- Chimera-users - RBVI Mailing Lists

Transform Molecule Coordinates
by rkhayat＠scripps.edu 19 Apr '07

19 Apr '07

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

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Re: [Chimera-users] rotating maps in chimera
by Tom Goddard 19 Apr '07

19 Apr '07

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(a)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 > > > > > >

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rotating 2 models side-by-side
by jean-francois menetret 19 Apr '07

19 Apr '07

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(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Proper display of oligosaccharide
by Greg Couch 18 Apr '07

18 Apr '07

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

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Proper display of oligosaccharide
by R. Andrew Byrd 18 Apr '07

18 Apr '07

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.

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using different scale for 2 models
by jean-francois menetret 17 Apr '07

17 Apr '07

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(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Rotate or rock commands for making movie?
by Elaine Meng 17 Apr '07

17 Apr '07

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(a)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

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Help with installing DMS and Chimera
by Ben Keshet 17 Apr '07

17 Apr '07

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

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switching object on/off at the command line
by jean-francois menetret 16 Apr '07

16 Apr '07

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(a)bu.edu Mailing address: 715 Albany Street

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gromacs trajectory - only atoms, no bonds
by Moo Cow 16 Apr '07

16 Apr '07

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

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Re: [Chimera-users] Ribosomal RNA depiction
by Tom Goddard 13 Apr '07

13 Apr '07

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* <goddard(a)cgl.ucsf.edu > <mailto:goddard@cgl.ucsf.edu>> 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 > >

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questions using chimera
by Xiaoyun Chen 12 Apr '07

12 Apr '07

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

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Ribosomal RNA depiction
by Thomas Goddard 12 Apr '07

12 Apr '07

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-François Ménétret, PhD > Boston University School of Medicine

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exporting ".pov" session
by Tom Goddard 12 Apr '07

12 Apr '07

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

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Suggestion on biological assembly load
by Miguel Ortiz-Lombardia 11 Apr '07

11 Apr '07

-----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/<ID>.mmol where <ID> 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=<ID> Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGGL+gF6oOrDvhbQIRAtQ2AKCi9oIpIJffYwshk1PgB2aiG4e9rgCghjzZ Uz0yTug1VXEHXNP2MG2HsmI= =EGzy -----END PGP SIGNATURE-----

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exporting a mineral structure as VRML
by Janet Iwasa 11 Apr '07

11 Apr '07

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

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Extra Chimera marker attributes
by Tom Goddard 10 Apr '07

10 Apr '07

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#descri… 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

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transparency factor
by jean-francois menetret 09 Apr '07

09 Apr '07

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(a)bu.edu Mailing address: 715 Albany Street

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Fetch EMDB map by id
by Thomas Goddard 09 Apr '07

09 Apr '07

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

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Re: [Chimera-users] hkcage command
by Thomas Goddard 09 Apr '07

09 Apr '07

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

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GIF animations in Chimera
by Tom Goddard 09 Apr '07

09 Apr '07

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

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[Fwd: Re: GIF animations in Chimera]
by Thomas Goddard 09 Apr '07

09 Apr '07

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(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] [chimera-dev] Building a multimer model
by Elaine Meng 07 Apr '07

07 Apr '07

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(a)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(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Re: [Chimera-users] viewing & comparison of multiple overlay structures
by Roberta King 04 Apr '07

04 Apr '07

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@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(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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render several models by attribute on an absolute scale
by E. Merkley 03 Apr '07

03 Apr '07

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

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