From christian.martinoli at unipv.it Wed Oct 2 09:51:35 2013 From: christian.martinoli at unipv.it (Christian Martinoli) Date: Wed, 2 Oct 2013 18:51:35 +0200 Subject: [Chimera-users] info pivotting on a single atom Message-ID: dear all, I have troubles in setting the center of rotation on a single atom of my model. i'm working with the command line to build up a short clip at the end.what i would need is pivotting the whole model on the three axes, rather than in 2D as seems work with cofr command. any help? Thanks in advance Christian -- Christian Martinoli University Of Pavia Dept. of Biology and Biotechnology "Lazzaro Spallanzani" Structural Biology Lab. Via Ferrata 1, 27100 Pavia Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 2 10:30:28 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Oct 2013 10:30:28 -0700 Subject: [Chimera-users] info pivotting on a single atom In-Reply-To: References: Message-ID: <101C5CE9-70B9-46A9-B0CC-6C5B1C8860D0@cgl.ucsf.edu> Dear Christian, The center of rotation is in 3D, not 2D. I"m not sure what you are doing, but some ways to set the center of rotation to a single atom are: (1) select atom, choose menu: Actions... Set Pivot (2) select atom, use command: cofr sel (3) or for command-line only (as in a script), name the atom directly in the command, e.g.: cofr #0:25.a at ca Even if you accidentally specified more than one atom in the command, it would still use the center of the bounding sphere of the atom(s) for 3D rotation. Maybe the issue is in your subsequent rotation commands. The "turn" "rock" and "roll" commands all take an axis specification, which could be simply x, y, z, or something more complicated to indicate any possible direction. Also, you can specify center of rotation directly within those commands instead of separately with the "cofr" command. See their manual pages for more information. 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 Oct 2, 2013, at 9:51 AM, Christian Martinoli wrote: > dear all, > I have troubles in setting the center of rotation on a single atom of my model. i'm working with the command line to build up a short clip at the end.what i would need is pivotting the whole model on the three axes, rather than in 2D as seems work with cofr command. any help? > Thanks in advance > Christian From uschulze-gahmen at lbl.gov Wed Oct 2 14:51:29 2013 From: uschulze-gahmen at lbl.gov (Ursula Schulze-Gahmen) Date: Wed, 2 Oct 2013 14:51:29 -0700 Subject: [Chimera-users] electrostatic surface calculation Message-ID: I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 2 15:51:35 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Oct 2013 15:51:35 -0700 Subject: [Chimera-users] electrostatic surface calculation In-Reply-To: References: Message-ID: Hi Ursula, The molecular surface calculation is the same regardless of what coloring is done. Thus there must be some difference in the atomic coordinates for which the surface is calculated. I am guessing one surface is for the coordinates returned by PDB2PQR and another is calculated from the original coordinates. You could try looking at those two sets of coordinates (not the surfaces) to see if there are any differences. However, I can only imagine that PDB2PQR would ignore/omit coordinates, not acquire additional coordinates as compared to the original coordinates. It omits residues not handled by the designated force field. My only other idea is that even if they contain the same number of protein atoms, one set of coordinates has been transformed (rotated and/or translated) differently than the other. It is best to figure out what is going on, but I should also note you can re-color the same surface model that was colored by Coulombic ESP with the APBS ESP instead. Which surface model to color is specified in the Surface Color (Electrostatic Surface Coloring) dialog. 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 Oct 2, 2013, at 2:51 PM, Ursula Schulze-Gahmen wrote: > I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? > > Thanks > > Ursula > > -- > Ursula Schulze-Gahmen, Ph.D. > Assistant Researcher > UC Berkeley, QB3 > 356 Stanley Hall #3220 > Berkeley, CA 94720-3220 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From matthew.k.thompson at Vanderbilt.Edu Wed Oct 2 14:35:39 2013 From: matthew.k.thompson at Vanderbilt.Edu (Thompson, Matthew K) Date: Wed, 2 Oct 2013 21:35:39 +0000 Subject: [Chimera-users] Stereoscope viewing Message-ID: Can anyone recommend the best camera settings for stereoscope glasses? Mine just don't seem to turn out right. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 2 15:55:31 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Oct 2013 15:55:31 -0700 Subject: [Chimera-users] electrostatic surface calculation In-Reply-To: References: Message-ID: <154F802F-553E-4572-A1CF-52007CA558F3@cgl.ucsf.edu> One more idea. Sometimes the molecular surface calculation chokes up on some singularity and generates a weird shape in a small area. Even if the coordinates are essentially the same, very small rounding differences might lead to this problem with one set and not the other. I feel that this is fairly unlikely, but if you think that it is the problem, just use the surface that looks good for both types of coloring. Elaine On Oct 2, 2013, at 3:51 PM, Elaine Meng wrote: > Hi Ursula, > The molecular surface calculation is the same regardless of what coloring is done. Thus there must be some difference in the atomic coordinates for which the surface is calculated. I am guessing one surface is for the coordinates returned by PDB2PQR and another is calculated from the original coordinates. > > You could try looking at those two sets of coordinates (not the surfaces) to see if there are any differences. > > However, I can only imagine that PDB2PQR would ignore/omit coordinates, not acquire additional coordinates as compared to the original coordinates. It omits residues not handled by the designated force field. My only other idea is that even if they contain the same number of protein atoms, one set of coordinates has been transformed (rotated and/or translated) differently than the other. > > It is best to figure out what is going on, but I should also note you can re-color the same surface model that was colored by Coulombic ESP with the APBS ESP instead. Which surface model to color is specified in the Surface Color (Electrostatic Surface Coloring) dialog. > 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 Oct 2, 2013, at 2:51 PM, Ursula Schulze-Gahmen wrote: > >> I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? >> >> Thanks >> >> Ursula >> >> -- >> Ursula Schulze-Gahmen, Ph.D. >> Assistant Researcher >> UC Berkeley, QB3 >> 356 Stanley Hall #3220 >> Berkeley, CA 94720-3220 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From gregc at cgl.ucsf.edu Wed Oct 2 16:10:10 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 02 Oct 2013 16:10:10 -0700 Subject: [Chimera-users] Stereoscope viewing In-Reply-To: References: Message-ID: <524CA7D2.5060208@cgl.ucsf.edu> On 10/02/2013 02:35 PM, Thompson, Matthew K wrote: > Can anyone recommend the best camera settings for stereoscope > glasses? Mine just don't seem to turn out right. > Double check that the Stereo parameters in the Camera tool are reasonable for your setup. The other thing to check is where the focal plane is -- use the SideView tool and switch the side from 'right' to 'top'. The dashed vertical line, representing the focal plane, should be placed on the near clipping plane to avoid any parallax problems, but some parallax is usually good, so move the focal plane back a bit to cause some of the graphics to pop out of the screen. HTH, Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From jprocter at compbio.dundee.ac.uk Thu Oct 3 03:33:28 2013 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Thu, 03 Oct 2013 11:33:28 +0100 Subject: [Chimera-users] Question about multi align viewer In-Reply-To: References: Message-ID: <524D47F8.6080208@compbio.dundee.ac.uk> Hello Sean, and Elaine. This is a bit late - but I thought I'd plug Jalview here since subfamily conservation is one of its key features. Although it doesn't (yet) link directly with Chimera, it is straightforward to visualize subfamily conservation and export it as a CSV. You can see how it has been used in this paper by Chen et al (2012) : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049679 If you want a less interactive - but phylogenetically rigorous approach, you should check out ConSurf - whose results Chimera can directly display ( http://www.cgl.ucsf.edu/chimera/consurf/consurf.html ). Hope this helps too! Jim. ps. as an aside - I'm working on having Chimera linked with Jalview sometime before the end of this year, which would allow you to interactively highlight conserved residues within subfamilies. Drop me a line if you are interested in test driving this! On 20/09/2013 17:41, Elaine Meng wrote: > On Sep 20, 2013, at 9:33 AM, Sean Connell wrote: > >> Hello I was wondering if it is possible to calculate conservation statistics using only subsets of the aligned sequence. The reason I ask is that in my alignment I have differently families of proteins that have slightly different functions and I would like to highlight residues that are conserved in one subset but not in the other? >> > Hi Sean, > Not directly. I believe you would have to create alignments of just those subsets. You could do that with some other program (including text-editor) before opening the alignment in Chimera, or you could do it in Chimera. Of course, keep the original file with the full alignment too! To edit in Chimera, open the full alignment and then from the sequence window menu choose "Edit... Delete Sequences/Gaps" and in the resulting dialog, choose which sequences to delete. > > > > > You can then continue working with the subset alignment in Chimera, including saving it to a new file (sequence window menu "File... Save As"). > 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 > > P.S. your original message was in an attachment, which was kind of weird, but I could view it by just clicking the attachment > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From JeanDidier.Marechal at uab.cat Thu Oct 3 06:09:01 2013 From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal) Date: Thu, 03 Oct 2013 15:09:01 +0200 Subject: [Chimera-users] command line to define a plane Message-ID: <474888348801.524d888d@uab.es> Dear all, is there a way to define a plane from the command line. Something that would work providing a list of atoms or a selection. Cheers, JD Dr. Jean-Didier Mar?chal Associate Professor The Computational Biotechnological Chemistry Team Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es www: http://asklipio.qf.uab.es From meng at cgl.ucsf.edu Thu Oct 3 08:40:56 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 3 Oct 2013 08:40:56 -0700 Subject: [Chimera-users] command line to define a plane In-Reply-To: <474888348801.524d888d@uab.es> References: <474888348801.524d888d@uab.es> Message-ID: Dear JD, Yes, there is actually a "define plane" command that takes an atom specification and various options. You can use the resulting plane (shown as a disc) for distance and angle measurements. It can also be done with the Axes/Planes/Centroids tool. 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 Oct 3, 2013, at 6:09 AM, Jean Didier Pie Marechal wrote: > Dear all, > > is there a way to define a plane from the command line. Something that would work providing a list of atoms or a selection. > Cheers, > JD From jeandidier.marechal at gmail.com Thu Oct 3 08:41:43 2013 From: jeandidier.marechal at gmail.com (=?ISO-8859-1?Q?Jean=2DDidier_Mar=E9chal?=) Date: Thu, 3 Oct 2013 17:41:43 +0200 Subject: [Chimera-users] command line to define a plane In-Reply-To: References: <474888348801.524d888d@uab.es> Message-ID: thanks a lot. Missed this one. JD **************************** Dr. Jean-Didier Mar?chal Associate Professor The Computational Biotechnological Chemistry Team Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es www: http://g ent.uab.cat/jdidier 2013/10/3 Elaine Meng > Dear JD, > Yes, there is actually a "define plane" command that takes an atom > specification and various options. You can use the resulting plane (shown > as a disc) for distance and angle measurements. > > > > It can also be done with the Axes/Planes/Centroids tool. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes > > > > 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 Oct 3, 2013, at 6:09 AM, Jean Didier Pie Marechal < > JeanDidier.Marechal at uab.cat> wrote: > > > Dear all, > > > > is there a way to define a plane from the command line. Something that > would work providing a list of atoms or a selection. > > Cheers, > > JD > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.hirabatool at ymail.com Fri Oct 4 02:26:22 2013 From: s.hirabatool at ymail.com (Syeda Hira Batool) Date: Fri, 4 Oct 2013 02:26:22 -0700 (PDT) Subject: [Chimera-users] Structural Allignment in Chimera Message-ID: <1380878782.80105.YahooMailNeo@web120901.mail.ne1.yahoo.com> Hello? I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Oct 4 09:17:40 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Oct 2013 09:17:40 -0700 Subject: [Chimera-users] Structural Allignment in Chimera In-Reply-To: <1380878782.80105.YahooMailNeo@web120901.mail.ne1.yahoo.com> References: <1380878782.80105.YahooMailNeo@web120901.mail.ne1.yahoo.com> Message-ID: <09F16633-9BE9-4E81-A919-AC508B9F2DE0@cgl.ucsf.edu> Hello, The source is included in the Chimera download, and the methods are described in the documentation; see here and follow the links from this page for further details: If the methods are suitable for your work, you could just use Chimera to do the alignments and RMSD calculations. However, maybe you are supposed to write your own code for some homework project. In that case, there may be more direct, basic information available on the Web (rather than digging into Chimera code). 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 Oct 4, 2013, at 2:26 AM, Syeda Hira Batool wrote: > Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. > Hira Batool > Student of BS-Bioinformatics > Biosciences Department > COMSATS Institute of Information Technology > Islamabad, PAKISTAN From christian.martinoli at unipv.it Fri Oct 4 01:29:37 2013 From: christian.martinoli at unipv.it (Christian Martinoli) Date: Fri, 4 Oct 2013 10:29:37 +0200 Subject: [Chimera-users] info pivotting on a single atom In-Reply-To: <101C5CE9-70B9-46A9-B0CC-6C5B1C8860D0@cgl.ucsf.edu> References: <101C5CE9-70B9-46A9-B0CC-6C5B1C8860D0@cgl.ucsf.edu> Message-ID: Dear Elaine, still, also with your suggestions, I could not overcome the problem. Since I need to write a script, I need to use just command lines not the graphic interface (where the pivot selection is working). Using cofr i expected that the selected atom would have taken as pivot of the entire molecule, which in my case is not. this is the exact line I 'm using. cofr #3:700.A at N10 the syntax seems correct but still the actual center of rotation is somewhere else any idea about? thankyou, Christian On 2 October 2013 19:30, Elaine Meng wrote: > Dear Christian, > The center of rotation is in 3D, not 2D. I"m not sure what you are doing, > but some ways to set the center of rotation to a single atom are: > > (1) select atom, choose menu: Actions... Set Pivot > (2) select atom, use command: cofr sel > (3) or for command-line only (as in a script), name the atom directly in > the command, e.g.: > cofr #0:25.a at ca > > Even if you accidentally specified more than one atom in the command, it > would still use the center of the bounding sphere of the atom(s) for 3D > rotation. > > > Maybe the issue is in your subsequent rotation commands. The "turn" "rock" > and "roll" commands all take an axis specification, which could be simply > x, y, z, or something more complicated to indicate any possible direction. > Also, you can specify center of rotation directly within those commands > instead of separately with the "cofr" command. See their manual pages for > more information. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands > > > > 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 Oct 2, 2013, at 9:51 AM, Christian Martinoli wrote: > > > dear all, > > I have troubles in setting the center of rotation on a single atom of my > model. i'm working with the command line to build up a short clip at the > end.what i would need is pivotting the whole model on the three axes, > rather than in 2D as seems work with cofr command. any help? > > Thanks in advance > > Christian > > -- Christian Martinoli University Of Pavia Dept. of Biology and Biotechnology "Lazzaro Spallanzani" Structural Biology Lab. Via Ferrata 1, 27100 Pavia Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Oct 4 13:53:21 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Oct 2013 13:53:21 -0700 Subject: [Chimera-users] info pivotting on a single atom In-Reply-To: References: <101C5CE9-70B9-46A9-B0CC-6C5B1C8860D0@cgl.ucsf.edu> Message-ID: <2E4EB300-BC7D-40CB-8DBC-EF82C8B04DFD@cgl.ucsf.edu> Dear Christian, If you use "select" instead of "cofr" does the command select the atom? I.e., command: select #3:700.A at N10 If it does not, there is something wrong with your specification. If it does, but the cofr command still doesn't work to put the center of rotation there, I have no idea about what could be happening. Your command seems correct. You could use menu: Help... Report a Bug, include short description with the cofr command that you tried and also attach your PDB file or a Chimera session file (because we can't fix a bug unless we can reproduce it). Also include your email address to get feedback about what happens with your bug report. 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 Oct 4, 2013, at 1:29 AM, Christian Martinoli wrote: > Dear Elaine, > still, also with your suggestions, I could not overcome the problem. > Since I need to write a script, I need to use just command lines not the graphic interface (where the pivot selection is working). Using cofr i expected that the selected atom would have taken as pivot of the entire molecule, which in my case is not. > this is the exact line I 'm using. > > cofr #3:700.A at N10 > > the syntax seems correct but still the actual center of rotation is somewhere else > > any idea about? > thankyou, > Christian From pett at cgl.ucsf.edu Sun Oct 6 10:25:15 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Sun, 6 Oct 2013 10:25:15 -0700 Subject: [Chimera-users] Structural Allignment in Chimera In-Reply-To: <09F16633-9BE9-4E81-A919-AC508B9F2DE0@cgl.ucsf.edu> References: <1380878782.80105.YahooMailNeo@web120901.mail.ne1.yahoo.com> <09F16633-9BE9-4E81-A919-AC508B9F2DE0@cgl.ucsf.edu> Message-ID: Specifically, the matching code is in /share/chimera/match.py. (On a Mac, "" would be Chimera.app/Contents/Resources.) --Eric Eric Pettersen UCSF Computer Graphics Lab On Oct 4, 2013, at 9:17 AM, Elaine Meng wrote: > Hello, > The source is included in the Chimera download, and the methods are described in the documentation; see here and follow the links from this page for further details: > > > If the methods are suitable for your work, you could just use Chimera to do the alignments and RMSD calculations. > > > However, maybe you are supposed to write your own code for some homework project. In that case, there may be more direct, basic information available on the Web (rather than digging into Chimera code). > 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 Oct 4, 2013, at 2:26 AM, Syeda Hira Batool wrote: > >> Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. >> Hira Batool >> Student of BS-Bioinformatics >> Biosciences Department >> COMSATS Institute of Information Technology >> Islamabad, PAKISTAN > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From ashok9869 at gmail.com Mon Oct 7 14:38:07 2013 From: ashok9869 at gmail.com (ashok rout) Date: Mon, 7 Oct 2013 14:38:07 -0700 Subject: [Chimera-users] want to converge 20 pdb files of a trimer Message-ID: Hi, I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer. Can you please assist me how to do this?? Thanks, Ashok -- thanks & regards, Ashok -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Oct 7 15:21:55 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 7 Oct 2013 15:21:55 -0700 Subject: [Chimera-users] want to converge 20 pdb files of a trimer In-Reply-To: References: Message-ID: <15C1E5E3-4472-4756-85E7-82EBFDE536A4@cgl.ucsf.edu> Hi Ashok, Not sure exactly what you mean by "converge" ... (A) If you mean to superimpose (to put on top of each other), you would probably want to use either MatchMaker or the command "match." The different methods for superimposing structures are described in this page and its links: With the "match" command you specify exactly which residues/atoms to use in the match. You would have to use it 19 times with the same single structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3, ...) Matchmaker only uses CA atoms and doesn't require specifying which residues to use, but optionally you can restrict it to use only a certain section with the "Further restrict matching to current selection" option. You can choose one structure as reference and the other 19 as structures to match. (B) If you mean to calculate an average, you can do that with the MD Movie tool, after opening the NMR file as a trajectory: 1. download the NMR structure PDB file to some location on your computer that you will be able to find later 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis) 3. choose to open "PDB, single file" and browse to open the NMR structure file 4. from the MD Movie menu, choose "Analysis... Average Structure" Be aware this is a simple Cartesian coordinate average and the result may be distorted. I don't think you can average just some part. Just average the whole thing and then you can delete the parts you don't want later. 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 Oct 7, 2013, at 2:38 PM, ashok rout wrote: > Hi, > I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer. > Can you please assist me how to do this?? > Thanks, > Ashok From ashok9869 at gmail.com Mon Oct 7 15:57:13 2013 From: ashok9869 at gmail.com (ashok rout) Date: Mon, 7 Oct 2013 15:57:13 -0700 Subject: [Chimera-users] want to converge 20 pdb files of a trimer In-Reply-To: <15C1E5E3-4472-4756-85E7-82EBFDE536A4@cgl.ucsf.edu> References: <15C1E5E3-4472-4756-85E7-82EBFDE536A4@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks for your reply. I am able to superimpose 2 pbd files by using command "match #0:379,400 #1:379,400", where #0 and #1 are 1st and 2nd pdb files. 379, 400 means I want to superimpose residues from 379 to 400. After that I have problem (error: an even number of space-separated atom specs are required) when I am trying to superimpose 3 pdb files using command "match #0:379,400 #1:379,400 #2:379,400". I am clearly writing you: I have 20 pdb files of the trimer. e.g 1.pdb, 2.pdb, 3.pdb .... 20.pdb Residues in the pdb file is from 369-410. I want to superimpose residues from 379-400. So what exactly the commands and steps. Thanks, Ashok On Mon, Oct 7, 2013 at 3:21 PM, Elaine Meng wrote: > Hi Ashok, > Not sure exactly what you mean by "converge" ... > > (A) If you mean to superimpose (to put on top of each other), you would > probably want to use either MatchMaker or the command "match." The > different methods for superimposing structures are described in this page > and its links: > > > With the "match" command you specify exactly which residues/atoms to use > in the match. You would have to use it 19 times with the same single > structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3, > ...) > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic > > > > Matchmaker only uses CA atoms and doesn't require specifying which > residues to use, but optionally you can restrict it to use only a certain > section with the "Further restrict matching to current selection" option. > You can choose one structure as reference and the other 19 as structures > to match. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html > > > > (B) If you mean to calculate an average, you can do that with the MD Movie > tool, after opening the NMR file as a trajectory: > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html > > > > 1. download the NMR structure PDB file to some location on your computer > that you will be able to find later > 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis) > 3. choose to open "PDB, single file" and browse to open the NMR structure > file > 4. from the MD Movie menu, choose "Analysis... Average Structure" > > Be aware this is a simple Cartesian coordinate average and the result may > be distorted. I don't think you can average just some part. Just average > the whole thing and then you can delete the parts you don't want later. > > 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 Oct 7, 2013, at 2:38 PM, ashok rout wrote: > > > Hi, > > I have a nmr structure of a protein which is a trimer. I want to > converge 20 pdb files of the trimer, by Chimera. And also want to converge > a specific region of the 20 pdb files of the trimer. > > Can you please assist me how to do this?? > > Thanks, > > Ashok > > -- thanks & regards, Ashok -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Oct 7 16:08:10 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 7 Oct 2013 16:08:10 -0700 Subject: [Chimera-users] want to converge 20 pdb files of a trimer In-Reply-To: References: <15C1E5E3-4472-4756-85E7-82EBFDE536A4@cgl.ucsf.edu> Message-ID: <7DE72FF7-D7B2-40E3-8233-26B5EA4244C6@cgl.ucsf.edu> Hi Ashok, As I said, you have to use the match command 19 times because it will only make a pairwise match. You have to decide which one you want to use as the reference and then match each of the other 19 to the reference in a separate match command. Also, your first command is wrong, should contain "-" instead of "," to use all the residues from 379 to 400 (instead of only two residues, 379 and 400). For example, if you want to make #0 the reference: match #1:379-400 #0:379-400 match #2:379-400 #0:379-400 [ ... etc. 18 more times ...] The above is if you had each NMR structure in its own separate PDB file. Usually NMR structures in the PDB are all in one file. In that case, it would be something like: match #0.2:379-400 #0.1:379-400 match #0.3:379-400 #0.1:379-400 [ ... etc. 18 more times ...] Elaine > > On Oct 7, 2013, at 3:57 PM, ashok rout wrote: > Hi Elaine, > Thanks for your reply. I am able to superimpose 2 pbd files by using command "match #0:379,400 #1:379,400", where #0 and #1 are 1st and 2nd pdb files. 379, 400 means I want to superimpose residues from 379 to 400. > After that I have problem (error: an even number of space-separated atom specs are required) when I am trying to superimpose 3 pdb files using command "match #0:379,400 #1:379,400 #2:379,400". > > I am clearly writing you: > I have 20 pdb files of the trimer. e.g 1.pdb, 2.pdb, 3.pdb .... 20.pdb > Residues in the pdb file is from 369-410. I want to superimpose residues from 379-400. > So what exactly the commands and steps. > Thanks, > Ashok > > > On Mon, Oct 7, 2013 at 3:21 PM, Elaine Meng wrote: > Hi Ashok, > Not sure exactly what you mean by "converge" ... > > (A) If you mean to superimpose (to put on top of each other), you would probably want to use either MatchMaker or the command "match." The different methods for superimposing structures are described in this page and its links: > > > With the "match" command you specify exactly which residues/atoms to use in the match. You would have to use it 19 times with the same single structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3, ...) > > > > Matchmaker only uses CA atoms and doesn't require specifying which residues to use, but optionally you can restrict it to use only a certain section with the "Further restrict matching to current selection" option. You can choose one structure as reference and the other 19 as structures to match. > > > (B) If you mean to calculate an average, you can do that with the MD Movie tool, after opening the NMR file as a trajectory: > > > 1. download the NMR structure PDB file to some location on your computer that you will be able to find later > 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis) > 3. choose to open "PDB, single file" and browse to open the NMR structure file > 4. from the MD Movie menu, choose "Analysis... Average Structure" > > Be aware this is a simple Cartesian coordinate average and the result may be distorted. I don't think you can average just some part. Just average the whole thing and then you can delete the parts you don't want later. > > 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 Oct 7, 2013, at 2:38 PM, ashok rout wrote: > > > Hi, > > I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer. > > Can you please assist me how to do this?? > > Thanks, > > Ashok > > > > > -- > thanks & regards, > Ashok > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From ashok9869 at gmail.com Mon Oct 7 17:16:23 2013 From: ashok9869 at gmail.com (ashok rout) Date: Mon, 7 Oct 2013 17:16:23 -0700 Subject: [Chimera-users] want to converge 20 pdb files of a trimer In-Reply-To: <7DE72FF7-D7B2-40E3-8233-26B5EA4244C6@cgl.ucsf.edu> References: <15C1E5E3-4472-4756-85E7-82EBFDE536A4@cgl.ucsf.edu> <7DE72FF7-D7B2-40E3-8233-26B5EA4244C6@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks a lot. Now it is working. Regards, Ashok On Mon, Oct 7, 2013 at 4:08 PM, Elaine Meng wrote: > Hi Ashok, > As I said, you have to use the match command 19 times because it will only > make a pairwise match. You have to decide which one you want to use as the > reference and then match each of the other 19 to the reference in a > separate match command. > > Also, your first command is wrong, should contain "-" instead of "," to > use all the residues from 379 to 400 (instead of only two residues, 379 and > 400). For example, if you want to make #0 the reference: > > match #1:379-400 #0:379-400 > match #2:379-400 #0:379-400 > [ ... etc. 18 more times ...] > > The above is if you had each NMR structure in its own separate PDB file. > Usually NMR structures in the PDB are all in one file. In that case, it > would be something like: > > match #0.2:379-400 #0.1:379-400 > match #0.3:379-400 #0.1:379-400 > [ ... etc. 18 more times ...] > > Elaine > > > > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic > > > > On Oct 7, 2013, at 3:57 PM, ashok rout wrote: > > > Hi Elaine, > > Thanks for your reply. I am able to superimpose 2 pbd files by using > command "match #0:379,400 #1:379,400", where #0 and #1 are 1st and 2nd pdb > files. 379, 400 means I want to superimpose residues from 379 to 400. > > After that I have problem (error: an even number of space-separated > atom specs are required) when I am trying to superimpose 3 pdb files using > command "match #0:379,400 #1:379,400 #2:379,400". > > > > I am clearly writing you: > > I have 20 pdb files of the trimer. e.g 1.pdb, 2.pdb, 3.pdb .... 20.pdb > > Residues in the pdb file is from 369-410. I want to superimpose residues > from 379-400. > > So what exactly the commands and steps. > > Thanks, > > Ashok > > > > > > On Mon, Oct 7, 2013 at 3:21 PM, Elaine Meng wrote: > > Hi Ashok, > > Not sure exactly what you mean by "converge" ... > > > > (A) If you mean to superimpose (to put on top of each other), you would > probably want to use either MatchMaker or the command "match." The > different methods for superimposing structures are described in this page > and its links: > > > > > > With the "match" command you specify exactly which residues/atoms to use > in the match. You would have to use it 19 times with the same single > structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3, > ...) > > > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic > > > > > > Matchmaker only uses CA atoms and doesn't require specifying which > residues to use, but optionally you can restrict it to use only a certain > section with the "Further restrict matching to current selection" option. > You can choose one structure as reference and the other 19 as structures > to match. > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html > > > > > > (B) If you mean to calculate an average, you can do that with the MD > Movie tool, after opening the NMR file as a trajectory: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html > > > > > > 1. download the NMR structure PDB file to some location on your computer > that you will be able to find later > > 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis) > > 3. choose to open "PDB, single file" and browse to open the NMR > structure file > > 4. from the MD Movie menu, choose "Analysis... Average Structure" > > > > Be aware this is a simple Cartesian coordinate average and the result > may be distorted. I don't think you can average just some part. Just > average the whole thing and then you can delete the parts you don't want > later. > > > > 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 Oct 7, 2013, at 2:38 PM, ashok rout wrote: > > > > > Hi, > > > I have a nmr structure of a protein which is a trimer. I want to > converge 20 pdb files of the trimer, by Chimera. And also want to converge > a specific region of the 20 pdb files of the trimer. > > > Can you please assist me how to do this?? > > > Thanks, > > > Ashok > > > > > > > > > > -- > > thanks & regards, > > Ashok > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- thanks & regards, Ashok -------------- next part -------------- An HTML attachment was scrubbed... URL: From ad2720 at columbia.edu Tue Oct 8 11:37:38 2013 From: ad2720 at columbia.edu (Amedee des Georges) Date: Tue, 8 Oct 2013 14:37:38 -0400 Subject: [Chimera-users] Packaging sessions Message-ID: Dear Chimera, Currently, Session saves don't save volume data, only link to them, which is an issue whenever one of those links is broken or when one wants to send a whole session to someone else. Would it be possible to have an additional saving option that could be called "Package session" (like in InDesign), where a folder is created and all the files associated to the session saved in it. This way, people could zip and send the package by email, or package their important sessions to make sure not to lose them, or just to move them around. By advance, many thanks, Amedee -- Amedee des Georges Frank lab Howard Hughes Medical Institute Dept. of Biochemistry and Molecular Biophysics 650 W 168th St, P&S Black Building room 221 New York, NY 10032 (T) 212 305-9527 (F) 212 305-9500 (E) ad2720 at columbia.edu http://franklab.cpmc.columbia.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Oct 8 18:27:19 2013 From: goddard at sonic.net (Tom Goddard) Date: Tue, 8 Oct 2013 18:27:19 -0700 Subject: [Chimera-users] Packaging sessions In-Reply-To: References: Message-ID: Hi Amedee, I agree that would be helpful for sharing Chimera sessions. I've made a feature request entry in our database for it. Another related solution to the same problem that I've thought about implementing for years is to have an option to embed all the density maps within the session file so the session is self-contained. I think your suggestions of putting the session and copying map files in the same directory is better in ways, since then the person receiving the data can easily open the individual map data sets if they choose to. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12426 http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763 Tom On Oct 8, 2013, at 11:37 AM, Amedee des Georges wrote: > Dear Chimera, > > Currently, Session saves don't save volume data, only link to them, which is an issue whenever one of those links is broken or when one wants to send a whole session to someone else. > > Would it be possible to have an additional saving option that could be called "Package session" (like in InDesign), where a folder is created and all the files associated to the session saved in it. > > This way, people could zip and send the package by email, or package their important sessions to make sure not to lose them, or just to move them around. > > By advance, many thanks, > > Amedee > > -- > Amedee des Georges > Frank lab > Howard Hughes Medical Institute > Dept. of Biochemistry and Molecular Biophysics > 650 W 168th St, P&S Black Building room 221 > New York, NY 10032 > http://franklab.cpmc.columbia.edu > > > > _______________________________________________ > 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 gregc at cgl.ucsf.edu Wed Oct 9 14:16:17 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 09 Oct 2013 14:16:17 -0700 Subject: [Chimera-users] font size in pull-down menus In-Reply-To: References: Message-ID: <5255C7A1.3000904@cgl.ucsf.edu> Hello everyone, Just wanted to let everyone know that in the Chimera daily builds since the end of June, the font sizes in the GUI should match the system's font sizes in most cases. So you should be able to use your system's mechanism for changing the default font size, and Chimera should pick that up. In particular, this helps Linux users, but it should help users on other platforms too. -- Greg On 01/24/2011 05:56 AM, Boaz Shaanan wrote: > Hi, > > Is there a way to change the font size of the pull-down menus? For > some reason on the Windows (XP) v.1.5.1 they seem smaller to me. > Nothing in terms of graphics (or my eyesight) has changed since I > upgraded to 1.5.1 recently. > > Thanks, > > Boaz > > Thanks, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > Phone: 972-8-647-2220 ; Fax: 646-1710 > Skype: boaz.shaanan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From psu4 at uic.edu Thu Oct 10 17:41:14 2013 From: psu4 at uic.edu (psu4 at uic.edu) Date: Thu, 10 Oct 2013 19:41:14 -0500 Subject: [Chimera-users] Chimera commands to record MD movies In-Reply-To: References: Message-ID: Dear Elaine and Eric, Really appreciate your kind help! Sorry for the late reply. We were busy on the other project. Our volunteer Kevin modified Eric's python script. Then we execute the remote headless Chimera by the command "chimera", and "open recoding_movie_kevin.py" *The following error message will pop out* : > open /work/02444/drugsu/recoding_movie_kevin.py Executing /work/02444/drugsu/recoding_movie_kevin.py... Reading Amber prmtop Done reading Amber prmtop Creating interface Creating bonds Bonds created Assigning chain ID A to 259 residues, e.g. GLY Model 2 (AAA_with_AAA_91_12A_prod_v0_l1.mdcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Computing secondary structure assignments... Computed secondary structure assignments (see reply log) Interface created Traceback (most recent call last): File "/work/02444/drugsu/chimera_headless/share/ReadStdin/__init__.py", line 79, in _runCommand chimera.runCommand(cmd) File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand makeCommand(*args, **kw) File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1570, in doOpen modelArg, noprefs) File "", line 1, in File "/work/02444/drugsu/chimera_headless/share/Midas/__init__.py", line 2090, in open noprefs=noprefs) File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1817, in open models = func(filename, *args, **kw) File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1196, in _openPython loadFunc(sandboxName, fileName, f) File "recoding_movie_kevin.py", line 39, in runCommand('preset apply pub 1') File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand makeCommand(*args, **kw) File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1676, in doPreset mgr.applyPreset(type, vals[1]) File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 107, in applyPreset func() File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 36, in lambda:preset(publication=True, depthCued=False), False) File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()): AttributeError: 'module' object has no attribute 'update' AttributeError: 'module' object has no attribute 'update' File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()): See reply log for Python traceback. If we use the GUI chimera and open this script, it will work properly. We have searched the mailing list but didn't see similar error messages. If not too much asking, could you kindly offer some solutions? Please forgive any ignorance, if any. Cheers, Pin-Chih On Wed, Sep 18, 2013 at 4:23 PM, Eric Pettersen wrote: > On Sep 18, 2013, at 12:11 PM, psu4 at uic.edu wrote: > > > Dear Chimera, > > > > Since we run a lot of Amber MD simulation in remote clusters, we > wonder if there is any Chimera command that can record the Amber MD > trajectories remotely and save them as avi (or any other movie file > formats)? If this is feasible, then we don't have to download all the > trajectories to local and make the trajectory movies manually. We have > searched the Chimera user manual but didn't see any command. If there are > related commands which we didn't see, please forgive us : ) Thanks. > > > > * There is a way to activate X11 forwarding and use remote Chimera > GUI to do this, but it's extremely slow and prone to freeze the computer. > > Hi Henry, > The trick is to get the trajectory loaded without using the > graphical user interface. When dinosaurs roamed the earth and the MD Movie > tool was being designed, we didn't recognize the importance of providing > command-line versions of all important functions and therefore the MD Movie > is very much unfriendly to non-GUI usage like what you are trying to do. > Nonetheless, in Python almost anything is possible and indeed non-GUI > loading of trajectories is possible using a short Python script. I've > attached such a script. You would need to edit the second line of the > script to specify where the topology and coordinate files are. Then you > can run it simply by opening it with the "open"command. > The other trick is that you will need to get the "headless" > version of Chimera from the download page in order to be able to save > images/movies without using the GUI. > Let me know if you run into any problems. > > --Eric > > > -- Pin-Chih Su (Henry Su) Ph.D. canditate Center for Pharmaceutical Biotechnology (MC 870) College of Pharmacy, University of Illinois at Chicago 900 South Ashland Avenue, Room 1052 Chicago, IL 60607-7173 office 312-996-5388 fax 312-413-9303 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: recording_movie_kevin.py Type: application/octet-stream Size: 2846 bytes Desc: not available URL: From pett at cgl.ucsf.edu Fri Oct 11 11:10:05 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 11 Oct 2013 11:10:05 -0700 Subject: [Chimera-users] Chimera commands to record MD movies In-Reply-To: References: Message-ID: Hi Pin-Chih, You should really report bugs to chimera-bugs instead of chimera-users. I will open a ticket for this problem in our bug-tracking database so you'll know when a fix gets done (and will show up in the next daily build). That said, I'm pretty sure the fix is for you to edit the file /work/02444/drugsu/chimera_headless/share/chimera/preset.py and just above line 183 (which should start with "with nested(NA?") put "import chimera.update" with the same indentation that the "with nested(NA?" line has. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 10, 2013, at 5:41 PM, psu4 at uic.edu wrote: > Dear Elaine and Eric, > > Really appreciate your kind help! Sorry for the late reply. We were busy on the other project. > > Our volunteer Kevin modified Eric's python script. Then we execute the remote headless Chimera by the command "chimera", and "open recoding_movie_kevin.py" > > The following error message will pop out : > > > open /work/02444/drugsu/recoding_movie_kevin.py > Executing /work/02444/drugsu/recoding_movie_kevin.py... > Reading Amber prmtop > Done reading Amber prmtop > Creating interface > Creating bonds > Bonds created > Assigning chain ID A to 259 residues, e.g. GLY > Model 2 (AAA_with_AAA_91_12A_prod_v0_l1.mdcrd) appears to be a protein without secondary structure assignments. > Automatically computing assignments using 'ksdssp' and parameter values: > energy cutoff -0.5 > minimum helix length 3 > minimum strand length 3 > Use command 'help ksdssp' for more information. > > Computing secondary structure assignments... > Computed secondary structure assignments (see reply log) > Interface created > > Traceback (most recent call last): > File "/work/02444/drugsu/chimera_headless/share/ReadStdin/__init__.py", line 79, in _runCommand > chimera.runCommand(cmd) > File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand > makeCommand(*args, **kw) > File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand > f(c, args) > File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1570, in doOpen > modelArg, noprefs) > File "", line 1, in > File "/work/02444/drugsu/chimera_headless/share/Midas/__init__.py", line 2090, in open > noprefs=noprefs) > File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1817, in open > models = func(filename, *args, **kw) > File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1196, in _openPython > loadFunc(sandboxName, fileName, f) > File "recoding_movie_kevin.py", line 39, in > runCommand('preset apply pub 1') > File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand > makeCommand(*args, **kw) > File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand > f(c, args) > File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1676, in doPreset > mgr.applyPreset(type, vals[1]) > File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 107, in applyPreset > func() > File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 36, in > lambda:preset(publication=True, depthCued=False), False) > File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset > with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()): > AttributeError: 'module' object has no attribute 'update' > > AttributeError: 'module' object has no attribute 'update' > > File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset > with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()): > > See reply log for Python traceback. > > If we use the GUI chimera and open this script, it will work properly. We have searched the mailing list but didn't see similar error messages. If not too much asking, could you kindly offer some solutions? Please forgive any ignorance, if any. > > Cheers, > Pin-Chih > > > On Wed, Sep 18, 2013 at 4:23 PM, Eric Pettersen wrote: > On Sep 18, 2013, at 12:11 PM, psu4 at uic.edu wrote: > > > Dear Chimera, > > > > Since we run a lot of Amber MD simulation in remote clusters, we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)? If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually. We have searched the Chimera user manual but didn't see any command. If there are related commands which we didn't see, please forgive us : ) Thanks. > > > > * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer. > > Hi Henry, > The trick is to get the trajectory loaded without using the graphical user interface. When dinosaurs roamed the earth and the MD Movie tool was being designed, we didn't recognize the importance of providing command-line versions of all important functions and therefore the MD Movie is very much unfriendly to non-GUI usage like what you are trying to do. Nonetheless, in Python almost anything is possible and indeed non-GUI loading of trajectories is possible using a short Python script. I've attached such a script. You would need to edit the second line of the script to specify where the topology and coordinate files are. Then you can run it simply by opening it with the "open"command. > The other trick is that you will need to get the "headless" version of Chimera from the download page in order to be able to save images/movies without using the GUI. > Let me know if you run into any problems. > > --Eric > > > > > > -- > > Pin-Chih Su (Henry Su) > > Ph.D. canditate > > Center for Pharmaceutical Biotechnology (MC 870) > > College of Pharmacy, University of Illinois at Chicago > > 900 South Ashland Avenue, Room 1052 > > Chicago, IL 60607-7173 > > office 312-996-5388 > > fax 312-413-9303 > > _______________________________________________ > 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 jack52577 at gmail.com Sun Oct 13 19:21:20 2013 From: jack52577 at gmail.com (Chao Wang) Date: Sun, 13 Oct 2013 22:21:20 -0400 Subject: [Chimera-users] Fwd: setting or hardware problem? In-Reply-To: References: Message-ID: Hi, chimera users I am starting to use ucsf chimera to analysis protein structure recently. It is an excellent software, and I have no problem using it at school. But when I try to use it on my other pc at home. It doesn't work properly. The ribbon looks flat and dull, not a 3D looking anymore, like the situation showed in pic1 and pic2. My hardwares: School PC: win7 64 bit,cpu E5-1606, Nvidia Quadro 5000, 4G Home PC: win7 64 bit, cpu i5-2500k, AMD Radeon HD6700, 8G I know the video card of school's pc is much better, but I checked the hardware list. HD6700 is also compatible. Can anyone tell me what is wrong? I really appreciate it. [image: Inline image 1] [image: Inline image 1] Jack Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pic2.jpg Type: image/jpeg Size: 1197973 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pic1.jpg Type: image/jpeg Size: 680648 bytes Desc: not available URL: From gregc at cgl.ucsf.edu Mon Oct 14 08:41:45 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 14 Oct 2013 08:41:45 -0700 Subject: [Chimera-users] Fwd: setting or hardware problem? In-Reply-To: References: Message-ID: <11eca2bff84ff44e838ed78b46f8e443.squirrel@plato-mail.cgl.ucsf.edu> Hi Jack, There is a problem with the current AMD graphics drivers, Catalyst 13.9 beta, and chimera. You need to downgrade to Catalyst 13.1 for Chimera to work properly. Usually, bugs like this are fixed by the vendor in the next release, but AMD has made several releases with this same bug, so please file a bug report with AMD to increase the chances that it will be fixed. -- Greg > Hi, chimera users > > I am starting to use ucsf chimera to analysis protein structure recently. > It is an excellent software, and I have no problem using it at school. But > when I try to use it on my other pc at home. It doesn't work properly. The > ribbon looks flat and dull, not a 3D looking anymore, like the situation > showed in pic1 and pic2. > My hardwares: > School PC: win7 64 bit,cpu E5-1606, Nvidia Quadro 5000, 4G > Home PC: win7 64 bit, cpu i5-2500k, AMD Radeon HD6700, 8G > I know the video card of school's pc is much better, but I checked the > hardware list. HD6700 is also compatible. > Can anyone tell me what is wrong? I really appreciate it. > [image: Inline image 1] [image: Inline image 1] > > > > Jack Wang > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From edward_elchamy at hotmail.com Sun Oct 13 15:32:30 2013 From: edward_elchamy at hotmail.com (edward el chamy) Date: Mon, 14 Oct 2013 00:32:30 +0200 Subject: [Chimera-users] (no subject) Message-ID: Hey i am a student using chimera 1.8 i have a question: how we find on a specific chain the different interaction domains? Thanks a lot -------------- next part -------------- An HTML attachment was scrubbed... URL: From apande at albany.edu Mon Oct 14 14:10:53 2013 From: apande at albany.edu (Pande, Ajay K) Date: Mon, 14 Oct 2013 21:10:53 +0000 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Message-ID: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 15 16:29:20 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 15 Oct 2013 16:29:20 -0700 Subject: [Chimera-users] finding interaction domains In-Reply-To: References: Message-ID: <4C71000E-85C2-4EE8-9BD0-2FCE9DB7C6C5@cgl.ucsf.edu> Hi Edward, I'm not sure exactly what you mean. If you mean you have a structure in which one chain is interacting with another and you want to find which atoms are interacting, you could use the Find Contacts/Clashes tool (in menu under Tools? Structure Analysis) or the "findclash" command: There are examples of using findclash in tutorials: (1) Opened Interface image tutorial, the command is used in the "Background and Setup" section (2) Structure Analysis and Comparison tutorial, the tool is used in the "Distances, H-Bonds, Contacts" section If you mean that some chain of your structure has different domains and you just want to see which parts of the chain are which domains, you may need to look up that information outside of Chimera. If the protein is annotated with domains in UniProt, there is a convenient way in Chimera: (a) start PDB/Uniprot Info (in Chimera menu under Tools? Sequence) and choose the chain of interest. Two additional windows should appear, the sequence of the chain and the Region Browser listing annotations of the chain. (b) In the Region Browser, scroll to find the domain annotation of interest, check its Shown box to show it as a colored box on the sequence (b) In the sequence window, click on the colored box to select all the corresponding residues in the structure If UniProt doesn't have domain annotations for that protein, however, you may need to look in some other resource outside of Chimera. For example, you could search for the structure in the SCOP database and then manually enter residue ranges in the Chimera command line to color or select that part of the structure. I hope this helps. If I answered something different than you were asking, you need to provide more information in your question. 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 Oct 13, 2013, at 3:32 PM, edward el chamy wrote: > Hey > i am a student using chimera 1.8 > i have a question: how we find on a specific chain the different interaction domains? > Thanks a lot From pett at cgl.ucsf.edu Tue Oct 15 16:48:01 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 15 Oct 2013 16:48:01 -0700 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> Message-ID: On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: > How would I draw a normal to the plane of an aromatic ring, at its centroid? Hi Ajay, There's not a 100% direct way in Chimera, but what you can do is this: 1) Define the plane of the aromatic ring using the Axes/Planes/Centroids tool. 2) Use that tool's Save button to save the plane info to a file. The info will include the plane center and normal. 3) Create a "BILD"-format file defining an arrow (BILD format here: BILD format). The start of the arrow would be at the center of the plane and the end (arrowhead) at the center plus some multiple of the normal. Since the normal is of length 1, maybe two or three times the normal would look okay. Also, the parameter that determines the width of the arrowhead should probably be reduced from the default value (4 times the arrow width) unless you make the arrow length considerably longer. Anyway, an example: .arrow 16.692 32.583 17.432 16.583 31.740 17.959 0.1 0.2 which shows a normal to the aromatic six-member ring of the ligand in PDB 121P. The plane info was: Planes plane name, center, normal, radius plane: ( 16.692, 32.583, 17.432) (-0.109, -0.843, 0.527) 1.446 3) Open the BILD file with the "open" or the File-Open menu item. Make sure the file name ends with ".bild". If the structure is the only other open model (or has the lowest model number), the arrow will be oriented correctly relative to the structure. Otherwise, you will either have to use an open command that also specifies that you want the BILD opened in the same model number as the structure (e.g. "open 5 myarrow.bild") or use the "transform as" button in the Model Panel to make the arrow have the same transformation matrix as the structure (which can also be accomplished with the matrixcopy command). --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 Oct 15 16:50:21 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 15 Oct 2013 16:50:21 -0700 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> Message-ID: On Oct 15, 2013, at 4:48 PM, Eric Pettersen wrote: > Open the BILD file with the "open" or ?with the "open" command or? --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Oct 15 17:09:44 2013 From: goddard at sonic.net (Tom Goddard) Date: Tue, 15 Oct 2013 17:09:44 -0700 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com> Message-ID: Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: > How would I draw a normal to the plane of an aromatic ring, at its centroid? > > Thanks > > Ajay Pande > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1a0m_ring_axis.jpg Type: image/jpg Size: 76334 bytes Desc: not available URL: From goddard at sonic.net Wed Oct 16 10:03:29 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 16 Oct 2013 10:03:29 -0700 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: <709c6acfefba4549b0833f520a1ed225@BN1PR04MB294.namprd04.prod.outlook.com> References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com>, <709c6acfefba4549b0833f520a1ed225@BN1PR04MB294.namprd04.prod.outlook.com> Message-ID: Hi Ajay, The example commands were if your molecule was model #0 and the two inertia ellipsoids were #1 and #2. But I see that if your molecule was #1 and the ellipsoids were #2 and #3 it still works but gives a fat long axis cylinder! You don't end up even using the second ellipsoid. The axis comes out fat and long because its size is based on the first model in the "measure rotation #1 #2" comand and that was your molecule model, instead of the much smaller ellipsoid model. As mentioned in the documentation on measure rotation it makes the axis length equal the size of the first model and the axis diameter equal 5% of that size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation Now that you've discovered the second ellipsoid is not needed the axis can be made with measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #2 #1 color pink where we assume #1 is your molecule model and #2 is the inertia ellipsoid model. Substitute the correct model numbers for your case by checking the numbers in Model Panel (Favorites menu). And here's a better explanation of this bit of trickery. Measure inertia shows an ellipsoid surface that matches the inertia of the selected ring atoms and that surface is a new model. Then the turn command rotates the ellipsoid about the axis perpendicular to the ring with center being the center of the ellipsoid, and it rotates only the ellipsoid, not the molecule, and the axis is specified in the coordinate system of the ellipsoid, and we rotate 90 degrees (although an non-zero angle will work). Then the measure rotation command shows the rotation axis for one model that is rotated relative to another. Tom On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K" wrote: > Hi Tom, > > I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! > > But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. > > Thanks > > Ajay > > > From: Tom Goddard > Sent: Tuesday, October 15, 2013 8:09 PM > To: Pande, Ajay K > Cc: chimera-users at cgl.ucsf.edu List > Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid > > Hi Ajay, > > Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then > > measure inertia sel > > This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: > > measure inertia sel > turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 > measure rotation #1 #2 color pink > > In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! > > Tom > > > <1a0m_ring_axis.jpg> > > > On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: > >> How would I draw a normal to the plane of an aromatic ring, at its centroid? >> >> Thanks >> >> Ajay Pande >> _______________________________________________ >> 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 divjak.m at wehi.EDU.AU Wed Oct 16 00:04:15 2013 From: divjak.m at wehi.EDU.AU (Maja Divjak) Date: Wed, 16 Oct 2013 18:04:15 +1100 Subject: [Chimera-users] Create a protein model using Chimera? Message-ID: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> Hello Chimera, I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. I look forward to your reply! Thank you and best wishes, Dr Maja Divjak, WEHI, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ From apande at albany.edu Wed Oct 16 03:31:41 2013 From: apande at albany.edu (Pande, Ajay K) Date: Wed, 16 Oct 2013 10:31:41 +0000 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com>, Message-ID: <709c6acfefba4549b0833f520a1ed225@BN1PR04MB294.namprd04.prod.outlook.com> Hi Tom, I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. Thanks Ajay ________________________________ From: Tom Goddard Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom [cid:4366A083-E964-4CE7-A651-B1F68AA4A781 at cgl.ucsf.edu] On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1a0m_ring_axis.jpg Type: image/jpg Size: 76334 bytes Desc: 1a0m_ring_axis.jpg URL: From ltartaglia at ufl.edu Wed Oct 16 11:35:18 2013 From: ltartaglia at ufl.edu (Tartaglia,Lawrence J) Date: Wed, 16 Oct 2013 14:35:18 -0400 Subject: [Chimera-users] Cross-section question Message-ID: <0af8b453dbede6e1996246d964ec5741@ufl.edu> Hello, I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? Thanks! Best, Lawrence -- Lawrence J. Tartaglia, Ph.D. Postdoctoral Scientist Agbandje-McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine, University of Florida From apande at albany.edu Wed Oct 16 17:41:17 2013 From: apande at albany.edu (Pande, Ajay K) Date: Thu, 17 Oct 2013 00:41:17 +0000 Subject: [Chimera-users] Normal to the plane of the aromatic ring at the centroid In-Reply-To: References: <4d9bdbb0197f4dd085c1bb6486be3ce7@DM2PR04MB301.namprd04.prod.outlook.com>, <709c6acfefba4549b0833f520a1ed225@BN1PR04MB294.namprd04.prod.outlook.com>, Message-ID: <901dd01c918f4f72b8e76fbaecfeb0f6@DM2PR04MB301.namprd04.prod.outlook.com> Thank you very much. It worked beautifully!! Ajay ________________________________ From: Tom Goddard Sent: Wednesday, October 16, 2013 1:03 PM To: Pande, Ajay K Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, The example commands were if your molecule was model #0 and the two inertia ellipsoids were #1 and #2. But I see that if your molecule was #1 and the ellipsoids were #2 and #3 it still works but gives a fat long axis cylinder! You don't end up even using the second ellipsoid. The axis comes out fat and long because its size is based on the first model in the "measure rotation #1 #2" comand and that was your molecule model, instead of the much smaller ellipsoid model. As mentioned in the documentation on measure rotation it makes the axis length equal the size of the first model and the axis diameter equal 5% of that size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation Now that you've discovered the second ellipsoid is not needed the axis can be made with measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #2 #1 color pink where we assume #1 is your molecule model and #2 is the inertia ellipsoid model. Substitute the correct model numbers for your case by checking the numbers in Model Panel (Favorites menu). And here's a better explanation of this bit of trickery. Measure inertia shows an ellipsoid surface that matches the inertia of the selected ring atoms and that surface is a new model. Then the turn command rotates the ellipsoid about the axis perpendicular to the ring with center being the center of the ellipsoid, and it rotates only the ellipsoid, not the molecule, and the axis is specified in the coordinate system of the ellipsoid, and we rotate 90 degrees (although an non-zero angle will work). Then the measure rotation command shows the rotation axis for one model that is rotated relative to another. Tom On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K" wrote: Hi Tom, I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. Thanks Ajay ________________________________ From: Tom Goddard Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom <1a0m_ring_axis.jpg> On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande _______________________________________________ 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 Thu Oct 17 09:29:47 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Oct 2013 09:29:47 -0700 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> References: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> Message-ID: Dear Dr Maja Divjak, Sorry, Chimera does not do de novo modeling. Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins. I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling. I have not done it myself, so I don't have any specific recommendations. Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net : 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 Oct 16, 2013, at 12:04 AM, Maja Divjak wrote: > Hello Chimera, > > I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. > > I look forward to your reply! > > Thank you and best wishes, > > Dr Maja Divjak, > WEHI, Melbourne, Australia From meng at cgl.ucsf.edu Thu Oct 17 09:39:48 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Oct 2013 09:39:48 -0700 Subject: [Chimera-users] Cross-section question In-Reply-To: <0af8b453dbede6e1996246d964ec5741@ufl.edu> References: <0af8b453dbede6e1996246d964ec5741@ufl.edu> Message-ID: <6B228C20-096C-4F83-8BC5-4E8CE79D62A6@cgl.ucsf.edu> Hello Lawrence, You may want to use Per-Model Clipping (in menu under Tools? Depiction, or as command "mclip"): Just make sure to specify the model that is your cryoEM surface. Whereas the global clipping planes in the SIde View affect everything and are always perpendicular to the line of sight, you can interactively position a per-model clipping plane at any angle, and it only affects one model (although each model can have its own). You can also erase an octant with "vop ~octant" and erase all but that octant with "vop octant" 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 Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: > Hello, > > I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? > > Thanks! > > Best, > > Lawrence > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida From goddard at sonic.net Thu Oct 17 09:43:43 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 17 Oct 2013 09:43:43 -0700 Subject: [Chimera-users] Cross-section question In-Reply-To: <0af8b453dbede6e1996246d964ec5741@ufl.edu> References: <0af8b453dbede6e1996246d964ec5741@ufl.edu> Message-ID: <5D1FDE6C-3041-4A13-A847-45122A94A185@sonic.net> Hi Lawrence, I'm not sure what you mean by "exact cross-section". Do you mean aligned to the virus map grid axes? If so the Orient button at the bottom of the volume viewer dialog will do that. But probably it is better to simply specify which planes to show using the Region Bounds panel of the volume viewer dialog (Features menu) - specify a z range 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane). This will be better than using clip planes. Tom On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: > Hello, > > I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? > > Thanks! > > Best, > > Lawrence > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From divjak.m at wehi.EDU.AU Fri Oct 18 01:28:59 2013 From: divjak.m at wehi.EDU.AU (Maja Divjak) Date: Fri, 18 Oct 2013 19:28:59 +1100 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: References: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> Message-ID: Hi Elaine, Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. Thank you and best wishes, Maja On Oct 18, 2013, at 3:29 AM, Elaine Meng wrote: > Dear Dr Maja Divjak, > Sorry, Chimera does not do de novo modeling. Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins. > > > I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling. I have not done it myself, so I don't have any specific recommendations. Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net : > > 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 Oct 16, 2013, at 12:04 AM, Maja Divjak wrote: > >> Hello Chimera, >> >> I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. >> >> I look forward to your reply! >> >> Thank you and best wishes, >> >> Dr Maja Divjak, >> WEHI, Melbourne, Australia > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ From divjak.m at wehi.EDU.AU Fri Oct 18 02:26:32 2013 From: divjak.m at wehi.EDU.AU (Maja Divjak) Date: Fri, 18 Oct 2013 20:26:32 +1100 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: References: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> Message-ID: <477534FC-9505-40B8-BCF6-62AA56A77F31@wehi.edu.au> Hello again Elaine, And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte... I look forward to your reply, Thank you and best wishes, Maja On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote: > Hi Elaine, > > Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. > > Thank you and best wishes, > > Maja > > On Oct 18, 2013, at 3:29 AM, Elaine Meng wrote: > >> Dear Dr Maja Divjak, >> Sorry, Chimera does not do de novo modeling. Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins. >> >> >> I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling. I have not done it myself, so I don't have any specific recommendations. Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net : >> >> 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 Oct 16, 2013, at 12:04 AM, Maja Divjak wrote: >> >>> Hello Chimera, >>> >>> I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. >>> >>> I look forward to your reply! >>> >>> Thank you and best wishes, >>> >>> Dr Maja Divjak, >>> WEHI, Melbourne, Australia >> > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ From meng at cgl.ucsf.edu Fri Oct 18 10:02:11 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Oct 2013 10:02:11 -0700 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: <477534FC-9505-40B8-BCF6-62AA56A77F31@wehi.edu.au> References: <0FF15CD9-1735-47F8-8C68-BF5D4F7795A8@wehi.edu.au> <477534FC-9505-40B8-BCF6-62AA56A77F31@wehi.edu.au> Message-ID: <89393ECB-7957-4D2A-916B-072B9E32ADEA@cgl.ucsf.edu> Hello Maja, It depends if there are atoms of overlap between the two parts. If there are overlapping parts, for example one structure is residues 1-15 and the other is residues 12-500: you can position the structures relative to each other by superimposing just the overlapping atoms using the "match" command (for example, something like "match #0:12-15 at n,ca,c,o #1:12-15 at n,ca,c,o"). Note the numbering won't necessarily be the same in the two structures, so you need to check on exactly which residues should be superimposed. Then you would delete the overlapping atoms from one structure (since the "same" atoms are already in the other structure), combine the two structures into one model, and then add a bond between the two parts. This could all be done in Chimera (see commands "delete" "combine" "bond", or graphical interfaces for the latter two are Favorites...Model Panel "copy/combine" function and Tools...Structure Editing... Build Structure, Adjust Bonds tab), OR it could be done by manually text-editing PDB files, after the matching step described above and then saving one structure as PDB "relative to" the other structure. Documentation for commands, command-line atom specification, and Build Structure: If there are not overlapping parts, for example one structure is residues 1-15 and the other is residues 16-500, you would just use the Join Models tab in the Build Structure tool mentioned above: YOu can see there are fewer steps in the latter, but it can be hard to fully specify the correct geometry at the join. Thus when overlapping atoms in similar conformations are available, that more complicated overlapping procedure may produce better results than simply deleting the redundant atoms and using the second approach. 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 Oct 18, 2013, at 2:26 AM, Maja Divjak wrote: > Hello again Elaine, > > And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte... > > I look forward to your reply, > > Thank you and best wishes, > > Maja > > On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote: > >> Hi Elaine, >> >> Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. >> >> Thank you and best wishes, >> >> Maja From darrellh at niaid.nih.gov Fri Oct 18 10:28:02 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Fri, 18 Oct 2013 17:28:02 +0000 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: <89393ECB-7957-4D2A-916B-072B9E32ADEA@cgl.ucsf.edu> Message-ID: Hi Maja, At the risk of straying too much from the Chimera listserv,if you are willing to go outside of Chimera, there are some additional tools that you could try: (1) For the homology modeling, give the Protein Model Portal a try: http://www.proteinmodelportal.org (2) For the assembly of the complex, you can follow Elaine's excellent instructions below and then accommodate the overlapping portions using a "perturbation docking" server, such as the docking server at ROSIE: http://rosie.graylab.jhu.edu Hope that helps, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Elaine Meng > Reply-To: "chimera-users at cgl.ucsf.edu Mailing List" > Date: Friday, October 18, 2013 1:02 PM To: Maja Divjak > Cc: "chimera-users at cgl.ucsf.edu List" >, Maja Divjak > Subject: Re: [Chimera-users] Create a protein model using Chimera? Hello Maja, It depends if there are atoms of overlap between the two parts. If there are overlapping parts, for example one structure is residues 1-15 and the other is residues 12-500: you can position the structures relative to each other by superimposing just the overlapping atoms using the "match" command (for example, something like "match #0:12-15 at n,ca,c,o #1:12-15 at n,ca,c,o"). Note the numbering won't necessarily be the same in the two structures, so you need to check on exactly which residues should be superimposed. Then you would delete the overlapping atoms from one structure (since the "same" atoms are already in the other structure), combine the two structures into one model, and then add a bond between the two parts. This could all be done in Chimera (see commands "delete" "combine" "bond", or graphical interfaces for the latter two are Favorites...Model Panel "copy/combine" function and Tools...Structure Editing... Build Structure, Adjust Bonds tab), OR it could be done by manually text-editing PDB files, after the matching step descr! ibed above and then saving one structure as PDB "relative to" the other structure. Documentation for commands, command-line atom specification, and Build Structure: If there are not overlapping parts, for example one structure is residues 1-15 and the other is residues 16-500, you would just use the Join Models tab in the Build Structure tool mentioned above: YOu can see there are fewer steps in the latter, but it can be hard to fully specify the correct geometry at the join. Thus when overlapping atoms in similar conformations are available, that more complicated overlapping procedure may produce better results than simply deleting the redundant atoms and using the second approach. 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 Oct 18, 2013, at 2:26 AM, Maja Divjak wrote: Hello again Elaine, And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte... I look forward to your reply, Thank you and best wishes, Maja On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote: Hi Elaine, Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. Thank you and best wishes, Maja _______________________________________________ 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 Oct 18 11:06:58 2013 From: goddard at sonic.net (Tom Goddard) Date: Fri, 18 Oct 2013 11:06:58 -0700 Subject: [Chimera-users] Cross-section question In-Reply-To: References: <0af8b453dbede6e1996246d964ec5741@ufl.edu> <5D1FDE6C-3041-4A13-A847-45122A94A185@sonic.net> Message-ID: <7181366B-B7F9-4499-ACDC-432BEDDF4BE1@sonic.net> Hi Lawrence, Sure it is easy to see plane 72. Use the Volume Viewer dialog, show the planes panel (menu Features / Planes), press the "One" plane button in that panel and set the plane number entry field to 72. To assure you see the full resolution data make sure "Step" is set to 1 above the volume dialog density map histogram, and that "depth" is set to 1 in the Planes panel. This and other Chimera density map features are described in the Chimera guide to volume data display http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom On Oct 18, 2013, at 10:09 AM, "Tartaglia,Lawrence J" wrote: > Hi Tom, > > Thank you for getting back to me. I should have been a bit more clear. What I want is the exact "central" section. I'm not sure if you are familiar with cryo-electron microscopy? I used a box size of 143 pixels to box my virus particles. What I would like to see if image 72 (central section) of my reconstruction. Is there a way to do that? I've attached an image of an example central section (left hand side) using the program IMOD. I'm sorry for the confusion... > > Best, > > Lawrence > > > On Thu, 17 Oct 2013 09:43:43 -0700, Tom Goddard wrote: >> Hi Lawrence, >> >> I'm not sure what you mean by "exact cross-section". Do you mean >> aligned to the virus map grid axes? If so the Orient button at the >> bottom of the volume viewer dialog will do that. But probably it is >> better to simply specify which planes to show using the Region Bounds >> panel of the volume viewer dialog (Features menu) - specify a z range >> 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane). >> This will be better than using clip planes. >> >> Tom >> >> >> On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: >> >>> Hello, >>> >>> I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? >>> >>> Thanks! >>> >>> Best, >>> >>> Lawrence >>> -- >>> Lawrence J. Tartaglia, Ph.D. >>> Postdoctoral Scientist >>> Agbandje-McKenna Lab >>> Department of Biochemistry and Molecular Biology >>> College of Medicine, University of Florida >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida From meng at cgl.ucsf.edu Fri Oct 18 11:14:13 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Oct 2013 11:14:13 -0700 Subject: [Chimera-users] Cross-section question In-Reply-To: <7181366B-B7F9-4499-ACDC-432BEDDF4BE1@sonic.net> References: <0af8b453dbede6e1996246d964ec5741@ufl.edu> <5D1FDE6C-3041-4A13-A847-45122A94A185@sonic.net> <7181366B-B7F9-4499-ACDC-432BEDDF4BE1@sonic.net> Message-ID: <563EF033-7C21-4249-91C8-FCE2A5D1BBD5@cgl.ucsf.edu> On Oct 18, 2013, at 11:06 AM, Tom Goddard wrote: > This and other Chimera density map features are described in the Chimera guide to volume data display > http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html The Volume Viewer documentation also includes a section on Planes: Elaine From goddard at sonic.net Fri Oct 18 11:18:59 2013 From: goddard at sonic.net (Tom Goddard) Date: Fri, 18 Oct 2013 11:18:59 -0700 Subject: [Chimera-users] Cross-section question In-Reply-To: <563EF033-7C21-4249-91C8-FCE2A5D1BBD5@cgl.ucsf.edu> References: <0af8b453dbede6e1996246d964ec5741@ufl.edu> <5D1FDE6C-3041-4A13-A847-45122A94A185@sonic.net> <7181366B-B7F9-4499-ACDC-432BEDDF4BE1@sonic.net> <563EF033-7C21-4249-91C8-FCE2A5D1BBD5@cgl.ucsf.edu> Message-ID: Hi Elaine, Sorry I often reference the volume guide and am too lazy to also reference the user's guide page. Usually my reason for mentioning volume guide is to get the ignorant up to speed on the available features so they don't pester us, not to provide the in-depth knowledge where the User's Guide excels. Tom On Oct 18, 2013, at 11:14 AM, Elaine Meng wrote: > On Oct 18, 2013, at 11:06 AM, Tom Goddard wrote: > >> This and other Chimera density map features are described in the Chimera guide to volume data display >> http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html > > The Volume Viewer documentation also includes a section on Planes: > > > > > Elaine > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From divjak.m at wehi.EDU.AU Fri Oct 18 21:32:49 2013 From: divjak.m at wehi.EDU.AU (Maja Divjak) Date: Sat, 19 Oct 2013 15:32:49 +1100 Subject: [Chimera-users] Create a protein model using Chimera? In-Reply-To: References: Message-ID: <93E29F16-43A9-419F-AB9F-0D3349EAA8B8@wehi.edu.au> Hello Elaine and Darrell, Thank you both so much for your help, I have managed to join the two molecules together using build, join models to give a convincing structure. Now I just need to get it out as a PDB that Maya can read. Problems every step of the way. Grrrr! You're both brilliant! Have a great weekend, Maja On Oct 19, 2013, at 4:28 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Maja, > > At the risk of straying too much from the Chimera listserv,if you are willing to go outside of Chimera, there are some additional tools that you could try: > > (1) For the homology modeling, give the Protein Model Portal a try: > http://www.proteinmodelportal.org > > (2) For the assembly of the complex, you can follow Elaine's excellent instructions below and then accommodate the overlapping portions using a "perturbation docking" server, such as the docking server at ROSIE: > http://rosie.graylab.jhu.edu > > Hope that helps, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: Elaine Meng > > Reply-To: "chimera-users at cgl.ucsf.edu Mailing List" > > Date: Friday, October 18, 2013 1:02 PM > To: Maja Divjak > > Cc: "chimera-users at cgl.ucsf.edu List" >, Maja Divjak > > Subject: Re: [Chimera-users] Create a protein model using Chimera? > > Hello Maja, > It depends if there are atoms of overlap between the two parts. > > If there are overlapping parts, for example one structure is residues 1-15 and the other is residues 12-500: you can position the structures relative to each other by superimposing just the overlapping atoms using the "match" command (for example, something like "match #0:12-15 at n,ca,c,o #1:12-15 at n,ca,c,o"). Note the numbering won't necessarily be the same in the two structures, so you need to check on exactly which residues should be superimposed. Then you would delete the overlapping atoms from one structure (since the "same" atoms are already in the other structure), combine the two structures into one model, and then add a bond between the two parts. This could all be done in Chimera (see commands "delete" "combine" "bond", or graphical interfaces for the latter two are Favorites...Model Panel "copy/combine" function and Tools...Structure Editing... Build Structure, Adjust Bonds tab), OR it could be done by manually text-editing PDB files, after the matching step descr! > ibed above and then saving one structure as PDB "relative to" the other structure. Documentation for commands, command-line atom specification, and Build Structure: > > > > > If there are not overlapping parts, for example one structure is residues 1-15 and the other is residues 16-500, you would just use the Join Models tab in the Build Structure tool mentioned above: > > > YOu can see there are fewer steps in the latter, but it can be hard to fully specify the correct geometry at the join. Thus when overlapping atoms in similar conformations are available, that more complicated overlapping procedure may produce better results than simply deleting the redundant atoms and using the second approach. > > 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 Oct 18, 2013, at 2:26 AM, Maja Divjak wrote: > > Hello again Elaine, > And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte... > I look forward to your reply, > Thank you and best wishes, > Maja > On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote: > Hi Elaine, > Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models. > Thank you and best wishes, > Maja > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ From wigge.christoph at gmail.com Tue Oct 22 04:37:04 2013 From: wigge.christoph at gmail.com (Christoph Wigge) Date: Tue, 22 Oct 2013 13:37:04 +0200 Subject: [Chimera-users] Constrainted fitting Message-ID: Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge From meng at cgl.ucsf.edu Tue Oct 22 15:46:20 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 22 Oct 2013 15:46:20 -0700 Subject: [Chimera-users] Constrainted fitting In-Reply-To: References: Message-ID: Hi Christoph, If you have the monomers already in the desired positions relative to one another, you could combine them into a single model (for example using the "copy/combine" function in the Model Panel), and then fit the single model as a rigid body into the map. However, if you meant you only wanted to constrain the distance between the monomers but not fully fix (freeze) their relative positions, you may need to use some program other than Chimera. Chimera doesn't do flexible fitting with constraints. Besides simple rigid-body fitting, the options in Chimera are: sequential fitting of multiple structures (find good position for one rigid body, then find nonoverlapping good position for next rigid body, ...) and symmetric fitting of rigid-body copies of the same structure. I'm not qualified to make recommendations in this area, and can only mention a few programs that might be relevant: PyRy3D (Monte Carlo fitting with restraints) has a plugin to use Chimera as the graphical interface: IMP: Molecular Dynamics Flexible Fitting (MDFF): 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 Oct 22, 2013, at 4:37 AM, Christoph Wigge wrote: > Dear all, > I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. > Bests > Christoph Wigge From evan.kantrowitz at bc.edu Wed Oct 23 07:55:26 2013 From: evan.kantrowitz at bc.edu (Evan Kantrowitz) Date: Wed, 23 Oct 2013 14:55:26 +0000 Subject: [Chimera-users] Chimera and Mac Mavericks Message-ID: <9B6C21A20C8D6648B4ACDBB730277AA368FC3778@EBHAZARD04.bc.edu> I just install Mavericks on my Mac. Chimera starts OK, but if you try to type into a field, like the PDB fetch field, entering key strokes is very hard. 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 wigge.christoph at gmail.com Wed Oct 23 00:01:35 2013 From: wigge.christoph at gmail.com (Christoph Wigge) Date: Wed, 23 Oct 2013 09:01:35 +0200 Subject: [Chimera-users] Constrainted fitting In-Reply-To: References: Message-ID: Hi Elaine, Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution? Bests Christoph Am 23.10.2013 um 00:46 schrieb Elaine Meng: > Hi Christoph, > If you have the monomers already in the desired positions relative to one another, you could combine them into a single model (for example using the "copy/combine" function in the Model Panel), and then fit the single model as a rigid body into the map. > > However, if you meant you only wanted to constrain the distance between the monomers but not fully fix (freeze) their relative positions, you may need to use some program other than Chimera. Chimera doesn't do flexible fitting with constraints. Besides simple rigid-body fitting, the options in Chimera are: sequential fitting of multiple structures (find good position for one rigid body, then find nonoverlapping good position for next rigid body, ...) and symmetric fitting of rigid-body copies of the same structure. > > > > > I'm not qualified to make recommendations in this area, and can only mention a few programs that might be relevant: > > PyRy3D (Monte Carlo fitting with restraints) has a plugin to use Chimera as the graphical interface: > > > > IMP: > > > Molecular Dynamics Flexible Fitting (MDFF): > > > 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 Oct 22, 2013, at 4:37 AM, Christoph Wigge wrote: > >> Dear all, >> I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. >> Bests >> Christoph Wigge > From meng at cgl.ucsf.edu Wed Oct 23 09:47:11 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Oct 2013 09:47:11 -0700 Subject: [Chimera-users] Constrainted fitting In-Reply-To: References: Message-ID: <162D4245-1C9F-46CD-A922-A72679CBE405@cgl.ucsf.edu> Hi Christoph, It depends on whether you believe your protein forms the dimer in the same way as the homolog with known dimeric structure. It sounds like a reasonable hypothesis, at least, and I believe other people have done similar things. You could try it and see if the shape of your modeled dimer appears to be compatible with the shape of the density. If the fit is very poor, then you might consider alternative hypotheses. 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 Oct 23, 2013, at 12:01 AM, Christoph Wigge wrote: > Hi Elaine, > Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution? > Bests > Christoph From sclassen at lbl.gov Wed Oct 23 09:43:28 2013 From: sclassen at lbl.gov (Scott Classen) Date: Wed, 23 Oct 2013 09:43:28 -0700 Subject: [Chimera-users] odd surface graphics artifact Message-ID: Hello, I'm trying to fade a surface to 100 transparent with the following command transparency 100,s #2 frames 30; wait 30 and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface: What is causing this and how can I eliminate it? Thanks, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: zero.png Type: image/png Size: 124780 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: one.png Type: image/png Size: 131990 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 4103 bytes Desc: not available URL: From s.molnar at sbcglobal.net Wed Oct 23 10:21:33 2013 From: s.molnar at sbcglobal.net (Stephen P. Molnar) Date: Wed, 23 Oct 2013 13:21:33 -0400 Subject: [Chimera-users] Problem with Chimera-1.8-linux-x86_64 Message-ID: <5268059D.1090802@sbcglobal.net> I have installed chimera-1.8-linux-x86_64 in VMware Player v-6.0.0 build-1295980 without any waning or error messages. When I start chimera I get the splash screen, then: ./chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x4000064 Serial number of failed request: 1352 Current serial number in output stream: 1358 computation at inga:~/Apps/chimera/bin$ Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemisry.com (614)312-7528(c) Skype: smolnar1 From zen.lu at roslin.ed.ac.uk Wed Oct 23 10:54:36 2013 From: zen.lu at roslin.ed.ac.uk (LU Zen) Date: Wed, 23 Oct 2013 18:54:36 +0100 Subject: [Chimera-users] hydrophopic interaction Message-ID: Hi All, I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However, I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. Any suggestion is appreciated. Thanks, ZL -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From meng at cgl.ucsf.edu Wed Oct 23 11:03:27 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Oct 2013 11:03:27 -0700 Subject: [Chimera-users] odd surface graphics artifact In-Reply-To: References: Message-ID: Hi Scott, Short answer is I have no idea what could be happening. I tried to reproduce the problem, but in my case making the surface transparent didn't make any part of it disappear. I tried to use a similar situation (partial surface, gradient background, etc.) It may be something specific to your computer or the structure, which we would need to be able to reproduce to solve. You could save session with the surface at zero transparency, then use Help... Report a Bug, including your email address and a short description of the problem and how to reveal it starting from that session (e.g. command: transparency 1,s), and of course attaching the session file. 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 Oct 23, 2013, at 9:43 AM, Scott Classen wrote: > Hello, > I'm trying to fade a surface to 100 transparent with the following command > > transparency 100,s #2 frames 30; wait 30 > > and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface: > > > > > What is causing this and how can I eliminate it? > > Thanks, > Scott From meng at cgl.ucsf.edu Wed Oct 23 11:10:53 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Oct 2013 11:10:53 -0700 Subject: [Chimera-users] hydrophopic interaction In-Reply-To: References: Message-ID: <2F822AD0-BCFF-4268-A6FF-F9D4D12F15EB@cgl.ucsf.edu> Hi ZL, The way that you would identify only the hydrophobic contacts is to only designate hydrophobic atoms for checking. For example, if you consider the carbons to be the hydrophobic atoms, you would first select all the carbons in your protein, "designate" them for checking, choose the option to check against "second set of designated atoms," then select all the carbons in the membrane and designate them as the second set. In the "Treatment" section, the "Draw pseudobonds" option means to draw the lines. You can turn that off if you don't want to draw lines, and/or you can color the contacting atoms, and/or select them for subsequent actions such as residue label display. There is no quantification of the possible energy contributions, sorry. It is all based on distances between VDW surfaces of the atoms. 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 Oct 23, 2013, at 10:54 AM, LU Zen wrote: > Hi All, > I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However, I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. > Any suggestion is appreciated. > Thanks, > ZL > From pett at cgl.ucsf.edu Wed Oct 23 11:43:19 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 23 Oct 2013 11:43:19 -0700 Subject: [Chimera-users] Chimera and Mac Mavericks In-Reply-To: <9B6C21A20C8D6648B4ACDBB730277AA368FC3778@EBHAZARD04.bc.edu> References: <9B6C21A20C8D6648B4ACDBB730277AA368FC3778@EBHAZARD04.bc.edu> Message-ID: <07269901-E258-4D3A-980B-906DD3E48BFB@cgl.ucsf.edu> Hi Evan, We have gotten a could of reports of crashes on Mavericks while opening PDB files, but nothing about typing difficulty. Can you describe what it means when you say entering keystrokes is hard? Do you have to type a key multiple times to get it to show up? Is it difficult to click into the field with the mouse to start typing? What exactly? Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 23, 2013, at 7:55 AM, Evan Kantrowitz wrote: > I just install Mavericks on my Mac. Chimera starts OK, but if you try to type into a field, like the PDB fetch field, entering key strokes is very hard. > > Evan From gregc at cgl.ucsf.edu Wed Oct 23 11:59:50 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 23 Oct 2013 11:59:50 -0700 Subject: [Chimera-users] Problem with Chimera-1.8-linux-x86_64 In-Reply-To: <5268059D.1090802@sbcglobal.net> References: <5268059D.1090802@sbcglobal.net> Message-ID: <52681CA6.5030604@cgl.ucsf.edu> So in general, we don't recommend running Chimera within vmware (or any other virtual machine, like virtualbox) because Chimera needs direct access to the graphics hardware for the best performance. That said, to get it to work, you'll need to read the vmware documentation to figure out how to enable "accelerated 3D graphics". It will probably requiring installing an appropriate graphics driver in your Linux virtual machine, and might require a newer version Linux in your virtual machine, or possibly a newer version of vmware. Some links I found: VMware Horizon View 5.2 and Hardware Accelerated 3D Graphics , VMware Fusion Help > Configuring Your Virtual Machines , X.org Drivers for VMware virtual graphics , How to fix 3D Acceleration for Vmware Workstation 9? , VMware promises better 3D graphics on virtualized desktops . It appears that 3D graphics in vmware is still a "work in progress". Perhaps someone who has configured vmware for 3D will speak up. Good luck, Greg On 10/23/2013 10:21 AM, Stephen P. Molnar wrote: > I have installed chimera-1.8-linux-x86_64 in VMware Player v-6.0.0 > build-1295980 without any waning or error messages. > > When I start chimera I get the splash screen, then: > > ./chimera > X Error of failed request: BadDrawable (invalid Pixmap or Window > parameter) > Major opcode of failed request: 72 (X_PutImage) > Resource id in failed request: 0x4000064 > Serial number of failed request: 1352 > Current serial number in output stream: 1358 > computation at inga:~/Apps/chimera/bin$ > > Please advise. > > Thanks in advance. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 23 15:50:38 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 23 Oct 2013 15:50:38 -0700 Subject: [Chimera-users] Chimera crashes on Mac OS 10.9 Mavericks Message-ID: For those updating to the newly released Mac operating system Mavericks (10.9), we already have several reports that Chimera crashes showing any molecule due to a graphics driver bug in the new Mac operating system. I suggest not updating to Mavericks immediately if you want Chimera to continue to work. Only Apple can fix this bug. But we will disable the advanced graphics that leads to the crash in tonight's daily build. So if you already updated to Mavericks you can try the Chimera daily build (available about 16 hours after this post) instead of the Chimera 1.8 release. If you want the Chimera 1.8 release to work in Mavericks you'll need to disable DrawElementsInstanced in the Chimera debug graphics driver dialog. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html Disabling this graphics feature (which is what the daily build will do automatically) will cause rendering of large molecules to be slower when atoms are shown as spheres/balls or bonds are shown as cylinders, about 30 times slower. Still it should be as fast as the older Chimera 1.6 version where we did not use this advanced graphics feature at all. Tom From goddard at sonic.net Wed Oct 23 15:55:14 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 23 Oct 2013 15:55:14 -0700 Subject: [Chimera-users] odd surface graphics artifact In-Reply-To: References: Message-ID: <4D0C201F-B85B-4050-8973-1222319C8DB4@sonic.net> Hi Scott, This looks to me like a graphics driver bug, and you should use the Chimera Report a Bug dialog if you wish to discuss it further with us. Probably updating your graphics driver is the only hope of fixing it. If you have another computer you can try it on, you can see if it depends on the computer which would support the theory that it is the system graphics driver at fault. Tom On Oct 23, 2013, at 11:03 AM, Elaine Meng wrote: > Hi Scott, > Short answer is I have no idea what could be happening. I tried to reproduce the problem, but in my case making the surface transparent didn't make any part of it disappear. I tried to use a similar situation (partial surface, gradient background, etc.) It may be something specific to your computer or the structure, which we would need to be able to reproduce to solve. > > You could save session with the surface at zero transparency, then use Help... Report a Bug, including your email address and a short description of the problem and how to reveal it starting from that session (e.g. command: transparency 1,s), and of course attaching the session file. > 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 Oct 23, 2013, at 9:43 AM, Scott Classen wrote: > >> Hello, >> I'm trying to fade a surface to 100 transparent with the following command >> >> transparency 100,s #2 frames 30; wait 30 >> >> and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface: >> >> >> >> >> What is causing this and how can I eliminate it? >> >> Thanks, >> Scott > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Wed Oct 23 16:32:21 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 23 Oct 2013 16:32:21 -0700 Subject: [Chimera-users] Constrainted fitting In-Reply-To: References: Message-ID: Hi Christoph, If I understand your question you have two PDB files of monomers that form a dimer and you want to fit them into a density map as a rigid unit without disturbing how they bind to each other. This is easy to do in Chimera. If you are using the Fit in Map dialog just select both monomers (e.g. command "select #1,2") then use the Fit "selected atoms" setting in the dialog. This will move selected two monomers rigidly as one unit to the locally optimal position in the density map. You can do this with a command instead of the fitting dialog "fit #1,2 #3". Tom On Oct 22, 2013, at 4:37 AM, Christoph Wigge wrote: > Dear all, > > I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. > > Bests > > Christoph Wigge > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meetpavithramsc at gmail.com Wed Oct 23 18:01:19 2013 From: meetpavithramsc at gmail.com (Pavithra) Date: Thu, 24 Oct 2013 10:01:19 +0900 Subject: [Chimera-users] BadStatusLine error Message-ID: Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. -- regards, Pavithra.K.B. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meetpavithramsc at gmail.com Wed Oct 23 18:04:10 2013 From: meetpavithramsc at gmail.com (Pavithra) Date: Thu, 24 Oct 2013 10:04:10 +0900 Subject: [Chimera-users] Fwd: BadStatusLine error In-Reply-To: References: Message-ID: Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. The detailed error is given below Exception in Tk callback Function: > (type: ) Args: (,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "C:\Program Files\Chimera 1.7\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.7\share\Midas\midas_ui.py", line 270, in processCommand midas_text.makeCommand(cmdText) File "C:\Program Files\Chimera 1.7\share\Midas\midas_text.py", line 69, in makeCommand f(c, args) File "C:\Program Files\Chimera 1.7\share\Midas\midas_text.py", line 1449, in doOpen modelArg, noprefs) File "", line 1, in None File "C:\Program Files\Chimera 1.7\share\Midas\__init__.py", line 2033, in open noprefs=noprefs) File "C:\Program Files\Chimera 1.7\share\chimera\__init__.py", line 1745, in open models = func(filename, *args, **kw) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\ChimeraExtension.py", line 27, in showUniprotSeq self.module().showUniprotSeq(ident) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\__init__.py", line 302, in showUniprotSeq acc = mapUniprotNameID(ident) File "C:\Program Files\Chimera 1.7\share\SeqAnnotations\__init__.py", line 62, in mapUniprotNameID response = urllib2.urlopen(request) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 406, in open response = meth(req, response) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 519, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 438, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 378, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 625, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 400, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 418, in _open '_open', req) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 378, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 1207, in http_open return self.do_open(httplib.HTTPConnection, req) File "C:\Program Files\Chimera 1.7\bin\lib\urllib2.py", line 1180, in do_open r = h.getresponse(buffering=True) File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 1030, in getresponse response.begin() File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 407, in begin version, status, reason = self._read_status() File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) : '' ================================================ Event contents: char: delta: 13 height: ?? keycode: 13 keysym: Return keysym_num: 65293 num: ?? serial: 38444 state: 8 time: 69416531 type: 2 widget: .44391680.76326552.76670056.76670616.76670816 width: ?? x: 174 x_root: 227 y: 13 y_root: 942 BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. -- regards, Pavithra.K.B. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 23 18:18:48 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Oct 2013 18:18:48 -0700 Subject: [Chimera-users] BadStatusLine error In-Reply-To: References: Message-ID: <83D10236-99AC-44C2-A718-29ECDED38B26@cgl.ucsf.edu> Hi Pavithra, I can't reproduce this problem -- the fetch of UniProt oprd_human is successful for me in Chimera 1.7 and newer versions of Chimera. I don't know what preference you are talking about... if you meant the download directory, that only specifies a local directory for saving the files and should not have "http" in it. In general, you should report problems using the Chimera menu: Help... Report a Bug instead of sending email to this address. In the report form, you can include a description of what you did and your email (if you want feedback). Some other things to try and maybe mention in the report: can you fetch anything from UniProt? Can you fetch anything from any database (PDB, etc.)? 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote: > Dear chimera users, > > I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. > > Steps followed: > Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) > > Error: > > > BadStatusLine: '' > > File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status > raise BadStatusLine(line) > > See reply log for Python traceback. > > I tried changing the preference to use "http" but nothing fix it. please help. > > -- > regards, > Pavithra.K.B. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meetpavithramsc at gmail.com Wed Oct 23 19:12:09 2013 From: meetpavithramsc at gmail.com (Pavithra) Date: Thu, 24 Oct 2013 11:12:09 +0900 Subject: [Chimera-users] BadStatusLine error In-Reply-To: <83D10236-99AC-44C2-A718-29ECDED38B26@cgl.ucsf.edu> References: <83D10236-99AC-44C2-A718-29ECDED38B26@cgl.ucsf.edu> Message-ID: Dear Dr. Elaine, Thank you for the reply. I tried to report the bug before I mailed this group. To be exact for the past two days, I tried to report the bug. But, It didn't work. The preference I was talking about is the "web access" in which i changed the http proxy true and tried. I have tried Fetching pdb, Emdb, which was successful. But, with uniprot I'm getting the previously mentioned error. I have tried different uniprot Ids but I get the same error. On Thu, Oct 24, 2013 at 10:18 AM, Elaine Meng wrote: > Hi Pavithra, > I can't reproduce this problem -- the fetch of UniProt oprd_human is > successful for me in Chimera 1.7 and newer versions of Chimera. I don't > know what preference you are talking about... if you meant the download > directory, that only specifies a local directory for saving the files and > should not have "http" in it. > > In general, you should report problems using the Chimera menu: Help... > Report a Bug instead of sending email to this address. In the report form, > you can include a description of what you did and your email (if you want > feedback). Some other things to try and maybe mention in the report: can > you fetch anything from UniProt? Can you fetch anything from any database > (PDB, etc.)? > 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote: > > > Dear chimera users, > > > > I'm trying comparative modeling tutorial in chimera tutorials and I'm > getting the following error in using fetch uniprot id. > > > > Steps followed: > > Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried > all combinations) > > > > Error: > > > > > > BadStatusLine: '' > > > > File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in > _read_status > > raise BadStatusLine(line) > > > > See reply log for Python traceback. > > > > I tried changing the preference to use "http" but nothing fix it. please > help. > > > > -- > > regards, > > Pavithra.K.B. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- regards, Pavithra.K.B. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.maly at ujep.cz Thu Oct 24 02:10:10 2013 From: marek.maly at ujep.cz (Marek Maly) Date: Thu, 24 Oct 2013 11:10:10 +0200 Subject: [Chimera-users] rotation of the molecule using plane and the axis ? Message-ID: Hello, if I define plane "p" using 3 atoms of the given molecule, is there any possibility to rotate consequently molecule into the position in which the chosen axis of the coordinate system (x or y or z) is perpendicular to the plane "p" ? (Of course except slow and not accurate "manual" rotation by mouse). Than you, Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From goddard at sonic.net Thu Oct 24 11:03:46 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 24 Oct 2013 11:03:46 -0700 Subject: [Chimera-users] Typing broken in Mac Mavericks (10.9) with 64-bit Chimera Message-ID: <82F1C4F7-C56C-4466-B4C5-6E1E56CBF791@sonic.net> With the new Mac operating system Mavericks (Mac OS 10.9), typing into Chimera entry fields is not working in 64-bit Chimera but works correctly in 32-bit Chimera. Also as reported earlier a Mavericks graphics driver bug causes Chimera 1.8 to crash displaying any atoms or bonds. The crashing problem has been fixed in today's Chimera daily build (by disabling an advanced graphics feature automatically on Mac 10.9). So the only Mac Chimera that will work correctly on Mavericks is today's 32-bit daily build (or newer). Tom From pett at cgl.ucsf.edu Thu Oct 24 12:37:54 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 24 Oct 2013 12:37:54 -0700 Subject: [Chimera-users] BadStatusLine error In-Reply-To: References: <83D10236-99AC-44C2-A718-29ECDED38B26@cgl.ucsf.edu> Message-ID: <6F1D1CA3-986E-4F30-937D-E3749A0A3246@cgl.ucsf.edu> Hi Pavithra, Thanks for reporting the error via the bug-reporting mechanism. Since this problem seems to be affecting no one else, we'll work on it via the bug report rather than via the users list. Expect mail via the bug report soon. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 23, 2013, at 7:12 PM, Pavithra wrote: > Dear Dr. Elaine, > > Thank you for the reply. > I tried to report the bug before I mailed this group. To be exact for the past two days, I tried to report the bug. But, It didn't work. > The preference I was talking about is the "web access" in which i changed the http proxy true and tried. > I have tried Fetching pdb, Emdb, which was successful. But, with uniprot I'm getting the previously mentioned error. > I have tried different uniprot Ids but I get the same error. > > > On Thu, Oct 24, 2013 at 10:18 AM, Elaine Meng wrote: > Hi Pavithra, > I can't reproduce this problem -- the fetch of UniProt oprd_human is successful for me in Chimera 1.7 and newer versions of Chimera. I don't know what preference you are talking about... if you meant the download directory, that only specifies a local directory for saving the files and should not have "http" in it. > > In general, you should report problems using the Chimera menu: Help... Report a Bug instead of sending email to this address. In the report form, you can include a description of what you did and your email (if you want feedback). Some other things to try and maybe mention in the report: can you fetch anything from UniProt? Can you fetch anything from any database (PDB, etc.)? > 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 Oct 23, 2013, at 6:01 PM, Pavithra wrote: > > > Dear chimera users, > > > > I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. > > > > Steps followed: > > Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) > > > > Error: > > > > > > BadStatusLine: '' > > > > File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status > > raise BadStatusLine(line) > > > > See reply log for Python traceback. > > > > I tried changing the preference to use "http" but nothing fix it. please help. > > > > -- > > regards, > > Pavithra.K.B. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > regards, > Pavithra.K.B. > _______________________________________________ > 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 p.qian at sheffield.ac.uk Fri Oct 25 04:25:39 2013 From: p.qian at sheffield.ac.uk (Pu Qian) Date: Fri, 25 Oct 2013 12:25:39 +0100 Subject: [Chimera-users] chimera in mac osx 10.9 Message-ID: Hi, I upgraded my mac to 10.9 Marvericks. Chimera does not show up input text in Command windows or other text windows properly. I'm using version 1.9, 2013-10-24, 64-bit for mac OSX. It would be a great appreciated if you could tell me which version I should use for this new OSX. Thanks. Best regards Pu Qian The University of Sheffield, UK -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.qian at sheffield.ac.uk Fri Oct 25 06:16:30 2013 From: p.qian at sheffield.ac.uk (Pu Qian) Date: Fri, 25 Oct 2013 14:16:30 +0100 Subject: [Chimera-users] chimera in mac osx 10.9 In-Reply-To: References: Message-ID: 32-bit latest version seems OK for Mac OSX 10.9 Marvericks. Qian On 25 October 2013 12:25, Pu Qian wrote: > Hi, > > I upgraded my mac to 10.9 Marvericks. Chimera does not show up input text > in Command windows or other text windows properly. > > I'm using version 1.9, 2013-10-24, 64-bit for mac OSX. > > It would be a great appreciated if you could tell me which version I > should use for this new OSX. Thanks. > > Best regards > > Pu Qian > The University of Sheffield, UK > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Oct 25 10:10:18 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 25 Oct 2013 10:10:18 -0700 Subject: [Chimera-users] can get sequence from UniProt website Message-ID: <8C9E07F1-4EA3-4C0B-A7CB-2C83788135A4@cgl.ucsf.edu> Hi Pavithra, I forgot to mention that you could just go to the UniProt web site and save the sequence as a file, then open the file in Chimera. For example, I went to UniProt, searched for oprd_human, then in the Sequences section of the oprd_human page, clicked "FASTA" to get to the URL below, contents of which you can save as plain text file named ending in .fa or .fasta and then open in Chimera with File... Open. It would not have the annotations mentioned in the comparative modeling tutorial, but those aren't important for doing the tutorial. After opening the FAST file as described above, you can then carry on with the tutorial starting with the fourth paragraph in the "Blast Search for Templates" section ("The next step...". 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 From pett at cgl.ucsf.edu Fri Oct 25 16:24:24 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 25 Oct 2013 16:24:24 -0700 Subject: [Chimera-users] rotation of the molecule using plane and the axis ? In-Reply-To: References: Message-ID: On Oct 24, 2013, at 2:10 AM, Marek Maly wrote: > Hello, > > if I define plane "p" using 3 atoms of the given molecule, is there > any possibility to rotate consequently molecule into the position > in which the chosen axis of the coordinate system (x or y or z) is perpendicular > to the plane "p" ? (Of course except slow and not accurate "manual" rotation by mouse). Hi Marek, My interpretation of your question is that you define a plane in one molecule, and then want to position another molecule so that it's X (or Y, or Z) axis is aligned with the normal of the plane (possibly also positioning the origin of the axis with the origin of the plane). If I've misinterpreted the question, let me know. Anyway, I've appended a Python script that does that. You run it simply by opening it with File->Open or with the "open" command. It assumes you have exactly one plane defined, and that you want to move the model with the highest model ID so that its X axis is aligned with the plane normal and its coordinate system origin is coincident with the plane origin. If you look at the script I think it's obvious how change X axis to other axes (though nothing else is obvious!). Hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- A non-text attachment was scrubbed... Name: alignAxis.py Type: text/x-python-script Size: 941 bytes Desc: not available URL: From mmatho at liai.org Fri Oct 25 13:57:36 2013 From: mmatho at liai.org (Michael Matho) Date: Fri, 25 Oct 2013 13:57:36 -0700 (PDT) Subject: [Chimera-users] Need help with fit into segment function In-Reply-To: <1788367215.69747703.1382734327704.JavaMail.root@liai.org> Message-ID: <487591229.69748380.1382734656330.JavaMail.root@liai.org> Hello, I have an EM map segmented in 5 segments I need to fit 5 molecules into. I'm trying to select a specific segment in order to fit each molecule individually, one after the other. After reading the tutorial, I still cannot figure out how to select only one segment of the map: If I try selecting from "Render/select by attribute" and choose "Segmentation regions" (and I do have the 5 segments ready), only the full map shows up, not the segments! In the "fit to segment" window, I select the molecule to fit and click on Fit... then there's a bug. I'd appreciate your help on how to finalize my fit. Thanks, Michael H. Matho, Ph.D. | Research Associate | Department of Cell Biology La Jolla Institute for Allergy and Immunology 9420 Athena Circle | La Jolla, CA, 92037 Tel: (858) 752-6631 | mmatho at liai.org -------------- next part -------------- A non-text attachment was scrubbed... Name: group4_stage1.png Type: image/png Size: 884794 bytes Desc: not available URL: From meng at cgl.ucsf.edu Sun Oct 27 10:37:35 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 27 Oct 2013 10:37:35 -0700 Subject: [Chimera-users] Need help with fit into segment function In-Reply-To: <487591229.69748380.1382734656330.JavaMail.root@liai.org> References: <487591229.69748380.1382734656330.JavaMail.root@liai.org> Message-ID: <3023ED86-093A-4133-A9DD-33B8B067CABC@cgl.ucsf.edu> Hi Michael, Just select the desired segment with the mouse (Ctrl-click) in the graphics window. If you want more than one segment selected at a time, Shift-Ctrl-click to add to your selection. In the picture you sent, I only see one surface (not 5 segmentation surfaces) but maybe you just meant to show your whole map. Presumably you used "Segment Map" to produce separate regions before using "Fit to Segment." The 5 segmentation regions with separate surfaces should show up when you used Segment Map. I'm not sure which tutorial you are viewing, but just now I tried segmenting a map, selecting a segment with Ctrl-click, opening a molecule, and using the "Fit" button without problems. To report problems, use "Help... Report a Bug" in the Chimera menu and include whatever is needed to reproduce the problem, including data or session and description of steps causing the problem. That also sends us information on what type of computer and version of Chimera you are using. 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 Oct 25, 2013, at 1:57 PM, Michael Matho wrote: > Hello, > I have an EM map segmented in 5 segments I need to fit 5 molecules into. > > I'm trying to select a specific segment in order to fit each molecule individually, one after the other. > > After reading the tutorial, I still cannot figure out how to select only one segment of the map: > > If I try selecting from "Render/select by attribute" and choose "Segmentation regions" (and I do have the 5 segments ready), only the full map shows up, not the segments! > > In the "fit to segment" window, I select the molecule to fit and click on Fit... then there's a bug. > > I'd appreciate your help on how to finalize my fit. > > Thanks, > > Michael H. Matho, Ph.D. | Research Associate | Department of Cell Biology > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle | La Jolla, CA, 92037 > Tel: (858) 752-6631 | mmatho at liai.org From Yanyong.Kang at vai.org Sat Oct 26 15:34:16 2013 From: Yanyong.Kang at vai.org (Kang, Yanyong) Date: Sat, 26 Oct 2013 22:34:16 +0000 Subject: [Chimera-users] Morph movie issue Message-ID: <9DB4E3B1F4210F4BA65CC1756DB1EE5C188F61@VAIEXMB02.vai.org> Dear Chimera developer, I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much Best, Yanyong Dr. Yanyong Kang Laboratory of Structural Sciences Van Andel Research Institute Tel, 616-234-5446 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Oct 28 10:29:34 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 28 Oct 2013 10:29:34 -0700 Subject: [Chimera-users] Morph movie issue In-Reply-To: <9DB4E3B1F4210F4BA65CC1756DB1EE5C188F61@VAIEXMB02.vai.org> References: <9DB4E3B1F4210F4BA65CC1756DB1EE5C188F61@VAIEXMB02.vai.org> Message-ID: <9B2FC505-BBF3-4101-9EAA-6C954E9446FE@cgl.ucsf.edu> From the help page for the Morph Conformations tool: MD Movie does not automatically re-evaluate secondary structure. MD Movie does not automatically recompute secondary structure assignments as coordinates change across a trajectory. This is relevant when ribbons are displayed and the conformational changes are large enough to alter secondary structure assignments. To recompute secondary structure at each frame, use a per-frame script in MD Movie that includes the Chimera command ksdssp. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 26, 2013, at 3:34 PM, "Kang, Yanyong" wrote: > Dear Chimera developer, > > I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much > > Best, > > Yanyong > > Dr. Yanyong Kang > Laboratory of Structural Sciences > Van Andel Research Institute > Tel, 616-234-5446 > > > _______________________________________________ > 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 mmatho at liai.org Mon Oct 28 11:42:30 2013 From: mmatho at liai.org (Michael Matho) Date: Mon, 28 Oct 2013 11:42:30 -0700 (PDT) Subject: [Chimera-users] Need help with fit into segment function In-Reply-To: <3023ED86-093A-4133-A9DD-33B8B067CABC@cgl.ucsf.edu> Message-ID: <1661165723.70239358.1382985750289.JavaMail.root@liai.org> Thanks so much Elaine. I had figured it out over the week end, but your explanations are spot on. I do have another question: I discovered that my map's resolution is too low to embed the molecules accurately (i.e that the interface between molecules corresponds to the known amino acid interface definition, which was determined via other methods (DXMS, X-ray crystallography, alanine scan and mutation analysis). Is there a way to guide the embedding process by giving interface definitions as input? I would rather not just do it manually so I can explain my protocol in a manuscript. That would be of tremendous help. Alternatively, I requested "Dock" software, in order to previously dock the molecules to each other (using the interface as ligand, and then superimposing the whole molecule to the 'ligand'). The problem is, it said that it worked for OSX but on the download page it doesn't offer OSX as an option, only the source. Do I have to download the source or is there another page to download the OSX version? Thanks so much, Michael ----- Original Message ----- From: "Elaine Meng" To: "Michael Matho" Cc: chimera-users at cgl.ucsf.edu Sent: Sunday, October 27, 2013 10:37:35 AM Subject: Re: [Chimera-users] Need help with fit into segment function Hi Michael, Just select the desired segment with the mouse (Ctrl-click) in the graphics window. If you want more than one segment selected at a time, Shift-Ctrl-click to add to your selection. In the picture you sent, I only see one surface (not 5 segmentation surfaces) but maybe you just meant to show your whole map. Presumably you used "Segment Map" to produce separate regions before using "Fit to Segment." The 5 segmentation regions with separate surfaces should show up when you used Segment Map. I'm not sure which tutorial you are viewing, but just now I tried segmenting a map, selecting a segment with Ctrl-click, opening a molecule, and using the "Fit" button without problems. To report problems, use "Help... Report a Bug" in the Chimera menu and include whatever is needed to reproduce the problem, including data or session and description of steps causing the problem. That also sends us information on what type of computer and version of Chimera you are using. 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 Oct 25, 2013, at 1:57 PM, Michael Matho wrote: > Hello, > I have an EM map segmented in 5 segments I need to fit 5 molecules into. > > I'm trying to select a specific segment in order to fit each molecule individually, one after the other. > > After reading the tutorial, I still cannot figure out how to select only one segment of the map: > > If I try selecting from "Render/select by attribute" and choose "Segmentation regions" (and I do have the 5 segments ready), only the full map shows up, not the segments! > > In the "fit to segment" window, I select the molecule to fit and click on Fit... then there's a bug. > > I'd appreciate your help on how to finalize my fit. > > Thanks, > > Michael H. Matho, Ph.D. | Research Associate | Department of Cell Biology > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle | La Jolla, CA, 92037 > Tel: (858) 752-6631 | mmatho at liai.org From meng at cgl.ucsf.edu Mon Oct 28 11:53:38 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Oct 2013 11:53:38 -0700 Subject: [Chimera-users] Need help with fit into segment function In-Reply-To: <1661165723.70239358.1382985750289.JavaMail.root@liai.org> References: <1661165723.70239358.1382985750289.JavaMail.root@liai.org> Message-ID: Hi Michael, Chimera's fitting doesn't have options to constrain the fits to make specific residues close to one another. To do something like that, you may want to look into some other programs, such as mentioned in this recent post: DOCK development is by a separate group, so you'd probably want to ask them about the download. (I don't know the answer.) 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 Oct 28, 2013, at 11:42 AM, Michael Matho wrote: > Thanks so much Elaine. > > I had figured it out over the week end, but your explanations are spot on. > > I do have another question: I discovered that my map's resolution is too low to embed the molecules accurately (i.e that the interface between molecules corresponds to the known amino acid interface definition, which was determined via other methods (DXMS, X-ray crystallography, alanine scan and mutation analysis). > > Is there a way to guide the embedding process by giving interface definitions as input? I would rather not just do it manually so I can explain my protocol in a manuscript. > > That would be of tremendous help. > > Alternatively, I requested "Dock" software, in order to previously dock the molecules to each other (using the interface as ligand, and then superimposing the whole molecule to the 'ligand'). > > The problem is, it said that it worked for OSX but on the download page it doesn't offer OSX as an option, only the source. > > Do I have to download the source or is there another page to download the OSX version? > > Thanks so much, > > Michael From bobwohlhueter at earthlink.net Mon Oct 28 12:55:54 2013 From: bobwohlhueter at earthlink.net (Robert Wohlhueter) Date: Mon, 28 Oct 2013 15:55:54 -0400 Subject: [Chimera-users] no moleculr dispay with version 1.8 In-Reply-To: References: Message-ID: <526EC14A.2040907@earthlink.net> I have chimera-1.5.3 running on my Linux-AMD64 Ubuntu (12.10) computer. It works fine in every respect. Recently I installed version 1.8, with runs, but with one fatal flaw. By "runs", I mean the chimera screen comes up, the menus display. If I load (say, a pdb file), it seems to be there in the sense, for example, that I can open and view its sequence. BUT the molecule display window is absolutely blank (black). I suspect it has either to do with my python installation, or with my NVIDIA graphics driver. But whatever the problem, it effects only v. 1.8, not v. 1.5.3. For NVIDIA driver I'm using version 310.14. For python, I understand chimera uses 2.7. My python executable is indeed set as version 2.7.3 (that is, `python --version1 returns 2.7.3), though I have version 3 installed, and it could be used, if needed. I'm not all so clear on how envars PYTHONHOME and PYTHONPATH may or may not effect chimera. Of course, the easy way out is to stick with chimera-1.5.3 -- but one likes to stay up-to-date. Thanks in advance for any profound wisdom. Bob Wohlhueter From goddard at sonic.net Mon Oct 28 15:54:06 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 28 Oct 2013 15:54:06 -0700 Subject: [Chimera-users] no moleculr dispay with version 1.8 In-Reply-To: <526EC14A.2040907@earthlink.net> References: <526EC14A.2040907@earthlink.net> Message-ID: <8B222161-EA99-47FC-97CB-73C316F75ACA@sonic.net> Hi Bob, This is certainly a graphics driver problem. For more help on it use Chimera menu entry Help / Report a Bug? and say the graphics is black in the description. The report will tell us what graphics driver you are using. The probable solution is to update your graphics driver. Chimera 1.5.3 is 2 years old and we rewrote much of the molecular graphics to use more modern (faster and simpler) OpenGL (3-d graphics library) in Chimera 1.7 and 1.8 and your driver is having trouble doing the modern graphics. The specific issue is probably that programs that run on the graphics chip are not working. You can disable that by turning off "Shading" in the Chimera debug graphics driver dialog. This will make the graphics slower, so updating your graphics driver is the preferred solution. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html Tom On Oct 28, 2013, at 12:55 PM, Robert Wohlhueter wrote: > I have chimera-1.5.3 running on my Linux-AMD64 Ubuntu (12.10) computer. It works fine in every respect. Recently I installed version 1.8, with runs, but with one fatal flaw. By "runs", I mean the chimera screen comes up, the menus display. If I load (say, a pdb file), it seems to be there in the sense, for example, that I can open and view its sequence. > > BUT the molecule display window is absolutely blank (black). I suspect it has either to do with my python installation, or with my NVIDIA graphics driver. But whatever the problem, it effects only v. 1.8, not v. 1.5.3. > > For NVIDIA driver I'm using version 310.14. > > For python, I understand chimera uses 2.7. My python executable is indeed set as version 2.7.3 (that is, `python --version1 returns 2.7.3), though I have version 3 installed, and it could be used, if needed. I'm not all so clear on how envars PYTHONHOME and PYTHONPATH may or may not effect chimera. > > Of course, the easy way out is to stick with chimera-1.5.3 -- but one likes to stay up-to-date. > > Thanks in advance for any profound wisdom. > > Bob Wohlhueter > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gregc at cgl.ucsf.edu Mon Oct 28 16:12:26 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 28 Oct 2013 16:12:26 -0700 Subject: [Chimera-users] no moleculr dispay with version 1.8 In-Reply-To: <526EC14A.2040907@earthlink.net> References: <526EC14A.2040907@earthlink.net> Message-ID: <526EEF5A.3080803@cgl.ucsf.edu> As you guessed, the problem is probably with the graphics driver. So the first thing to try is to update your graphics driver. Since you are using Ubuntu, use the Additional Drivers panel to switch which proprietary driver you are using. Ubuntu provides several choices. Don't forget to reboot after changing the driver. I'm upgrading a 32-bit Ubuntu 12.04 machine to 12.10 to see if I can reproduce the problem, we've already upgraded our 64-bit NVIDIA test machine to 13.04, and there no problems there, so that might be an alternative solution. HTH, Greg On 10/28/2013 12:55 PM, Robert Wohlhueter wrote: > I have chimera-1.5.3 running on my Linux-AMD64 Ubuntu (12.10) > computer. It works fine in every respect. Recently I installed > version 1.8, with runs, but with one fatal flaw. By "runs", I mean > the chimera screen comes up, the menus display. If I load (say, a pdb > file), it seems to be there in the sense, for example, that I can open > and view its sequence. > > BUT the molecule display window is absolutely blank (black). I > suspect it has either to do with my python installation, or with my > NVIDIA graphics driver. But whatever the problem, it effects only v. > 1.8, not v. 1.5.3. > > For NVIDIA driver I'm using version 310.14. > > For python, I understand chimera uses 2.7. My python executable is > indeed set as version 2.7.3 (that is, `python --version1 returns > 2.7.3), though I have version 3 installed, and it could be used, if > needed. I'm not all so clear on how envars PYTHONHOME and PYTHONPATH > may or may not effect chimera. > > Of course, the easy way out is to stick with chimera-1.5.3 -- but one > likes to stay up-to-date. > > Thanks in advance for any profound wisdom. > > Bob Wohlhueter > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From bala.biophysics at gmail.com Tue Oct 29 07:52:22 2013 From: bala.biophysics at gmail.com (Bala subramanian) Date: Tue, 29 Oct 2013 15:52:22 +0100 Subject: [Chimera-users] Symmetry generation question Message-ID: Hello, 1) I have modelled one chain of a multimer. Since this is a modelled structure I dnt have any symmetry information in my pdb. In such case, how can I generate the symmetry related copies. Say I want to apply a fivefold symmetry along z-axis, how can I achieve it ? 2) I used a template structure from PDB to model my structure. What is the correct way to apply the symmetry of existing pdb model to my modeled chain. I tried this as follows, I opened my model as #0 and then the template pdb structure #1 and tried the following sym command and obtained an error as '#0 has no biological unit info.' sym #0 #1 Thanks, Bala -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 29 09:10:33 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 29 Oct 2013 09:10:33 -0700 Subject: [Chimera-users] coloring plane by ESP In-Reply-To: <08103BD2-903C-4CD8-A02F-26B105C9DF4C@cgl.ucsf.edu> References: <08103BD2-903C-4CD8-A02F-26B105C9DF4C@cgl.ucsf.edu> Message-ID: <6BFA01B3-48FC-4BFE-AD7A-B670D4053D81@cgl.ucsf.edu> Hi Marek, Just thought I'd mention that in Chimera you can color a plane that is in any orientation by the values in an ESP map. Unfortunately it doesn't work with the planes from Axes/Planes/Centroids, but you can create a rectangular plane with specified height and width with command "shape rectangle". Then you can open the molecule and the ESP map, activate/deactivate models (freeze/unfreeze them) and use the mouse to position the rectangle however you like in relationship to the molecule. Then you can use the "Surface Color" tool (aka Electrostatic Surface Coloring) to color the rectangle by the ESP map values. If you didn't already have an ESP map, you could use the PQR and APBS tools in Chimera to calculate one with APBS, or use the Coulombic Surface Coloring tool with option to "Compute grid" (i.e. make ESP map). Attached image is for 3eeb chain B, ESP map file 3eebB.phi ( available from link near bottom of the Surface Properties image tutorial ), and rectangle created with command: shape rectangle height 50 width 50 widthdiv 100 heightdiv 100 center protein It shows the area of strong positive potential near where the highly negatively charged ligand binds. 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 -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: planeESP.png Type: image/png Size: 48180 bytes Desc: not available URL: From meng at cgl.ucsf.edu Tue Oct 29 09:28:02 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 29 Oct 2013 09:28:02 -0700 Subject: [Chimera-users] Symmetry generation question In-Reply-To: References: Message-ID: Hi Bala, I believe you would need: sym #0 group #1 ? assuming the template model #1 has biological unit information (REMARK 350 BIOMT) information in its header. If the template instead has symmetry information in other types of symmetry records, you may need to take a slightly longer approach: (a) show symmetry copies of the template, e.g. with the Unit Cell tool (b) open extra copies of your modeled protein (c ) superimpose the copies of the modeled protein onto those of the template. Probably the matchmaker approach would be easiest. If the template does not have symmetry information in its header, you would need to somehow obtain a PDB file with the template already in the multimeric state (possibly hand-modeled) and then proceed with the third step above, or you could specify symmetry directly in the sym command with various keywords (group, axis, center?), but that can be difficult. 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 Oct 29, 2013, at 7:52 AM, Bala subramanian wrote: > Hello, > 1) I have modelled one chain of a multimer. Since this is a modelled structure I dnt have any symmetry information in my pdb. In such case, how can I generate the symmetry related copies. Say I want to apply a fivefold symmetry along z-axis, how can I achieve it ? > > 2) I used a template structure from PDB to model my structure. What is the correct way to apply the symmetry of existing pdb model to my modeled chain. > > I tried this as follows, I opened my model as #0 and then the template pdb structure #1 and tried the following sym command and obtained an error as '#0 has no biological unit info.' > > sym #0 #1 > > Thanks, > Bala From jholien at svi.edu.au Tue Oct 29 17:57:59 2013 From: jholien at svi.edu.au (Jessica Holien) Date: Wed, 30 Oct 2013 11:57:59 +1100 (EST) Subject: [Chimera-users] Fitting models into density - meaning of values Message-ID: <1171522057.23545.1383094679205.JavaMail.root@zstore.medstv.unimelb.edu.au> I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks From goddard at sonic.net Tue Oct 29 18:22:32 2013 From: goddard at sonic.net (Tom Goddard) Date: Tue, 29 Oct 2013 18:22:32 -0700 Subject: [Chimera-users] Fitting models into density - meaning of values In-Reply-To: <1171522057.23545.1383094679205.JavaMail.root@zstore.medstv.unimelb.edu.au> References: <1171522057.23545.1383094679205.JavaMail.root@zstore.medstv.unimelb.edu.au> Message-ID: Hi Jessica, The "average map" value reported by Chimera is only useful for comparing different fits in the same map. The values in a density map normalized in ways that differ from map to map, so the absolute value is meaningless. What is sometimes reported in the literature is correlation coefficient, ranging from -1 to 1. The Chimera fitting will report this if you use the Options button on the Fit Map dialog and enable "Use simulated map ? with resolution 23". The correlation compares a simulated map from your atomic model to the experimental map. Values like 0.8 and higher are often considered "good". But unfortunately this is a very poor indicator too for several reasons. First it depends on the region in space over which the correlation was measured. In Chimera this will be the grid points within the displayed contour of the simulated map. (You'll have to show the simulated map using the volume dialog or model panel to see that contour level.) Higher contour levels use fewer grid points and often give a much higher correlation value. Another reason this is a poor measure is that it doesn't tell you if there are 5 other very different fits with equally good correlation value. For a low resolution map like 23 Angstroms, there may be many equally good and very different fits. The short answer is that it is hard to say if a fit to a low resolution map is good in a convincing way, and the research community does not have standard measures for this. To make your best effort I would try to produce 2nd and 3rd best fits and see if the 1st best one stands out as a visibly better match (and corresponding higher correlation) than the 2nd and 3rd best fits. Tom On Oct 29, 2013, at 5:57 PM, Jessica Holien wrote: > I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jholien at svi.edu.au Tue Oct 29 18:39:37 2013 From: jholien at svi.edu.au (Jessica Holien) Date: Wed, 30 Oct 2013 12:39:37 +1100 (EST) Subject: [Chimera-users] Fitting models into density - meaning of values In-Reply-To: Message-ID: <614196792.23935.1383097177423.JavaMail.root@zstore.medstv.unimelb.edu.au> Thanks Tom - so within my map I can say the higher the value the "better" the fit? Luckily we have a fair bit of biological data which adds to the modelling. I have used the authors "suggested" contour level and knew that the correlation should be around 0.8 (or higher) - which it is for these models at this level. This is my first attempt at EM density fitting and thought Chimera was very user friendly! Jess Dr. Jessica Holien, PhD Research Officer Biota Structural Biology Laboratory ACRF Rational Drug Discovery Centre St. Vincent's Institute of Medical Research Address: 9 Princes St, Fitzroy, Victoria, Australia 3065 Postal: 41 Victoria St, Fitzroy, Victoria, Australia 3065 Telephone: +61 3 9288 2685 Email: jholien at svi.edu.au ----- Original Message ----- From: "Tom Goddard" To: "Jessica Holien" Cc: chimera-users at cgl.ucsf.edu Sent: Wednesday, 30 October, 2013 12:22:32 PM Subject: Re: [Chimera-users] Fitting models into density - meaning of values Hi Jessica, The "average map" value reported by Chimera is only useful for comparing different fits in the same map. The values in a density map normalized in ways that differ from map to map, so the absolute value is meaningless. What is sometimes reported in the literature is correlation coefficient, ranging from -1 to 1. The Chimera fitting will report this if you use the Options button on the Fit Map dialog and enable "Use simulated map ? with resolution 23". The correlation compares a simulated map from your atomic model to the experimental map. Values like 0.8 and higher are often considered "good". But unfortunately this is a very poor indicator too for several reasons. First it depends on the region in space over which the correlation was measured. In Chimera this will be the grid points within the displayed contour of the simulated map. (You'll have to show the simulated map using the volume dialog or model panel to see that contour level.) Higher contour levels use fewer grid points and often give a much higher correlation value. Another reason this is a poor measure is that it doesn't tell you if there are 5 other very different fits with equally good correlation value. For a low resolution map like 23 Angstroms, there may be many equally good and very different fits. The short answer is that it is hard to say if a fit to a low resolution map is good in a convincing way, and the research community does not have standard measures for this. To make your best effort I would try to produce 2nd and 3rd best fits and see if the 1st best one stands out as a visibly better match (and corresponding higher correlation) than the 2nd and 3rd best fits. Tom On Oct 29, 2013, at 5:57 PM, Jessica Holien wrote: > I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From berenger at riken.jp Wed Oct 30 00:29:25 2013 From: berenger at riken.jp (Francois Berenger) Date: Wed, 30 Oct 2013 16:29:25 +0900 Subject: [Chimera-users] color a small molecule in a .mol2 file by red to blue gradient of the partial charges Message-ID: <5270B555.1030607@riken.jp> Is it possible to do this in Chimera? I'd like a white background too. Thanks a lot, F. From gtseng at vcu.edu Wed Oct 30 06:58:56 2013 From: gtseng at vcu.edu (Gea-Ny Tseng/FS/VCU) Date: Wed, 30 Oct 2013 09:58:56 -0400 Subject: [Chimera-users] how to make the background of Chimera-generated images transparent Message-ID: Dear Chimera developers and users: I would like to know how to make the background of Chimera-generated images transparent. I used to be able to do this with an older version of Chimera. But with Chimera 1.8, I could not figure out how to do this. There are options in the 'Color/Background' to adjust 'Opacity', which to me means that I could make the background transparent by using 'zero'. But this did not happen. Could you please advise? Thank you. Gea-Ny Tseng, PhD Dept of Physiology & Biophysics Virginia Commonwealth University -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 30 09:35:18 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 30 Oct 2013 09:35:18 -0700 Subject: [Chimera-users] how to make the background of Chimera-generated images transparent In-Reply-To: References: Message-ID: <06BACD89-849C-4B0D-995D-BA6E8A8FC54C@sonic.net> Hi Gea-Ny, To save an image having a transparent background in Chimera 1.8 use File / Save Image? and click the "Transparent background" option in that dialog. Tom On Oct 30, 2013, at 6:58 AM, Gea-Ny Tseng/FS/VCU wrote: > Dear Chimera developers and users: > > I would like to know how to make the background of Chimera-generated images transparent . I used to be able to do this with an older version of Chimera. But with Chimera 1.8, I could not figure out how to do this. There are options in the 'Color/Background' to adjust 'Opacity', which to me means that I could make the background transparent by using 'zero'. But this did not happen. Could you please advise? > > Thank you. > > Gea-Ny Tseng, PhD > Dept of Physiology & Biophysics > Virginia Commonwealth University > _______________________________________________ > 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 Wed Oct 30 10:03:54 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 30 Oct 2013 10:03:54 -0700 Subject: [Chimera-users] color a small molecule in a .mol2 file by red to blue gradient of the partial charges In-Reply-To: <5270B555.1030607@riken.jp> References: <5270B555.1030607@riken.jp> Message-ID: Hi Francois, Yes, you can color by values of attributes such as charge with either the Render by Attribute tool (in menu under Tools... Depiction) or with the command "rangecolor". When you read in a mol2 file with charge values the "charge" attribute is automatically assigned. There are several examples of using these in the tutorials. The attributes tutorial part 1 uses both: The rangecolor example in that tutorial specifies particular values for red and blue, but as the man page says, you can also use the words "min" and "max" to mean the minimum and maximum charge values present in your molecule, e.g.: rangecolor charge min red 0 white max blue The GUI (Render by Attribute tool) has the advantage of showing you the range in a histogram and also displaying the names of the various attributes, although in this case it's just "charge". There are more examples of coloring by attribute in the attributes tutorial part 2 and the surface properties tutorial. There are several ways to switch to white background, including any of the publication presets and command "background solid white": The image tips page covers many image-related topics such as background color. You can just click the "Tips" button on the image-saving dialog to show 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 Oct 30, 2013, at 12:29 AM, Francois Berenger wrote: > Is it possible to do this in Chimera? > > I'd like a white background too. > > Thanks a lot, > F. > _______________________________________________ > 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 Wed Oct 30 10:10:19 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 30 Oct 2013 10:10:19 -0700 Subject: [Chimera-users] color a small molecule in a .mol2 file by red to blue gradient of the partial charges In-Reply-To: References: <5270B555.1030607@riken.jp> Message-ID: P.S. If your mol2 file didn't already have charges, you can add them in Chimera (menu: Tools... Structure Editing... Add Charge, or command: addcharge). It may call another tool to add hydrogens first if your structure doesn't already have them. On Oct 30, 2013, at 10:03 AM, Elaine Meng wrote: > Hi Francois, > Yes, you can color by values of attributes such as charge with either the Render by Attribute tool (in menu under Tools... Depiction) or with the command "rangecolor". When you read in a mol2 file with charge values the "charge" attribute is automatically assigned. > > > > > There are several examples of using these in the tutorials. The attributes tutorial part 1 uses both: > > > The rangecolor example in that tutorial specifies particular values for red and blue, but as the man page says, you can also use the words "min" and "max" to mean the minimum and maximum charge values present in your molecule, e.g.: > > rangecolor charge min red 0 white max blue > > The GUI (Render by Attribute tool) has the advantage of showing you the range in a histogram and also displaying the names of the various attributes, although in this case it's just "charge". There are more examples of coloring by attribute in the attributes tutorial part 2 and the surface properties tutorial. > > > > There are several ways to switch to white background, including any of the publication presets and command "background solid white": > > > The image tips page covers many image-related topics such as background color. You can just click the "Tips" button on the image-saving dialog to show 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 Oct 30, 2013, at 12:29 AM, Francois Berenger wrote: > >> Is it possible to do this in Chimera? >> >> I'd like a white background too. >> >> Thanks a lot, >> F. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Wed Oct 30 11:37:14 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 30 Oct 2013 11:37:14 -0700 Subject: [Chimera-users] Coloring distance lines between atoms In-Reply-To: <5268F2BC.3070206@fourmentinguilbert.org> References: <5268F2BC.3070206@fourmentinguilbert.org> Message-ID: <22736859-E590-4FB8-B25C-97348210C131@sonic.net> Hi Damien, Here is a Chimera Python script colordist.py that lets you color distance lines between atoms based on how long the distance is. The colors update as you move one model relative to another. After showing some distances, for instance with the "distance" command you would use command runscript colordist.py 8.5 green red to color the distance lines less than 8.5 Angstroms green, and longer ones red. The script needs to be in the directory you started Chimera in (e.g. on Linux), or you can specify a full path to the script "runscript /Users/Smith/colordist.py ?", or use the Chimera "cd" command to change to the directory containing the script. You can select specific distance lines to color with the mouse and use runscript colordist.py 8.5 green red sel You can stop the color updating using runscript colordist.py or for just selected distance lines runscript colordist.py sel Tom -------------- next part -------------- A non-text attachment was scrubbed... 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Name: colordist.py Type: text/x-python-script Size: 3509 bytes Desc: not available URL: -------------- next part -------------- On Oct 24, 2013, at 3:13 AM, Damien Larivi?re wrote: > Hi Tom, > > So, here is a reminder for the script we talked about. > > The idea is as follows: > > Once I have loaded several proteins in Chimera, once I have calculated distances between residue pairs that are displayed in the distance popup window, once I have displayed visually the distance as a colored stick pseudobond, then I would like a switch of the pseudobond color to occur when the distance is higher than a given value as I'm moving the proteins. > So, in my current manual modeling, I'm calculating a total of 24 distances between 5 proteins, I ask Chimera to display 24 pseudobond, most of them are initially let'say red, I load the script after having editing it with the distances and the associated maximal values, I move the proteins and the pseudobond color turn from red to yellow when the distance get lower than the maximal value defined for this distance in the script. And inversely, a pseudobond turns to red from yellow when it gets higher than a maximum distance. > > Let me know if you need more explanations. > > Many thanks for your help, > > Damien > From goddard at sonic.net Wed Oct 30 15:10:38 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 30 Oct 2013 15:10:38 -0700 Subject: [Chimera-users] Fitting models into density - meaning of values In-Reply-To: <614196792.23935.1383097177423.JavaMail.root@zstore.medstv.unimelb.edu.au> References: <614196792.23935.1383097177423.JavaMail.root@zstore.medstv.unimelb.edu.au> Message-ID: <12CFBFF4-CA5C-4A2B-8D3D-89F762BC509E@sonic.net> Hi Jess, The "average map value" that Chimera fitting reports just means the density map value averaged over the center positions of all the fit atoms. So a higher value means the atoms sit in higher density, and that should be a better fit since the protein density is higher than the solvent density. Also higher correlation is better. Tom On Oct 29, 2013, at 6:39 PM, Jessica Holien wrote: > Thanks Tom - so within my map I can say the higher the value the "better" the fit? Luckily we have a fair bit of biological data which adds to the modelling. I have used the authors "suggested" contour level and knew that the correlation should be around 0.8 (or higher) - which it is for these models at this level. This is my first attempt at EM density fitting and thought Chimera was very user friendly! > > Jess > > Dr. Jessica Holien, PhD > Research Officer > Biota Structural Biology Laboratory > ACRF Rational Drug Discovery Centre > St. Vincent's Institute of Medical Research > > Address: 9 Princes St, Fitzroy, Victoria, Australia 3065 > Postal: 41 Victoria St, Fitzroy, Victoria, Australia 3065 > Telephone: +61 3 9288 2685 > > ----- Original Message ----- > From: "Tom Goddard" > To: "Jessica Holien" > Cc: chimera-users at cgl.ucsf.edu > Sent: Wednesday, 30 October, 2013 12:22:32 PM > Subject: Re: [Chimera-users] Fitting models into density - meaning of values > > Hi Jessica, > > The "average map" value reported by Chimera is only useful for comparing different fits in the same map. The values in a density map normalized in ways that differ from map to map, so the absolute value is meaningless. What is sometimes reported in the literature is correlation coefficient, ranging from -1 to 1. The Chimera fitting will report this if you use the Options button on the Fit Map dialog and enable "Use simulated map ? with resolution 23". The correlation compares a simulated map from your atomic model to the experimental map. Values like 0.8 and higher are often considered "good". But unfortunately this is a very poor indicator too for several reasons. First it depends on the region in space over which the correlation was measured. In Chimera this will be the grid points within the displayed contour of the simulated map. (You'll have to show the simulated map using the volume dialog or model panel to see that contour level.) Higher contour levels use fewer grid points and often give a much higher correlation value. Another reason this is a poor measure is that it doesn't tell you if there are 5 other very different fits with equally good correlation value. For a low resolution map like 23 Angstroms, there may be many equally good and very different fits. The short answer is that it is hard to say if a fit to a low resolution map is good in a convincing way, and the research community does not have standard measures for this. To make your best effort I would try to produce 2nd and 3rd best fits and see if the 1st best one stands out as a visibly better match (and corresponding higher correlation) than the 2nd and 3rd best fits. > > Tom > > > > On Oct 29, 2013, at 5:57 PM, Jessica Holien wrote: > >> I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >