From marek.maly at ujep.cz Mon Sep 3 06:28:58 2012 From: marek.maly at ujep.cz (Marek Maly) Date: Mon, 03 Sep 2012 15:28:58 +0200 Subject: [Chimera-users] H-bond analysis in case of TIP4P water model ? Message-ID: Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From maryvjes1985 at yahoo.co.in Mon Sep 3 23:18:25 2012 From: maryvjes1985 at yahoo.co.in (MARY VARUGHESE) Date: Tue, 4 Sep 2012 14:18:25 +0800 (SGT) Subject: [Chimera-users] saving spheres Message-ID: <1346739505.71489.YahooMailNeo@web193606.mail.sg3.yahoo.com> Hi, I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. Thanking You. -------------- next part -------------- An HTML attachment was scrubbed... URL: From miromoman at gmail.com Tue Sep 4 05:40:53 2012 From: miromoman at gmail.com (Miro Moman) Date: Tue, 04 Sep 2012 14:40:53 +0200 Subject: [Chimera-users] Ligand parametrization Message-ID: <5045F6D5.1070408@gmail.com> Hello, When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: Are parameters computed in the same way? If not, what are the differences? Maybe a different forcefield version? In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? Kind regards, Miro From goddard at sonic.net Tue Sep 4 09:13:29 2012 From: goddard at sonic.net (Tom Goddard) Date: Tue, 4 Sep 2012 09:13:29 -0700 Subject: [Chimera-users] Fwd: Installation problems In-Reply-To: References: Message-ID: <2678D7D8-942D-4631-B4B6-271842C0E041@sonic.net> I've seen this error when trying to install 64-bit Chimera on a 32-bit Linux or 32-bit Chimera on a 64-bit Linux that does not include 32-bit libraries. So you might try 32-bit Chimera. Tom On Aug 31, 2012, at 9:50 AM, prashant kurkute wrote: > Respected sir, > > Sorry for making you disturb. > I am novice to linux. > I am trying to install chimera in ubuntu 12.04 LTS. > > I follow following instruction. > > sudo chmod +x chimera-1.6.2-linux_x86_64.bin > ./chimera-1.6.2-linux_x86_64.bin > > (I also triied with root sudo ./chimera-1.6.2-linux_x86_64.bin) > > I got following reply > bash: ./chimera-1.6.2-linux_x86_64.bin: cannot execute binary file > > Sir please help me to solve problem. > I will be greatly thankful to your help. > > With Best wishes and regards. > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue Sep 4 09:26:21 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Sep 2012 09:26:21 -0700 Subject: [Chimera-users] saving spheres In-Reply-To: <1346739505.71489.YahooMailNeo@web193606.mail.sg3.yahoo.com> References: <1346739505.71489.YahooMailNeo@web193606.mail.sg3.yahoo.com> Message-ID: <812F0943-6B18-4D91-8DB5-CE05E59EA1EA@cgl.ucsf.edu> Hi Mary, In Chimera each cluster is a different model (something like model numbers #0.1, #0.2, #0.3, ...), so if you wanted to write two clusters as a single cluster, you would first need to combine them into a single model (for example, #0.1 and #0.2 could be combined into a new model #1). You can see what models are present by looking in the Model Panel (in menu under Tools.. Favorites), and you can combine models by using the Model Panel function "copy/combine". For details, see "Editing Sphere Clusters": Alternatively, instead of using Chimera, you could just text-edit the sphere file to put all the spheres in a single cluster. The sphere file has lines like: cluster 3 number of spheres in cluster 50 ...and you could just remove the second such line and update the sphere count in the first such line to include all the spheres in the file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 3, 2012, at 11:18 PM, MARY VARUGHESE wrote: > Hi, > I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. > Thanking You. From pett at cgl.ucsf.edu Tue Sep 4 13:13:29 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 4 Sep 2012 13:13:29 -0700 Subject: [Chimera-users] Ligand parametrization In-Reply-To: <5045F6D5.1070408@gmail.com> References: <5045F6D5.1070408@gmail.com> Message-ID: <3615F88F-17AF-4B88-AB9E-540ED8C1B7EB@cgl.ucsf.edu> On Sep 4, 2012, at 5:40 AM, Miro Moman wrote: > Hello, > > When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. > > However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. > > Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: > > Are parameters computed in the same way? > > If not, what are the differences? Maybe a different forcefield version? Parameters are not computed in the same way for Write Prmtop / sleap as they are for Minimize Structure / MMTK. For Write Prmtop, Chimera relies on sleap's built-in parmchk to generate missing parameters. sleap runs parmchk on a per-residue basis. This means that parameters can be missing for bonds/angles/torsions that cross the boundary between the non-standard residue and any connected residues. Since many non-standard residues are not connected to other residues (e.g. they are ligands), this isn't as big a problem as one might think, but it is still a problem. For Minimize Structure, Chimera finds the entire connected chain that contains the non-standard residue and runs parmchk on that. In fact, it runs it on all such chains at once. This means that for structures that contain many chains with non-standard residues, the parmchk process can take a long time. Nonetheless, the parmchk will produce a complete set of parameters. We hope to make Chimera run parmchk on a per-chain basis sometime soon (parmchk execution time seems to scale exponentially with the number of atoms involved). > In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? There is always a way. Well, almost always. There is this time at least! You would need to edit Chimera's Python code so that it doesn't remove the parmchk output once it's done with it. For Write Prmtop, there is a _clean function defined near line 95 of /share/WritePrmtop/__init__.py. You would add these lines at the beginning of the function to show the temp folder name in the reply log and to prevent it from being removed: print tempDir return (indented appropriately) Similarly, for Minimize Structure, there is a _removeTempDir function defined near line 301 of /share/MMMD/MMTKinter.py. Add these lines near the beginning of that function: print self.tempDir return (also indented appropriately) The frcmod file left in the temp dir has the generated parameters. Other parameters are just the standard ones provided with the force field chosen. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 4 13:50:22 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 4 Sep 2012 13:50:22 -0700 Subject: [Chimera-users] H-bond analysis in case of TIP4P water model ? In-Reply-To: References: Message-ID: On Sep 3, 2012, at 6:28 AM, Marek Maly wrote: > Hello, > > it seem to me that Chimera is not able to do H-bond analysis between > water molecules when TIP4P water model is used. Am I right or I overlooked something ? Hi Marek, I am not aware of any such problem. Could you use Help->Report A Bug to send in a bug report, and provide more details about the problem you are having (what structure you used, what you did, what happened)? Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 4 14:02:58 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 4 Sep 2012 14:02:58 -0700 Subject: [Chimera-users] H-bond analysis in case of TIP4P water model ? In-Reply-To: References: Message-ID: <839DDF3F-0D4D-46A7-A9C0-440A567ED500@cgl.ucsf.edu> On Sep 3, 2012, at 6:28 AM, Marek Maly wrote: > Hello, > > it seem to me that Chimera is not able to do H-bond analysis between > water molecules when TIP4P water model is used. Am I right or I overlooked something ? Upon further review, I can reproduce the problem you're having. The "extra point" of the TIP4P water (atom "EPW") is screwing up Chimera's H-bond finding. You need to delete that "atom" ("del @epw" in the command line), then Chimera will be able to find the inter-water H bonds. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtzotzos at me.com Wed Sep 5 05:36:45 2012 From: gtzotzos at me.com (George Tzotzos) Date: Wed, 05 Sep 2012 14:36:45 +0200 Subject: [Chimera-users] Fwd: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission) References: <042.706e4d5b93266becbfaaf549bb4c78dc@cgl.ucsf.edu> Message-ID: <41CB0FD9-F5E4-4690-8681-1200767E9C8E@me.com> Apologies for sending this to the List but I haven't received any information regarding the bug report below. Maybe I missed the mail. I have reinstalled Chimera but I get the same error message. Any suggestions how to solve this problem? Many thanks George Begin forwarded message: > From: Chimera > Subject: Re: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission) > Date: August 27, 2012 7:12:02 PM GMT+02:00 > To: Undisclosed recipients: ; > Reply-To: chimera-bugs at cgl.ucsf.edu > > #11323: Chimera using local GLUT installation > ---------------------------------+------------------------------------- > Reporter: gtzotzos@? | Owner: gregc > Type: defect | Status: assigned > Priority: normal | Milestone: Release 1.7 > Component: Platform | Version: 1.6.2 (b36855) > Severity: normal | Resolution: > Keywords: | Blocked By: > Blocking: | Notify when closed: > Platform: Mac OS X (Cocoa 64) | Project: chimera > ---------------------------------+------------------------------------- > Changes (by pett): > > * status: new => assigned > * component: Unassigned => Platform > * project: => chimera > * platform: => Mac OS X (Cocoa 64) > * version: => 1.6.2 (b36855) > * milestone: => Release 1.7 > * owner: pett => gregc > > > -- > Ticket URL: > Chimera > Chimera Issue Tracker -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtzotzos at me.com Thu Sep 6 02:26:21 2012 From: gtzotzos at me.com (George Tzotzos) Date: Thu, 06 Sep 2012 11:26:21 +0200 Subject: [Chimera-users] Distance between two benzene rings Message-ID: <2A881019-EC3F-47A9-9ABA-E75E8CDF5947@me.com> Hi everybody, I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue? Your help suggestions / help much appreciated as always Regards George From meng at cgl.ucsf.edu Thu Sep 6 08:43:20 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 6 Sep 2012 08:43:20 -0700 Subject: [Chimera-users] Distance between two benzene rings In-Reply-To: <2A881019-EC3F-47A9-9ABA-E75E8CDF5947@me.com> References: <2A881019-EC3F-47A9-9ABA-E75E8CDF5947@me.com> Message-ID: <6BABB9BD-A3FB-49BB-851C-CBDD75FD2A16@cgl.ucsf.edu> Hi George, You can define centroids for the rings and then measure the distance between those centroid objects. See "Axes/Planes/Centroids" (under Tools... Structure Analysis) and/or command "define": The objects you have defined will be listed in a dialog, and you can measure distance simply by choosing two objects (rows) in the dialog, or by using the "distance" command. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 6, 2012, at 2:26 AM, George Tzotzos wrote: > Hi everybody, > > I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue? > > Your help suggestions / help much appreciated as always > > Regards > > George > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From danielgurnon at depauw.edu Fri Sep 7 13:19:03 2012 From: danielgurnon at depauw.edu (Daniel Gurnon) Date: Fri, 7 Sep 2012 16:19:03 -0400 Subject: [Chimera-users] color by RMSD Message-ID: Hi everyone, To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script: mm #0 #1 show true rangecolor mavRMSD min white mid pink max red This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window? thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon at depauw.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From emailanindito at yahoo.co.in Sun Sep 9 07:54:57 2012 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Sun, 9 Sep 2012 22:54:57 +0800 (SGT) Subject: [Chimera-users] selection of multiple atoms in a session with multiple pdb structures Message-ID: <1347202497.85664.YahooMailNeo@web193104.mail.sg3.yahoo.com> Dear All, I have a Chimera session where 4 different atomic structures ?(pdb files) ?are docked in the computed density map of a macromolecular complex. I need to select multiple amino acids positioned at different places of the different docked atomic structures. To explain the situation- Say the 4 docked Atomic structures are A, B, C & D I need to select 276aa of A, 15aa of B, 246aa of C and so on... How can I do that ? Thanks ? Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kay_jay at earthlink.net Sun Sep 9 10:09:08 2012 From: kay_jay at earthlink.net (Kenward Vaughan) Date: Sun, 9 Sep 2012 10:09:08 -0700 Subject: [Chimera-users] selection of multiple atoms in a session with multiple pdb structures In-Reply-To: <1347202497.85664.YahooMailNeo@web193104.mail.sg3.yahoo.com> References: <1347202497.85664.YahooMailNeo@web193104.mail.sg3.yahoo.com> Message-ID: <20120909100908.047958d6@dobby.vaughan.home> On Sun, 9 Sep 2012 22:54:57 +0800 (SGT) Anindito Sen wrote: > Dear All, > > I have a Chimera session where 4 different atomic structures ?(pdb > files) ?are docked in the computed density map of a macromolecular > complex. I need to select multiple amino acids positioned at > different places of the different docked atomic structures. > > To explain the situation- > > Say the 4 docked Atomic structures are A, B, C & D > > I need to select 276aa of A, 15aa of B, 246aa of C and so on... > > How can I do that ? > > Thanks Hi Anindito! Just playing around with the select command on a session with 2 loaded pdb files gave me the following: select #0:105.a #1:77.c #1:82 #:5 In other words, spaces between the different residues being picked allows you to pick from multiple models on the same line. With this command, I selected residue 105 on chain A of model 0, residue 77 on chain C of model 1, residue 82 on all chains of model 1, and residue 5 on all chains on both models. Since you label your pdb files as A, B, C, ... I assume that these would be numbered as 0, 1, 2, ... by Chimera, depending on the order they were read into the session. You would then enter the following: select #0:276 #1:15 #2:246 ... While I have not played with such situations, the origin of your particular set of pdb structures may have Chimera classify the chains as submodels of one large model, instead of distinctly different molecules. If that is true, then I believe the above becomes: select #.0:276 #.1:15 #.2:246 ... This is explained (much) more fully on the Atom Specification page of the help system. Final thought: if you know which residues you want to grab because you can see them in the structure, and this is a one time sort of thing, I'd honestly just select the residues with the mouse (with a cleared selection, Ctrl-Shift click on an atom of each residue, then up-arrow the results to grab the whole residues) ... Hope this works for you! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca From vamseedharr at gmail.com Mon Sep 10 12:59:59 2012 From: vamseedharr at gmail.com (vamsee) Date: Mon, 10 Sep 2012 13:59:59 -0600 Subject: [Chimera-users] Ribbon gradient coloring Message-ID: Hi All, Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? Thanks in advance Vamsee -------------- next part -------------- An HTML attachment was scrubbed... URL: From nirodion at syr.edu Mon Sep 10 14:06:08 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Mon, 10 Sep 2012 21:06:08 +0000 Subject: [Chimera-users] Visualization of protein aqueous solution Message-ID: Hi all, Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. Much Thanks! Nikolay Rodionov -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 10 14:39:26 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 10 Sep 2012 14:39:26 -0700 Subject: [Chimera-users] Ribbon gradient coloring In-Reply-To: References: Message-ID: Hi Vamsee, You can assign "attribute" values to the residues ... then map attribute value to colors using "Render by Attribute" or command "rangecolor" It depends what you mean by gradient: While the mapping of values to colors is continuous (colors will be interpolated), the ribbon "piece" for each residue is only a single color, so you will see color boundaries between residues unless their values are very similar. For example, the following command would color a ribbon by the built-in attribute named kdHydrophobicity (amino acid hydrophobicity on the Kyte-Doolittle scale). Values -4 and lower would be shown with lime green, then up to 0 gradually interpolated to white, then up to 4 r interpolated up to orange. rangecol kdHydrophobicity,r -4 lime green 0 white 4 orange There is a simple format for reading in your own custom attributes: ... or if you have only a few values to assign, you can do them one at a time with command "setattr": See also tutorials, including: B-factor coloring Surface properties Attributes I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 10, 2012, at 12:59 PM, vamsee wrote: > Hi All, > Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? > Thanks in advance > Vamsee From meng at cgl.ucsf.edu Mon Sep 10 14:42:30 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 10 Sep 2012 14:42:30 -0700 Subject: [Chimera-users] Visualization of protein aqueous solution In-Reply-To: References: Message-ID: <356FCF7D-C513-4EC2-AC48-A2B87B88912F@cgl.ucsf.edu> Hi Nikolay, Other than Add Ions, the only other thing I can think of is to manually add atoms one by one at the desired x,y,z coordinates, which can be done with Build Structure, the "Start Structure" section. Of course, you could also do that by just text-editing your PDB file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 10, 2012, at 2:06 PM, Nikolay Igorovich Rodionov wrote: > Hi all, > Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. > > I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. > > Much Thanks! > Nikolay Rodionov From meng at cgl.ucsf.edu Mon Sep 10 14:54:31 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 10 Sep 2012 14:54:31 -0700 Subject: [Chimera-users] Visualization of protein aqueous solution In-Reply-To: <356FCF7D-C513-4EC2-AC48-A2B87B88912F@cgl.ucsf.edu> References: <356FCF7D-C513-4EC2-AC48-A2B87B88912F@cgl.ucsf.edu> Message-ID: <8DEBDE89-957A-4B9C-987B-D4102A6D17B7@cgl.ucsf.edu> Hi Nikolay, One more idea: since this is just for display, you could use "Volume Tracer" to place "markers" (which are essentially fake atoms) interactively in space. Although it is called volume tracer, you can place markers in space independent of any volume data. menu: Tools... Volume Data... Volume Tracer in that dialog's Mouse menu, turn off all settings except turn on "Place markers outside data" ... then proceed to place markers interactively. You can move them around, change radii and color, etc. Elaine On Sep 10, 2012, at 2:42 PM, Elaine Meng wrote: > Hi Nikolay, > Other than Add Ions, the only other thing I can think of is to manually add atoms one by one at the desired x,y,z coordinates, which can be done with Build Structure, the "Start Structure" section. > > > > Of course, you could also do that by just text-editing your PDB file. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 10, 2012, at 2:06 PM, Nikolay Igorovich Rodionov wrote: > >> Hi all, >> Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. >> >> I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. >> >> Much Thanks! >> Nikolay Rodionov From pett at cgl.ucsf.edu Mon Sep 10 15:06:11 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 10 Sep 2012 15:06:11 -0700 Subject: [Chimera-users] color by RMSD In-Reply-To: References: Message-ID: <8CCB4E74-0A9D-41E8-A13F-A7CFE4F774C4@cgl.ucsf.edu> On Sep 7, 2012, at 1:19 PM, Daniel Gurnon wrote: > Hi everyone, > > To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script: > > mm #0 #1 show true > rangecolor mavRMSD min white mid pink max red > > > This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window? Hi Dan, The way Chimera is currently structured, there is no way to get that RMSD attribute assignment without creating the MAV window. Now I could give you a script that closes the open MAV windows, which you could insert into your per-frame commands, but if I'm going to give you a script I might as well give you one that entirely bypasses the matchmaker/mav steps (which do a lot more work than strictly necessary for your purposes). I've attached such a script. Assuming you saved that script into the "Documents" folder of your home directory, your per-frame command would change to: runscript ~/Documents/md-rmsd.py rangecolor trajRMSD min white mid pink max red As you might surmise from the rangecolor command above the script defines a "trajRMSD" attribute. Also, I think you want to use actual specific numeric values rather than min/mid/max, since even matching against the reference frame can produce small numeric differences (due to PDB precision roundoff) which will nonetheless look just as big as much larger differences elsewhere in the trajectory. Now, I'm not certain for what purpose you are making this RMSD depiction, but I thought I should point out that in the daily build you can plot the RMSD difference for any set of atoms in a particular frame against the rest of the trajectory. That feature is in MD Movie's Analysis->Plot menu. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: md-rmsd.py Type: text/x-python-script Size: 633 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Sep 10 16:48:37 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 10 Sep 2012 16:48:37 -0700 Subject: [Chimera-users] Visualization of protein aqueous solution In-Reply-To: References: Message-ID: On Sep 10, 2012, at 2:06 PM, Nikolay Igorovich Rodionov wrote: > I've tried using add-ion but I haven't had good results. So what was the problem with the results? The results seem good to me if I add a specific number of ions (depends on the system; in the attached image: 50). If you add ions to neutralize the charge you will get a relatively small number clustered around the solute rather than a larger number spaced throughout the solution. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 554103 bytes Desc: not available URL: From pett at cgl.ucsf.edu Wed Sep 12 14:10:51 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 12 Sep 2012 14:10:51 -0700 Subject: [Chimera-users] Match->Align command line option? In-Reply-To: References: Message-ID: <216BA665-6BFA-4FA7-AA63-EE54227F063C@cgl.ucsf.edu> On Sep 12, 2012, at 11:16 AM, Chetanya Pandya wrote: > Hello, > > I want to superimpose multiple structure sets and get the corresponding multiple sequence alignments using Chimera. I've been using the Match->Align option from the Tools menu. Now, I want to automate the process using the Python interface. > > Unfortunately, I'm unable to find a command line option which does this. Can you help me out with this? Hi Chetanya, It's a little ambiguous if you are asking about a command version of Match->Align, or how to call it from Python. The issue is moot though since there currently is no command version of Match->Align, so you have to call it from Python! I don't know how familiar you are with Python or programming with Python, but the Chimera Programmer's Guide has some info to help. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html If you don't know Python at all, follow the link in the Guide to the Python Tutorial and work through that, or at least the first few sections of that. Then for some Chimera-specific info, look at some of the Examples and the "basic primer" linked on the page. Assuming you've written a script that has gotten to the stage where the structures are already open and superimposed, here's the info you'll need to use the Match->Align API: 1) Getting the list of open molecules: from chimera import openModels, Molecule mols = openModels.list(modelTypes=[Molecule]) 2) Getting the list of chains to use. This example code assumes they're chain A: chains = [m.sequence('A') for m in mols] 3) Call Match->Align to create the alignment. from StructSeqAlign import makeAlignment mav = makeAlignment(chains) Note that the makeAlignment call will only return the Multalign Viewer instance starting with tomorrow's daily build (i.e. I made that change today!). Also, the makeAlignment call has a lot of optional arguments to change the parameters used in computing the alignment (e.g. cutoff, iteration, reference chain). Look at /share/StructSeqAlign/__init__.py to see what the options are if you need to change the default behavior. (On a Mac, "" is Chimera.app/Contents/Resources). 4) Save the alignment to a FASTA format file (named "x.fa") and Quit the MAV instance: f = open("x.fa", "w") from MultAlignViewer.formatters.saveFASTA import save save(f, mav, mav.seqs, mav.fileMarkups) f.close() mav.Quit() I hope this helps. Since this is pretty Python-intensive, I set followups to go to the chimera-dev mailing list rather than chimera-users. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotikats at pharm.auth.gr Thu Sep 13 05:40:41 2012 From: sotikats at pharm.auth.gr (Sotirios Katsamakas) Date: Thu, 13 Sep 2012 15:40:41 +0300 Subject: [Chimera-users] chimera utility help Message-ID: <20120913154041.74704syion5ptw09@webmail.auth.gr> Dear sir or madam, I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem. Best Regards, Sotirios Katsamakas -------------- next part -------------- A non-text attachment was scrubbed... Name: 1HVY-reconstructed_pdbv3.pdb Type: chemical/x-pdb Size: 399940 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Sep 13 09:17:55 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Sep 2012 09:17:55 -0700 Subject: [Chimera-users] chimera utility help In-Reply-To: <20120913154041.74704syion5ptw09@webmail.auth.gr> References: <20120913154041.74704syion5ptw09@webmail.auth.gr> Message-ID: Dear Sotirios Katsamakas, You didn't say how you added the 25 amino acids. If I were adding them in Chimera, I would: (1) first build a peptide of the 25 amino acids as a separate model, using Build Structure (under Tools... Structure Editing), Start Structure section, "peptide sequence" -- this lets you specify all the phi and psi angles before the peptide is created (2) join the original protein and the new peptide using Build Structure, Join Models section So one possibility is to delete the 25 amino acids from that structure and build them again in Chimera as described above. A second possibility is to rotate each phi and psi angle in your current structure, using either Build Structure, Adjust Torsions section, or the "rotation" command. However, I think that would be difficult, or at least quite tedious and labor-intensive. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 5:40 AM, Sotirios Katsamakas wrote: > Dear sir or madam, > I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem. > > Best Regards, > Sotirios Katsamakas > > <1HVY-reconstructed_pdbv3.pdb> From pett at cgl.ucsf.edu Thu Sep 13 11:16:04 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 13 Sep 2012 11:16:04 -0700 Subject: [Chimera-users] chimera utility help In-Reply-To: References: <20120913154041.74704syion5ptw09@webmail.auth.gr> Message-ID: On Sep 13, 2012, at 9:17 AM, Elaine Meng wrote: > A second possibility is to rotate each phi and psi angle in your current structure, using either Build Structure, Adjust Torsions section, or the "rotation" command. However, I think that would be difficult, or at least quite tedious and labor-intensive. Along these same lines, since phi/psi angles are residue attributes, you can use the setattr command to set them. For instance, an alpha helix has phi/psi angles of -57/-47. So your original extended structure that looked like this: Could at least be changed into a couple of alpha helical segments like so: Your extended structure has a lot of prolines in it, which means it cannot easily be made into one helix since prolines cannot have their phi angles changed without corresponding adjustments to the side chain ring (which is why prolines are known as "helix breaking" residues), so maybe the other approaches that Elaine suggested are better here. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16390 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen shot 2012-09-13 at 11.09.14 AM.png Type: image/png Size: 173424 bytes Desc: not available URL: From filip.vanpetegem at gmail.com Thu Sep 13 12:24:48 2012 From: filip.vanpetegem at gmail.com (Filip Van Petegem) Date: Thu, 13 Sep 2012 12:24:48 -0700 Subject: [Chimera-users] saving a rotated map Message-ID: Dear chimera users, I have a problem with saving a cryoEM map after rotating/translating it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 format) This seems to work fine, but when I save the reoriented map (in any of the available formats), and try to open it, it is back to the original position. Is there any way to save the reoriented map file? Best regards, Filip Van Petegem -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem at gmail.com http://crg.ubc.ca/VanPetegem/ From meng at cgl.ucsf.edu Thu Sep 13 12:53:00 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Sep 2012 12:53:00 -0700 Subject: [Chimera-users] saving a rotated map In-Reply-To: References: Message-ID: <287A3F4F-4CB6-4732-AFFE-69341BEC1246@cgl.ucsf.edu> Hi Filip, Ah yes, a commonly asked question. The problem is that map formats do not accomodate rotation information. Please see here for solutions for "saving maps after fitting": Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 12:24 PM, Filip Van Petegem wrote: > Dear chimera users, > > I have a problem with saving a cryoEM map after rotating/translating > it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 > format) This seems to work fine, but when I save the reoriented map > (in any of the available formats), and try to open it, it is back to > the original position. > > Is there any way to save the reoriented map file? > > Best regards, > > Filip Van Petegem > From pett at cgl.ucsf.edu Thu Sep 13 13:50:33 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 13 Sep 2012 13:50:33 -0700 Subject: [Chimera-users] Gromac .xtc format Message-ID: <84BB07C4-53AF-4D87-A4DA-E29B3909EB4E@cgl.ucsf.edu> Hi, For you Chimera/Gromacs users out there, the current daily build allows you to use .xtc format coordinates now as an alternative to .trr . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From brianfochtman at gmail.com Thu Sep 13 15:32:59 2012 From: brianfochtman at gmail.com (Brian Fochtman) Date: Thu, 13 Sep 2012 18:32:59 -0400 Subject: [Chimera-users] sphgen format Message-ID: Hello, I read in the release notes for version 1.6 that Chimera is now able to input files in the dock .sph format. Thank you for this feature, it will be very helpful. Unfortunately I am having some trouble using it. (File -> Open -> file.sph) declares a syntax error for the following file (I've only included the beginning of the file because the output says the synax error is on line 2). Is there another method to read in these files? Thank you, Brian Fochtman cluster 1 number of spheres in cluster 72 1 20.51900 -17.55400 15.86300 0.700 1 2 21.04300 -18.55700 16.07400 0.700 2 3 22.17700 -17.60500 16.24100 0.700 3 4 22.17500 -17.84200 15.30900 0.700 4 5 21.41300 -20.08800 15.15700 0.700 5 6 20.64000 -20.83100 16.58800 0.700 6 7 21.63200 -18.65500 14.15300 0.700 7 8 23.13800 -16.98900 16.54500 0.700 8 9 21.18800 -21.21200 14.71200 0.700 9 10 17.88800 -26.45300 19.89900 0.700 10 11 21.83900 -17.33000 12.81300 0.700 11 12 21.28600 -20.42100 13.28900 0.700 12 13 23.77100 -15.65400 16.91100 0.700 13 14 21.15100 -21.76500 13.92000 0.700 14 15 21.38500 -19.46300 12.20200 0.700 15 16 20.39500 -21.75600 13.41100 0.700 16 -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Thu Sep 13 16:17:20 2012 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Thu, 13 Sep 2012 16:17:20 -0700 Subject: [Chimera-users] sphgen format In-Reply-To: References: Message-ID: <50526980.8050007@cgl.ucsf.edu> Hi, Brian. According to documentation (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphgenOutput), the first line of a sphgen file is supposed to be a header. There should also be eight fields in each sphere line, although the last two probably aren't used often. I've updated the code so that it will handle missing headers and sphere fields. If you can try out tomorrow's daily build at http://www.cgl.ucsf.edu/chimera/download.html#daily (should be dated Sep 14, 2012), it should work better. (I assume the file contents you sent is just the start of the file. If there are really only sixteen points in a cluster declared to have 72, Chimera will still complain and not open it.) Conrad On 9/13/12 3:32 PM, Brian Fochtman wrote: > Hello, > I read in the release notes for version 1.6 that Chimera is now able > to input files in the dock .sph format. Thank you for this feature, it > will be very helpful. Unfortunately I am having some trouble using it. > (File -> Open -> file.sph) declares a syntax error for the following > file (I've only included the beginning of the file because the output > says the synax error is on line 2). Is there another method to read in > these files? > Thank you, > Brian Fochtman > > > cluster 1 number of spheres in cluster 72 > 1 20.51900 -17.55400 15.86300 0.700 1 > 2 21.04300 -18.55700 16.07400 0.700 2 > 3 22.17700 -17.60500 16.24100 0.700 3 > 4 22.17500 -17.84200 15.30900 0.700 4 > 5 21.41300 -20.08800 15.15700 0.700 5 > 6 20.64000 -20.83100 16.58800 0.700 6 > 7 21.63200 -18.65500 14.15300 0.700 7 > 8 23.13800 -16.98900 16.54500 0.700 8 > 9 21.18800 -21.21200 14.71200 0.700 9 > 10 17.88800 -26.45300 19.89900 0.700 10 > 11 21.83900 -17.33000 12.81300 0.700 11 > 12 21.28600 -20.42100 13.28900 0.700 12 > 13 23.77100 -15.65400 16.91100 0.700 13 > 14 21.15100 -21.76500 13.92000 0.700 14 > 15 21.38500 -19.46300 12.20200 0.700 15 > 16 20.39500 -21.75600 13.41100 0.700 16 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From dobry at g.pl Thu Sep 13 18:26:04 2012 From: dobry at g.pl (=?ISO-8859-2?Q?Mateusz_Dobrych=B3op?=) Date: Fri, 14 Sep 2012 03:26:04 +0200 Subject: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file Message-ID: Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz -------------- next part -------------- An HTML attachment was scrubbed... URL: From vamseedharr at gmail.com Thu Sep 13 18:31:18 2012 From: vamseedharr at gmail.com (vamsee) Date: Thu, 13 Sep 2012 19:31:18 -0600 Subject: [Chimera-users] Denaturing a protein In-Reply-To: References: Message-ID: Hi Elaine, Thanks for the answer for the previous question. I am back with one more :) Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? Thanks again Vamsee -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 14 10:55:20 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Sep 2012 10:55:20 -0700 Subject: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file In-Reply-To: References: Message-ID: <31DA36FA-C8EF-4C06-B283-47BB960A3D71@cgl.ucsf.edu> Hi Mateusz, To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 6:26 PM, Mateusz Dobrych?op wrote: > Hello, > I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? > Mateusz From meng at cgl.ucsf.edu Fri Sep 14 10:56:49 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Sep 2012 10:56:49 -0700 Subject: [Chimera-users] Denaturing a protein In-Reply-To: References: Message-ID: <4B87CE6B-93B1-480E-B288-6DD5170ABB87@cgl.ucsf.edu> Hi Vamsee, Sorry no, there is no way to do those kinds of calculations in Chimera. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 6:31 PM, vamsee wrote: > Hi Elaine, > Thanks for the answer for the previous question. I am back with one more :) > > Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? > Thanks again > Vamsee From dobry at g.pl Fri Sep 14 11:26:53 2012 From: dobry at g.pl (=?ISO-8859-2?Q?Mateusz_Dobrych=B3op?=) Date: Fri, 14 Sep 2012 20:26:53 +0200 Subject: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file In-Reply-To: <31DA36FA-C8EF-4C06-B283-47BB960A3D71@cgl.ucsf.edu> References: <31DA36FA-C8EF-4C06-B283-47BB960A3D71@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you for your reply! I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software. What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window. Is there maybe a way to move (not save) the structures relatively to one of them? Mateusz 2012/9/14 Elaine Meng > Hi Mateusz, > To retain the spatial relationships between the structures when you have > moved them independently, you need to save the PDBs "relative to" the same > model. For example, save models 0,1,2 all relative to 0. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 13, 2012, at 6:26 PM, Mateusz Dobrych?op wrote: > > > Hello, > > I load 3 protein models into Chimera and enter several "move" commands. > The structures change their positions. Then, I save them as a PDB file, and > immediately open the PDB file. The structures are not overlapping > (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this > and what can I do to obtain accurate coordinates on my screen without > re-opening the model (after I finish my sequence of translations)? > > Mateusz > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nadir.Mrabet at univ-lorraine.fr Fri Sep 14 11:18:54 2012 From: Nadir.Mrabet at univ-lorraine.fr (Nadir T. Mrabet) Date: Fri, 14 Sep 2012 20:18:54 +0200 Subject: [Chimera-users] Denaturing a protein In-Reply-To: <4B87CE6B-93B1-480E-B288-6DD5170ABB87@cgl.ucsf.edu> References: <4B87CE6B-93B1-480E-B288-6DD5170ABB87@cgl.ucsf.edu> Message-ID: <5053750E.8020106@univ-lorraine.fr> Why is that? Simply, because the denaturate state is difficult to define as it certainly correspond to a multitude of conformations including some of the native state. Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 14/09/2012 19:56, Elaine Meng wrote: > Hi Vamsee, > Sorry no, there is no way to do those kinds of calculations in Chimera. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 13, 2012, at 6:31 PM, vamsee wrote: > >> Hi Elaine, >> Thanks for the answer for the previous question. I am back with one more :) >> >> Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? >> Thanks again >> Vamsee > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Fri Sep 14 12:43:58 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Sep 2012 12:43:58 -0700 Subject: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file In-Reply-To: References: <31DA36FA-C8EF-4C06-B283-47BB960A3D71@cgl.ucsf.edu> Message-ID: Maybe I'm not understanding the question. You could make a Chimera command file (just a text file, filename ending in .com or .cmd) that has the move commands in it. You could first open the original structures and then open the Chimera command file, which would execute the commands. If you are making an animation with a script, those commands could be at the beginning of the script before the recording. My only other idea is to just save a Chimera session, which can later be restored. Elaine On Sep 14, 2012, at 11:26 AM, Mateusz Dobrych?op wrote: > Hi Elaine, > > Thank you for your reply! > > I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software. > > What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window. > > Is there maybe a way to move (not save) the structures relatively to one of them? > > Mateusz > > 2012/9/14 Elaine Meng > Hi Mateusz, > To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 13, 2012, at 6:26 PM, Mateusz Dobrych?op wrote: > > > Hello, > > I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? > > Mateusz > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Fri Sep 14 13:17:17 2012 From: goddard at sonic.net (Tom Goddard) Date: Fri, 14 Sep 2012 13:17:17 -0700 Subject: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file In-Reply-To: References: <31DA36FA-C8EF-4C06-B283-47BB960A3D71@cgl.ucsf.edu> Message-ID: <505390CD.2050602@sonic.net> Hi Mateusz, I don't understand exactly what is going wrong for you. But maybe an example will help. If you have two models #0 and #1 you can move #1 relative to #0 in 100 steps each 0.5 Angstrom along the x axis with a command move x 0.5 100 model #1 coord #0 The "coord #0" option is important here. It says move along the x-axis of the model #0 coordinate system. If you leave off that option it moves along the horizontal axis displayed on the screen. That is different from the x-axis of model #0 if you have rotated the models. The "turn" command also accepts the coordinate system option. Here is documentation for the move command http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html and examples of other commands useful in movie making http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file From: Mateusz Dobrych?op To: UCSF Chimera Mailing List Date: 9/14/12 11:26 AM > Hi Elaine, > > Thank you for your reply! > > I'm trying to recreate the components' moves from another software (in > order to record it and export it to a movie file). The software > generates a text "history" file with a list of all the moves the > components make and a PDB file which is a result of those > transformations. After applying all the transformations listed in the > history file using Chimera, the stuff that's displayed on screen does > not match the "result" model from this other software. Hovewer, if I > save the result of my Chimera transformations into a PDB file, it > perfectly matches the result file from the other software. > > What I'm trying to say is that the PDB file that I create is actually > okay, but I'm trying to generate an animation so I much more care > about the things that are displayed in Chimera window. > > Is there maybe a way to move (not save) the structures relatively to > one of them? > > Mateusz > > 2012/9/14 Elaine Meng > > Hi Mateusz, > To retain the spatial relationships between the structures when > you have moved them independently, you need to save the PDBs > "relative to" the same model. For example, save models 0,1,2 all > relative to 0. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 13, 2012, at 6:26 PM, Mateusz Dobrych?op wrote: > > > Hello, > > I load 3 protein models into Chimera and enter several "move" > commands. The structures change their positions. Then, I save them > as a PDB file, and immediately open the PDB file. The structures > are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). > Why does it work like this and what can I do to obtain accurate > coordinates on my screen without re-opening the model (after I > finish my sequence of translations)? > > Mateusz > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 17 09:38:51 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 17 Sep 2012 09:38:51 -0700 Subject: [Chimera-users] chimera utility help In-Reply-To: <20120917191041.69801vjpfjz0zdkx@webmail.auth.gr> References: <20120913154041.74704syion5ptw09@webmail.auth.gr> <20120917191041.69801vjpfjz0zdkx@webmail.auth.gr> Message-ID: <0E4F57FD-B4DC-424A-A34D-4C7BD1B19E91@cgl.ucsf.edu> Dear Sotirios, You would use Join Models option "C-N peptide bond" as described in these instructions: "C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond." If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version. If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport. I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure. Thanks! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote: > Dear Elaine C. Meng, > I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25 at C) and the N terminus of the protein (#1:26 at N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you. > > Best Regards, > Sotirios Katsamakas. From dieter.blaas at meduniwien.ac.at Tue Sep 18 08:47:24 2012 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Tue, 18 Sep 2012 17:47:24 +0200 Subject: [Chimera-users] Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems Message-ID: <5058978C.2020901@meduniwien.ac.at> Those who encountered lots of problems with the graphics when running chimera remotely for example you receive error messages like this one: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 might be interested in the following solution: 1) install VirtualGL (http://www.virtualgl.org/) on both PCs 2) outcomment the indicated lines in the 'chimera' startup script 3) connect to the server by using 'vglconnect' 4) start chimera on the server with 'vglrun chimera' that's it! if [ -z "$nogui" ] then case "`uname -s`" in Linux) # preload our C++ runtime to avoid # ATI graphics driver bug # LD_PRELOAD=libotf.so <<<<<<<<< # export LD_PRELOAD <<<<<<<<< if test -e "$CHIMERA/bin/python2.7" then python="$CHIMERA/bin/python2.7" else in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! Best, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ From pett at cgl.ucsf.edu Wed Sep 19 17:10:48 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 19 Sep 2012 17:10:48 -0700 Subject: [Chimera-users] Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems In-Reply-To: <5058978C.2020901@meduniwien.ac.at> References: <5058978C.2020901@meduniwien.ac.at> Message-ID: Interesting. Note that in the 1.7 builds libotf is no longer preloaded, so step #2 will not be needed for those. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 18, 2012, at 8:47 AM, Dieter Blaas wrote: > Those who encountered lots of problems with the graphics when running chimera remotely > > for example you receive error messages like this one: > > X Error of failed request: GLXBadContextTag > Major opcode of failed request: 153 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 1352 > Current serial number in output stream: 1352 > > might be interested in the following solution: > > 1) install VirtualGL (http://www.virtualgl.org/) on both PCs > 2) outcomment the indicated lines in the 'chimera' startup script > 3) connect to the server by using 'vglconnect' > 4) start chimera on the server with 'vglrun chimera' > > that's it! > > if [ -z "$nogui" ] > then > case "`uname -s`" in > Linux) > # preload our C++ runtime to avoid > # ATI graphics driver bug > # LD_PRELOAD=libotf.so <<<<<<<<< > # export LD_PRELOAD <<<<<<<<< > if test -e "$CHIMERA/bin/python2.7" > then > python="$CHIMERA/bin/python2.7" > else > > in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! > > Best, Dieter > > -- > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: dieter.blaas at meduniwien.ac.at > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From coyote_v2002 at yahoo.com Thu Sep 20 02:25:47 2012 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Thu, 20 Sep 2012 02:25:47 -0700 (PDT) Subject: [Chimera-users] solvation box transformed Message-ID: <1348133147.50358.YahooMailNeo@web111722.mail.gq1.yahoo.com> Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis -------------- next part -------------- An HTML attachment was scrubbed... URL: From coyote_v2002 at yahoo.com Thu Sep 20 02:38:55 2012 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Thu, 20 Sep 2012 02:38:55 -0700 (PDT) Subject: [Chimera-users] solvation box transformed In-Reply-To: <1348133147.50358.YahooMailNeo@web111722.mail.gq1.yahoo.com> References: <1348133147.50358.YahooMailNeo@web111722.mail.gq1.yahoo.com> Message-ID: <1348133935.89145.YahooMailNeo@web111705.mail.gq1.yahoo.com> I am very sorry for bothering the list members with my previous email. I figured this myself, I just need to "reset" from the command line. Sincerely, Vis To: "chimera-users at cgl.ucsf.edu" Sent: Thursday, September 20, 2012 12:25 PM Subject: solvation box transformed Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis -------------- next part -------------- An HTML attachment was scrubbed... URL: From rice at nysbc.org Thu Sep 20 07:29:24 2012 From: rice at nysbc.org (William Rice) Date: Thu, 20 Sep 2012 10:29:24 -0400 Subject: [Chimera-users] saving a rotated map In-Reply-To: References: Message-ID: <505B2844.30009@nysbc.org> Hi Filip, Another way to do it, if you are somewhat comfortable with python, is to use sparx, as described on this page: http://sparx-em.org/sparxwiki/align_chimera This will give you the Euler angles which describe the rotations, and can be converted to most of the common angle conventions (spider, EMAN, imagic, ...). Bill Filip Van Petegem wrote: > Dear chimera users, > > I have a problem with saving a cryoEM map after rotating/translating > it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 > format) This seems to work fine, but when I save the reoriented map > (in any of the available formats), and try to open it, it is back to > the original position. > > Is there any way to save the reoriented map file? > > Best regards, > > Filip Van Petegem > > > -- William J. Rice, Ph.D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, NY, NY 10027 From rmcnulty at scripps.edu Thu Sep 20 08:00:33 2012 From: rmcnulty at scripps.edu (Reginald McNulty) Date: Thu, 20 Sep 2012 08:00:33 -0700 Subject: [Chimera-users] icosahedral reconstruction volume color Message-ID: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu> Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie -- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Molecular Biology La Jolla, California 92037 Email: rmcnulty at scripps.edu From meng at cgl.ucsf.edu Thu Sep 20 09:22:45 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Sep 2012 09:22:45 -0700 Subject: [Chimera-users] icosahedral reconstruction volume color In-Reply-To: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu> References: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: <1D0871F4-33C7-48C8-9E04-91DBFCB7F88E@cgl.ucsf.edu> Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me. You can open and display the vol file in Chimera, assuming it is the SPIDER format: You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane radial coloring = coloring by distance from a point, where the point is the center of symmetry I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote: > Dear Users, > I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? > Kind regards, > Reggie From rmcnulty at scripps.edu Thu Sep 20 10:04:26 2012 From: rmcnulty at scripps.edu (Reginald McNulty) Date: Thu, 20 Sep 2012 10:04:26 -0700 Subject: [Chimera-users] icosahedral reconstruction volume color In-Reply-To: <1D0871F4-33C7-48C8-9E04-91DBFCB7F88E@cgl.ucsf.edu> References: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu>, <1D0871F4-33C7-48C8-9E04-91DBFCB7F88E@cgl.ucsf.edu> Message-ID: <2639CB5887B7B844A85E581C733BA684213DB7DCF2@EXCH-CCR01.lj.ad.scripps.edu> Hi Elaine, I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red. Reggie ______________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Thursday, September 20, 2012 9:22 AM To: Reginald McNulty Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] icosahedral reconstruction volume color Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me. You can open and display the vol file in Chimera, assuming it is the SPIDER format: You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane radial coloring = coloring by distance from a point, where the point is the center of symmetry I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote: > Dear Users, > I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? > Kind regards, > Reggie From meng at cgl.ucsf.edu Thu Sep 20 10:37:55 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Sep 2012 10:37:55 -0700 Subject: [Chimera-users] icosahedral reconstruction volume color In-Reply-To: <2639CB5887B7B844A85E581C733BA684213DB7DCF2@EXCH-CCR01.lj.ad.scripps.edu> References: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu>, <1D0871F4-33C7-48C8-9E04-91DBFCB7F88E@cgl.ucsf.edu> <2639CB5887B7B844A85E581C733BA684213DB7DCF2@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: Hi Reggie, I can't think of a way to do that directly, but here are some related ideas: (a) for visualizing the 5-fold and 6-fold vertices, the command "hkcage" can be used to create an icosahedral mesh of hexagons and pentagons - you specify radius, h and k values (where virus T number = h^2 + hk +k^2). It makes a wire model which could be converted to sticks with command "meshmol". The difficulty would probably be in getting the orientation and placement of the cage to match that of your reconstruction. (b) "Color Zone" colors surfaces to match nearby atoms or pseudoatomic "markers" -- theoretically you could use "Volume Tracer" to place a red marker at each 5-fold vertex and then use Color Zone to color those regions of the surface red, and then undisplay the atoms or markers. (These tools are in the menu under Tools... Volume Data.) However, the difficulty I see is in placing the markers exactly symmetrically so each vertex would get the same amount of coloring. If you knew coordinates for the vertices (again the hard part) you could just create a PDB file with those fake atoms, color them red, ... (c) there is a "Cage Builder" (menu under Tools... Higher-Order Structure) that lets you interactively construct a cage of hexagons and pentagons. This is an additional method of generating markers. The "Create Mesh...." option would generate single edges and vertices from the initially generated doubled set (you'd have to look at the figure in the docs to understand that part) and in the result, you could color the 5-fold vertices red and proceed as above with Color Zone. The difficulty may be in building/scaling/positioning the cage to coincide correctly with your reconstruction. Sorry I haven't come up with simpler solutions, Elaine On Sep 20, 2012, at 10:04 AM, Reginald McNulty wrote: > Hi Elaine, > I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red. > Reggie > ______________ > From: Elaine Meng [meng at cgl.ucsf.edu] > Sent: Thursday, September 20, 2012 9:22 AM > To: Reginald McNulty > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] icosahedral reconstruction volume color > > Dear Reggie, > I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me. > > You can open and display the vol file in Chimera, assuming it is the SPIDER format: > > > You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". > > > > These support coloring by > (a) map value or gradient norm > (b) distance from a point, axis or plane > > radial coloring = coloring by distance from a point, where the point is the center of symmetry > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote: > >> Dear Users, >> I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? >> Kind regards, >> Reggie From evan.kantrowitz at bc.edu Thu Sep 20 13:18:19 2012 From: evan.kantrowitz at bc.edu (Evan Kantrowitz) Date: Thu, 20 Sep 2012 20:18:19 +0000 Subject: [Chimera-users] arrow heads for pipes and planks Message-ID: <9B6C21A20C8D6648B4ACDBB730277AA31ACD96C9@EBHAZARD04.bc.edu> Hi, Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N?C directionality. These are not on the pipes and planks tool. What is the format on the command line to use this commands I tried Show arrow on helix Show arrow on helix true Thanks Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz at bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 ------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Sep 20 13:50:43 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Sep 2012 13:50:43 -0700 Subject: [Chimera-users] arrow heads for pipes and planks In-Reply-To: <9B6C21A20C8D6648B4ACDBB730277AA31ACD96C9@EBHAZARD04.bc.edu> References: <9B6C21A20C8D6648B4ACDBB730277AA31ACD96C9@EBHAZARD04.bc.edu> Message-ID: <2D6E006E-006E-4F0E-B73F-419135A935BA@cgl.ucsf.edu> Hi Evan, Probably you are looking at documentation that is newer than your version of Chimera. The Pipes & Planks arrowheads are in Chimera 1.7 daily builds, not the 1.6 production release. Pipes & Planks has been improved significantly since the 1.6 release. However, this feature is not available as a command, sorry. If you use the documentation in the Help menu (or from clicking the Help button on a dialog) it should be fairly well synchronized with whatever version you have downloaded. daily build download: "what's new in daily builds" (vs. current production release): I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2012, at 1:18 PM, Evan Kantrowitz wrote: > Hi, > Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info > > Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N?C directionality. > > These are not on the pipes and planks tool. > What is the format on the command line to use this commands > > I tried > Show arrow on helix > Show arrow on helix true > > Thanks > Evan From meng at cgl.ucsf.edu Thu Sep 20 13:57:08 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Sep 2012 13:57:08 -0700 Subject: [Chimera-users] arrow heads for pipes and planks In-Reply-To: <2D6E006E-006E-4F0E-B73F-419135A935BA@cgl.ucsf.edu> References: <9B6C21A20C8D6648B4ACDBB730277AA31ACD96C9@EBHAZARD04.bc.edu> <2D6E006E-006E-4F0E-B73F-419135A935BA@cgl.ucsf.edu> Message-ID: <19BCFAA9-559B-4B22-B559-0DE4E286C750@cgl.ucsf.edu> whoops, I was on the wrong site when I added the links... doh! corrections below Elaine daily build download: "what's new in daily builds" (vs. current production release): From adavenpo at ucsd.edu Thu Sep 20 17:20:46 2012 From: adavenpo at ucsd.edu (Amy Davenport) Date: Thu, 20 Sep 2012 17:20:46 -0700 Subject: [Chimera-users] =?iso-8859-1?q?Calculation_of_SASA_with_probe_siz?= =?iso-8859-1?q?e_of_0=2E8=C5?= Message-ID: Hi all, I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8? to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. Thank you, Amy Davenport Migliori UCSD -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Sep 20 17:51:36 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Sep 2012 17:51:36 -0700 Subject: [Chimera-users] =?iso-8859-1?q?Calculation_of_SASA_with_probe_siz?= =?iso-8859-1?q?e_of_0=2E8=C5?= In-Reply-To: References: Message-ID: Hi Amy, It sounds like you may be using the "Area/Volume from Web" tool in Chimera, which in turn uses the StrucTools web server at NIH. In that case, you are limited to the options that the server provides. However, you do not need to use that tool in Chimera to get SASA. If you can just display a molecular surface for your protein in Chimera, you will automatically get the area of both the SES (solvent-excluded surface = molecular surface, corresponding to what is displayed) and the SAS. Both totals are reported in the Reply Log (under Favorites in the menu). If your protein has hydrogens, the surfaces will include them. "Components" means disconnected parts, so if values are reported for more than one component, you may want to use only the largest. The others are generally interior bubbles. Surface calculation parameters such as probe radius can be changed by selecting the surface (Ctrl-click), opening the Selection Inspector (for example by clicking the green magnifying glass at the bottom right of the Chimera window), and in that dialog inspecting "MSMS surface" and changing the values. Note: sometimes surface calculation fails numerically. If it fails but still shows the surface you expect, the failure is for the interior bubbles only, and you can proceed if you didn't need the surface areas to include those. However, in some cases you may not get any surface or values reported. Using a small probe may make such failures more likely. In the case of complete failure, see: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2012, at 5:20 PM, Amy Davenport wrote: > Hi all, > I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8? to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. > Thank you, > Amy Davenport Migliori > UCSD From jvald040 at fiu.edu Thu Sep 20 07:08:59 2012 From: jvald040 at fiu.edu (James Valdes) Date: Thu, 20 Sep 2012 16:08:59 +0200 Subject: [Chimera-users] Modeller-Chimera interface Message-ID: Hello Chimera, I'm using the Modeller interface via Chimera and I was wondering if the models produced takes into account multiple templates (e.g., selecting all) from a multiple alignment produced by MAFFT (http://mafft.cbrc.jp/alignment/software/). I appreciate any insight you may provide. Cheers, James Jason Vald?s, Ph.D. From cs.fernandes at campus.fct.unl.pt Fri Sep 21 07:26:15 2012 From: cs.fernandes at campus.fct.unl.pt (Claudia Fernandes) Date: Fri, 21 Sep 2012 15:26:15 +0100 Subject: [Chimera-users] Estimated RMSD after using Modeller feature Message-ID: I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. Any help would be welcome. Regards, Cl?udia Fernandes -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 21 10:35:58 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Sep 2012 10:35:58 -0700 Subject: [Chimera-users] Modeller-Chimera interface In-Reply-To: References: Message-ID: <309D5651-E5DE-41C5-99A4-094633D36CE2@cgl.ucsf.edu> Hi James, Yes, you can specify multiple templates in the Modeller interface -- you must have those structures already open in Chimera before you can choose them in the dialog. It doesn't matter where the sequence alignment came from: you just need to have it open in Chimera and associated with the structure(s), also open in Chimera, that you want to use as template(s). Click the Help button on the Modeller dialog or see documentation here: ... and here is a little more about sequence-structure association in Chimera: I would only note that if your sequence alignment is huge (has lots of sequences), it may be quite slow to interact with it in Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2012, at 7:08 AM, James Valdes wrote: > Hello Chimera, > I'm using the Modeller interface via Chimera and I was wondering if > the models produced takes into account multiple templates (e.g., > selecting all) from a multiple alignment produced by MAFFT > (http://mafft.cbrc.jp/alignment/software/). I appreciate any insight > you may provide. > Cheers, > James Jason Vald?s, Ph.D. From meng at cgl.ucsf.edu Fri Sep 21 10:50:16 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Sep 2012 10:50:16 -0700 Subject: [Chimera-users] Estimated RMSD after using Modeller feature In-Reply-To: References: Message-ID: <2B464BB2-C267-4A41-BA8B-702368411641@cgl.ucsf.edu> Hi Claudia, The "estimated RMSD" is a model quality score calculated by the Sali lab's Model Evaluation Server. For descriptions of scores, literature references, and links to more information at the Sali lab website, click the Help button on the Model List dialog in Chimera or see here: "Estimated RMSD - TSVMod predicted C? root-mean-square deviation (RMSD) of the model from the native structure (see Eramian et al., Protein Sci 17:1881 (2008))" So if you follow the link to the Eramian paper (from the URL above) it should explain more about the calculation. I don't know the exact answer to your question, but I imagine there may be additional restraints from the extra N-terminal residues. Also, the model-building involves some randomization, so even multiple models from the same template would have different scores, including different estimated RMSD values. Finally, this estimated RMSD is not relative to the template, but relative to the (unknown) "real" structure of the protein you are trying to model. That is why it is "estimated" rather than an exact calculation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 21, 2012, at 7:26 AM, Claudia Fernandes wrote: > I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. > > I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? > As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. > > Any help would be welcome. > Regards, > Cl?udia Fernandes From adavenpo at ucsd.edu Fri Sep 21 11:35:23 2012 From: adavenpo at ucsd.edu (Amy Davenport) Date: Fri, 21 Sep 2012 11:35:23 -0700 Subject: [Chimera-users] =?iso-8859-1?q?Calculation_of_SASA_with_probe_siz?= =?iso-8859-1?q?e_of_0=2E8=C5?= In-Reply-To: References: Message-ID: Thanks Elaine! Ok, so now that I have gotten the surface to work by playing with settings, is there a way to write out the SASA per atom? Thanks Amy On Sep 20, 2012, at 5:51 PM, Elaine Meng wrote: > Hi Amy, > It sounds like you may be using the "Area/Volume from Web" tool in Chimera, which in turn uses the StrucTools web server at NIH. In that case, you are limited to the options that the server provides. > > > However, you do not need to use that tool in Chimera to get SASA. If you can just display a molecular surface for your protein in Chimera, you will automatically get the area of both the SES (solvent-excluded surface = molecular surface, corresponding to what is displayed) and the SAS. Both totals are reported in the Reply Log (under Favorites in the menu). If your protein has hydrogens, the surfaces will include them. "Components" means disconnected parts, so if values are reported for more than one component, you may want to use only the largest. The others are generally interior bubbles. > > > Surface calculation parameters such as probe radius can be changed by selecting the surface (Ctrl-click), opening the Selection Inspector (for example by clicking the green magnifying glass at the bottom right of the Chimera window), and in that dialog inspecting "MSMS surface" and changing the values. > > > > Note: sometimes surface calculation fails numerically. If it fails but still shows the surface you expect, the failure is for the interior bubbles only, and you can proceed if you didn't need the surface areas to include those. However, in some cases you may not get any surface or values reported. Using a small probe may make such failures more likely. In the case of complete failure, see: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Sep 20, 2012, at 5:20 PM, Amy Davenport wrote: > >> Hi all, >> I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8? to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. >> Thank you, >> Amy Davenport Migliori >> UCSD > From meng at cgl.ucsf.edu Fri Sep 21 11:47:31 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Sep 2012 11:47:31 -0700 Subject: [Chimera-users] =?iso-8859-1?q?Calculation_of_SASA_with_probe_siz?= =?iso-8859-1?q?e_of_0=2E8=C5?= In-Reply-To: References: Message-ID: <1DDCC994-FC29-4E06-8F53-B79DEC500FA7@cgl.ucsf.edu> Hi Amy, You can save attributes such as per-atom areaSAS and areaSES using Render by Attribute. Open that tool (from menu under Tools... Structure Analysis) and in its menu choose "File... Save Attributes." In the save dialog specify which attribute you want, probably "areaSAS" of "atoms". General explanation of attributes: Saving attributes: Elaine On Sep 21, 2012, at 11:35 AM, Amy Davenport wrote: > Thanks Elaine! > Ok, so now that I have gotten the surface to work by playing with settings, is there a way to write out the SASA per atom? > Thanks > Amy From nirodion at syr.edu Fri Sep 21 16:32:49 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Fri, 21 Sep 2012 23:32:49 +0000 Subject: [Chimera-users] Potential Energy Calculations Message-ID: Hi all, I was wondering the there is a tool in chimera that can find the net interaction potential energy between models, something like Lennard Jones Potential. Specifically, I need to measure the interaction potential between a protein and water in a solvated system. Thanks! Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 21 17:23:40 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Sep 2012 17:23:40 -0700 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: References: Message-ID: <8BE40059-8B9D-4CA6-9185-1A05125073D5@cgl.ucsf.edu> Hi Nikolay, Sorry, no. Although the minimizer reports an energy, it is the total energy of the system, and no breakdown is available. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote: > Hi all, > I was wondering the there is a tool in chimera that can find the net interaction potential energy between models, something like Lennard Jones Potential. Specifically, I need to measure the interaction potential between a protein and water in a solvated system. > Thanks! > Nikolay Rodionov From nirodion at syr.edu Fri Sep 21 17:30:32 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 00:30:32 +0000 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: <8BE40059-8B9D-4CA6-9185-1A05125073D5@cgl.ucsf.edu> Message-ID: Would it be make sense to compute the total energy for the protein w/o water and then loaded with water, and then take the difference to be energy due to interaction? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu On 9/21/12 8:23 PM, "Elaine Meng" wrote: >Hi Nikolay, >Sorry, no. Although the minimizer reports an energy, it is the total >energy of the system, and no breakdown is available. >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > >On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote: > >> Hi all, >> I was wondering the there is a tool in chimera that can find the net >>interaction potential energy between models, something like Lennard >>Jones Potential. Specifically, I need to measure the interaction >>potential between a protein and water in a solvated system. >> Thanks! >> Nikolay Rodionov > > From meng at cgl.ucsf.edu Fri Sep 21 17:41:19 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Sep 2012 17:41:19 -0700 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: References: Message-ID: <35CF14B0-2ACF-4F08-A7FE-BA22922BFA57@cgl.ucsf.edu> In my opinion, no. Maybe you could ask for recommendations of what program(s) would be more appropriate on ccl.net -- we're getting into the territory of general computational chemistry issues that are probably beyond the scope of this forum. Best, Elaine On Sep 21, 2012, at 5:30 PM, Nikolay Igorovich Rodionov wrote: > Would it be make sense to compute the total energy for the protein w/o > water and then loaded with water, and then take the difference to be > energy due to interaction? > > Thanks! > > > Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 > Martin J. Whitman School of Management & L.C. Smith College of Engineering > at Syracuse University > > Syracuse, New York 13244 > Phone: 281.301.9401| Email: Nirodion at syr.edu > > > > > > > > On 9/21/12 8:23 PM, "Elaine Meng" wrote: > >> Hi Nikolay, >> Sorry, no. Although the minimizer reports an energy, it is the total >> energy of the system, and no breakdown is available. >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote: >> >>> Hi all, >>> I was wondering the there is a tool in chimera that can find the net >>> interaction potential energy between models, something like Lennard >>> Jones Potential. Specifically, I need to measure the interaction >>> potential between a protein and water in a solvated system. >>> Thanks! >>> Nikolay Rodionov >> >> > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From nirodion at syr.edu Fri Sep 21 17:49:00 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 00:49:00 +0000 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: <35CF14B0-2ACF-4F08-A7FE-BA22922BFA57@cgl.ucsf.edu> Message-ID: Okay will do, thanks for the advice! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu On 9/21/12 8:41 PM, "Elaine Meng" wrote: >In my opinion, no. Maybe you could ask for recommendations of what >program(s) would be more appropriate on ccl.net -- we're getting into the >territory of general computational chemistry issues that are probably >beyond the scope of this forum. >Best, >Elaine > >On Sep 21, 2012, at 5:30 PM, Nikolay Igorovich Rodionov wrote: > >> Would it be make sense to compute the total energy for the protein w/o >> water and then loaded with water, and then take the difference to be >> energy due to interaction? >> >> Thanks! >> >> >> Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 >> Martin J. Whitman School of Management & L.C. Smith College of >>Engineering >> at Syracuse University >> >> Syracuse, New York 13244 >> Phone: 281.301.9401| Email: Nirodion at syr.edu >> >> >> >> >> >> >> >> On 9/21/12 8:23 PM, "Elaine Meng" wrote: >> >>> Hi Nikolay, >>> Sorry, no. Although the minimizer reports an energy, it is the total >>> energy of the system, and no breakdown is available. >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote: >>> >>>> Hi all, >>>> I was wondering the there is a tool in chimera that can find the net >>>> interaction potential energy between models, something like Lennard >>>> Jones Potential. Specifically, I need to measure the interaction >>>> potential between a protein and water in a solvated system. >>>> Thanks! >>>> Nikolay Rodionov >>> >>> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From nirodion at syr.edu Fri Sep 21 20:33:06 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 03:33:06 +0000 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: <35CF14B0-2ACF-4F08-A7FE-BA22922BFA57@cgl.ucsf.edu> Message-ID: Hi Elaine, I posted my question on the ccl mail server, but I have one more question for you. I realize that this might be entirely appropriate for this mailing list but regarding my previous proposal, what if I modify the method to create 3 files. One file will be with just the protein, one with the solvated protein, and one it just the water molecules isolated from the solvated model. If I calculate the net energy in the each system, and then subtract the net energies of the protein only and water only systems from the net energy of the protein & water system, shouldn't this leave me with just interaction energy? I was also thinking about putting all of the water molecules into an energy minima orientation in both files with water by first running the minimization function in the file with water & protein, and then isolating the water molecules and writing them into a separate PDB for the water-only file since the energy minima orientation will change based on the environment. Thanks for pointing me to a great resource by the way. Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu On 9/21/12 8:41 PM, "Elaine Meng" wrote: >In my opinion, no. Maybe you could ask for recommendations of what >program(s) would be more appropriate on ccl.net -- we're getting into the >territory of general computational chemistry issues that are probably >beyond the scope of this forum. >Best, >Elaine > >On Sep 21, 2012, at 5:30 PM, Nikolay Igorovich Rodionov wrote: > >> Would it be make sense to compute the total energy for the protein w/o >> water and then loaded with water, and then take the difference to be >> energy due to interaction? >> >> Thanks! >> >> >> Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 >> Martin J. Whitman School of Management & L.C. Smith College of >>Engineering >> at Syracuse University >> >> Syracuse, New York 13244 >> Phone: 281.301.9401| Email: Nirodion at syr.edu >> >> >> >> >> >> >> >> On 9/21/12 8:23 PM, "Elaine Meng" wrote: >> >>> Hi Nikolay, >>> Sorry, no. Although the minimizer reports an energy, it is the total >>> energy of the system, and no breakdown is available. >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote: >>> >>>> Hi all, >>>> I was wondering the there is a tool in chimera that can find the net >>>> interaction potential energy between models, something like Lennard >>>> Jones Potential. Specifically, I need to measure the interaction >>>> potential between a protein and water in a solvated system. >>>> Thanks! >>>> Nikolay Rodionov >>> >>> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From nirodion at syr.edu Sat Sep 22 09:11:07 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 16:11:07 +0000 Subject: [Chimera-users] "No MMTK name for atom "H" in standard residue "G" " Message-ID: Hi could someone help me with this error: No MMTK name for atom "H" in standard residue "G" I get this error when running the minimize structure function. Does anyone know a work around or how I can fix the problem? Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Sep 22 10:38:50 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 22 Sep 2012 10:38:50 -0700 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: References: Message-ID: <0D6FFAC7-6982-4F34-8DF6-B0980B4AC4D4@cgl.ucsf.edu> Hi Nikolay, There are a lot of levels to this question -- I hesitate to get into it, because it could be very complicated (and it's not a Chimera question per se). Concerns are why you want to calculate this quantity and whether it has any physical meaning. If you are trying to calculate a solvation energy, there are many well-established computational approaches involving MD or MC simulations, or continuum dielectric calculations. What you describe is only for a single configuration, without sampling or entropy considerations. I would recommend thinking carefully about what quantity you are calculating, how it relates to any real property, and then investigating in the literature (or computational chemistry textbooks), on the web, and by questions to email lists such as CCL how best to proceed in terms of calculations. Probably to get helpful answers from email lists, you should give some rationale, and solicit suggestions about your strategy as well as what programs to use to execute that strategy. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 21, 2012, at 8:33 PM, Nikolay Igorovich Rodionov wrote: > Hi Elaine, > I posted my question on the ccl mail server, but I have one more question > for you. I realize that this might be entirely appropriate for this > mailing list but regarding my previous proposal, what if I modify the > method to create 3 files. > > One file will be with just the protein, one with the solvated protein, and > one it just the water molecules isolated from the solvated model. If I > calculate the net energy in the each system, and then subtract the net > energies of the protein only and water only systems from the net energy of > the protein & water system, shouldn't this leave me with just interaction > energy? > > I was also thinking about putting all of the water molecules into an > energy minima orientation in both files with water by first running the > minimization function in the file with water & protein, and then isolating > the water molecules and writing them into a separate PDB for the > water-only file since the energy minima orientation will change based on > the environment. > > Thanks for pointing me to a great resource by the way. > Nikolay Rodionov From meng at cgl.ucsf.edu Sat Sep 22 10:43:23 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 22 Sep 2012 10:43:23 -0700 Subject: [Chimera-users] "No MMTK name for atom "H" in standard residue "G" " In-Reply-To: References: Message-ID: <145EE871-EDC2-4675-9BD4-A3D7E3FC7A02@cgl.ucsf.edu> Hi Nikolay, It is not possible to figure out errors like this without the data. You would need to use Help... Report a Bug in the Chimera menu, attach the data file such as the PDB or the Chimera session, describe what you did that generated the error, and include your email address on the report if you want feedback. That would automatically also tell us your Chimera version and type of computer, which are often also needed. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 22, 2012, at 9:11 AM, Nikolay Igorovich Rodionov wrote: > Hi could someone help me with this error: > No MMTK name for atom "H" in standard residue "G" > > I get this error when running the minimize structure function. Does anyone know a work around or how I can fix the problem? > > Nikolay Rodionov From nirodion at syr.edu Sat Sep 22 11:02:02 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 18:02:02 +0000 Subject: [Chimera-users] Potential Energy Calculations In-Reply-To: <0D6FFAC7-6982-4F34-8DF6-B0980B4AC4D4@cgl.ucsf.edu> Message-ID: I recognize that the approach is limited in that scope but I am working with a highly stable macro protein structure and I am not expecting any immense configurational changes when I study the system in MD. I simply trying to redefine the surface of the molecule based on the extent of solvent interaction within the macrostructure. I feel as though an analysis of a generalized energy minimal state will give me a good approximation of how deep interactions persist and give me a better idea of the "surface" atoms than MSMS analysis which simply accounts for VDW size and not VDW interactions per say. The structure is tubular so I was going to create multiple analysis states with atomic cutoffs at varying distances from the center of the energy minimized structure and then compare the relative energies of the systems as I described before. Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu On 9/22/12 1:38 PM, "Elaine Meng" wrote: >Hi Nikolay, >There are a lot of levels to this question -- I hesitate to get into it, >because it could be very complicated (and it's not a Chimera question per >se). > >Concerns are why you want to calculate this quantity and whether it has >any physical meaning. If you are trying to calculate a solvation energy, >there are many well-established computational approaches involving MD or >MC simulations, or continuum dielectric calculations. What you describe >is only for a single configuration, without sampling or entropy >considerations. > >I would recommend thinking carefully about what quantity you are >calculating, how it relates to any real property, and then investigating >in the literature (or computational chemistry textbooks), on the web, and >by questions to email lists such as CCL how best to proceed in terms of >calculations. Probably to get helpful answers from email lists, you >should give some rationale, and solicit suggestions about your strategy >as well as what programs to use to execute that strategy. >Best, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > >On Sep 21, 2012, at 8:33 PM, Nikolay Igorovich Rodionov wrote: > >> Hi Elaine, >> I posted my question on the ccl mail server, but I have one more >>question >> for you. I realize that this might be entirely appropriate for this >> mailing list but regarding my previous proposal, what if I modify the >> method to create 3 files. >> >> One file will be with just the protein, one with the solvated protein, >>and >> one it just the water molecules isolated from the solvated model. If I >> calculate the net energy in the each system, and then subtract the net >> energies of the protein only and water only systems from the net energy >>of >> the protein & water system, shouldn't this leave me with just >>interaction >> energy? >> >> I was also thinking about putting all of the water molecules into an >> energy minima orientation in both files with water by first running the >> minimization function in the file with water & protein, and then >>isolating >> the water molecules and writing them into a separate PDB for the >> water-only file since the energy minima orientation will change based on >> the environment. >> >> Thanks for pointing me to a great resource by the way. >> Nikolay Rodionov > > -------------- next part -------------- A non-text attachment was scrubbed... Name: VDI.tif Type: image/tiff Size: 379502 bytes Desc: VDI.tif URL: From nirodion at syr.edu Sat Sep 22 11:02:40 2012 From: nirodion at syr.edu (Nikolay Igorovich Rodionov) Date: Sat, 22 Sep 2012 18:02:40 +0000 Subject: [Chimera-users] "No MMTK name for atom "H" in standard residue "G" " In-Reply-To: <145EE871-EDC2-4675-9BD4-A3D7E3FC7A02@cgl.ucsf.edu> Message-ID: Will do. Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion at syr.edu On 9/22/12 1:43 PM, "Elaine Meng" wrote: >Hi Nikolay, >It is not possible to figure out errors like this without the data. You >would need to use Help... Report a Bug in the Chimera menu, attach the >data file such as the PDB or the Chimera session, describe what you did >that generated the error, and include your email address on the report if >you want feedback. That would automatically also tell us your Chimera >version and type of computer, which are often also needed. >Thanks, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > >On Sep 22, 2012, at 9:11 AM, Nikolay Igorovich Rodionov wrote: > >> Hi could someone help me with this error: >> No MMTK name for atom "H" in standard residue "G" >> >> I get this error when running the minimize structure function. Does >>anyone know a work around or how I can fix the problem? >> >> Nikolay Rodionov > > From bala.biophysics at gmail.com Mon Sep 24 09:17:36 2012 From: bala.biophysics at gmail.com (Bala subramanian) Date: Mon, 24 Sep 2012 18:17:36 +0200 Subject: [Chimera-users] drawing circles Message-ID: Friends, I want to draw concentric circles of increasing sizes around the protein. To achieve this, i used the 'define plane' option to draw disk choosing I three reference atoms and drew the disks of increasing sizes and choose two different color for the inner and outer disk. Since the reference atoms are the same. If i change the color of the bigger disk, i get a weird appearance of the inner disk. I dnt know how to resolve this problem. I would like to know if i can do something like making the disk transparent/removing the fill color of the disk. thanks, Bala -- C. Balasubramanian From meng at cgl.ucsf.edu Mon Sep 24 09:46:08 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 24 Sep 2012 09:46:08 -0700 Subject: [Chimera-users] drawing circles In-Reply-To: References: Message-ID: Hi Bala, You can change the color (including transparency) of planes, axes, centroids by clicking a color well in the table of such objects and using the Color Editor. However, there is no separate fill, it is just the color of the whole object. (In recent versions of Chimera you can also just select the plane with mouse Ctrl-click and use the menu, Actions... Color... from editor) Alternative ways to draw rings: (1) just add a 2D Label circle symbol, increase font size and color as desired. You can have multiple labels of different font sizes and colors. As the name suggests, 2D labels exist only in the 2D plane and do not move along with the 3D Chimera view... however, you can drag each to the desired X,Y location: You can copy-and-paste into the label field, for example from this page of symbols. The circle is the top symbol in the "Miscellaneous" column: (2) create a surface model shaped like a ring by opening the attached python script. Inner/outer radii and color can be changed by editing the script. This will exist in 3D, so if you want it to look like a circle be careful to only translate (not rotate) it. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: annulus.py Type: text/x-python-script Size: 1266 bytes Desc: not available URL: -------------- next part -------------- On Sep 24, 2012, at 9:17 AM, Bala subramanian wrote: > Friends, > I want to draw concentric circles of increasing sizes around the > protein. To achieve this, i used the 'define plane' option to draw > disk choosing I three reference atoms and drew the disks of increasing > sizes and choose two different color for the inner and outer disk. > Since the reference atoms are the same. If i change the color of the > bigger disk, i get a weird appearance of the inner disk. I dnt know > how to resolve this problem. > I would like to know if i can do something like making the disk > transparent/removing the fill color of the disk. > thanks, > Bala > -- > C. Balasubramanian From pett at cgl.ucsf.edu Mon Sep 24 10:22:25 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 24 Sep 2012 10:22:25 -0700 Subject: [Chimera-users] drawing circles In-Reply-To: References: Message-ID: <5677EDC1-5F5A-4794-AC03-01D93202039F@cgl.ucsf.edu> As you define the disks, you can make the inner one thicker, which will guarantee that it's color will show through and not be "mixed" with the outer one's color. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 24, 2012, at 9:17 AM, Bala subramanian wrote: > Friends, > I want to draw concentric circles of increasing sizes around the > protein. To achieve this, i used the 'define plane' option to draw > disk choosing I three reference atoms and drew the disks of increasing > sizes and choose two different color for the inner and outer disk. > Since the reference atoms are the same. If i change the color of the > bigger disk, i get a weird appearance of the inner disk. I dnt know > how to resolve this problem. > > I would like to know if i can do something like making the disk > transparent/removing the fill color of the disk. > > thanks, > Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Sep 24 14:25:25 2012 From: goddard at sonic.net (Tom Goddard) Date: Mon, 24 Sep 2012 14:25:25 -0700 Subject: [Chimera-users] icosahedral reconstruction volume color In-Reply-To: References: <2639CB5887B7B844A85E581C733BA684213DB7DCF1@EXCH-CCR01.lj.ad.scripps.edu>, <1D0871F4-33C7-48C8-9E04-91DBFCB7F88E@cgl.ucsf.edu> <2639CB5887B7B844A85E581C733BA684213DB7DCF2@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: <5060CFC5.9080606@sonic.net> Hi Reggie, The following video shows how to place markers on your icosahedral map, replicate them using symmetry, then use the Color Zone tool to color part of the map near chosen markers. http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html The video is trying to solve a different problem from what you want but the same techniques will do the job. Tom -------- Original Message -------- Subject: Re: [Chimera-users] icosahedral reconstruction volume color From: Elaine Meng To: Reginald McNulty Date: 9/20/12 10:37 AM > Hi Reggie, > I can't think of a way to do that directly, but here are some related ideas: > > (a) for visualizing the 5-fold and 6-fold vertices, the command "hkcage" can be used to create an icosahedral mesh of hexagons and pentagons - you specify radius, h and k values (where virus T number = h^2 + hk +k^2). It makes a wire model which could be converted to sticks with command "meshmol". The difficulty would probably be in getting the orientation and placement of the cage to match that of your reconstruction. > > > (b) "Color Zone" colors surfaces to match nearby atoms or pseudoatomic "markers" -- theoretically you could use "Volume Tracer" to place a red marker at each 5-fold vertex and then use Color Zone to color those regions of the surface red, and then undisplay the atoms or markers. (These tools are in the menu under Tools... Volume Data.) However, the difficulty I see is in placing the markers exactly symmetrically so each vertex would get the same amount of coloring. If you knew coordinates for the vertices (again the hard part) you could just create a PDB file with those fake atoms, color them red, ... > > > (c) there is a "Cage Builder" (menu under Tools... Higher-Order Structure) that lets you interactively construct a cage of hexagons and pentagons. This is an additional method of generating markers. The "Create Mesh...." option would generate single edges and vertices from the initially generated doubled set (you'd have to look at the figure in the docs to understand that part) and in the result, you could color the 5-fold vertices red and proceed as above with Color Zone. The difficulty may be in building/scaling/positioning the cage to coincide correctly with your reconstruction. > > > Sorry I haven't come up with simpler solutions, > Elaine > > On Sep 20, 2012, at 10:04 AM, Reginald McNulty wrote: > >> Hi Elaine, >> I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red. >> Reggie >> ______________ >> From: Elaine Meng [meng at cgl.ucsf.edu] >> Sent: Thursday, September 20, 2012 9:22 AM >> To: Reginald McNulty >> Cc: chimera-users at cgl.ucsf.edu >> Subject: Re: [Chimera-users] icosahedral reconstruction volume color >> >> Dear Reggie, >> I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me. >> >> You can open and display the vol file in Chimera, assuming it is the SPIDER format: >> >> >> You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". >> >> >> >> These support coloring by >> (a) map value or gradient norm >> (b) distance from a point, axis or plane >> >> radial coloring = coloring by distance from a point, where the point is the center of symmetry >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote: >> >>> Dear Users, >>> I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? >>> Kind regards, >>> Reggie > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Sep 24 13:50:39 2012 From: goddard at sonic.net (Tom Goddard) Date: Mon, 24 Sep 2012 13:50:39 -0700 Subject: [Chimera-users] drawing circles In-Reply-To: References: Message-ID: <5060C79F.6070002@sonic.net> Hi Bala, I think the easiest way to show circles is to use the shape command to show a cylinder, for example. shape cylinder radius 20 height 1 slab 1 color pink I guess you want to have it perpendicular to the screen and centered on some atoms. That bit is slightly tricky. You can use shape cylinder radius 20 height 1 slab 1 color pink center #3:82-84 at CA but the plane of the circle will be perpendicular to the z-axis of the molecule #3 coordinate system which won't be the same as the z-axis of the screen if you did any rotation. A trick to handle this problem is open your molecule and don't rotate, make the circle, and set the center of rotation to the center of the circle (cofr #3:82-84 at CA), freeze the circle (Favorites / Model Panel, deactivate cylinder), then rotate the molecule to the orientation you want. If you translate the molecule make sure to unfreeze the circle first. Tom -------- Original Message -------- Subject: Re: [Chimera-users] drawing circles From: Elaine Meng To: Bala subramanian Date: 9/24/12 9:46 AM > Hi Bala, > You can change the color (including transparency) of planes, axes, centroids by clicking a color well in the table of such objects and using the Color Editor. However, there is no separate fill, it is just the color of the whole object. > > (In recent versions of Chimera you can also just select the plane with mouse Ctrl-click and use the menu, Actions... Color... from editor) > > Alternative ways to draw rings: > > (1) just add a 2D Label circle symbol, increase font size and color as desired. You can have multiple labels of different font sizes and colors. As the name suggests, 2D labels exist only in the 2D plane and do not move along with the 3D Chimera view... however, you can drag each to the desired X,Y location: > > > You can copy-and-paste into the label field, for example from this page of symbols. The circle is the top symbol in the "Miscellaneous" column: > > > (2) create a surface model shaped like a ring by opening the attached python script. Inner/outer radii and color can be changed by editing the script. This will exist in 3D, so if you want it to look like a circle be careful to only translate (not rotate) it. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Sep 24, 2012, at 9:17 AM, Bala subramanian wrote: > >> Friends, >> I want to draw concentric circles of increasing sizes around the >> protein. To achieve this, i used the 'define plane' option to draw >> disk choosing I three reference atoms and drew the disks of increasing >> sizes and choose two different color for the inner and outer disk. >> Since the reference atoms are the same. If i change the color of the >> bigger disk, i get a weird appearance of the inner disk. I dnt know >> how to resolve this problem. >> I would like to know if i can do something like making the disk >> transparent/removing the fill color of the disk. >> thanks, >> Bala >> -- >> C. Balasubramanian > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From 70padillasan at cardinalmail.cua.edu Mon Sep 24 11:20:01 2012 From: 70padillasan at cardinalmail.cua.edu (Victor Padilla-Sanchez) Date: Mon, 24 Sep 2012 14:20:01 -0400 Subject: [Chimera-users] E. coli cells Message-ID: Dear UCSF Chimera, Could you tell me where to find chimera maps of E. coli cell(s) ? Or could you send me some maps ? Thank you very much Victor Padilla-Sanchez -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 24 15:37:12 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 24 Sep 2012 15:37:12 -0700 Subject: [Chimera-users] E. coli cells In-Reply-To: References: Message-ID: Dear Victor, We provide the Chimera program for viewing and analyzing data, but we do not provide the data, sorry. You could search the literature for papers describing such data and then see if it is publicly available or ask the authors if they are willing to send it to you. There are also public databases of maps (e.g. EMDB ), but I believe they are mainly for macromolecules and their complexes, not whole cells. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 24, 2012, at 11:20 AM, Victor Padilla-Sanchez wrote: > Dear UCSF Chimera, > > Could you tell me where to find chimera maps of E. coli cell(s) ? > Or could you send me some maps ? > > Thank you very much > > Victor Padilla-Sanchez From almeida at cim.sld.cu Wed Sep 26 11:04:25 2012 From: almeida at cim.sld.cu (Yasser Almeida Hernandez) Date: Wed, 26 Sep 2012 18:04:25 +0000 Subject: [Chimera-users] Measuring angles between atoms pairs Message-ID: Dear Chimerians... I'm running an analysis about H-bonds geometries in several models. I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. How could I do that in a python IDLE/script? In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? Thanks in advance Yasser -- Yasser Almeida Hern?ndez, BSc. Center of Molecular Immunology (CIM) Tumor Biology Department 216 St.& 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3178 almeida at cim.sld.cu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 26 10:52:06 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 26 Sep 2012 10:52:06 -0700 Subject: [Chimera-users] Measuring angles between atoms pairs In-Reply-To: References: Message-ID: <7537CF79-5F48-4CDD-A017-EB82FEACF49F@cgl.ucsf.edu> Hi Yasser, It does not matter if the atoms are bonded or not. You could name any 3 or 4 atoms (for "valence" or "torsion" type of angle), for example with command: angle :2.a at ca:4.a at ca:6.b at ca (angle formed by three CA atoms: in residue 2 chain A, residue 4 chain A, residue 6 chain B) Or, instead of using names, you could select atoms (in order) with the mouse and then use: angle sel Angle command: How to specify atoms by name: I can't answer the Python part, except that there are some basic scripting instructions here: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 26, 2012, at 11:04 AM, Yasser Almeida Hernandez wrote: > Dear Chimerians... > > I'm running an analysis about H-bonds geometries in several models. > > I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. > How could I do that in a python IDLE/script? > > In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? > > Thanks in advance > > Yasser > From pett at cgl.ucsf.edu Wed Sep 26 11:25:49 2012 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 26 Sep 2012 11:25:49 -0700 Subject: [Chimera-users] Measuring angles between atoms pairs In-Reply-To: References: Message-ID: <5EFC944F-62DB-4F7A-96C3-E24BE369D149@cgl.ucsf.edu> On Sep 26, 2012, at 11:04 AM, Yasser Almeida Hernandez wrote: > Dear Chimerians... > > I'm running an analysis about H-bonds geometries in several models. > > I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. > How could I do that in a python IDLE/script? > > In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? In regards to the Python part, probably the single most salient fact is that there is an "angle" function in the chimera module, i.e.: chimera.angle(a1.coord(), a2.coord(), a3.coord()) returns the a1-a2-a3 angle in degrees formed by the Python Atom objects. If the Atoms could be in different models, then use .xformCoord() rather than .coord(). So, how to get an Atom object? Let's say you've selected the Atom by some means, then: a = chimera.selection.currentAtoms()[0] would get you the selected Atom object. Along the same lines, if you've selected a (covalent) Bond, then: b = chimera.selection.currentBonds()[0] a1, a2 = b.atoms would get you the two Atoms that form the bond. If the third Atom of interest is a neighbor of a1 or a2 then you could look through a1.neighbors or a2.neighbors to find it (FYI an Atom's name is a.name). Hydrogen bonds are PseudoBonds, so an analogous procedure could be used with chimera.selection.currentPseudobonds(). It sounds like you may want to run the hydrogen-bond finding code directly in your Python script, which will return a list of donor/acceptor Atom pairs, which you could then use in your angle call once you've found the third atom that you care about. This is how: from FindHBond import findHBonds da_list = findHBonds(chimera.openModels.list(modelTypes=[chimera.Molecule])) that call will return only hbonds meeting the strict angle/distance cutoff parameters. If you want to use the default GUI/command relaxed parameters (+0.4 angstroms / +20 degrees), then use this code instead: from FindHBonds import findHBonds, recDistSlop, recAngleSlop da_list = findHBonds(chimera.openModels.list(modelTypes=[chimera.Molecule]), distSlop=recDistSlop, angleSlop=recAngleSlop) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From vamseedharr at gmail.com Wed Sep 26 23:44:12 2012 From: vamseedharr at gmail.com (vamsee) Date: Thu, 27 Sep 2012 00:44:12 -0600 Subject: [Chimera-users] Silhouette color change Message-ID: Hi Elaine, I need to change the silhouette color of individual models and if possible for individual representations (ribbon, surface or atoms). Is there a command line option that I could use? (maybe set?) Thanks in advance Vamsee -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Sep 27 09:14:46 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 27 Sep 2012 09:14:46 -0700 Subject: [Chimera-users] Silhouette color change In-Reply-To: References: Message-ID: <3A54952A-64F5-4293-B155-49F61B4AED32@cgl.ucsf.edu> Hi Vamsee, Command "help set" will show you the "set" manual page -- the option is "set silhouetteColor" e.g. set silhouetteColor hot pink set silhouetteColor 0,.8,.7 However, there is only one silhouette color for everything: you can't use a different color for different models or representations. You might be able to fake having two different colors by using the selection outline. You can change the selection outline color in the Preferences (under Favorites in menu), category: Background. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 26, 2012, at 11:44 PM, vamsee wrote: > Hi Elaine, > I need to change the silhouette color of individual models and if possible for individual representations (ribbon, surface or atoms). Is there a command line option that I could use? (maybe set?) > Thanks in advance > Vamsee From coyote_v2002 at yahoo.com Fri Sep 28 00:34:17 2012 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Fri, 28 Sep 2012 00:34:17 -0700 (PDT) Subject: [Chimera-users] Met CH3 and NH3+ hydrogen optimization Message-ID: <1348817657.30944.YahooMailNeo@web111712.mail.gq1.yahoo.com> Dear colleagues, Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand.? I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:) Best regards, Vis Kairys Institute of Biotechnology Vilnius University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashley.pike at sgc.ox.ac.uk Fri Sep 28 08:38:05 2012 From: ashley.pike at sgc.ox.ac.uk (Ashley Pike) Date: Fri, 28 Sep 2012 15:38:05 +0000 Subject: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential Message-ID: <96D4B2775AB2BB499763EA2F174A0D7606018E@MBX06.ad.oak.ox.ac.uk> Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Sep 28 09:34:08 2012 From: goddard at sonic.net (Tom Goddard) Date: Fri, 28 Sep 2012 09:34:08 -0700 Subject: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential In-Reply-To: <96D4B2775AB2BB499763EA2F174A0D7606018E@MBX06.ad.oak.ox.ac.uk> References: <96D4B2775AB2BB499763EA2F174A0D7606018E@MBX06.ad.oak.ox.ac.uk> Message-ID: <5065D180.1050301@sonic.net> Hi Ashley, You can get a single color clipped cap by doing the electrostatic surface coloring with a command scolor #0 volume #1 cmap -10,red:0,white:10,blue autoUpdate false where #0 is the molecular surface and #1 is the electrostatic map (*.dx file). The key here is the "autoUpdate false" option. That means the coloring on the clip surface won't be updated as the clip plane is moved. The above command will still color the current clip surface and you'll have to move the clip plane to make it a single color. The Surface Color dialog does not offer control over the "autoUpdate" option so it can only be done with a command. Tom > Hi -- Can't find answer to this question in manual. Is it possible to > assign a uniform solid colour to a surface cap when the (clipped) > surface is coloured by electrostatic potential (using external .dx > file)? I know such capping can be done when the surface is coloured by > some other attribute but have not found a way to specify in the above > case. > > Any hints gratefully received. > > Many thanks, > > Ashley > > -- > > Dr. Ashley Pike > > Membrane Protein Crystallography | Structural Genomics Consortium | > University of Oxford > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 28 09:53:26 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 28 Sep 2012 09:53:26 -0700 Subject: [Chimera-users] Met CH3 and NH3+ hydrogen optimization In-Reply-To: <1348817657.30944.YahooMailNeo@web111712.mail.gq1.yahoo.com> References: <1348817657.30944.YahooMailNeo@web111712.mail.gq1.yahoo.com> Message-ID: <52BDB405-0F48-4265-91E9-AC807C41D68A@cgl.ucsf.edu> Dear Vis Kairys, AddH does try to avoid clashes where possible. It may be that your specific structure had other constraints, or that you ran into limitations of the clash-avoidance algorithm. Besides rotating manually, other approaches include: (a) energy minimization (you can freeze parts of the structure, for example to allow only hydrogens to move) (b) adding hydrogens instead with the Richardson program "Reduce" (see the bottom of the AddH manual page linked above). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 28, 2012, at 12:34 AM, Visvaldas K. wrote: > Dear colleagues, > Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand. I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:) > Best regards, > Vis Kairys > Institute of Biotechnology > Vilnius University From ashley.pike at sgc.ox.ac.uk Fri Sep 28 11:02:06 2012 From: ashley.pike at sgc.ox.ac.uk (Ashley Pike) Date: Fri, 28 Sep 2012 18:02:06 +0000 Subject: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential In-Reply-To: <5065D180.1050301@sonic.net> References: <96D4B2775AB2BB499763EA2F174A0D7606018E@MBX06.ad.oak.ox.ac.uk> <5065D180.1050301@sonic.net> Message-ID: <96D4B2775AB2BB499763EA2F174A0D760604EC@MBX06.ad.oak.ox.ac.uk> OK I see. This gives me a single colour clipped cap *BUT* the colouring of my surface is now very different from the result I see when colouring using the SurfaceColor dialog panel (with the same values -10,0,10). The colours generated by the suggested command are very intense rather than smeared out. For example a hydrophobic surface when coloured via the panel appears virtually white when coloured according to electrostatic potential (what one would expect) but from command line the same region appears as a patchwork of red/white and blue? I suspect some scaling is going on when colouring invoked from command line? I have played with qualifier 'cmapRange full' but this doesn't seem to do the job. From: Tom Goddard [mailto:goddard at sonic.net] Sent: 28 September 2012 17:34 To: Ashley Pike Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential Hi Ashley, You can get a single color clipped cap by doing the electrostatic surface coloring with a command scolor #0 volume #1 cmap -10,red:0,white:10,blue autoUpdate false where #0 is the molecular surface and #1 is the electrostatic map (*.dx file). The key here is the "autoUpdate false" option. That means the coloring on the clip surface won't be updated as the clip plane is moved. The above command will still color the current clip surface and you'll have to move the clip plane to make it a single color. The Surface Color dialog does not offer control over the "autoUpdate" option so it can only be done with a command. Tom Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashley.pike at sgc.ox.ac.uk Fri Sep 28 11:39:57 2012 From: ashley.pike at sgc.ox.ac.uk (Ashley Pike) Date: Fri, 28 Sep 2012 18:39:57 +0000 Subject: [Chimera-users] FW: Specifying colour of surface cap when surface coloured by electrostatic potential References: <96D4B2775AB2BB499763EA2F174A0D7606018E@MBX06.ad.oak.ox.ac.uk> <5065D180.1050301@sonic.net> Message-ID: <96D4B2775AB2BB499763EA2F174A0D76060506@MBX06.ad.oak.ox.ac.uk> Have sorted out the problem. Just needed to add the 'offset 1.4' to command (The SurfaceColor dialog panel has a surface offset parameter (default value of 1.4 gives the 'smearing' effect I mentioned - essentially has the effect of colouring the molecular surface as though it is a solvent-accessible surface)........ From: Ashley Pike Sent: 28 September 2012 19:02 To: 'Tom Goddard' Cc: chimera-users at cgl.ucsf.edu Subject: RE: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential OK I see. This gives me a single colour clipped cap *BUT* the colouring of my surface is now very different from the result I see when colouring using the SurfaceColor dialog panel (with the same values -10,0,10). The colours generated by the suggested command are very intense rather than smeared out. For example a hydrophobic surface when coloured via the panel appears virtually white when coloured according to electrostatic potential (what one would expect) but from command line the same region appears as a patchwork of red/white and blue? I suspect some scaling is going on when colouring invoked from command line? I have played with qualifier 'cmapRange full' but this doesn't seem to do the job. From: Tom Goddard [mailto:goddard at sonic.net] Sent: 28 September 2012 17:34 To: Ashley Pike Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential Hi Ashley, You can get a single color clipped cap by doing the electrostatic surface coloring with a command scolor #0 volume #1 cmap -10,red:0,white:10,blue autoUpdate false where #0 is the molecular surface and #1 is the electrostatic map (*.dx file). The key here is the "autoUpdate false" option. That means the coloring on the clip surface won't be updated as the clip plane is moved. The above command will still color the current clip surface and you'll have to move the clip plane to make it a single color. The Surface Color dialog does not offer control over the "autoUpdate" option so it can only be done with a command. Tom Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Sep 29 16:50:39 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 29 Sep 2012 16:50:39 -0700 Subject: [Chimera-users] [chimera-dev] The style of Ribbon in alpha 1.7 version In-Reply-To: References: Message-ID: Hi Cheng, Actually the ribbon shape has not changed, but a bug in the lighting that made the ribbon look rounder than it really was has been fixed. (see release notes "general changes" http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#general ) You could use Ribbon Style Editor to make something that looks more similar to the old ribbon. I tried making a ribbon style shaped like a football (named "football") and combined that with a ribbon scaling with larger height for helix, sheet, and arrow base (named "fat"). I wasn't very careful drawing the football so you could probably make it better by drawing it more carefully. I attached a file you could use as your preferences file (although you would then lose your own earlier preferences), or you could text-edit to insert all of the lines in the attached file *except* the top and bottom lines into your existing preferences file. Either way, you should save a copy of your existing preferences file first so you don't lose your settings. Or, you could just make a fatter scaling and football-shaped cross section (style) in Ribbon Style Editor yourself, without using the attached file. If you do use the attached file, you could apply everything with commands: ribscale fat ribrepr football Chimera-dev is for programming questions - I'll CC the chimera-users email address since that is more appropriate for this issue, and others on the list may be interested. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: prefs.football Type: application/octet-stream Size: 971 bytes Desc: not available URL: -------------- next part -------------- On Sep 29, 2012, at 3:17 PM, Cheng Wang wrote: > Dear Chimera Team, > Hi. > The ribbon style in 1.6 version is a little round for helix, while it is really flat in 1.7 version. I want to use v1.7 since several commands are really good for movie making eg. format option and transparency. However the ribbon style for helix is not as nice as it in 1.6. I am wondering how could I change the style of ribbon in 1.7 to be the same as in 1.6 since the ribbon style seams the same in the panel for both versions. > Many thanks. > Best, > Cheng From rainy908 at yahoo.com Sat Sep 29 17:07:31 2012 From: rainy908 at yahoo.com (rainy908 at yahoo.com) Date: Sat, 29 Sep 2012 17:07:31 -0700 Subject: [Chimera-users] crystal structure reconstruction Message-ID: Hi, I am new to Chimera. I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol. However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions. To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera. I suspect this is either the 'molmap' or "Fit in Map" feature? Sincerely, Lili -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Sun Sep 30 01:50:57 2012 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 30 Sep 2012 10:50:57 +0200 Subject: [Chimera-users] Error inizializing OpenGL Message-ID: Hello: Following and upgrading of Debian GNU-Linux i386 testing (= wheezy) of my old PC francesco at deb32:~$ lspci | grep VGA 01:00.0 VGA compatible controller: NVIDIA Corporation NV11DDR [GeForce2 MX200] (rev b2) francesco at deb32:~$ with modern kernel francesco at deb32:~$ uname -r 3.2.0-3-686-pae francesco at deb32:~$ chimera francesco at deb32:~$ chimera --version chimera production version 1.6.1 (build 35849) 2012-03-13 22:24:07 UTC francesco at deb32:~$ does not start anymore: Error inizializing OpenGl. Couldn't configure togl widget. Before I go messing the system, may be I can get advice on where to put the hands. libgotl is not installed, but the same occurs with my GTX-680 amd64 system, where chimera works fine. Thanks francesco pietra From meng at cgl.ucsf.edu Sun Sep 30 10:47:47 2012 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 30 Sep 2012 10:47:47 -0700 Subject: [Chimera-users] crystal structure reconstruction In-Reply-To: References: Message-ID: <67B80C50-4FB8-4083-94A9-E9E592332120@cgl.ucsf.edu> Hi Lili, I'm not sure what the person advising you meant -- I don't think it would make any sense to use molmap, since that would just simulate a density map from the coordinates, which are what you are unsure about in the first place. My only ideas for examining this possibly dubious helical assignment are: (a) look at B-factor values for the loop, which will give some idea of disorder, for example command: rangecolor bfactor min blue mid red max yellow (or see graphical interface "Render by Attribute" under Tools... Structure Analysis. It shows a histogram of the values.) However, if the loop is constrained by the crystal structure, it may still have low B-factors, and ** there is nothing in Chimera that will predict for you the intrinsic flexibility of the loop **. I believe you would need to use some other program that simulates motions or uses some empirical criteria to predict flexibility. ... if your doubts are more toward whether the coordinates are really helical or whether they well represent the original density map, the following may be useful ... (b) re-run secondary structure assignment calculations in Chimera. Different methods produce partially different results even for exactly the same atomic coordinates because their criteria differ, so where the authors thought there was a helix, other methods might not. If you open Model Panel (from Favorites menu) there is a "compute SS" button on the right with which you can try recalculating secondary structure. (c) if your structure is from the Protein Data Bank, you may be able to also get the corresponding experimental electron density map and see how well it agrees with the coordinates in the PDB file. menu: File... Fetch by ID, database: EDS (2fo-fc), enter the same 4 digits as the PDB entry. However, not all PDB entries have corresponding maps at EDS. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 29, 2012, at 5:07 PM, rainy908 at yahoo.com wrote: > Hi, > I am new to Chimera. I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol. However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions. > To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera. I suspect this is either the 'molmap' or "Fit in Map" feature? > Sincerely, > Lili From rainy908 at yahoo.com Sun Sep 30 17:07:25 2012 From: rainy908 at yahoo.com (rainy908 at yahoo.com) Date: Sun, 30 Sep 2012 17:07:25 -0700 Subject: [Chimera-users] crystal structure reconstruction In-Reply-To: <67B80C50-4FB8-4083-94A9-E9E592332120@cgl.ucsf.edu> References: <67B80C50-4FB8-4083-94A9-E9E592332120@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you for the detailed suggestions. Following your directions, I re-ran secondary structure calculations in Chimera, and the structure of the loop region did not change. Unfortunately, there is no experimental density map corresponding to the PDB. I performed B-factor analysis on the entire protein, and interestingly, the loop region has the highest B-factor values (yellow) of out all the other regions, including other loops on the protein. I'd like to clarify that this alpha-helical region corresponds to only 2 amino acids (the entire loop is 9 residues). Given the high B-factor of the loop, if I were to run an MD simulation on this protein to witness conformational changes (~10 ns), I would suspect that the atomic positions of the loop would change anyway? In other words, the ordered behavior of the 2 residues is transient? Thanks again! Lili On 30 September 2012 10:47, Elaine Meng wrote: > Hi Lili, > I'm not sure what the person advising you meant -- I don't think it would > make any sense to use molmap, since that would just simulate a density map > from the coordinates, which are what you are unsure about in the first > place. > > My only ideas for examining this possibly dubious helical assignment are: > > (a) look at B-factor values for the loop, which will give some idea of > disorder, for example command: > rangecolor bfactor min blue mid red max yellow > (or see graphical interface "Render by Attribute" under Tools... Structure > Analysis. It shows a histogram of the values.) > > > However, if the loop is constrained by the crystal structure, it may still > have low B-factors, and ** there is nothing in Chimera that will predict > for you the intrinsic flexibility of the loop **. I believe you would need > to use some other program that simulates motions or uses some empirical > criteria to predict flexibility. > > ... if your doubts are more toward whether the coordinates are really > helical or whether they well represent the original density map, the > following may be useful ... > > (b) re-run secondary structure assignment calculations in Chimera. > Different methods produce partially different results even for exactly the > same atomic coordinates because their criteria differ, so where the authors > thought there was a helix, other methods might not. If you open Model Panel > (from Favorites menu) there is a "compute SS" button on the right with > which you can try recalculating secondary structure. > > > (c) if your structure is from the Protein Data Bank, you may be able to > also get the corresponding experimental electron density map and see how > well it agrees with the coordinates in the PDB file. menu: File... Fetch by > ID, database: EDS (2fo-fc), enter the same 4 digits as the PDB entry. > However, not all PDB entries have corresponding maps at EDS. > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 29, 2012, at 5:07 PM, rainy908 at yahoo.com wrote: > > > Hi, > > I am new to Chimera. I have a PDB of a protein comprising of a loop > region that appears to have slight alpha-helical behavior when visualized > in Pymol. However, I doubt that this region is actually structured, and > that this alpha-helical behavior is actually an artifact from experimental > conditions. > > To double-check the validity of this loop, I was broadly advised that > "crystal structure reconstruction" can be performed in Chimera. I suspect > this is either the 'molmap' or "Fit in Map" feature? > > Sincerely, > > Lili > > -------------- next part -------------- An HTML attachment was scrubbed... URL: