Chimera-users] Sequence alignment Message-ID: <6638778774B9F14997D316BCC99504CE3AF1F1@hermes.mcb.ucdavis.edu> Hi, I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window. David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX) From meng at cgl.ucsf.edu Thu Dec 1 10:55:45 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 1 Dec 2005 10:55:45 -0800 Subject: [Chimera-users] Sequence alignment In-Reply-To: <6638778774B9F14997D316BCC99504CE3AF1F1@hermes.mcb.ucdavis.edu> References: <6638778774B9F14997D316BCC99504CE3AF1F1@hermes.mcb.ucdavis.edu> Message-ID: <7EA61019-83D6-4799-8374-BF79D30397FB@cgl.ucsf.edu> Hi David, Any selection on the structure is automatically shown in the associated sequence in the alignment. The default is a dark green outline box. If you open the Region Browser (from the sequence window menu, Tools... Region Browser) you can see the region, named "Chimera selection," and its border color and interior color settings. If you want a different color scheme to be used, click on the color wells and edit the colors as desired. Best, Elaine On Dec 1, 2005, at 9:48 AM, David G. Morgan wrote: > Hi, > > I'm learning to use the sequence alignment tools in chimera. I > know that I can highlight sequences in the alignment window and select > residues in the structure, but is it possible to do the opposite? In > other words, I'd like to box or otherwise select some residue(s) in > the > structure and have that region highlighted or otherwise marked in the > aligned sequence window. > > David Gene Morgan > Advanced Microscopy & Proteomics > Molecular & Cellular Biology > University of California at Davis > 530 752 2693 (lab) > 530 752 3085 (FAX) > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 meng at cgl.ucsf.edu Thu Dec 1 11:14:21 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 1 Dec 2005 11:14:21 -0800 Subject: [Chimera-users] Sequence alignment In-Reply-To: <6638778774B9F14997D316BCC99504CE3AF1F1@hermes.mcb.ucdavis.edu> References: <6638778774B9F14997D316BCC99504CE3AF1F1@hermes.mcb.ucdavis.edu> Message-ID: <2158DA18-F24A-41B6-987C-ABF40CF20E77@cgl.ucsf.edu> Hi David, I'd like to add that although the "Chimera selection" region will always keep track of the current Chimera selection, you can copy the region to another name to preserve it (click Copy on the Region Browser). We've been using the word "region" to mean boxed areas on the sequence alignment, and a single region can actually include more than one disjoint box. Here is an example of why you'd want to copy the region: if you wanted to keep a region with all residues near a ligand, you could first select those residues and then Copy the "Chimera selection" region to another name, say, "binding site." Then even when you change the current Chimera selection, the "binding site" region will stay the same. You will want to make the border and interior colors of the copy or copies different from one another, however, so it will not be visually confusing. You can also toggle between showing and not showing a region in the alignment with the "Shown" checkboxes in the Region Browser. Best, Elaine On Dec 1, 2005, at 9:48 AM, David G. Morgan wrote: > Hi, > > I'm learning to use the sequence alignment tools in chimera. I > know that I can highlight sequences in the alignment window and select > residues in the structure, but is it possible to do the opposite? In > other words, I'd like to box or otherwise select some residue(s) in > the > structure and have that region highlighted or otherwise marked in the > aligned sequence window. > > David Gene Morgan > Advanced Microscopy & Proteomics > Molecular & Cellular Biology > University of California at Davis > 530 752 2693 (lab) > 530 752 3085 (FAX) > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 svozil at uochb.cas.cz Fri Dec 2 06:53:48 2005 From: svozil at uochb.cas.cz (Daniel Svozil) Date: Fri, 02 Dec 2005 15:53:48 +0100 Subject: [Chimera-users] Add hydrogens to get -NH2 group Message-ID: <43905FFC.7020404@uochb.cas.cz> Hi all, if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly? Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312 From pett at cgl.ucsf.edu Fri Dec 2 15:06:14 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 2 Dec 2005 15:06:14 -0800 Subject: [Chimera-users] Add hydrogens to get -NH2 group In-Reply-To: <43905FFC.7020404@uochb.cas.cz> References: <43905FFC.7020404@uochb.cas.cz> Message-ID: <3B5B1667-3A7E-4E57-8AC4-EA069DFC215F@cgl.ucsf.edu> Hi Dan, Chimera assumes that sp3 nitrogens bonded only to sp3 carbons and/or hydrogens are positively charged at physiological pH. That means that their idatmType attribute is "N3+". If you actually do want to use the neutral species, you need to get the idatmType changed to "N3" before adding hydrogens. Here is some Python code that will change all selected nitrogens' idatmType to "N3": --- start code --- import chimera for a in chimera.selection.currentAtoms(): if a.element.name != "N": continue a.idatmType = "N3" --- end code --- You could either type that code into the IDLE interpreter (Tools- >General Controls->IDLE) or put it in a .py file and open that file with File...Open or with Chimera's command line. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 2, 2005, at 6:53 AM, Daniel Svozil wrote: > Hi all, > > if I use addH tool on the C-N, I would expect to get C-NH2, but I get > C-NH3 instead. How should I proceed to get C-NH2 correctly? > > Thanks > Dan > > -- > Daniel Svozil, PhD > Institute of Organic Chemistry and Biochemistry > Center for Biomolecules and Complex Molecular Systems > http://www.molecular.cz/~svozil > Czech Republic > > phone: +420-220 410 312 > _______________________________________________ > 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 cyberworm_upm at yahoo.com Sun Dec 4 17:42:31 2005 From: cyberworm_upm at yahoo.com (Reiner Villavicencio) Date: Mon, 5 Dec 2005 01:42:31 +0000 (GMT) Subject: [Chimera-users] Data reporting In-Reply-To: Message-ID: <20051205014232.82186.qmail@web31609.mail.mud.yahoo.com> Dear all, I have learned that 3D results/data from molecular dynamics or docking can be compressed to produce informative 2D diagrams for publication. Can anyone recommend such a program? Thank you and good day "Its hard to hold on to something that can never be yours in anyway you want... something that wasn?t really yours to begin with... you just have to go on and accept the fact that while good things never last some don?t even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From azelter at u.washington.edu Tue Dec 6 12:53:37 2005 From: azelter at u.washington.edu (Alex Zelter) Date: Tue, 06 Dec 2005 12:53:37 -0800 Subject: [Chimera-users] chimera for linux ppc Message-ID: <4395FA51.8040806@u.washington.edu> Hi, I was wondering if it would be possible for the developers to compile a binary version of chimer for use on linux ppc architecture seeing as it is not possible for a user to compile for themselves due to the proprietary solvent-accessible molecular surfacing library. I know this is not a common architecture, but some people do use it. Thanks in advance, Alex Zelter From luke.kontogiannis at bioch.ox.ac.uk Wed Dec 7 01:39:48 2005 From: luke.kontogiannis at bioch.ox.ac.uk (Luke Kontogiannis) Date: Wed, 07 Dec 2005 09:39:48 +0000 Subject: [Chimera-users] Missing tools Message-ID: <1133948388.8257.6.camel@localhost.localdomain> Hi all, I installed chimera on windows and everything works fine. However, I installed it on ubuntu linux 5.10 yesterday and there are some tools that are missing such as multiscale. Is the windows version of chimera simply more capable or have I done something wrong? I simply ran the chimeral.exe file as root and it seemed to install fine. I even tried replacing the share directory on the linux box at work with the one from the windows version but that gave errors upon launching. Any ideas? Thanks Luke From luke.kontogiannis at bioch.ox.ac.uk Wed Dec 7 02:16:10 2005 From: luke.kontogiannis at bioch.ox.ac.uk (Luke Kontogiannis) Date: Wed, 07 Dec 2005 10:16:10 +0000 Subject: [Chimera-users] Missing tools Message-ID: <1133950570.8257.12.camel@localhost.localdomain> I had installed the current production release chimera-1.2184-linux.exe. Just now I downloaded and installed the latest snapshot release chimera-1.2186-linux.exe and this version has the multiscale tool under Tools -> Higher-order structure Luke From conrad at cgl.ucsf.edu Wed Dec 7 09:33:18 2005 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 7 Dec 2005 09:33:18 -0800 Subject: [Chimera-users] chimera for linux ppc In-Reply-To: <4395FA51.8040806@u.washington.edu> References: <4395FA51.8040806@u.washington.edu> Message-ID: <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> Which flavor of Linux are you using? For Windows, we have been building on RedHat Linux 7.1, which seems to create executables that run across a large variety of Linux distributions. Is there a similar platform for Linux PPC? Conrad On Dec 6, 2005, at 12:53 PM, Alex Zelter wrote: > Hi, > I was wondering if it would be possible for the developers to > compile a > binary version of chimer for use on linux ppc architecture seeing > as it > is not possible for a user to compile for themselves due to the > proprietary solvent-accessible molecular surfacing library. I know > this > is not a common architecture, but some people do use it. > Thanks in advance, > Alex Zelter > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From azelter at u.washington.edu Wed Dec 7 09:44:17 2005 From: azelter at u.washington.edu (A. Zelter) Date: Wed, 7 Dec 2005 09:44:17 -0800 (PST) Subject: [Chimera-users] chimera for linux ppc In-Reply-To: <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> References: <4395FA51.8040806@u.washington.edu> <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> Message-ID: > Which flavor of Linux are you using? For Windows, we have been building on > RedHat Linux 7.1, which seems to create executables that run across a large > variety of Linux distributions. Is there a similar platform for Linux PPC? >> I was wondering if it would be possible for the developers to compile a >> binary version of chimer for use on linux ppc architecture seeing as it >> is not possible for a user to compile for themselves due to the Hi Conrad, Thanks for your reply. I'm not sure I understand the question. I am running Ubuntu linux with the 2.6.12-10-powerpc kernel. Redhat make a PPC distro, as do SuSE, Debian and many others. Changing to RedHat wouldn't solve the problem however, which is that you offer 2 linux binaries. One for 32 bit x86 architecture and one for 64 bit architecture. For me to be able to run Chimera on my machine I would need a binary compiled for Mac PPC architecture (my processor is a G3). This would still be true if I were running RedHat on my Mac. Thanks, Alex From wathen at physics.arizona.edu Wed Dec 7 10:54:14 2005 From: wathen at physics.arizona.edu (Geoffrey H Wathen) Date: Wed, 7 Dec 2005 10:54:14 -0800 Subject: [Chimera-users] chimera for linux ppc In-Reply-To: References: <4395FA51.8040806@u.washington.edu> <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> Message-ID: <0857820F-CF3D-4D92-9749-9E8458282515@physics.arizona.edu> I've used YellowDog in the past, and I think it is a good dist. I wouldn't mind seeing a PPC Linux version of Chimera, either. Geoff. On Dec 7, 2005, at 10:50 AM, A. Zelter wrote: >> I think Conrad is saying that on the x86 architecture they can >> compile for RedHat and it will run on most distributions of x86 >> Linux. He's asking if there's a similar situation on PPC Linux, >> and which distribution of PPC Linux would provide the best >> prospects for such coverage. It seems to me that this is to >> minimize the occurrence of someone saying "I see you have the >> binaries for XYZ PPC Linux, but they don't run on my distribution >> of ABC PPC Linux. Could you please compile it for ABC PPC Linux?" > > Ahhh thanks. I knew I didn't get something. Well, I'm no expert on > that kind of thing, but Fedora Core 4 has a ppc version. I think > this is a little more modern than Red Hat Linux 7.1 - it runs > kernel 2.6.11. However, RedHat did make a PPC version of their 7.1 > distro (Red Hat Linux 7.1 for pSeries). I suppose that would be > equivalent. Another good bet might be yellowdog linux. The latest > version is 4.0.1, and it uses kernel 2.6.10. Yellowdog is based on > redhat but built specifically for Macs. This is probably what I > would try using. > Alex > > From goddard at cgl.ucsf.edu Wed Dec 7 10:56:24 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 7 Dec 2005 10:56:24 -0800 (PST) Subject: [Chimera-users] Missing tools In-Reply-To: <1133950570.8257.12.camel@localhost.localdomain> (message from Luke Kontogiannis on Wed, 07 Dec 2005 10:16:10 +0000) References: <1133950570.8257.12.camel@localhost.localdomain> Message-ID: <200512071856.jB7IuOhM1639939@guanine.cgl.ucsf.edu> Hi Luke, The Chimera distributions on all the platforms (Windows, Mac, Linux, ...) have the same set of features and the same menu entries. The Chimera Tools menu was rearranged several months ago and the Multiscale tool is now under Tools / Higher-Order Structure. Before it was under Tools / Multiscale. The Chimera 1.2184 version has Multiscale but it is in the new location. Apologies for rearranging menu entries. As we get more tools the old Tools categories didn't seem the best. Tom From goddard at cgl.ucsf.edu Wed Dec 7 15:50:51 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 7 Dec 2005 15:50:51 -0800 (PST) Subject: [Chimera-users] chimera for linux ppc In-Reply-To: <0857820F-CF3D-4D92-9749-9E8458282515@physics.arizona.edu> (message from Geoffrey H Wathen on Wed, 7 Dec 2005 10:54:14 -0800) References: <4395FA51.8040806@u.washington.edu> <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> <0857820F-CF3D-4D92-9749-9E8458282515@physics.arizona.edu> Message-ID: <200512072350.jB7NopxR2087515@guanine.cgl.ucsf.edu> Here's an an overview of possible new platforms for Chimera distributions. Currently we distribute Chimera binaries for: Windows (x86, 32-bit app) Mac OS X (PPC, requires X windows) Linux (x86, 32-bit) SGI Irix Alpha Tru64 Additional platforms that we do not currently distribute for are: Mac OS X Aqua (PPC, no X windows) Mac OS X, Intel Linux 64-bit kernel Windows 64-bit Linux, PPC There are two obstacles to supporting a new platform. We want to have the target system in our lab for building and testing. This is the case for all our current distributions. And we have to put in work to build the following 28 third-party packages that Chimera uses: TclTk Togl Tix Pmw PyOpenGL zlib Python Numeric jpeg tiff freetype Imaging netcdf Scientific MMTK HappyDoc tr openssl ftgl omni msms otf autostereo swish-e FFmpeg al2co expat qhull And we will update versions of these third party packages and will have to get them to work on all distributed platforms in the future. Currently it is not possible for outsiders to compile Chimera. One reason is that one package, msms molecular surface calculation, cannot be distributed. But the real practical obstacle is that it would take some debugging to successfully compile all the third-party packages on a new platform. Chimera has makefiles to build all the third-party packages but a few of them are likely to fail to build on any new platform and some building expertise will be needed to resolve the problems. Here are a few comments on the possible new platforms. We have built Mac OS X Aqua versions of Chimera. Because of many problems with the Tk window toolkit we did not distribute it. That was 2 years ago and many of the problems may be fixed. We have built 64-bit Linux versions of Chimera. The 32-bit linux Chimera will run on those machines. The reason for building a 64-bit version is to handle very large data sets (> 4 Gbytes). The 64-bit pointers are needed to have an address space bigger than 4 Gbytes. The large data sets are primarily density maps. The Mac OS X Intel platform will become important in under a year and we will have to support it. The Linux PPC platform seems likely to become less common with Apple no longer producing PPC machines in the near future. I'm not sure there are enough potential Linux PPC Chimera users to make supporting this platform worthwhile. In summary, I think Mac Aqua and Mac Intel are the next 2 platforms we are likely to support. Tom From goddard at cgl.ucsf.edu Wed Dec 7 19:10:49 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 7 Dec 2005 19:10:49 -0800 (PST) Subject: [Chimera-users] chimera for linux ppc In-Reply-To: (azelter@u.washington.edu) References: <4395FA51.8040806@u.washington.edu> <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> <0857820F-CF3D-4D92-9749-9E8458282515@physics.arizona.edu> <200512072350.jB7NopxR2087515@guanine.cgl.ucsf.edu> Message-ID: <200512080310.jB83An6F1623154@guanine.cgl.ucsf.edu> Hi Alex, We have a problem where the msms molecular surface code crashes and takes down Chimera with it, so moving it out of Chimera as a separate binary might be helpful for that problem too. We'll keep in mind the desirability of making Chimera compilable by outsiders while we figure out how to fix the molecular surface problems. Thanks for the suggestion. Tom From goddard at cgl.ucsf.edu Wed Dec 7 19:13:56 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 7 Dec 2005 19:13:56 -0800 (PST) Subject: [Chimera-users] Moving selected atoms Message-ID: <200512080313.jB83Dugs1618332@guanine.cgl.ucsf.edu> I wrote a Chimera extension that allows moving just selected atoms with the mouse. This is for modifying molecular structures. Here is the code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds mouse modes to move selected atoms. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last two are for shifting and rotating selected atoms. Reassign mouse buttons (say buttons 1 and 2) to these modes and you can move selected atoms. There is no undo. I'll have to make this easier to use and put it into Chimera. Tom From goddard at cgl.ucsf.edu Thu Dec 8 11:16:55 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 8 Dec 2005 11:16:55 -0800 (PST) Subject: [Chimera-users] Moving selected atoms Message-ID: <200512081916.jB8JGtnr1739763@guanine.cgl.ucsf.edu> I improved the mouse mode for moving selected atoms so if no atoms are selected it moves everything like the normal rotation and translation mouse modes -- all active models are moved. The new code is http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar For installation instructions see my previous chimera-users message. http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000609.html The new behaviour makes it easy to move some atoms, then rotate the view, then move the atoms again. After moving the atoms you can clear the selection using ctrl-click on the background of the graphics window, then rotate everything to the new view point, then press the left arrow key (undo selection) to revert to the previous selection, and continue moving the atoms. Tom From rquiroga at immf.uncor.edu Thu Dec 8 16:26:38 2005 From: rquiroga at immf.uncor.edu (rquiroga at immf.uncor.edu) Date: Thu, 08 Dec 2005 21:26:38 -0300 Subject: [Chimera-users] Concerns regarding secondary structure Message-ID: <1134087998.4398cf3e8bda8@www.immf.uncor.edu> Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga From azelter at u.washington.edu Wed Dec 7 19:01:02 2005 From: azelter at u.washington.edu (A. Zelter) Date: Wed, 7 Dec 2005 19:01:02 -0800 (PST) Subject: [Chimera-users] chimera for linux ppc In-Reply-To: <200512072350.jB7NopxR2087515@guanine.cgl.ucsf.edu> References: <4395FA51.8040806@u.washington.edu> <058F8EC5-9AFD-413C-8D2C-A7FB580B11D9@cgl.ucsf.edu> <0857820F-CF3D-4D92-9749-9E8458282515@physics.arizona.edu> <200512072350.jB7NopxR2087515@guanine.cgl.ucsf.edu> Message-ID: > There are two obstacles to supporting a new platform. We want to > have the target system in our lab for building and testing. This is the > case for all our current distributions. And we have to put in work to > build the following 28 third-party packages that Chimera uses: Hi Tom, Thanks for the information. That sounds fair enough - ppc architecture will be less important soon and even now only a small proportion of linux users use that architecture. I have one more thought about support for different platforms though. Could you have a binary just for the msms molecular surface calculation package, and then the other packages as source plus makefiles. That would probably be much less work for you, and then whoever wanted to spend the time trying to get it to work could do, but you wouldn't have to be involved or support it in any way? You might even find others identify and fix problems on these new platforms - saving work for the Chimera team. Just a thought. Thanks for your consideration. Alex From rquiroga at immf.uncor.edu Thu Dec 8 16:16:59 2005 From: rquiroga at immf.uncor.edu (rquiroga at immf.uncor.edu) Date: Thu, 08 Dec 2005 21:16:59 -0300 Subject: [Chimera-users] Concerns regarding secondary structure Message-ID: <1134087419.4398ccfb2a4ff@www.immf.uncor.edu> I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga From meng at cgl.ucsf.edu Thu Dec 8 15:58:13 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Dec 2005 15:58:13 -0800 Subject: [Chimera-users] Concerns regarding secondary structure In-Reply-To: <1134087998.4398cf3e8bda8@www.immf.uncor.edu> References: <1134087998.4398cf3e8bda8@www.immf.uncor.edu> Message-ID: Hi Rodrigo, If a PDB file doesn't have HELIX and SHEET information in it, the ksdssp program is used to detect the secondary structure. Ksdssp uses the 3D structure (it doesn't matter what the sequence is). However, even if the 3D structure looks almost the same in the new model as in the original, there are reasons the assignments might be different: (a) the original structure has HELIX and SHEET information in it, and the person who determined that information used a different method than ksdssp, or different parameters (b) the structures are slightly different, causing the strands not to be predicted in the new structure There are some ways you can change the HELIX and SHEET assignments if you feel they are not right: (a) select the residues you think should be in beta-strands, open the Selection Inspector (click the button on the bottom right corner of the Chimera window), Inspect "Residue", set "is strand" to "true" (b) re-run the ksdssp algorithm but with different parameters. Open the Model Panel (Favorites... Model Panel), switch to the "infrequently used" list of functions, choose "compute SS". Try Apply-ing different parameters. If you want particular values of these parameters to always be used (for any proteins without HELIX and SHEET info), you can click "Save as Defaults" I hope this helps, Elaine On Dec 8, 2005, at 4:26 PM, rquiroga at immf.uncor.edu wrote: > Greetings, > > I have some concerns with Chimera's secondary structure detection/ > depiction. > > I am using Modeller to predict some 3D structures. > > I open my predicted structure in pdb file in Chimera along with the > original > structure I based my prediction on, and find that my predicted > structure lacks > two beta sheets that the model protein has, though the AA that > compose the > B-sheet are identical for the two proteins when I compare sequences > with > Matchmaker. > > I tried opening my predicted structure in MolMol and it detects the > B-sheet, > though I hugely prefer Chimera, so if you could solve this problem > for me I > would be very greatful. > > Thanks in advance, and regards > > Rodrigo Quiroga > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 rquiroga at immf.uncor.edu Mon Dec 12 10:55:27 2005 From: rquiroga at immf.uncor.edu (rquiroga at immf.uncor.edu) Date: Mon, 12 Dec 2005 15:55:27 -0300 Subject: [Chimera-users] Concerns regarding secondary structure In-Reply-To: References: <1134087998.4398cf3e8bda8@www.immf.uncor.edu> Message-ID: <1134413727.439dc79f8963c@www.immf.uncor.edu> Thanks a lot for your help, Dr. Meng. I truly appreciate it. Rodrigo Quiroga From cwmoad at gmail.com Wed Dec 14 05:54:18 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Wed, 14 Dec 2005 08:54:18 -0500 Subject: [Chimera-users] new version available In-Reply-To: <200510251849.j9PIn30N1767656@guanine.cgl.ucsf.edu> References: <6382066a0510240800r7c4bda37l8caf015f5d1f0b3f@mail.gmail.com> <435D3A7F.6020106@lbl.gov> <6382066a0510241322o2e2a0cd3u83e95ed51e07c167@mail.gmail.com> <200510242207.j9OM7YPc1748671@guanine.cgl.ucsf.edu> <6382066a0510250955j310a7886s6ef237284a9f38e6@mail.gmail.com> <6382066a0510251038s37534cc1ife4b4a02f741cf8f@mail.gmail.com> <200510251849.j9PIn30N1767656@guanine.cgl.ucsf.edu> Message-ID: <6382066a0512140554p2d31cd14p7487a746f7f6c35c@mail.gmail.com> I have had great success building an integrating matplotlib into a plugin. I was able to build a binary plugin for windows and linux. Now I am curious what header files I will need for osx/x11. Do I just need a different pyconfig.h file? Thanks, Charlie On 10/25/05, Thomas Goddard wrote: > Hi Charlie, > > As noted by Greg and Eric the Python configuration header file pyconfig.h > depends on the operating system. It is created when Python is configured. > > To handle this I have changed our source code download page to provide > header distributions for different platforms. When that page is updated > tonight it will have the Tru64 headers and Linux headers. > > Thanks for your patience. Our C++ and header source code distributions > are new and we're still figuring out how to make this work. > > Tom > From goddard at cgl.ucsf.edu Wed Dec 14 09:43:27 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 14 Dec 2005 09:43:27 -0800 (PST) Subject: [Chimera-users] new version available In-Reply-To: <6382066a0512140554p2d31cd14p7487a746f7f6c35c@mail.gmail.com> (message from Charlie Moad on Wed, 14 Dec 2005 08:54:18 -0500) References: <6382066a0510240800r7c4bda37l8caf015f5d1f0b3f@mail.gmail.com> <435D3A7F.6020106@lbl.gov> <6382066a0510241322o2e2a0cd3u83e95ed51e07c167@mail.gmail.com> <200510242207.j9OM7YPc1748671@guanine.cgl.ucsf.edu> <6382066a0510250955j310a7886s6ef237284a9f38e6@mail.gmail.com> <6382066a0510251038s37534cc1ife4b4a02f741cf8f@mail.gmail.com> <200510251849.j9PIn30N1767656@guanine.cgl.ucsf.edu> <6382066a0512140554p2d31cd14p7487a746f7f6c35c@mail.gmail.com> Message-ID: <200512141743.jBEHhRXo1709158@guanine.cgl.ucsf.edu> Hi Charlie, You will need the Mac Python configuration header file pyconfig.h to compile your Python module on the Mac and have it work with Chimera. I added Chimera and third party header files for the Mac to our source code download page: http://www.cgl.ucsf.edu/chimera/sourcecode.html Compiling a python module on the Mac also involves some special linking flags. The Mac has "dynamic libraries" and "bundles" and as far as I know Python can only import bundles. That was the case a few years ago. Here are a couple link examples that make bundles on the Mac. gcc -I/usr/local/src/staff/goddard/mac-10.4/build/include -L/usr/local/src/staff/goddard/mac-10.4/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -bundle -bundle_loader /usr/local/src/staff/goddard/mac-10.4/foreign/Python-2.4/bin/python2.4 Scientific_netcdf.o -Lnetcdf/lib -lnetcdf -o Scientific_netcdf.so cc -bundle -bundle_loader /usr/local/src/staff/goddard/builds/mac-10.3/chimera-2095/build/bin/python2.4 -o _contour.so -O -Wall -Wno-long-double contourdata.o pycontour.o _contour.o ContourObject.o -L/usr/local/src/staff/goddard/builds/mac-10.3/chimera-2095/build/lib -L../_volumearray -lrcarray -lwrappy -lstdc++ The flags -bundle and -bundle_loader are the important ones. These replace the usual -shared on other platforms. I'm not sure about -DUSE_DYLD_GLOBAL_NAMESPACE -- we don't use that for building the python modules we write but it appears that third-party packages we use define that macro. Tom From Bernard_Heymann at nih.gov Wed Dec 14 14:41:54 2005 From: Bernard_Heymann at nih.gov (Bernard Heymann) Date: Wed, 14 Dec 2005 17:41:54 -0500 Subject: [Chimera-users] Fit Models Message-ID: I'm interested in using the "Fit Models in Maps" feature in Chimera. However, the version I installed (release 1.2184) under Mac OSX 10.4 does not have this in the Tools/Volume Data menu as described in the documentation. Can anyone tell me if this is intentional or can I get this feature? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892 Tel. 301-451-8241, Fax. 301-480-7629 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Dec 14 14:52:29 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 14 Dec 2005 14:52:29 -0800 (PST) Subject: [Chimera-users] Fit Models In-Reply-To: (message from Bernard Heymann on Wed, 14 Dec 2005 17:41:54 -0500) References: Message-ID: <200512142252.jBEMqToY1842827@guanine.cgl.ucsf.edu> Hi Bernard, The "fit models in maps" tool is in Chimera version 1.2186 but not in the earlier version 1.2184. You were probably looking at the current development documentation on our web site which covers the latest features. The 1.2186 version is a snapshot and appears in the "Snapshot Releases" section of the Chimera download page below the "Production Releases" section. Tom From sabuj.pattanayek at vanderbilt.edu Mon Dec 19 10:59:40 2005 From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek) Date: Mon, 19 Dec 2005 12:59:40 -0600 Subject: [Chimera-users] how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog Message-ID: <43A7031C.7070308@vanderbilt.edu> Hi, I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog? It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command. Thanks, Sabuj Pattanayek From pett at cgl.ucsf.edu Mon Dec 19 12:04:26 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 19 Dec 2005 12:04:26 -0800 Subject: [Chimera-users] how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog In-Reply-To: <43A7031C.7070308@vanderbilt.edu> References: <43A7031C.7070308@vanderbilt.edu> Message-ID: <83648929-200A-45B6-A906-ADC9F1245ACC@cgl.ucsf.edu> Hi Sabuj, The save dialog does not allow for what you want. Do you think it's something that people in general would want to do, or is it fairly specific to something you're doing? You can do what you want using the command line with a mixture of the 'write' and 'system' commands: write relative 0 1 /usr/tmp/x ; system egrep -v ^HELIX\|^SHEET\| ^CONECT /usr/tmp/x > out.pdb which will write model 1 relative to model 0 into out.pdb. Now, I'm guessing you are going to do this repeatedly or you wouldn't have bothered asking on the list about it. You can reduce the above into a much shorter command using 'alias' and save that alias into a file that the command line reads at startup so it is always available. Here's the alias that redefines the above as the command 'minsave': alias ^minsave write relative $1 $2 /usr/tmp/x ; system egrep -v ^HELIX\|^SHEET\|^CONECT /usr/tmp/x > $3 With the above alias, "minsave 0 2 xyz.pdb" will write model 2 relative to model 0 into the file xyz.pdb. If you put this alias into ~/.chimera/midasrc or into ~/.chmidasrc (changeable using the Midas preference category) then the alias will always be available. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 19, 2005, at 10:59 AM, Sabuj Pattanayek wrote: > Hi, > > I was wondering how it might be possible to not include the CONECT, > RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save > pdb > file dialog? > > It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v > SHEET" > ...etc but I can't save the pdb model relative to another model on the > screen using that command. > > Thanks, > Sabuj Pattanayek > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfyang at gmail.com Wed Dec 21 14:28:42 2005 From: mfyang at gmail.com (Mingfeng Yang) Date: Wed, 21 Dec 2005 17:28:42 -0500 Subject: [Chimera-users] Help or feature request Message-ID: <43A9D71A.4060109@gmail.com> It's a very common problem to calculate the twist angle between to beta-strands or two alpha-helix. So I am wondering if Chimera can fit a group of atoms into a straight line, and give the angle of two fitted line. If chimera does do this, hopefully somebody can tell me how to do this. If not, it would be worthwhile to add this function in. Thank you very much! Happy holiday! Mingfeng From juhan at cires.colorado.edu Wed Dec 21 11:27:52 2005 From: juhan at cires.colorado.edu (Juhan Kim/CIRES) Date: Wed, 21 Dec 2005 12:27:52 -0700 Subject: [Chimera-users] Save image from Chimera Message-ID: <000001c60664$aba3e8e0$a28810ac@cires.edu> Hello, Does anybody know how to save the image from the chimera? I'm using PC version of Chimera and whenever I'm trying to save the image using the menu file>save image, I always fail to save the image and only get the following "reply log" ----reply log----- Opening "file.pdb" Done opening "file.pdb" Unable to save image: (0, 'Error') Unable to save image: encoder error -2 when writing image file Unable to save image: encoder error -2 when writing image file Unable to save image: (0, 'Error') If anybody knows how to solve this please let me know. Thank you. Juhan UCB, Boulder -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Dec 22 10:43:57 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 22 Dec 2005 10:43:57 -0800 Subject: [Chimera-users] Save image from Chimera In-Reply-To: <000001c60664$aba3e8e0$a28810ac@cires.edu> References: <000001c60664$aba3e8e0$a28810ac@cires.edu> Message-ID: <80805EA5-CB39-4C6D-93B3-6B363C41D509@cgl.ucsf.edu> Hi Juhan, Does it fail for every image format, or just one (e.g. jpeg)? Can you tell me what version of Chimera you are running (Help->About UCSF Chimera will report the version)? --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 21, 2005, at 11:27 AM, Juhan Kim/CIRES wrote: > Hello, > > Does anybody know how to save the image from the chimera? > > I?m using PC version of Chimera and whenever I?m trying to save the > image using > the menu file>save image, I always fail to save the image and only > get the following > ?reply log? > > ----reply log----- > > Opening ?file.pdb? > > Done opening ?file.pdb? > > Unable to save image: (0, 'Error') > > Unable to save image: encoder error -2 when writing image file > > Unable to save image: encoder error -2 when writing image file > > Unable to save image: (0, 'Error') > > > If anybody knows how to solve this please let me know. > > Thank you. > > Juhan > > UCB, Boulder > > _______________________________________________ > 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 meng at cgl.ucsf.edu Thu Dec 22 10:46:02 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 22 Dec 2005 10:46:02 -0800 Subject: [Chimera-users] Help or feature request In-Reply-To: <43A9D71A.4060109@gmail.com> References: <43A9D71A.4060109@gmail.com> Message-ID: > > It's a very common problem to calculate the twist angle between to > beta-strands or two alpha-helix. So I am wondering if Chimera can > fit a > group of atoms into a straight line, and give the angle of two fitted > line. If chimera does do this, hopefully somebody can tell me how > to do > this. If not, it would be worthwhile to add this function in. Thank > you > very much! > Happy holiday! > Mingfeng Hi Minfeng, Currently Chimera does not do these things, but this is a good suggestion, and we will put it on our requested features list. You can see the axes of strands and helices and measure the distances and angles between them using WebMol. I think the axes are not always one straight line - sometimes different straight segments are joined together to make a "bent" axis - but otherwise it sounds just like what you wanted. You can try WebMol at http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl Enter your PDB ID of interest, and after it shows up in WebMol, pick Msure ... Pack from the WebMol interface. The axes will be drawn on the structure, and the values of the measurements will be shown in a separate text window. Happy Holidays to you too! 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