From molatwork at yahoo.es Sun Apr 1 00:50:07 2007 From: molatwork at yahoo.es (Miguel Ortiz-Lombardia) Date: Sun, 01 Apr 2007 09:50:07 +0200 Subject: [Chimera-users] error parsing ATOM record when coordinate long-ish Message-ID: <460F642F.8000007@yahoo.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I can't read a particular atom line that looks like: ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 C I presume that the reason is that the y-coordinate forms a continuous string with the x-coordinate. However, this line complies with the PDB format; I quote from the RCBS site: 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms I realize that this may be seldom a problem, but I think it should be tackled. In my case, this is a dummy atom to represent a dipole moment vector with quite a big magnitude. I have the same problem in the last and the previous snapshot versions of chimera (both in linux and MacOSX) Thank you in advance, Miguel - -- Miguel Ortiz Lombard?a Centro de Investigaciones Oncol?gicas C/ Melchor Fern?ndez Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork at yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste f?t fort, on a fait que ce qui est fort f?t juste. Blaise Pascal, Pens?es -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2QuF6oOrDvhbQIRApSSAJ94MwNKKsPowzYE/k61g9Yen1PArwCfSnWJ gUXmMlHVsrRuLscR3IWg/tQ= =6/U1 -----END PGP SIGNATURE----- From molatwork at yahoo.es Sun Apr 1 01:22:20 2007 From: molatwork at yahoo.es (Miguel Ortiz-Lombardia) Date: Sun, 01 Apr 2007 10:22:20 +0200 Subject: [Chimera-users] error parsing ATOM record when coordinate long-ish (II) Message-ID: <460F6BBC.9050300@yahoo.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi again, I forgot to mention that I solved my particular problem by using a bild object to depict the vector. Just thought that the parsing of the ATOM record should be fixed. Cheers, Miguel - -- Miguel Ortiz Lombard?a Centro de Investigaciones Oncol?gicas C/ Melchor Fern?ndez Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork at yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste f?t fort, on a fait que ce qui est fort f?t juste. Blaise Pascal, Pens?es -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2u7F6oOrDvhbQIRAvWJAJ9UiNDLaAv9yDbf6HPoNyhHVaGAmwCfd1SF ZHM9NIY3QX5mjFVqNdvvTQk= =Gbf0 -----END PGP SIGNATURE----- From pett at cgl.ucsf.edu Mon Apr 2 16:40:47 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 2 Apr 2007 16:40:47 -0700 Subject: [Chimera-users] error parsing ATOM record when coordinate long-ish In-Reply-To: <460F642F.8000007@yahoo.es> References: <460F642F.8000007@yahoo.es> Message-ID: <88881246-04EB-44D3-B826-EEB4C2095ED9@cgl.ucsf.edu> On Apr 1, 2007, at 12:50 AM, Miguel Ortiz-Lombardia wrote: > I can't read a particular atom line that looks like: > > ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 > C > > I presume that the reason is that the y-coordinate forms a continuous > string with the x-coordinate. However, this line complies with the PDB > format; I quote from the RCBS site: > > 39 - 46 Real(8.3) y Orthogonal coordinates for > Y in > Angstroms Hi Miguel, The problem isn't with the numbers running together, it's that they're in the wrong columns. If you count it out, you'll find that your Y coordinate is in columns 38-45 rather than 39-46. This becomes obvious if you put your line next to one from a standard PDB file (such as 1GCN, below): ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 ATOM 1 N HIS 1 49.668 24.248 10.436 1.00 25.00 1 1GCN 50 If I insert a space before the start of your coordinates, Chimera reads the line okay. --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 rking at uri.edu Tue Apr 3 13:47:49 2007 From: rking at uri.edu (Roberta King) Date: Tue, 3 Apr 2007 16:47:49 -0400 Subject: [Chimera-users] viewing & comparison of multiple overlay structures Message-ID: <002c01c77631$58ad0e80$e81414ac@RKD420> Hello, I am relatively new to Chimera (and the user group), but am using it to compare ligand binding pockets for multiple (36) structures of related proteins. My proteins overlay nicely based on alignment, but I am having difficulty with the comparisons of multiple structures at once. First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? I appreciate any help provided. Roberta ******************************** Roberta S. King, Ph.D. Assistant Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island -------------- next part -------------- An HTML attachment was scrubbed... URL: From edm4 at u.washington.edu Tue Apr 3 15:59:58 2007 From: edm4 at u.washington.edu (E. Merkley) Date: Tue, 3 Apr 2007 15:59:58 -0700 (PDT) Subject: [Chimera-users] render several models by attribute on an absolute scale Message-ID: Hello Chimera users, I am using the "Define Attribute" and "Render by Attribute" features to color structures by number of native contacts observed during a molecular dynamics simulation. I would like to compare several simulations at once, applying a single color scale to several (~6) models at once. It seems that this can't be done using a separate attribute file for each model: The "render by attribute" dialog doesn't let you change the limits past the min and max of the data in the attribute file, but each simulation (and hence each attribute file) has a different range. Any suggestions? Thanks, Eric From pett at cgl.ucsf.edu Tue Apr 3 16:57:06 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Apr 2007 16:57:06 -0700 Subject: [Chimera-users] viewing & comparison of multiple overlay structures In-Reply-To: <002c01c77631$58ad0e80$e81414ac@RKD420> References: <002c01c77631$58ad0e80$e81414ac@RKD420> Message-ID: <26F84F4B-2912-4EAE-8FE7-E958D4FC0E37@cgl.ucsf.edu> On Apr 3, 2007, at 1:47 PM, Roberta King wrote: > First, After overlaying multiple protein (pdb) structures with > ligands using MultiAlign based on alignment, how does one easily > view only the overlaid ligands? [Note: I have up to 36 structures > overlaid, each with 0-2 ligands.] Hi Roberta, Using the command line (Favorites->Command Line), typing "~disp; show ligand" will hide all structures and then show only the ligands. If every structure had a ligand you would only need "show ligand" since the show command hides parts of structures that aren't to be shown, but if no part of a structure matches the show criteria, the structure isn't changed -- so you need the "~disp" also to guarantee that ligand-less structures get hidden. This is also doable with the menus by Select->Structure->ligand followed by Select->Invert Selection (or shift-right-arrow instead to invert the selection in all models) and then Actions->Atoms/Bonds->hide. From there, you will probably want to select the ligand clump by control dragging the mouse across the clump (there will be a green box outline as you drag the mouse) and then use Actions->Focus to zoom in on the clump and make it the center of rotation. > Secondly, can chimera then calculate a solvent-accessible closed > surface for the protein cavity surrounding each ligand? > Alternatively, I could calculate the cavity first, then overlay > based on alignment. The goal is to view the overlaid cavities for > visual comparison. It depends. If the cavity is actually completely enclosed then Chimera won't depict it. If there is some channel to the binding pocket, then it should be depicted. I say "should" because the surfacing library we are currently using (MSMS) is known to have problems when there are narrow channels in a surface. We are working on a replacement library that should solve both these problems, but it's not ready yet. Providing that MSMS doesn't fail, your pockets should be depicted. It is also sometimes possible to work around the MSMS problem by adding hydrogens to a structure or by slightly changing VDW radii (with the vdwdefine command) -- but you have to do this before any surfaces fail because after a failure surfacing won't work again until you restart Chimera. You create a surface with Actions->Surface->show or the "surf" command. If with experience you know that surfacing certain models is problematic, you can restrict the surfacing to particular models by selecting them before using the menus or providing the model numbers as arguments to the surf command (e.g. "surf #0,3-7,9"). > Thirdly, can chimera calculate electrostatic charge on amino acids > surrounding a binding cavity and reflect that charge onto the > closed cavity surface? Can this surface be included in overlay view? You can use the Add Charge tool (in the Structure Editing category) to add partial charges to all atoms. You can then use the Render By Attribute tool (Structure Analysis category) to color the surface and/ or atoms based on the partial charges. For more precise electrostatics, you can use an external tool such as APBS or Delphi to generate an electrostatic grid, and open that in Chimera and then use the Electrostatic Surface Coloring tool (Surface/ Binding Analysis category) to color the surface with the grid data. You can certainly show the surface(s) with the ligands overlaid. You would probably only want to show a few surfaces at most simultaneously for understandability (see next answer). > Given the number of structures, I would much appreciate any advice > on how to make this manageable. If Chimera cannot do the > calculations, can it import multiple structures saved by another > capable software, then overlay them using MultiAlign (including the > surfaces)? Depending on the speed of your computer, its amount of memory and its graphics card, working with 36 structures and their surfaces at once may or may not be satisfactory (and unless you have a real high- end machine my guess would be not). You will want to use the Model Panel (under Favorites) to control which surfaces/structures are being shown -- particularly which surfaces since I imagine that looking at more than a few would be incredibly confusing. Another thing that will help is to delete parts of structures that you aren't interested in. One trick here is to use MultAlign Viewer to select one residue in each structure (create a region by mouse dragging that covers one column in the alignment -- those residues will be selected), then select the corresponding chains by clicking into the main window and hitting the up-arrow key, then right-arrow to invert the selection, and finally Actions->Atoms/Bonds->delete to delete all atoms that are not part of chains in the alignment. Hopefully your ligands will have the same chain ID as the chain in the alignment and therefore will not be deleted. You might want to look at your ligands after you've inverted the selection and make sure none are selected for the following deletion. If some are selected, deselect them with "~select ligand". As a quasi-extreme measure you could prune away parts of the structure more than a certain distance from the ligands. Select the ligand clump and use Select->Zone... to select residues further than a certain distance from the clump and then delete the selected residues. --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 pett at cgl.ucsf.edu Tue Apr 3 17:11:53 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Apr 2007 17:11:53 -0700 Subject: [Chimera-users] render several models by attribute on an absolute scale In-Reply-To: References: Message-ID: <09BDA570-B3A3-4904-874E-29BE16C4D232@cgl.ucsf.edu> Hi Eric, I am aware of this limitation in the interface and intend to remedy it. Until then, you can instead use the "rangecolor" command to make your color range span any set of values. "help rangecolor" in the command line will bring up the documentation for the rangecolor command. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Apr 3, 2007, at 3:59 PM, E. Merkley wrote: > Hello Chimera users, > > I am using the "Define Attribute" and "Render by Attribute" > features to > color structures by number of native contacts observed during a > molecular > dynamics simulation. I would like to compare several simulations > at once, > applying a single color scale to several (~6) models at once. It > seems > that this can't be done using a separate attribute file for each > model: > The "render by attribute" dialog doesn't let you change the limits > past > the min and max of the data in the attribute file, but each simulation > (and hence each attribute file) has a different range. > > Any suggestions? > > Thanks, > Eric > > _______________________________________________ > 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 rking at uri.edu Wed Apr 4 06:19:40 2007 From: rking at uri.edu (Roberta King) Date: Wed, 4 Apr 2007 09:19:40 -0400 Subject: [Chimera-users] viewing & comparison of multiple overlay structures Message-ID: <001801c776bb$e82c5590$e81414ac@RKD420> Thank you Eric for your very detailed answers to my several questions. It will take me a few days to work through the suggestions. If I have any more troubles, I will contact you next week. Thanks very much, Roberta King ******************************** Roberta S. King, Ph.D. Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king _____ From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Tuesday, April 03, 2007 7:57 PM To: Roberta King Cc: Chimera BB Subject: Re: [Chimera-users] viewing & comparison of multiple overlay structures On Apr 3, 2007, at 1:47 PM, Roberta King wrote: First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Hi Roberta, Using the command line (Favorites->Command Line), typing "~disp; show ligand" will hide all structures and then show only the ligands. If every structure had a ligand you would only need "show ligand" since the show command hides parts of structures that aren't to be shown, but if no part of a structure matches the show criteria, the structure isn't changed -- so you need the "~disp" also to guarantee that ligand-less structures get hidden. This is also doable with the menus by Select->Structure->ligand followed by Select->Invert Selection (or shift-right-arrow instead to invert the selection in all models) and then Actions->Atoms/Bonds->hide. From there, you will probably want to select the ligand clump by control dragging the mouse across the clump (there will be a green box outline as you drag the mouse) and then use Actions->Focus to zoom in on the clump and make it the center of rotation. Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. It depends. If the cavity is actually completely enclosed then Chimera won't depict it. If there is some channel to the binding pocket, then it should be depicted. I say "should" because the surfacing library we are currently using (MSMS) is known to have problems when there are narrow channels in a surface. We are working on a replacement library that should solve both these problems, but it's not ready yet. Providing that MSMS doesn't fail, your pockets should be depicted. It is also sometimes possible to work around the MSMS problem by adding hydrogens to a structure or by slightly changing VDW radii (with the vdwdefine command) -- but you have to do this before any surfaces fail because after a failure surfacing won't work again until you restart Chimera. You create a surface with Actions->Surface->show or the "surf" command. If with experience you know that surfacing certain models is problematic, you can restrict the surfacing to particular models by selecting them before using the menus or providing the model numbers as arguments to the surf command (e.g. "surf #0,3-7,9"). Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? You can use the Add Charge tool (in the Structure Editing category) to add partial charges to all atoms. You can then use the Render By Attribute tool (Structure Analysis category) to color the surface and/or atoms based on the partial charges. For more precise electrostatics, you can use an external tool such as APBS or Delphi to generate an electrostatic grid, and open that in Chimera and then use the Electrostatic Surface Coloring tool (Surface/Binding Analysis category) to color the surface with the grid data. You can certainly show the surface(s) with the ligands overlaid. You would probably only want to show a few surfaces at most simultaneously for understandability (see next answer). Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? Depending on the speed of your computer, its amount of memory and its graphics card, working with 36 structures and their surfaces at once may or may not be satisfactory (and unless you have a real high-end machine my guess would be not). You will want to use the Model Panel (under Favorites) to control which surfaces/structures are being shown -- particularly which surfaces since I imagine that looking at more than a few would be incredibly confusing. Another thing that will help is to delete parts of structures that you aren't interested in. One trick here is to use MultAlign Viewer to select one residue in each structure (create a region by mouse dragging that covers one column in the alignment -- those residues will be selected), then select the corresponding chains by clicking into the main window and hitting the up-arrow key, then right-arrow to invert the selection, and finally Actions->Atoms/Bonds->delete to delete all atoms that are not part of chains in the alignment. Hopefully your ligands will have the same chain ID as the chain in the alignment and therefore will not be deleted. You might want to look at your ligands after you've inverted the selection and make sure none are selected for the following deletion. If some are selected, deselect them with "~select ligand". As a quasi-extreme measure you could prune away parts of the structure more than a certain distance from the ligands. Select the ligand clump and use Select->Zone... to select residues further than a certain distance from the clump and then delete the selected residues. --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 meng at cgl.ucsf.edu Thu Apr 5 10:16:24 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Apr 2007 10:16:24 -0700 Subject: [Chimera-users] [chimera-dev] Building a multimer model In-Reply-To: <1f3c0be50704050010v4a1c1d0bh90925afa6c80b3ee@mail.gmail.com> References: <1f3c0be50704050010v4a1c1d0bh90925afa6c80b3ee@mail.gmail.com> Message-ID: Hi Benjamin, There is probably more than one way to do this in Chimera, but I'd open the protein of interest six times and match it to the six monomers of the related protein. Let's call your protein "A" and the similar protein "B" (for which a hexamer is available or can be easily constructed from matrices in the PDB file). Since you didn't mention the specifics, I didn't try the whole process outlined below (not having a good example to work with), but have used the tools in other contexts. This is kind of a brute force approach. Someone else may know of a more elegant way... Making the hexamer of B: If the PDB file doesn't already have a hexamer, it should have matrix information that allows it to be constructed. If BIOMT, use Multiscale Models (under Tools... Higher-Order Structure). Initially, this doesn't copy all the atoms but just makes surfaces for computational expediency. Since you will need copies of all the atoms for matching, using the Multiscale Models GUI: select "All" chains, change their style to anything other than surface (e.g. Show... Ribbons). You can see the model IDs of the copies of B in the Model Panel (under Favorites). If SMTRY, CRYST1, or MTRIX you could use the Unit Cell tool (under Tools... Higher-Order Structure) instead of Multiscale Models. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ unitcell.html Matching the 6 copies of A to the monomers of B: Options for matching are the "match" command or MatchMaker (GUI under Tools... Structure Comparison, also implemented as a command, "matchmaker"). If you wanted to name specific atoms to use for fitting, you'd use the "match" command. That can be tedious, and I'd try MatchMaker first - if there is some sequence similarity, even fairly low, it usually works quite well. By default, it iterates the fit so that only residues that match well in space are ultimately used to superimpose the proteins. That means the parts that are different should not interfere with a good fit of the parts that are the same. You can adjust several parameters, but for example if B is model 0, chains A-F and copies of A are models 1-6, these commands would use the matchmaker defaults: matchmaker #0:.a #1 pair ss matchmaker #0:.b #2 pair ss matchmaker #0:.c #3 pair ss matchmaker #0:.d #4 pair ss matchmaker #0:.e #5 pair ss matchmaker #0:.f #6 pair ss (pair ss just means to use the specified chains rather than trying all chain combinations between the models) You could specify other parameters with various keywords, for example the stringency to use when iterating the fit, how much weight secondary structure should have vs. the residue types in the sequence, etc. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html 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 Apr 5, 2007, at 12:10 AM, Benjamin G.S. Horsman wrote: > Hello, > > My name is Benjamin Horsman and I am a student at the University of > Toronto. I have what should be a basic (possibly naive) question > regarding protein modelling that I was hoping you might be able to > answer for me or point my in the right direction. I have been > studying the structure of a bacterial protein complex, trying to > understand how it interacts with several known binding partners. The > complex is known to be a hexameric homomultimer. Recently the > structure of the subunit protein was solved. However, only the > monomeric form of the protein was determined, and the corresponding > PDB file does not contain coordinates for the multimer (i.e., no > BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a > model of the hexameric complex for visual inspection and for some > docking studies. What would be the best way to accomplish this? > > There are several structures in the PDB of hexameric protein complexes > composed of subunits with very close structural alignment to my > protein of interest, differing in two regions of the protein that are > outside of the multimer binding regions. I believe that my protein > complex posses very similar or nearly identical geometry to these > known complexes. Is there any way to basically insert my protein into > this geometry? Can this be done in Chimera? If not, is there any > program or web server that allows this to be done? Or are you aware > of a better way to get this done? > > Thank you for your time. Any help is greatly appreciated. > > > Benjamin Horsman > _______________________________________________ > Chimera-dev mailing list > Chimera-dev at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev From goddard at cgl.ucsf.edu Fri Apr 6 16:23:03 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 06 Apr 2007 16:23:03 -0700 Subject: [Chimera-users] GIF animations in Chimera Message-ID: <4616D657.7070106@cgl.ucsf.edu> Anyone interested in GIF animation output from Chimera? Their main appeal is that they play directly in most web browsers (like banner ads). It was easy to add to the Chimera movie recorder using ffmpeg which is included in the Chimera distribution. But ffmpeg uses a fixed color palette causing severe color banding and does not offer LZW compression resulting in large file sizes. That option looks unusable. I tried another approach using a separate program called "gifsicle". That gave decent coloring and compression but it would require adding gifsicle to the Chimera distribution. I am reluctant to do that (entails future maintenance) unless there is strong interest in making GIF animations. Tom From menetret at bu.edu Sat Apr 7 14:03:35 2007 From: menetret at bu.edu (jean-francois menetret) Date: Sat, 7 Apr 2007 17:03:35 -0400 (EDT) Subject: [Chimera-users] transparency factor Message-ID: Is it possible to change the transparency factor of a volume at the command line ? Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From molatwork at yahoo.es Sun Apr 8 03:10:40 2007 From: molatwork at yahoo.es (Miguel Ortiz-Lombardia) Date: Sun, 08 Apr 2007 12:10:40 +0200 Subject: [Chimera-users] Suggestion on biological assembly load Message-ID: <4618BFA0.6010706@yahoo.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I have small suggestion to make that I would find helpful if implemented in chimera: I think it would be great if the "biological assembly" could be fetched by ID from the File menu, just as it goes now for the pdb coordinates file from the RCSB site. Such assemblies are kept at the PQS database at the EBI (Cambridge). The links there follow this syntax: http://pqs.ebi.ac.uk/pqs-doc/macmol/.mmol where is obviously that of the PDB structure. Despite the extension, it is a plain PDB file. The CRYST1 record (for crystallographic structures) of such coordinates files has been modified to space group P1, since the crystallographic operations of the original structure don't hold. A potential problem if these files is that they don't seem to care about having duplicated atom numbers... These assemblies are most often correct and validated by experiments. However, you might want to add a caveat or, even better, an intermediate window with a link to the place where the PQS explains how that particular oligomer was generated and why it is considered biologically relevant: http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename= Best regards, Miguel - -- Miguel Ortiz Lombard?a Centro de Investigaciones Oncol?gicas C/ Melchor Fern?ndez Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork at yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste f?t fort, on a fait que ce qui est fort f?t juste. Blaise Pascal, Pens?es -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGGL+gF6oOrDvhbQIRAtQ2AKCi9oIpIJffYwshk1PgB2aiG4e9rgCghjzZ Uz0yTug1VXEHXNP2MG2HsmI= =EGzy -----END PGP SIGNATURE----- From benjamin.horsman at utoronto.ca Sat Apr 7 20:34:01 2007 From: benjamin.horsman at utoronto.ca (Benjamin G.S. Horsman) Date: Sat, 7 Apr 2007 23:34:01 -0400 Subject: [Chimera-users] [chimera-dev] Building a multimer model In-Reply-To: References: <1f3c0be50704050010v4a1c1d0bh90925afa6c80b3ee@mail.gmail.com> Message-ID: <1f3c0be50704072034l880175dhd7559ca6e70df152@mail.gmail.com> Hi Elaine, Your method worked perfectly. Thanks for help! Ben On 4/5/07, Elaine Meng wrote: > Hi Benjamin, > There is probably more than one way to do this in Chimera, but I'd > open the protein of interest six times and match it to the six > monomers of the related protein. Let's call your protein "A" and the > similar protein "B" (for which a hexamer is available or can be > easily constructed from matrices in the PDB file). Since you didn't > mention the specifics, I didn't try the whole process outlined below > (not having a good example to work with), but have used the tools in > other contexts. > > This is kind of a brute force approach. Someone else may know of a > more elegant way... > > Making the hexamer of B: > If the PDB file doesn't already have a hexamer, it should have matrix > information that allows it to be constructed. If BIOMT, use > Multiscale Models (under Tools... Higher-Order Structure). > Initially, this doesn't copy all the atoms but just makes surfaces > for computational expediency. Since you will need copies of all the > atoms for matching, using the Multiscale Models GUI: select "All" > chains, change their style to anything other than surface (e.g. > Show... Ribbons). You can see the model IDs of the copies of B in > the Model Panel (under Favorites). If SMTRY, CRYST1, or MTRIX you > could use the Unit Cell tool (under Tools... Higher-Order Structure) > instead of Multiscale Models. Relevant manual pages: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ > framemulti.html > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ > unitcell.html > > Matching the 6 copies of A to the monomers of B: > Options for matching are the "match" command or MatchMaker (GUI under > Tools... Structure Comparison, also implemented as a command, > "matchmaker"). If you wanted to name specific atoms to use for > fitting, you'd use the "match" command. That can be tedious, and I'd > try MatchMaker first - if there is some sequence similarity, even > fairly low, it usually works quite well. By default, it iterates the > fit so that only residues that match well in space are ultimately > used to superimpose the proteins. That means the parts that are > different should not interfere with a good fit of the parts that are > the same. You can adjust several parameters, but for example if B is > model 0, chains A-F and copies of A are models 1-6, these commands > would use the matchmaker defaults: > matchmaker #0:.a #1 pair ss > matchmaker #0:.b #2 pair ss > matchmaker #0:.c #3 pair ss > matchmaker #0:.d #4 pair ss > matchmaker #0:.e #5 pair ss > matchmaker #0:.f #6 pair ss > (pair ss just means to use the specified chains rather than trying > all chain combinations between the models) You could specify other > parameters with various keywords, for example the stringency to use > when iterating the fit, how much weight secondary structure should > have vs. the residue types in the sequence, etc. Relevant manual pages: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ > matchmaker.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html > > 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 Apr 5, 2007, at 12:10 AM, Benjamin G.S. Horsman wrote: > > > Hello, > > > > My name is Benjamin Horsman and I am a student at the University of > > Toronto. I have what should be a basic (possibly naive) question > > regarding protein modelling that I was hoping you might be able to > > answer for me or point my in the right direction. I have been > > studying the structure of a bacterial protein complex, trying to > > understand how it interacts with several known binding partners. The > > complex is known to be a hexameric homomultimer. Recently the > > structure of the subunit protein was solved. However, only the > > monomeric form of the protein was determined, and the corresponding > > PDB file does not contain coordinates for the multimer (i.e., no > > BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a > > model of the hexameric complex for visual inspection and for some > > docking studies. What would be the best way to accomplish this? > > > > There are several structures in the PDB of hexameric protein complexes > > composed of subunits with very close structural alignment to my > > protein of interest, differing in two regions of the protein that are > > outside of the multimer binding regions. I believe that my protein > > complex posses very similar or nearly identical geometry to these > > known complexes. Is there any way to basically insert my protein into > > this geometry? Can this be done in Chimera? If not, is there any > > program or web server that allows this to be done? Or are you aware > > of a better way to get this done? > > > > Thank you for your time. Any help is greatly appreciated. > > > > > > Benjamin Horsman > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev at cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > From goddard at cgl.ucsf.edu Mon Apr 9 10:42:58 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 09 Apr 2007 10:42:58 -0700 Subject: [Chimera-users] transparency factor In-Reply-To: References: Message-ID: <461A7B22.8020406@cgl.ucsf.edu> Hi Jean-Francois, There is not yet a command in the standard Chimera distribution to change volume surface transparency. There is such a command in the optional package called "Animation Commands" on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html You can install this with your current Chimera and then use "transition transparency". Tom From goddard at cgl.ucsf.edu Mon Apr 9 14:12:36 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 14:12:36 -0700 Subject: [Chimera-users] [Fwd: Re: GIF animations in Chimera] Message-ID: <461AAC44.4080607@cgl.ucsf.edu> Miguel uses ImageMagick to make GIF animations from Chimera movie frames. Tom -------- Original Message -------- Subject: Re: [Chimera-users] GIF animations in Chimera Date: Sat, 07 Apr 2007 09:09:43 +0200 From: Miguel Ortiz-Lombardia To: Tom Goddard Hi Tom, I make animated GIFs with Chimera by simply saving the frames and using convert (from ImageMagick). I run an extremely simple script to do so and the results are up to my needs. Cheers, Miguel En/na Tom Goddard ha escrit: > Anyone interested in GIF animation output from Chimera? Their main > appeal is that they play directly in most web browsers (like banner ads). > > It was easy to add to the Chimera movie recorder using ffmpeg which is > included in the Chimera distribution. But ffmpeg uses a fixed color > palette causing severe color banding and does not offer LZW compression > resulting in large file sizes. That option looks unusable. I tried > another approach using a separate program called "gifsicle". That gave > decent coloring and compression but it would require adding gifsicle to > the Chimera distribution. I am reluctant to do that (entails future > maintenance) unless there is strong interest in making GIF animations. > > Tom > > _______________________________________________ > 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 Apr 9 15:04:24 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 15:04:24 -0700 Subject: [Chimera-users] Suggestion on biological assembly load In-Reply-To: <4618BFA0.6010706@yahoo.es> References: <4618BFA0.6010706@yahoo.es> Message-ID: <461AB868.8040506@cgl.ucsf.edu> Hi Miguel, Adding a fetch by id option for PQS biological assembly PDB files looks like a good idea. I'll put it on the requested features list. Some of those files reuse atom serial numbers and reuse chain identifiers. For example, satellite tobacco mosaic virus 1a34 which involves 60 copies of the asymmetric unit (4 chains) has more than 200,000 atoms and hundreds of chains. The PDB file format can't handle that correctly. Still the file displays in Chimera although it can be hard to select just a single capsid protein since it shares a chain identifier with other subunits. This is a very small virus. Bigger viruses just don't have PQS entries -- they probably set a size limit. So this isn't a good way to handled icosahedral viruses. But probably most other PDB entries will not have size problems. Another issue is that PQS has more than one biological assembly for some PDB entries. For example, 1a6v has 3 assemblies, with files called 1a6v_1.mmol, 1a6v_2.mmol and 1a6v_3.mmol. I guess it would make sense to load all of the assemblies as separate Chimera models in those cases. Thanks for the suggestion. Tom From menetret at bu.edu Mon Apr 9 15:08:54 2007 From: menetret at bu.edu (jean-francois menetret) Date: Mon, 9 Apr 2007 18:08:54 -0400 (EDT) Subject: [Chimera-users] transparency factor In-Reply-To: <461A7B22.8020406@cgl.ucsf.edu> References: <461A7B22.8020406@cgl.ucsf.edu> Message-ID: Yes this is just what I need; but I cannot see any new tool appearing what I install it ... On Mon, 9 Apr 2007, Tom Goddard wrote: > Hi Jean-Francois, > > There is not yet a command in the standard Chimera distribution to change > volume surface transparency. There is such a command in the optional package > called "Animation Commands" on the experimental features web page: > > http://www.cgl.ucsf.edu/chimera/experimental/experimental.html > > http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html > > You can install this with your current Chimera and then use "transition > transparency". > > Tom > From goddard at cgl.ucsf.edu Mon Apr 9 15:14:02 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 15:14:02 -0700 Subject: [Chimera-users] GIF animations in Chimera In-Reply-To: <4616D657.7070106@cgl.ucsf.edu> References: <4616D657.7070106@cgl.ucsf.edu> Message-ID: <461ABAAA.7070708@cgl.ucsf.edu> Cathy Lawson also makes animated gif files from Chimera image sequences using standalone programs. --- Hi Tom, Sometimes I do like to make simple gif animations but then generally I have simply imported frames to a separate program to make the animation. Since my recent switch from pc to mac I am not entirely sure what program I would now adopt for this purpose but I am sure there is something suitable. If I were to make a more complex movie that I wanted to post on the web then I don't think I would use gif format. Cathy From goddard at cgl.ucsf.edu Mon Apr 9 15:28:25 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 15:28:25 -0700 Subject: [Chimera-users] Fetch EMDB map by id In-Reply-To: <48E3C03A-ED3D-4CE7-9D73-B5023A767406@rutgers.edu> References: <461AAC44.4080607@cgl.ucsf.edu> <48E3C03A-ED3D-4CE7-9D73-B5023A767406@rutgers.edu> Message-ID: <461ABE09.30705@cgl.ucsf.edu> Hi Cathy, It is a good idea to allow fetching EMDB maps by id in the current File / Fetch by ID dialog. Their are two issues related to the large size of some maps that I would like to solve to make that work well. First I would like Chimera not to freeze while the fetching is done. That is what currently happens when fetching files. Instead it could show a progress dialog with a cancel button (like a web browser) and open the map when it finally arrives. Second I would like the map to be saved on your local machine so that you don't have to fetch the same large file more than once. Perhaps the way that would work is the the first time you fetch any file it asks you where to save this and future fetched files, and there will be an option not to save them. This would be remembered in your Chimera preferences file. When you subsequently used the fetch dialog it could first look in the directory where you save fetched files and use the copy there if available. Thanks for the suggestion. It is on my requested features list. Tom From goddard at cgl.ucsf.edu Mon Apr 9 15:35:39 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 15:35:39 -0700 Subject: [Chimera-users] hkcage command In-Reply-To: References: Message-ID: <461ABFBB.3010003@cgl.ucsf.edu> Hi Padma, The code for the hkcage command had to be changed for Chimera version 1.2348 and newer because we switched from using the Numeric Python array package to its not completely compatible successor called NumPy. The new code for the hkcage command is on the experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Use that new code with Chimera 1.2363. I have not had time to try flattening an icosahedral map. I made a small step toward another request of yours, plotting radial density. I tried a Python 2-d plotting library called matplotlib that could be used for making radial density plots. It is a pretty big package so we have not decided whether to include it in Chimera. Tom From cathy.lawson at rutgers.edu Mon Apr 9 15:36:05 2007 From: cathy.lawson at rutgers.edu (Cathy Lawson) Date: Mon, 9 Apr 2007 18:36:05 -0400 Subject: [Chimera-users] Fetch EMDB map by id In-Reply-To: <461ABE09.30705@cgl.ucsf.edu> References: <461AAC44.4080607@cgl.ucsf.edu> <48E3C03A-ED3D-4CE7-9D73-B5023A767406@rutgers.edu> <461ABE09.30705@cgl.ucsf.edu> Message-ID: <0A45A8EA-3F77-42F0-A552-A1C21D5EE0BF@rutgers.edu> I really like your suggestions about downloading maps, particularly having a progress dialog and being able to save the files. It would be great to apply these to other downloads as well! On Apr 9, 2007, at 6:28 PM, Thomas Goddard wrote: > Hi Cathy, > > It is a good idea to allow fetching EMDB maps by id in the > current File / Fetch by ID dialog. Their are two issues related to > the large size of some maps that I would like to solve to make that > work well. First I would like Chimera not to freeze while the > fetching is done. That is what currently happens when fetching > files. Instead it could show a progress dialog with a cancel > button (like a web browser) and open the map when it finally > arrives. Second I would like the map to be saved on your local > machine so that you don't have to fetch the same large file more > than once. Perhaps the way that would work is the the first time > you fetch any file it asks you where to save this and future > fetched files, and there will be an option not to save them. This > would be remembered in your Chimera preferences file. When you > subsequently used the fetch dialog it could first look in the > directory where you save fetched files and use the copy there if > available. > > Thanks for the suggestion. It is on my requested features list. > > Tom /////////////////////////////////////////////////////// cathy.lawson at rutgers.edu http://rutchem.rutgers.edu/~lawson -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Apr 9 15:44:31 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 09 Apr 2007 15:44:31 -0700 Subject: [Chimera-users] transparency factor In-Reply-To: References: <461A7B22.8020406@cgl.ucsf.edu> Message-ID: <461AC1CF.3040709@cgl.ucsf.edu> Hi Jean-Francois, The "Animations Commands" plugin on the Chimera experimental features page adds the "transition" command. There is no new tool in the menus. The details link on the exper features web page explains its use http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html Make sure you get the version that is compatible with your Chimera version. See the "older versions" link on the exper features page if you are using Chimera older than version 1.2348 (Feb 2007). Tom From goddard at cgl.ucsf.edu Tue Apr 10 12:47:47 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 10 Apr 2007 12:47:47 -0700 Subject: [Chimera-users] Extra Chimera marker attributes In-Reply-To: <461BDA22.4040400@rice.edu> References: <45C9513B.5040900@rice.edu> <45C95B04.8060104@cgl.ucsf.edu> <45DA1A61.5050703@rice.edu> <45DB3908.9000104@cgl.ucsf.edu> <461BDA22.4040400@rice.edu> Message-ID: <461BE9E3.6020603@cgl.ucsf.edu> Hi Jeff, The Chimera path tracer markers accommodate extra attributes that are read and written to the XML marker files. There is no user interface to define new marker attributes in Chimera. A user interface to define new marker attributes does not seem hard. You could specify an attribute name and value in a command or dialog that assigns that attribute for all selected markers. For these new attributes to be of any use within Chimera more capabilities would be needed. For example some command or dialog that would allow you to select all markers with a certain attribute and value (e.g. is_filament = true). These kinds of capabilities already exist for attributes of atoms of molecules. For example, see the "setattr" and "defattr" commands, and "Render/Select by Attribute" tool, and atom specifiers that can test for specific attribute values. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors These will work with path tracer markers since markers are implemented as atoms. But there are problems. For example "defattr" uses names of atoms and the names of the path tracer atoms are not meaningful. Probably "setattr" is more useful and you can set an attribute for all currently selected atoms. The main weakness is that these atom attributes will not be saved in marker XML files. That is probably easy to fix but I would need to investigate how atom attributes are implemented. For markers the attributes are kept in a Python dictionary marker.extra_attributes. I do not know if atom attributes on markers will be saved in Chimera session files. Would have to test that. Tom Jeff wrote: > Tom, > > how hard would it be to add other attribute(s) to the markers > generated with the volume path tracer tool, aside from > marker-to-marker connectivity? Such as the ability to enumerate > individual filaments/objects within a single marker set, or a flag > that would tell whether a set/group is composed of filaments, or > surfaces, or just a point cloud? Either of of these (enumeration, or > object type) could be stored as an integer. > > -Jeff From goddard at cgl.ucsf.edu Tue Apr 10 13:41:02 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 10 Apr 2007 13:41:02 -0700 Subject: [Chimera-users] Extra Chimera marker attributes In-Reply-To: <461BE9E3.6020603@cgl.ucsf.edu> References: <45C9513B.5040900@rice.edu> <45C95B04.8060104@cgl.ucsf.edu> <45DA1A61.5050703@rice.edu> <45DB3908.9000104@cgl.ucsf.edu> <461BDA22.4040400@rice.edu> <461BE9E3.6020603@cgl.ucsf.edu> Message-ID: <461BF65E.8060103@cgl.ucsf.edu> Hi Jeff, I checked with Eric Pettersen and found that Chimera sessions do not contain atom attributes set with "setattr" or "defattr". So there is currently no convenient way to save an manipulate marker attributes. Tom From goddard at cgl.ucsf.edu Tue Apr 10 17:55:30 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 10 Apr 2007 17:55:30 -0700 Subject: [Chimera-users] Extra Chimera marker attributes In-Reply-To: <461BF65E.8060103@cgl.ucsf.edu> References: <45C9513B.5040900@rice.edu> <45C95B04.8060104@cgl.ucsf.edu> <45DA1A61.5050703@rice.edu> <45DB3908.9000104@cgl.ucsf.edu> <461BDA22.4040400@rice.edu> <461BE9E3.6020603@cgl.ucsf.edu> <461BF65E.8060103@cgl.ucsf.edu> Message-ID: <461C3202.6060506@cgl.ucsf.edu> Jeff wrote: > do you think there is a way to address the request with minimal effort > from the developers? > Hi Jeff, The code could be changed so that whenever you open markers (XML file or session) their extra attributes become atom attributes, and whenever you save markers (XML file or session) the atom attributes become marker attributes (hence are saved). This would be trivial except that the implementation of atom attributes is hard to use. Finding atom attributes involves checking all the Python attributes of each atom and throwing out ones based on "smart" rules: the name can't start with "_" or with a capital letter, can't be in a standard list (radius, serialNumber, drawMode, ...), has to have a numeric value, .... All of these rules are currently inaccessible to other code in the render by attribute tool, though that could be changed. If all these special rules about atom attributes in the future are not adequate then when you save markers you will get unintended junk attributes in your XML files and sessions. If the above change were made it still looks cumbersome to use -- so cumbersome that noone would use it. Could you explain just how you would use it? including all commands you would type, what would get selected by hand, how you would operationally use the attributes. Tom From jiwasa at gmail.com Wed Apr 11 09:52:10 2007 From: jiwasa at gmail.com (Janet Iwasa) Date: Wed, 11 Apr 2007 12:52:10 -0400 Subject: [Chimera-users] exporting a mineral structure as VRML Message-ID: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> Hello, I'm trying to use Chimera to export a mineral file ( http://virtual-museum.soils.wisc.edu/soil_smectite/soil_smectite.pdb) as a ball and stick VRML structure, but I'm running into a bit of difficulty since some of the bonds don't get made into sticks -- rather, they appear as purple dotted lines in the viewer. Any suggestions on how to get these bonds to be made into geometry? thanks! Janet Iwasa -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Apr 11 11:22:19 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 11 Apr 2007 11:22:19 -0700 (PDT) Subject: [Chimera-users] exporting a mineral structure as VRML In-Reply-To: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> References: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> Message-ID: On Wed, 11 Apr 2007, Janet Iwasa wrote: > I'm trying to use Chimera to export a mineral file ( > http://virtual-museum.soils.wisc.edu/soil_smectite/soil_smectite.pdb) as a > ball and stick VRML structure, but I'm running into a bit of difficulty > since some of the bonds don't get made into sticks -- rather, they appear as > purple dotted lines in the viewer. Any suggestions on how to get these > bonds to be made into geometry? Hi Janet! There are two ways to convert the dashed lines in the metal coordination complexes to sticks: 1) Select one of the lines with the mouse, type the up-arrow key, to select all of the similar bonds, then use the selection inspector (button at bottom right of main window), to change the bond style to stick. In your example there are three different groups, one each for Al, Fe, and Mg. 2) Use the Tools / General Controls / PseudoBond Panel dialog, select each coordination complex in turn and click the attributes... button, then click the Component PseudoBond Attributes button to expose the bond style option and change the bond style to stick. Once the dashed lines are converted to sticks, they will export as sticks. - Greg From goddard at cgl.ucsf.edu Wed Apr 11 11:26:45 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 11 Apr 2007 11:26:45 -0700 Subject: [Chimera-users] exporting a mineral structure as VRML In-Reply-To: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> References: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> Message-ID: <461D2865.9050006@cgl.ucsf.edu> Hi Janet, Those purple dotted lines indicate metal coordination and are not covalent bonds. Apparently the dotted lines don't go into the VRML. You can change them to cylinders by selecting them and using the selection inspector. First ctrl-click on one dotted line. Then press the up-arrow key a few times to select all dotted lines. Then press the selection inspector button in the bottom right corner of the window that says "256 pbonds" (means pseudo-bonds). In the dialog that appears change "bond style" to "stick" and you might also change the radius (maybe from 0.2 to 0.05) so the look different then the real covalent bonds. The stick display of the pseudo-bonds does appear in the VRML. Tom From pett at cgl.ucsf.edu Wed Apr 11 11:29:39 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 11 Apr 2007 11:29:39 -0700 Subject: [Chimera-users] exporting a mineral structure as VRML In-Reply-To: References: <37ce55880704110952m70765d09m398565e29f744000@mail.gmail.com> Message-ID: <2DBA46D6-A8E5-4019-BC17-D67C33E26B7F@cgl.ucsf.edu> Hi Janet, I have also fixed the code to skip forming these metal complexes for large inorganic residues. If you are going to be working with many of these files I can send you the fix. --Eric On Apr 11, 2007, at 11:22 AM, Greg Couch wrote: > On Wed, 11 Apr 2007, Janet Iwasa wrote: > >> I'm trying to use Chimera to export a mineral file ( >> http://virtual-museum.soils.wisc.edu/soil_smectite/ >> soil_smectite.pdb) as a >> ball and stick VRML structure, but I'm running into a bit of >> difficulty >> since some of the bonds don't get made into sticks -- rather, they >> appear as >> purple dotted lines in the viewer. Any suggestions on how to get >> these >> bonds to be made into geometry? > > Hi Janet! > > There are two ways to convert the dashed lines in the metal > coordination > complexes to sticks: > > 1) Select one of the lines with the mouse, type the up-arrow key, to > select all of the similar bonds, then use the selection inspector > (button > at bottom right of main window), to change the bond style to > stick. In > your example there are three different groups, one each for Al, Fe, > and > Mg. > > 2) Use the Tools / General Controls / PseudoBond Panel dialog, > select each > coordination complex in turn and click the attributes... button, then > click the Component PseudoBond Attributes button to expose the bond > style > option and change the bond style to stick. > > Once the dashed lines are converted to sticks, they will export as > sticks. > > - Greg > _______________________________________________ > 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 Wed Apr 11 16:11:04 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 11 Apr 2007 16:11:04 -0700 Subject: [Chimera-users] exporting ".pov" session In-Reply-To: References: Message-ID: <461D6B08.2040408@cgl.ucsf.edu> Jean-Francois asks about what is exported to POV-ray. jean-francois menetret wrote: > > Hi Thomas, > > I have a question about saving ".pov" session > > Items of the chimera window that are not shown at the time of the > export command are saved in the povray scene. > Is that normal ? How can I save one object at a time ? > > Jean-Francois From meng at cgl.ucsf.edu Wed Apr 11 16:46:17 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Apr 2007 16:46:17 -0700 Subject: [Chimera-users] exporting ".pov" session In-Reply-To: <461D6B08.2040408@cgl.ucsf.edu> References: <461D6B08.2040408@cgl.ucsf.edu> Message-ID: Hi Jean-Francois, In our early releases with direct POV-Ray image saving, the scale of the result was different - the POV-Ray result was about 75% the scale in Chimera, so you could see things around the edges you couldn't see in Chimera. Is that what you mean? This scaling difference has been fixed. The problem is still there in 1.2352 but it is fixed in 1.2363. If this does sound like the problem you were having, try getting snapshot 1.2363 or newer: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Also, a known current limitation is that things clipped away with the global clipping planes in Chimera will still be included in the POV- Ray result. If it is a different problem, maybe we could understand better if you send a Chimera session and the POV-Ray image file that came from it. 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 Apr 11, 2007, at 4:11 PM, Tom Goddard wrote: > Jean-Francois asks about what is exported to POV-ray. > > > jean-francois menetret wrote: >> >> Hi Thomas, >> >> I have a question about saving ".pov" session >> >> Items of the chimera window that are not shown at the time of the >> export command are saved in the povray scene. >> Is that normal ? How can I save one object at a time ? >> >> Jean-Francois > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From menetret at bu.edu Wed Apr 11 17:41:39 2007 From: menetret at bu.edu (jean-francois menetret) Date: Wed, 11 Apr 2007 20:41:39 -0400 (EDT) Subject: [Chimera-users] exporting ".pov" session In-Reply-To: References: <461D6B08.2040408@cgl.ucsf.edu> Message-ID: Hi Elaine, I understand what you are talking about and it is great that you fixed it but my question is not related to saving images but '.pov' files. If a chimera session has 2 objects A and B, can you unshow A and save a '.pov' sesion file containing only info from B ? Jean-Francois Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street On Wed, 11 Apr 2007, Elaine Meng wrote: > Hi Jean-Francois, > In our early releases with direct POV-Ray image saving, the scale of the > result was different - the POV-Ray result was about 75% the scale in > Chimera, so you could see things around the edges you couldn't see in > Chimera. Is that what you mean? > > This scaling difference has been fixed. The problem is still there in > 1.2352 but it is fixed in 1.2363. If this does sound like the problem you > were having, try getting snapshot 1.2363 or newer: > http://www.cgl.ucsf.edu/chimera/download.html#snapshots > > Also, a known current limitation is that things clipped away with the global > clipping planes in Chimera will still be included in the POV-Ray result. > > If it is a different problem, maybe we could understand better if you send a > Chimera session and the POV-Ray image file that came from it. > 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 Apr 11, 2007, at 4:11 PM, Tom Goddard wrote: > >> Jean-Francois asks about what is exported to POV-ray. >> >> >> jean-francois menetret wrote: >>> >>> Hi Thomas, >>> >>> I have a question about saving ".pov" session >>> >>> Items of the chimera window that are not shown at the time of the >>> export command are saved in the povray scene. >>> Is that normal ? How can I save one object at a time ? >>> >>> Jean-Francois >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From molatwork at yahoo.es Wed Apr 11 22:43:24 2007 From: molatwork at yahoo.es (Miguel Ortiz Lombardia) Date: Thu, 12 Apr 2007 07:43:24 +0200 Subject: [Chimera-users] Suggestion on biological assembly load In-Reply-To: <461AB868.8040506@cgl.ucsf.edu> References: <4618BFA0.6010706@yahoo.es> <461AB868.8040506@cgl.ucsf.edu> Message-ID: <461DC6FC.5000601@yahoo.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, Thanks for your interest! I think that a collection of models for the cases where there is more than one assembly is an excellent idea. On a related note, it's a pity that mmCIF files are not more widely used instead of the very limited PDB format. I like the fact that Chimera can handle them. Best regards, Miguel Thomas Goddard escribi?: > Hi Miguel, > > Adding a fetch by id option for PQS biological assembly PDB files > looks like a good idea. I'll put it on the requested features list. > > Some of those files reuse atom serial numbers and reuse chain > identifiers. For example, satellite tobacco mosaic virus 1a34 which > involves 60 copies of the asymmetric unit (4 chains) has more than > 200,000 atoms and hundreds of chains. The PDB file format can't handle > that correctly. Still the file displays in Chimera although it can be > hard to select just a single capsid protein since it shares a chain > identifier with other subunits. This is a very small virus. Bigger > viruses just don't have PQS entries -- they probably set a size limit. > So this isn't a good way to handled icosahedral viruses. But probably > most other PDB entries will not have size problems. > > Another issue is that PQS has more than one biological assembly for > some PDB entries. For example, 1a6v has 3 assemblies, with files called > 1a6v_1.mmol, 1a6v_2.mmol and 1a6v_3.mmol. I guess it would make sense > to load all of the assemblies as separate Chimera models in those cases. > > Thanks for the suggestion. > > Tom > - -- Miguel Ortiz Lombard?a Centro de Investigaciones Oncol?gicas C/ Melchor Fern?ndez Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork at yahoo.es www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouv? de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFGHcb8F6oOrDvhbQIRAoHnAJ952AbA01XpJmKp6ctyWyKrPJEOFwCgpSNu 0riRyAIZrocy+SACVZAiwM8= =mMMB -----END PGP SIGNATURE----- From goddard at cgl.ucsf.edu Wed Apr 11 23:15:22 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 11 Apr 2007 23:15:22 -0700 Subject: [Chimera-users] Suggestion on biological assembly load In-Reply-To: <461DC6FC.5000601@yahoo.es> References: <4618BFA0.6010706@yahoo.es> <461AB868.8040506@cgl.ucsf.edu> <461DC6FC.5000601@yahoo.es> Message-ID: <461DCE7A.8000003@cgl.ucsf.edu> Hi Miguel, The remediated mmCIF virus files contain matrices to specify the full capsid, a single pentamer, a 23 hexamer (I think 6 monomers about a 3-fold axis), and the crystal asym unit. I plan to allow the Chimera multiscale tool to list and display all these biological assemblies listed in mmCIF files. Tom From meng at cgl.ucsf.edu Thu Apr 12 09:37:22 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 Apr 2007 09:37:22 -0700 Subject: [Chimera-users] exporting ".pov" session In-Reply-To: References: <461D6B08.2040408@cgl.ucsf.edu> Message-ID: <852A09B7-0F36-49DB-B966-BC509B50125F@cgl.ucsf.edu> Hi Jean-Francois, If "A" and "B" are molecule models and/or molecular surfaces, yes. However, there is currently a bug that VRML models (such as generated by Nucleotides, PipesAndPlanks) are included in the pov file and resulting POV-Ray image even when they are not shown in Chimera. To work around this problem, I recommend first saving a session with all your models, then closing the models you don't want in your pov file and image, then saving the pov file. I'll submit a bug report. Thanks for pointing out this problem, 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 Apr 11, 2007, at 5:41 PM, jean-francois menetret wrote: > Hi Elaine, > I understand what you are talking about and it is great that you > fixed it > but my question is not related to saving images but '.pov' files. > If a chimera session has 2 objects A and B, can you unshow A and > save a '.pov' sesion file containing only info from B ? > Jean-Francois > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret at bu.edu > Mailing address: 715 Albany Street From goddard at cgl.ucsf.edu Thu Apr 12 10:01:50 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 12 Apr 2007 10:01:50 -0700 Subject: [Chimera-users] Ribosomal RNA depiction In-Reply-To: References: <200704112110.l3BLAnFx1722440@guanine.cgl.ucsf.edu> <461D8026.8070302@cgl.ucsf.edu> <461DC806.2070400@cgl.ucsf.edu> Message-ID: <461E65FE.8090204@cgl.ucsf.edu> Hi Jean-Francois, Here are some tips for showing coarse RNA depictions. I too had lots of different colors for the ribosome rna bases using the nucleic acid blobs tool but I changed them. Here was my procedure. 1. open 1s72 2. select chain 0 (menu Select / Chain / 0) 3. invert selection to select all proteins (menu Select / Invert) 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete 5. open reschains.py 6. open multiscale (menu Tools / Higher-order Structure / Multiscale Models) 7. select multiscale multimer type None and press Make models. 8. press multiscale select All button, change resolution to 2, press Resurface 9. ctrl-click on backbone to select it 10. invert selection (menu Select / Invert) 11. click multiscale color button and set color of all bases http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna.png Nicer simplified depictions can be made using ribbons with a single side chain atom as a sphere. The ribbon style editor (Tools / Depictions / Ribbon Style Editor) can fatten up the ribbon. Or for fancier bases shown as slabs use the Nucleotides tool (Tools / Depiction / Nucleotides), for example, http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/1a34.png Tom jean-francois menetret wrote: > > Hi Tom, > > the new reschains.py works well; but how did you specify the color > scheme in 1s72_rna.png using "multiscalemodel" option ? I am getting so > many different colours (see attached jpeg) > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine From goddard at cgl.ucsf.edu Thu Apr 12 10:11:07 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 12 Apr 2007 10:11:07 -0700 Subject: [Chimera-users] Ribosomal RNA depiction In-Reply-To: <461E65FE.8090204@cgl.ucsf.edu> References: <200704112110.l3BLAnFx1722440@guanine.cgl.ucsf.edu> <461D8026.8070302@cgl.ucsf.edu> <461DC806.2070400@cgl.ucsf.edu> <461E65FE.8090204@cgl.ucsf.edu> Message-ID: <461E682B.1060702@cgl.ucsf.edu> The reschains.py script mentioned in the preceding message comes from the nucleic acid blobs package http://www.cgl.ucsf.edu/chimera/experimental/nablobs/nablobs.html on the Chimera experimental features web page. Tom From xiaoyunc at umich.edu Thu Apr 12 11:29:38 2007 From: xiaoyunc at umich.edu (Xiaoyun Chen) Date: Thu, 12 Apr 2007 14:29:38 -0400 Subject: [Chimera-users] questions using chimera Message-ID: <20070412142938.bf1xo5lggks04kkw@web.mail.umich.edu> I have two questions: 1) Is there a way for chimera to display the x-y-z axes? For example, for a pdb file, all the x/y/z coordinates are referenced to the molecular coordinate system. In the chimera screen, we can rotate the molecules. I want to know the orientation of the molecular coordinate system in the laboratory/chimera coordinate system, but cannot find a way for the x/y/z to show up on the screen. Many other protein visualization software (VMD, Molw, etc) have this feature. 2) by default, the z coordinate point out from the screen. often i would like to see the protein with its z direction in the plane of the screen and pointing up. tools-viewing controls-side view allow me to get what i want, but the image is only the protein projected onto the y-z plane. but it would be nice if there are two side view panels, one with an image in the y-z plane, one with an image in the x-z plane. Thank you! Xiaoyun Chen From meng at cgl.ucsf.edu Thu Apr 12 15:46:09 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 Apr 2007 15:46:09 -0700 Subject: [Chimera-users] questions using chimera In-Reply-To: <20070412142938.bf1xo5lggks04kkw@web.mail.umich.edu> References: <20070412142938.bf1xo5lggks04kkw@web.mail.umich.edu> Message-ID: <6243F976-717D-4EE8-BACE-11EA2C5C3DA6@cgl.ucsf.edu> Hi Xiaoyun, (1) There is no function to display the axes currently, but I attached at the bottom of this message a BILD object file showing the X,Y,Z axes in red, yellow, and blue. BILD is a very simple text format, and simply opening the file in Chimera shows the object. The drawback is that the position and scale of this object are not automatically adjusted depending on what you have displayed. You could change its origin by editing the coordinates in the ".translate" line and its scale by editing the number in the ".scale" line. Format description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html (2) Funny you should ask, but we just added a "top view" option to the Side View. It is available in the most recent snapshots (dated Apr 11 for Windows and Linux, Mar 26 for OSX although the GUI text was a little different then). You can switch between the two views. The top view shows the XZ plane with Z pointing left, toward the viewer. Here is a picture and description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/topview.html snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots 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 Apr 12, 2007, at 11:29 AM, Xiaoyun Chen wrote: > I have two questions: > 1) Is there a way for chimera to display the x-y-z axes? For example, > for a pdb file, all the x/y/z coordinates are referenced to the > molecular coordinate system. In the chimera screen, we can rotate the > molecules. I want to know the orientation of the molecular coordinate > system in the laboratory/chimera coordinate system, but cannot find a > way for the x/y/z to show up on the screen. Many other protein > visualization software (VMD, Molw, etc) have this feature. > > 2) by default, the z coordinate point out from the screen. often i > would like to see the protein with its z direction in the plane of the > screen and pointing up. tools-viewing controls-side view allow me to > get what i want, but the image is only the protein projected onto the > y-z plane. but it would be nice if there are two side view panels, one > with an image in the y-z plane, one with an image in the x-z plane. > > Thank you! > Xiaoyun Chen -------------- next part -------------- A non-text attachment was scrubbed... Name: general-axes.bild Type: application/octet-stream Size: 148 bytes Desc: not available URL: -------------- next part -------------- From goddard at cgl.ucsf.edu Thu Apr 12 15:49:55 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 12 Apr 2007 15:49:55 -0700 Subject: [Chimera-users] questions using chimera In-Reply-To: <20070412142938.bf1xo5lggks04kkw@web.mail.umich.edu> References: <20070412142938.bf1xo5lggks04kkw@web.mail.umich.edu> Message-ID: <461EB793.9060108@cgl.ucsf.edu> Hi Xiaoyun, As Elaine points out the side view window can also show a top view in recent Chimera versions. But Chimera has only two windows for viewing the models. It is not possible to show 3 orthogonal views in 3 windows. Tom From goddard at cgl.ucsf.edu Fri Apr 13 11:38:04 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Apr 2007 11:38:04 -0700 Subject: [Chimera-users] Ribosomal RNA depiction In-Reply-To: <4f0f0cb0704131038j48b1d602vd4e8e65179a120bc@mail.gmail.com> References: <200704112110.l3BLAnFx1722440@guanine.cgl.ucsf.edu> <461D8026.8070302@cgl.ucsf.edu> <461DC806.2070400@cgl.ucsf.edu> <461E65FE.8090204@cgl.ucsf.edu> <4f0f0cb0704131038j48b1d602vd4e8e65179a120bc@mail.gmail.com> Message-ID: <461FCE0C.6090301@cgl.ucsf.edu> Hi Dave, The RNA display using surfaces for each base could be done easily in a Python script, but not with Chimera commands since those are not available for multiscale. The result could be exported to POV-ray, or since Chimera now includes POV-ray the raytraced image can be directly produced in Chimera. I still think that a fat tubular ribbon with a single base atom shown as sphere gives a cleaner coarse view of RNA that indicates base orientations. Here's a ribbon and sphere image, also a ribbon with surface bases, also an image with bases with NDB colors. http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna/1s72.html Tom David Konerding wrote: > > > On 4/12/07, *Thomas Goddard* > wrote: > > Hi Jean-Francois, > > Here are some tips for showing coarse RNA depictions. > > I too had lots of different colors for the ribosome rna bases using > the nucleic acid blobs tool but I changed them. Here was my > procedure. > > 1. open 1s72 > 2. select chain 0 (menu Select / Chain / 0) > 3. invert selection to select all proteins (menu Select / Invert) > 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete > 5. open reschains.py > 6. open multiscale (menu Tools / Higher-order Structure / > Multiscale Models) > 7. select multiscale multimer type None and press Make models. > 8. press multiscale select All button, change resolution to 2, press > Resurface > 9. ctrl-click on backbone to select it > 10. invert selection (menu Select / Invert) > 11. click multiscale color button and set color of all bases > > > Tom- > > This looks nice. I don't have a lot of time to look into the > implementation right now, > but can steps 6-11 be done programmatically easily? > > Will the resulting images export to povray? > > Dave > > From goddard at cgl.ucsf.edu Fri Apr 13 13:13:56 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Apr 2007 13:13:56 -0700 Subject: [Chimera-users] Ribosomal RNA depiction In-Reply-To: <461FCE0C.6090301@cgl.ucsf.edu> References: <200704112110.l3BLAnFx1722440@guanine.cgl.ucsf.edu> <461D8026.8070302@cgl.ucsf.edu> <461DC806.2070400@cgl.ucsf.edu> <461E65FE.8090204@cgl.ucsf.edu> <4f0f0cb0704131038j48b1d602vd4e8e65179a120bc@mail.gmail.com> <461FCE0C.6090301@cgl.ucsf.edu> Message-ID: <461FE484.8050605@cgl.ucsf.edu> Hi Dave, I added a raytraced version of the 1s72 image at the bottom of the following web page. http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna/1s72.html The shadows give a much better sense of depth. I had to modify the current Chimera POV-ray output commenting out assumed_gamma and doubling light intensity to get this image. Otherwise the colors were faded and dim. Tom From goddard at cgl.ucsf.edu Fri Apr 13 14:11:31 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Apr 2007 14:11:31 -0700 Subject: [Chimera-users] Ribosomal RNA depiction In-Reply-To: <461FE484.8050605@cgl.ucsf.edu> References: <200704112110.l3BLAnFx1722440@guanine.cgl.ucsf.edu> <461D8026.8070302@cgl.ucsf.edu> <461DC806.2070400@cgl.ucsf.edu> <461E65FE.8090204@cgl.ucsf.edu> <4f0f0cb0704131038j48b1d602vd4e8e65179a120bc@mail.gmail.com> <461FCE0C.6090301@cgl.ucsf.edu> <461FE484.8050605@cgl.ucsf.edu> Message-ID: <461FF203.7090501@cgl.ucsf.edu> Hi Dave, The POVray tweeks I did by hand to make the 1s72 image are done automatically by Chimera version 1.2379, but not in the latest snapshot on the web 1.2363. The next snapshot out will have the improved POVray color / lighting fidelity. Tom From moocow at mindless.com Mon Apr 16 01:29:47 2007 From: moocow at mindless.com (Moo Cow) Date: Mon, 16 Apr 2007 03:29:47 -0500 Subject: [Chimera-users] gromacs trajectory - only atoms, no bonds Message-ID: <20070416082947.55BC11C0A32@ws1-1.us4.outblaze.com> I believe one has to have a very recent chimera in order to be able to read gromacs trajectories. I have "beta version 1 build 2376 2007/04/11 It is terrific that chimera can read the trajectories (without problem), but it then does not seem to join the atoms with bonds (it certainly does so for normal pdb files). My trajectory is displayed as a set of lonely unbonded atoms. I believe I checked for obvious mistakes on my part. I went to the tutorial, found the lines repr stick and so on. They gave no error message, but did not help. Many thanks for any advice. = Search for products and services at: http://search.mail.com From pett at cgl.ucsf.edu Mon Apr 16 11:18:34 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 Apr 2007 11:18:34 -0700 Subject: [Chimera-users] gromacs trajectory - only atoms, no bonds In-Reply-To: <20070416082947.55BC11C0A32@ws1-1.us4.outblaze.com> References: <20070416082947.55BC11C0A32@ws1-1.us4.outblaze.com> Message-ID: <9969C2F2-9597-4C87-AD71-7BBDF247B056@cgl.ucsf.edu> Moo!, The .tpr file format is basically undocumented, so it's possible that I've done something wrong somewhere in my code that reads it. Nonetheless, every trajectory I have access to works correctly (bonds show up). Could you send me your .tpr file? It would also be nice if you could send a corresponding .trr file with a frame or two of your trajectory so I can verify that everything looks okay when I'm done, but it's not strictly necessary if it's hard for you to make one. It has been suggested that I support allowing the use of .gro files instead of .tpr files. WIth a .gro file I would have to guesstimate connectivity and chemical elements, but in some cases (possibly this one for instance) it may be preferable. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Apr 16, 2007, at 1:29 AM, Moo Cow wrote: > I believe one has to have a very recent chimera in order > to be able to read gromacs trajectories. > I have "beta version 1 build 2376 2007/04/11 > > It is terrific that chimera can read the trajectories > (without problem), but it then does not seem to join > the atoms with bonds (it certainly does so for normal > pdb files). My trajectory is displayed as a set of > lonely unbonded atoms. > > I believe I checked for obvious mistakes on my part. I > went to the tutorial, found the lines > repr stick > and so on. They gave no error message, but did not help. > Many thanks for any advice. > > > = > Search for products and services at: > http://search.mail.com > > _______________________________________________ > 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 menetret at bu.edu Mon Apr 16 16:29:53 2007 From: menetret at bu.edu (jean-francois menetret) Date: Mon, 16 Apr 2007 19:29:53 -0400 (EDT) Subject: [Chimera-users] switching object on/off at the command line Message-ID: Is it possible to switch a model on/off from the command line ? "objdisplay #model / ~objdisplay #model" sound promissing but it doesn't work ... Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From meng at cgl.ucsf.edu Mon Apr 16 16:54:34 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Apr 2007 16:54:34 -0700 Subject: [Chimera-users] switching object on/off at the command line In-Reply-To: References: Message-ID: Hi Jean-Francois, The "objdisplay" command works for non-molecule-type models (VRML, volume, and isosurface models). The "modeldisplay" command works for molecule models and MSMS molecular surfaces. However, if you want to control a MSMS surface separately from its corresponding molecule model (atomic coordinates), it is necessary to use the Model Panel (because those two models will have the same model number and "modeldisplay" uses the model number). 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 Apr 16, 2007, at 4:29 PM, jean-francois menetret wrote: > > Is it possible to switch a model on/off from the command line ? > "objdisplay #model / ~objdisplay #model" sound promissing but it > doesn't work ... > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret at bu.edu > Mailing address: 715 Albany > Street_______________________________________________ > 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 Mon Apr 16 16:59:03 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Apr 2007 16:59:03 -0700 Subject: [Chimera-users] switching object on/off at the command line In-Reply-To: References: Message-ID: <8AAF57E2-48AE-400E-A92D-0B7BEF29BB95@cgl.ucsf.edu> Small clarification: "modeldisplay" will work on all of the model types, including those affected by "objdisplay," see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/objdisplay.html Elaine From keshet1 at umbc.edu Mon Apr 16 19:47:34 2007 From: keshet1 at umbc.edu (Ben Keshet) Date: Mon, 16 Apr 2007 22:47:34 -0400 Subject: [Chimera-users] Help with installing DMS and Chimera Message-ID: <000b01c7809a$c1323340$29ad5582@umbc80a173302c> Hello everybody, I am a very inexperienced new user of Linux / cygwin and having problems in installing DMS and Chimera: 1. I am trying to install DMS but having problems with specifying correctly the pathway to the appropriate locations of the BINDIR and LIBDIR directories in the GNUmakefile. I am getting a message: "Cannot create directory. not such file or directory". I have tried it both on Linux enterprise 4 and on Windows using cygwin. My pathway includes spaces, i.e: /cygdrive/c/Documents and Settings/User Name/Desktop/dms/bin Can anyone please tell me how exactly I should enter the pathway (I think the spaces cause the problem but not sure)? 2. I am having problems running the chimera-installer.exe. file of Chimera on Linux. When I double-clicked on it, it tells me that I cannot execute the file, so as suggested in the instructions (http://www.cgl.ucsf.edu/chimera/1.2304/linux.html) I typed chmod +x 'filename' . When I checked the properties of the file after chmod, the box of 'execute' was checked (so I believe that I really changed the file's permissions). However, I am still getting the same error message when I double-click it. Does anyone know what am I doing wrong? Please consider my lack of experience in UNIX terminology if you try to answer one of my questions, Thanks a lot, Ben -------------- next part -------------- An HTML attachment was scrubbed... URL: From marlovits at imp.univie.ac.at Tue Apr 17 05:47:13 2007 From: marlovits at imp.univie.ac.at (Thomas C Marlovits) Date: Tue, 17 Apr 2007 14:47:13 +0200 Subject: [Chimera-users] new feature: conversion of atomic coordinates to electron density map Message-ID: Hi, I am not quite sure, whether this is possible with Chimera ... but it would be great if there is a feature that would allow to convert a .pdb structure (atomic coordinates) into a map usually obtained by electron microscopy (sections) - for example into mrc/ccp4 format. Even filtering this map then to different resolutions (including storing entire maps) would be an interesting feature. Thanks, -Thomas __________________________________________ Thomas C Marlovits, PhD, M.A.S IMP - Institute of Molecular Pathology IMBA - Institute of Molecular Biotechnology, Austrian Academy of Sciences Dr. Bohr-Gasse 3 A-1030 Vienna AUSTRIA marlovits at imp.univie.ac.at Tel (+ 43) 1 79044 4630 From pett at cgl.ucsf.edu Tue Apr 17 11:07:38 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 17 Apr 2007 11:07:38 -0700 Subject: [Chimera-users] Help with installing DMS and Chimera In-Reply-To: <000b01c7809a$c1323340$29ad5582@umbc80a173302c> References: <000b01c7809a$c1323340$29ad5582@umbc80a173302c> Message-ID: <69CC731C-8B92-4B2B-892F-EC8D4B0C609C@cgl.ucsf.edu> On Apr 16, 2007, at 7:47 PM, Ben Keshet wrote: > Hello everybody, > > I am a very inexperienced new user of Linux / cygwin and having > problems in installing DMS and Chimera: > > 1. I am trying to install DMS but having problems with specifying > correctly the pathway to the appropriate locations of the BINDIR > and LIBDIR directories in the GNUmakefile. I am getting a message: > ?Cannot create directory? not such file or directory?. I have > tried it both on Linux enterprise 4 and on Windows using cygwin. > My pathway includes spaces, i.e: /cygdrive/c/Documents and Settings/ > User Name/Desktop/dms/bin Can anyone please tell me how exactly I > should enter the pathway (I think the spaces cause the problem but > not sure)? Your assessment of spaces being the problem is probably correct. Try putting double quotes around the path (i.e. LIBDIR="path" and BINDIR="path"). > > 2. I am having problems running the chimera-installer.exe. file of > Chimera on Linux. When I double-clicked on it, it tells me that I > cannot execute the file, so as suggested in the instructions > (http://www.cgl.ucsf.edu/chimera/1.2304/linux.html) I typed chmod > +x ?filename? . When I checked the properties of the file after > chmod, the box of ?execute? was checked (so I believe that I really > changed the file?s permissions). However, I am still getting the > same error message when I double-click it. Does anyone know what > am I doing wrong? Some Linux desktop managers are "smart" and "know" that files that end in .exe are Windows executables and will not let you execute them no matter what. You could try removing the .exe from the name and see if you are allowed to start it then. Otherwise you will have to start a terminal (probably under some system tools menu) and go to your desktop (type: cd ~/Desktop) and execute the installer directly (type: ./chimera-installer.exe). Let me know if you need more help. --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 goddard at cgl.ucsf.edu Tue Apr 17 11:36:24 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 17 Apr 2007 11:36:24 -0700 Subject: [Chimera-users] new feature: conversion of atomic coordinates to electron density map In-Reply-To: References: Message-ID: <462513A8.20301@cgl.ucsf.edu> Hi Thomas, There is a Chimera extension that produces an MRC density map from a PDB file. It is part of the Analysis of Intermediate Resolution Structures (AIRS) toolkit that is distributed with the EM single article reconstruction package EMAN1. http://ncmi.bcm.tmc.edu/software/AIRS http://blake.bcm.tmc.edu/eman If you install EMAN and configure Chimera to find the EMAN / Chimera extensions as described here http://ncmi.bcm.tmc.edu/software/AIRS/doc_html then there will be a Chimera menu entry Tools / AIRS / PDB to MRC. It allows you to specify a resolution and number of angstroms per pixel for the map. This is a good bit of work to setup and I plan on including the ability to make a density map from a PDB model directly in Chimera distributions in the future. It will use a Gaussian for each atom. I'll add this to my list of requested Chimera features. http://www.cgl.ucsf.edu/chimera/plans.html Thanks for the suggestion. Tom From menetret at bu.edu Tue Apr 17 14:31:03 2007 From: menetret at bu.edu (jean-francois menetret) Date: Tue, 17 Apr 2007 17:31:03 -0400 (EDT) Subject: [Chimera-users] using different scale for 2 models Message-ID: Is it possible to vary the scale of one model in respect to another during a movie ? Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From meng at cgl.ucsf.edu Tue Apr 17 15:03:11 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Apr 2007 15:03:11 -0700 Subject: [Chimera-users] Rotate or rock commands for making movie? In-Reply-To: References: Message-ID: On Apr 17, 2007, at 2:14 PM, Walter wrote: > Hi Elaine, > > I would like to make a movie using CHIMERA, but can only figure out > how to > rotate the molecule by hand and it ends up looking sloppy. Are there > command line entries for smoothly rotating or rocking a molecule? > > Thanks for your help! > > Walt Hi Walter, Sounds like you are looking for the "roll" command. http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/midas/roll.html This page lists commands especially useful for scripting movies, and links to a few example command files: http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/movies.html 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 From meng at cgl.ucsf.edu Tue Apr 17 15:14:08 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Apr 2007 15:14:08 -0700 Subject: [Chimera-users] using different scale for 2 models In-Reply-To: References: Message-ID: <16148273-6735-4A7B-9911-A5C22BD4CB1F@cgl.ucsf.edu> Hi Jean-Francois, There is only one scale factor, and it applies to everything. However, you can "fake" a shrinking model by setting the clip planes very far apart, then moving one model very far away (assuming you have "perspective" turned on, which is the default). For example, this series of commands: open 1gcn open 1zik [that makes 1gcn model 0, 1zik model 1] thickness 10000 [that moves the clipping planes 10,000 A farther apart] ~select 0 [freezes 1gcn] move z -10 50 [that moves 1zik 10 A farther away 50x, a total of 500 A] Fun, huh? 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 Apr 17, 2007, at 2:31 PM, jean-francois menetret wrote: > > Is it possible to vary the scale of one model in respect to another > during a movie ? > > > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret at bu.edu > Mailing address: 715 Albany > Street_______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From rabyrd at ncifcrf.gov Tue Apr 17 20:10:05 2007 From: rabyrd at ncifcrf.gov (R. Andrew Byrd) Date: Tue, 17 Apr 2007 23:10:05 -0400 Subject: [Chimera-users] Proper display of oligosaccharide Message-ID: <6.2.1.2.2.20070417230346.03019e70@mail.ncifcrf.gov> We study protein:carbohydrate interactions, and we use chimera for protein displays. We have a model built for an oligosaccharide using the SWEET server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php The file is in pdb format, but it has neither amino acid residue names nor nucleotide names. Hence, the molecule is invisible in Chimera. How could we make this a recognizable molecule so that we can examine various visualizations and modeling efforts using Chimera? Thanks! Andy P.S. I can send the file if you want. From meng at cgl.ucsf.edu Wed Apr 18 09:21:03 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Apr 2007 09:21:03 -0700 Subject: [Chimera-users] Proper display of oligosaccharide In-Reply-To: <6.2.1.2.2.20070417230346.03019e70@mail.ncifcrf.gov> References: <6.2.1.2.2.20070417230346.03019e70@mail.ncifcrf.gov> Message-ID: <81872EC6-FDA1-4911-92B7-05AABD0ABEDD@cgl.ucsf.edu> Hi Andy, It does not matter what the atom and residue names are, as long as they occupy the correct columns of the file. I often view molecules that are not protein or nucleic acids. Most likely the oligosaccharide file does not follow the PDB format specification completely. I went to the SWEET web site and downloaded the first example PDB on this page: http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php? left=fexample.html&main=bsp%2Fpdb%2Fpdb.html Chimera does display all the atoms and bonds for this structure, but complained about each line: "bad PDB record." (I'm using version 1.2363 on Mac OSX, but I don't think PDB reading has changed much in recent versions.) Using a text editor to compare other PDB files with the file from SWEET, it is evident that the latter has 4-character residue names, while PDB format only includes three columns for residue names. Replacing the last character in the residue name with a space (because the subsequent columns are already in the right place) should suppress the complaining messages. However, since this file did display in Chimera, perhaps the file(s) you are working with have some different or additional problems. You can mail it to me if you'd like us to take a look. Here is a line from the SWEET example file (need to view this with constant width font!) ATOM 1 C1 adne 1 -0.937 -0.321 0.174 0.00 0.00 and from a different file from the PDB ATOM 1 N ALA 1 46.457 12.189 21.556 1.00 56.69 Description of PDB format: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ framepdbintro.html http://www.wwpdb.org/documentation/format23/sect9.html#ATOM http://www.wwpdb.org/documentation/format23/sect9.html#HETATM 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 Apr 17, 2007, at 8:10 PM, R. Andrew Byrd wrote: > We study protein:carbohydrate interactions, and we use chimera for > protein > displays. We have a model built for an oligosaccharide using the > SWEET > server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php > > The file is in pdb format, but it has neither amino acid residue > names nor > nucleotide names. Hence, the molecule is invisible in Chimera. > > How could we make this a recognizable molecule so that we can examine > various visualizations and modeling efforts using Chimera? > > Thanks! > Andy > > P.S. I can send the file if you want. > > > > _______________________________________________ > 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 Wed Apr 18 10:46:30 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 18 Apr 2007 10:46:30 -0700 (PDT) Subject: [Chimera-users] Proper display of oligosaccharide In-Reply-To: <81872EC6-FDA1-4911-92B7-05AABD0ABEDD@cgl.ucsf.edu> References: <6.2.1.2.2.20070417230346.03019e70@mail.ncifcrf.gov> <81872EC6-FDA1-4911-92B7-05AABD0ABEDD@cgl.ucsf.edu> Message-ID: Actually, chimera accepts 4 character residue names, it's a non-standard extension that we first had in our previous software, MidasPlus. The bad PDB records are the bogus AUTHOR, REMARK, and CONNECT records. AUTHOR and REMARK records have particular formats to be standard. And CONNECT is supposed to be spelled CONECT, and when it is, chimera uses those records for connectivity. That said, we'd still like to see the example that fails. Greg Couch UCSF Computer Graphics Lab On Wed, 18 Apr 2007, Elaine Meng wrote: > From: Elaine Meng > To: R. Andrew Byrd > Cc: chimera-users at cgl.ucsf.edu > Date: Wed, 18 Apr 2007 09:21:03 -0700 > Subject: Re: [Chimera-users] Proper display of oligosaccharide > Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted > mechanism) > Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted > mechanism) > > Hi Andy, > It does not matter what the atom and residue names are, as long as > they occupy the correct columns of the file. I often view molecules > that are not protein or nucleic acids. Most likely the > oligosaccharide file does not follow the PDB format specification > completely. > > I went to the SWEET web site and downloaded the first example PDB on > this page: > http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php? > left=fexample.html&main=bsp%2Fpdb%2Fpdb.html > > Chimera does display all the atoms and bonds for this structure, but > complained about each line: "bad PDB record." (I'm using version > 1.2363 on Mac OSX, but I don't think PDB reading has changed much in > recent versions.) Using a text editor to compare other PDB files with > the file from SWEET, it is evident that the latter has 4-character > residue names, while PDB format only includes three columns for > residue names. Replacing the last character in the residue name with > a space (because the subsequent columns are already in the right > place) should suppress the complaining messages. However, since this > file did display in Chimera, perhaps the file(s) you are working with > have some different or additional problems. You can mail it to me if > you'd like us to take a look. > > Here is a line from the SWEET example file (need to view this with > constant width font!) > ATOM 1 C1 adne 1 -0.937 -0.321 0.174 0.00 0.00 > and from a different file from the PDB > ATOM 1 N ALA 1 46.457 12.189 21.556 1.00 56.69 > > Description of PDB format: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ > framepdbintro.html > http://www.wwpdb.org/documentation/format23/sect9.html#ATOM > http://www.wwpdb.org/documentation/format23/sect9.html#HETATM > > 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 Apr 17, 2007, at 8:10 PM, R. Andrew Byrd wrote: > >> We study protein:carbohydrate interactions, and we use chimera for >> protein >> displays. We have a model built for an oligosaccharide using the >> SWEET >> server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php >> >> The file is in pdb format, but it has neither amino acid residue >> names nor >> nucleotide names. Hence, the molecule is invisible in Chimera. >> >> How could we make this a recognizable molecule so that we can examine >> various visualizations and modeling efforts using Chimera? >> >> Thanks! >> Andy >> >> P.S. I can send the file if you want. >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > 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 Wed Apr 18 11:57:31 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 18 Apr 2007 11:57:31 -0700 (PDT) Subject: [Chimera-users] Proper display of oligosaccharide Message-ID: To followup, I just tried the first Human milk saccarides example on the Sweet webside, 2'-Fucosyllactose, and the PDB file it generates doesn't display at all because of the non-standard data in columns 67-72. We have decided that we're being too strict in this case and will change chimera. In the iterim, if you're on a UNIX system (Linux, Mac OS X, etc.), you can truncate the lines with the following: awk '{if (/^ATOM/) print substr($0, 1, 67); else print $0}' < original > fixed with appropriate filename replacements for original and fixed. Greg Couch UCSF Computer Graphics Lab From menetret at bu.edu Thu Apr 19 05:59:10 2007 From: menetret at bu.edu (jean-francois menetret) Date: Thu, 19 Apr 2007 08:59:10 -0400 (EDT) Subject: [Chimera-users] rotating 2 models side-by-side Message-ID: How can I make two models rotate side-by-side around their respective centers using chimera ? Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From meng at cgl.ucsf.edu Thu Apr 19 09:09:26 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 19 Apr 2007 09:09:26 -0700 Subject: [Chimera-users] rotating 2 models side-by-side In-Reply-To: References: Message-ID: <63230563-DF1C-44F8-B2D0-A419988AD865@cgl.ucsf.edu> Hi Jean-Francois, Either set "center of rotation method" to "independent" in the Rotation tool (under Tools... Movement): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation or use the command "set independent": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html You can see this in action in the "COX Inhibitors Demo" (under Tools... Demos). ----- 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 Apr 19, 2007, at 5:59 AM, jean-francois menetret wrote: > > > How can I make two models rotate side-by-side around their > respective centers using chimera ? > > > > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret at bu.edu > Mailing address: 715 Albany > Street_______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From rkhayat at scripps.edu Thu Apr 19 08:56:54 2007 From: rkhayat at scripps.edu (rkhayat at scripps.edu) Date: Thu, 19 Apr 2007 08:56:54 -0700 (PDT) Subject: [Chimera-users] Transform Molecule Coordinates Message-ID: <31679.66.236.22.99.1176998214.squirrel@webmail.scripps.edu> Hi, I was wondering if there is a stand alone version of the "Transform Molecule Coordinates" Chimera extension available. Alternatively, how will I be able to use this feature outside of Chimera? Thanks. Reza From goddard at cgl.ucsf.edu Thu Apr 19 09:58:21 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 19 Apr 2007 09:58:21 -0700 Subject: [Chimera-users] Transform Molecule Coordinates In-Reply-To: <31679.66.236.22.99.1176998214.squirrel@webmail.scripps.edu> References: <31679.66.236.22.99.1176998214.squirrel@webmail.scripps.edu> Message-ID: <46279FAD.70401@cgl.ucsf.edu> Hi Reza, You can use the Chimera transform molecule coordinates tool to rotate a molecule using Euler angles without displaying the Chimera graphical interface. You need a Python script to do this. I've attached an example script rotatepdb.py that you would run from a terminal window as follows: $ chimera --nogui rotatepdb.py The --nogui flag means that Chimera should not display any windows. Chimera is needed because it contains the code that reads and writes PDB files and applies transformation matrices. Tom From goddard at cgl.ucsf.edu Thu Apr 19 10:30:34 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 19 Apr 2007 10:30:34 -0700 Subject: [Chimera-users] rotating maps in chimera In-Reply-To: <20070419130332.hxnjn70is4wwws4o@www.bu.edu> References: <20070419130332.hxnjn70is4wwws4o@www.bu.edu> Message-ID: <4627A73A.8070408@cgl.ucsf.edu> Hi Preethi, Here's what caused the misalignment when you opened "subtracted map 2", let's call that one map 3, into Chimera where the original map 2 and reoriented map 1 were already opened. When you open map 3 Chimera needed to give it an initial transformation. Maps 1 and 2 had different transforms. Chimera chooses the transform of the map with the lowest id number (shown in Model Panel, menu entry Favorites / Model Panel). Map 1 must have had the lowest id number, so it got the transform of map 1 instead of the transform of map 2. Chimera had no way of knowing that map 3 was just a modified version of map 2. When you open data in Chimera it assigns an id number to it (shown in Model Panel). The id number is 0 for the first opened data set, then 1 for the next, .... In general it assigns the lowest available id number when a new data set is opened. When restoring Chimera sessions maps get their original model id numbers in Chimera versions 1.2354 and later, but are assigned new model id numbers in older versions. Since the data sets with lowest id number determines the transform of all newly opened models it is best to think of that data set as defining the reference frame. You can use the Model Panel / Transform As... button to correct the transform of a newly opened model. In the case you described you would need to transform map 3 as map 2 to fix the misalignment. This is probably easier than editing a session file. Tom preethi at bu.edu wrote: > Hi Tom, > > Chris I think had already discussed with you about how we transform > the PDB files that were originally fit into a brix map so that it now > fits into an MRC file in chimera. > > I am just repeating that here because I came across a problem when I > did this. > > I saved a session in chimera where I had rotated a MRC map say map 1 > w.r.t another MRC map 2 and then used the "fit map into map" feature > to align map 1 into map 2.So I saved the session(which would save the > transformation matrix) and then used the matrix to move certain PDB > files(using "transform as"). > > Now I did some zoning and volume erasing on map 2(the unrotated map) > and then saved the resulting map and then with another program outside > chimera subtracted the zoned out volume from the whole volume of map 2. > > SO when I read in the subtracted file into chimera it is now rotated > w.r.t the map 2 instead of being read with the original matrix that > was used for map2. I fixed this problem by going into chimera session > file and maunally changing the rotation and translation values for > this map to match that of map2. > > Also, if I opened chimera afresh and didnt restore the session where I > had done all the transformations but just opened map 2 and the > subtracted map then it reads them correctly without displacing one map > w.r.t the other. > > So I was just wondering why chimera automatically rotates the > subsequent MRC files that are read into a session where a > transformation was applied to some files only ? > > -Preethi > > > > > > From rkhayat at scripps.edu Thu Apr 19 15:25:47 2007 From: rkhayat at scripps.edu (rkhayat at scripps.edu) Date: Thu, 19 Apr 2007 15:25:47 -0700 (PDT) Subject: [Chimera-users] Transform Molecule Coordinates In-Reply-To: <46279FAD.70401@cgl.ucsf.edu> References: <31679.66.236.22.99.1176998214.squirrel@webmail.scripps.edu> <46279FAD.70401@cgl.ucsf.edu> Message-ID: <49520.192.26.250.242.1177021547.squirrel@webmail.scripps.edu> Hi Tom, Thank you very much. Reza > Hi Reza, > > You can use the Chimera transform molecule coordinates tool to rotate > a molecule using Euler angles without displaying the Chimera graphical > interface. You need a Python script to do this. I've attached an > example script rotatepdb.py that you would run from a terminal window as > follows: > > $ chimera --nogui rotatepdb.py > > The --nogui flag means that Chimera should not display any windows. > > Chimera is needed because it contains the code that reads and writes > PDB files and applies transformation matrices. > > Tom > > From hsosa at aecom.yu.edu Fri Apr 20 16:54:11 2007 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Fri, 20 Apr 2007 19:54:11 -0400 Subject: [Chimera-users] Chimera crash Message-ID: <462952A3.60609@aecom.yu.edu> Hi, I'm having problems later with chimera. Sometimes when rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash with blue screen and reboot. It seems like a new problem as I've bee using chimera for a while and it didn't' happen before. As far as I know everything is the same in the computer. I'm running the latest snapshot release of chimera but that doesn't seem to be the problem. I deinstalled this version and installed the latest production release and got the same problem. Any ideas what the problem may be ?. Thanks Hernando System details UCSF chimera version 1.2382 (or 1.2304) OS: Windows XP service pack-2 Computer: Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.00.27.05 ForceWare version 91.36 -- ----------------------------------- 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 Fri Apr 20 18:16:46 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 20 Apr 2007 18:16:46 -0700 Subject: [Chimera-users] Chimera crash In-Reply-To: <462952A3.60609@aecom.yu.edu> References: <462952A3.60609@aecom.yu.edu> Message-ID: <462965FE.9040508@cgl.ucsf.edu> Hi Hernando, This is almost certainly a graphics driver problem. You could try updating your machine to a newer graphics driver such as 93.71 (most recent driver for your card) http://www.nvidia.com/object/winxp_2k_93.71.html and if that does not fix the problem try an older driver. Tom From pounjai at gmail.com Sat Apr 21 07:15:15 2007 From: pounjai at gmail.com (Puey Ounjai) Date: Sat, 21 Apr 2007 10:15:15 -0400 Subject: [Chimera-users] Chimera-users Digest, Vol 48, Issue 17 In-Reply-To: References: Message-ID: Dear all; I am wondering can we manually assign secondary structure to each residues in the PDB file in chimera? Thanks Puey -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Apr 21 16:21:45 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 21 Apr 2007 16:21:45 -0700 Subject: [Chimera-users] assigning secondary structure In-Reply-To: References: Message-ID: <6b3c9ac2719564411809bcbf01dfb96e@cgl.ucsf.edu> Hi Puey, Yes, there are many different ways to assign values of these residue attributes, named isHelix and isSheet (or isStrand). Here are five possible ways: (A) by editing/adding HELIX and SHEET records in the input PDB file http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ pdbintro.html#secondary (B) by running ksdssp in Chimera if you want the Kabsch & Sander DSSP method to figure out the assignments using your preferred parameter values http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html (C) by creating an attribute assignment file http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html#attrfile and reading it in with Define Attribute http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html (D) by using the command "setattr" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html For example: setattr r isHelix true :1-10.a,23-36.b setattr r isSheet false :1-10.a,23-36.b (E) by selecting residues, opening the Selection Inspector (one way is to click the button on the lower right corner of the Chimera window), and changing the "Residue" attributes "in helix" and "in strand" ** Be careful to avoid making both of those attributes true for the same residue, because Chimera will allow it. If a residue is first assigned as helix and you want it to be strand, you need to both set isHelix false and set isSheet true. ** 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 Apr 21, 2007, at 7:15 AM, Puey Ounjai wrote: > Dear all; > > I am wondering can we manually assign secondary structure to each > residues in the PDB file in chimera? > > Thanks > Puey > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From anat at chem.ch.huji.ac.il Sun Apr 22 01:31:49 2007 From: anat at chem.ch.huji.ac.il (anat at chem.ch.huji.ac.il) Date: Sun, 22 Apr 2007 11:31:49 +0300 Subject: [Chimera-users] Secondary Structure Editing Message-ID: <20070422113149.20vjovgv4g0cg0os@webmail.huji.ac.il> Hi, I would like to know if it's possible to edit (manually) the secondary structure attribute of single amino acid in the computed sequence given by Chimera (e.g. from strand to helix). Thank you for your help, Anat, the Hebrew university of Jerusalem. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From meng at cgl.ucsf.edu Mon Apr 23 09:51:24 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Apr 2007 09:51:24 -0700 Subject: [Chimera-users] Secondary Structure Editing In-Reply-To: <20070422113149.20vjovgv4g0cg0os@webmail.huji.ac.il> References: <20070422113149.20vjovgv4g0cg0os@webmail.huji.ac.il> Message-ID: <12AC1993-0F6E-4B41-B128-0EA0C9CDA52B@cgl.ucsf.edu> Hi Anat, See yesterday's message on this topic, especially methods (D) and (E): http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-April/001514.html Elaine On Apr 22, 2007, at 1:31 AM, anat at chem.ch.huji.ac.il wrote: > Hi, > > I would like to know if it's possible to edit (manually) the secondary > structure attribute of single amino acid in the computed sequence > given by Chimera (e.g. from strand to helix). > > Thank you for your help, > Anat, the Hebrew university of Jerusalem. > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From menetret at bu.edu Mon Apr 23 11:42:06 2007 From: menetret at bu.edu (jean-francois menetret) Date: Mon, 23 Apr 2007 14:42:06 -0400 (EDT) Subject: [Chimera-users] movie and 'side view' Message-ID: Is it possible to include the 'side view' during movie recording ? Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From goddard at cgl.ucsf.edu Mon Apr 23 11:49:52 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 23 Apr 2007 11:49:52 -0700 Subject: [Chimera-users] movie and 'side view' In-Reply-To: References: Message-ID: <462CFFD0.20106@cgl.ucsf.edu> Hi Jean-Francois, The Chimera movie recorder cannot record the side-view. And there is no Chimera capability to make an image of the side view. Tom From glaco at lecom.edu Mon Apr 23 17:07:23 2007 From: glaco at lecom.edu (Gary Laco) Date: Mon, 23 Apr 2007 20:07:23 -0400 Subject: [Chimera-users] mutating amino acid side chain_deleting single atom Message-ID: <20070424000129.89B89B7453@spam.lecom.edu> Hi, How can I mutate an amino acid side chain in a protein to another residue using Chimera? Also, how do I delete a single atom on an amino acid (for example a hydrogen). I looked through all the tools and did not find a way to do it. Thanks, Gary Gary S. Laco, Ph.D. Assistant Professor of Biochemistry Lake Erie College of Osteopathic Medicine-Bradenton 5000 Lakewood Ranch Blvd. Bradenton, FL 34211 Office: 941-782-5666 Fax: 941-782-5729 E-mail: glaco at lecom.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 24 10:01:49 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Apr 2007 10:01:49 -0700 Subject: [Chimera-users] mutating amino acid side chain_deleting single atom In-Reply-To: <20070424000129.89B89B7453@spam.lecom.edu> References: <20070424000129.89B89B7453@spam.lecom.edu> Message-ID: <3C5956B3-D940-4545-BD9F-FF2CDBA72E12@cgl.ucsf.edu> Hi Gary, (1) You can mutate an amino acid side chain with the command "swapaa": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html We are working on an interface to allow choosing favorable sidechain rotamers. However, that is not yet available, and swapaa does not make any effort to choose a favorable conformation. After swapping the residue, you can adjust the torsions if you want, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#adjust (2) There is no separate deletion tool, but you can either select the atom and use "Actions... Atoms/Bonds... delete" in the menu, or you can use the command "delete": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html You can see there are functions performed by commands and menu items that are not in the "Tools" (which generally have graphical interfaces). You can search for features using "Help... Search Documentation" in the Chimera menu, or in addition to the Tools, scan the commands index http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html 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 Apr 23, 2007, at 5:07 PM, Gary Laco wrote: > Hi, > > How can I mutate an amino acid side chain in a protein to another > residue using Chimera? Also, how do I delete a single atom on an > amino acid (for example a hydrogen). I looked through all the > tools and did not find a way to do it. > > Thanks, > > Gary > > > > Gary S. Laco, Ph.D. > > Assistant Professor of Biochemistry > > Lake Erie College of Osteopathic Medicine-Bradenton > > 5000 Lakewood Ranch Blvd. > > Bradenton, FL 34211 > > > > Office: 941-782-5666 > > Fax: 941-782-5729 > > E-mail: glaco at lecom.edu > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From jeandidier.marechal at uab.es Fri Apr 27 09:39:27 2007 From: jeandidier.marechal at uab.es (Jean-Didier Marechal) Date: Fri, 27 Apr 2007 18:39:27 +0200 Subject: [Chimera-users] Ligand structure minimization In-Reply-To: References: Message-ID: <1177691967.11432.17.camel@localhost> Dear all, I don't know whether my problem falls in "bug" or "user request" category, pcorry if I use the wrong list. I am preparing a course where students will perform some protein-ligand dockings. I was thinking in minimizing the ligand in chimera using the "minimize structure" tool. I have installed the 1.2356 (that's what I thought but the message in the "About UCSF Chimera" pop up window says 1.2376 actually) version of chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to have compatibility problems with numpy. I join here the message given in the reply log file: .... Charges for residue U0E determined Total charge for #0: 1.0000 Running PARMCHK for U0E1.pdb command: /usr/local/chimera/bin/antechamber/exe/parmchk -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0 -p /usr/local/chimera/share/MMMD/parm/gaff.dat Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for calculations. Numeric is only available in Chimera 1.2318 and earlier. Is there an easy way to move around this problem or should I install a earlier version of chimera for the moment? cheers, JD From coolaladdin at gmail.com Sat Apr 28 22:59:58 2007 From: coolaladdin at gmail.com (aladdin) Date: Sun, 29 Apr 2007 01:59:58 -0400 Subject: [Chimera-users] How does chimera invoke msms? Message-ID: <6ff244430704282259y6a532ce0m8dea704d8aed612b@mail.gmail.com> I need to know the solvent accessible surface of a protein, that means the info of solvent accessibility of residues or atoms . If I directly run "msms" with "-af" option, I can get an .area file in which stored such information. But in chimera's surface model, I cannot find what I need. How can I get the solvent accessible info in chimera? Thanks. liren -------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Apr 30 11:20:53 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 30 Apr 2007 11:20:53 -0700 Subject: [Chimera-users] How does chimera invoke msms? In-Reply-To: <6ff244430704282259y6a532ce0m8dea704d8aed612b@mail.gmail.com> References: <6ff244430704282259y6a532ce0m8dea704d8aed612b@mail.gmail.com> Message-ID: <5FBDF3F7-512E-49BB-A7CA-56A5BE96A0C1@cgl.ucsf.edu> Hi Liren, We had always intended to expose the surface-area info in Chimera, but once it became clear that we were going to replace MSMS with our own library (due to reliability issues) we decided to wait for the new library before doing that work. Unfortunately the new library has been a long time in coming and is still not ready. What you can do right now is use the Measure Volume and Area tool to get the area of an entire surface. If you need per-atom/residue values, then you can use Area/Volume from Web (which uses the NIH StrucTools server) to get per-atom values assigned as attributes to atoms. To get per-residue sums, you would use the sum() function of the Attribute Calculator tool to compute those and to save them (or the atom attibutes) to a file. Part II of the Attributes tutorial (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html#part2) covers using the Area/Volume from Web and Attribute Calculator tools, though it use them to compute a convexity attribute rather than the residue area. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Apr 28, 2007, at 10:59 PM, aladdin wrote: > I need to know the solvent accessible surface of a protein, that > means the info of solvent accessibility of residues or atoms . If I > directly run "msms" with "-af" option, I can get an .area file in > which stored such information. But in chimera's surface model, I > cannot find what I need. How can I get the solvent accessible info > in chimera? Thanks. > > liren > -------------------------------------------- > _______________________________________________ > 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: