From meng at cgl.ucsf.edu Mon Mar 4 09:14:33 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 4 Mar 2013 09:14:33 -0800 Subject: [Chimera-users] Question about using the volume command In-Reply-To: <8CBDB911-7247-441E-B81C-12EA594865F0@me.com> References: <8CBDB911-7247-441E-B81C-12EA594865F0@me.com> Message-ID: <2A90B639-0B3F-4F6E-8FD3-CB03FCE51A18@cgl.ucsf.edu> Please see previous response to duplicate question: ... culminating in: On Feb 28, 2013, at 2:24 AM, Henning Stahlberg wrote: > > The command > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be ". > What am I doing wrong? > > Thanks for any suggestions, Henning. From meng at cgl.ucsf.edu Mon Mar 4 09:17:26 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 4 Mar 2013 09:17:26 -0800 Subject: [Chimera-users] Thank You In-Reply-To: References: Message-ID: <8B5AEE6E-E808-43C8-B157-87FDC76535B5@cgl.ucsf.edu> Hi Noel, You're welcome -- we look forward to seeing your work! 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 Feb 27, 2013, at 5:33 PM, Noel Pace wrote: > thank you to all of you who helped me in compiling a DEMO which I will be using for my dissertation project. I will be making this DEMO public once it has been tested and modified accordingly. > > Noel Pace > Malta From goddard at sonic.net Mon Mar 4 13:38:19 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 04 Mar 2013 13:38:19 -0800 Subject: [Chimera-users] [chimera-dev] 2-D projection of volume in Chimera In-Reply-To: <24954B2B-9085-4DC1-8BAE-0B665D3AE770@cgl.ucsf.edu> References: <24954B2B-9085-4DC1-8BAE-0B665D3AE770@cgl.ucsf.edu> Message-ID: <5135144B.9030001@sonic.net> Hi Jesus, There is a tricky way to do a projection of a map in Chimera. You can use the map binning capability. For example, if map #0 has 144 planes along the z axis I can add all those planes with vop bin #0 binsize 1,1,144 This can be done with a dialog instead of a command using Tools / Volume Data / Volume Filter, filter type bin and type in the bin size as 1 1 144. You also want a view along an axis other than x, y or z it sounds like. To do that you would resample the map on a new rotated grid so that the z axis is along the desired projection axis. The following video shows how to use the Chimera volume dialog subregion selection capability to do that http://www.cgl.ucsf.edu/chimera/videodoc/rotatedbox/ Tom -------- Original Message -------- Subject: Re: [chimera-dev] 2-D projection of volume in Chimera From: Elaine Meng To: Jesus Montoya Date: 3/4/13 11:59 AM > Hi Jesus, > Sorry, I don't think there is a way, currently. Here is the most recent information I could find on that topic: > > > > Regards, > 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. For future questions, you may want to send to chimera-users at cgl.ucsf.edu (chimera-dev is mainly for programming questions). > > On Feb 26, 2013, at 5:28 PM, Jesus Montoya wrote: > >> Hi, >> >> Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? >> >> For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). >> Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. >> >> While a "solid" representation of the volume is similar, it is not exactly what I need... >> >> Thanks! >> >> From miromoman at gmail.com Tue Mar 5 13:03:40 2013 From: miromoman at gmail.com (Miro Moman) Date: Tue, 05 Mar 2013 22:03:40 +0100 Subject: [Chimera-users] Guessing net charge Message-ID: <51365DAC.9040508@gmail.com> Hello, When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Best regards, Miro Moman -- http://www.e-moman.eu From pett at cgl.ucsf.edu Tue Mar 5 13:59:00 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 5 Mar 2013 13:59:00 -0800 Subject: [Chimera-users] Guessing net charge In-Reply-To: <51365DAC.9040508@gmail.com> References: <51365DAC.9040508@gmail.com> Message-ID: <80526928-D26D-4A1B-9D2C-431955CF49DC@cgl.ucsf.edu> On Mar 5, 2013, at 1:03 PM, Miro Moman wrote: > Hello, > > When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. > > I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Hi Miro, Chimera makes an assessment of the atom types of the atoms of a structure as the structure is opened. Those atom types have an associated charge state and protonation state, which allows Chimera to guesstimate the formal charge of a structure as long as the original atom-type assessment was correct. The Python function that takes a set of atoms and returns the estimated formal charge is AddCharge.estimateNetCharge. I don't know how familiar you are with Python programming, but the Chimera Python code to run through all currently open structures and write their estimated formal charge to a file named "charge-estimates" in your home directory would be: from chimera import openModels, Molecule from AddCharge import estimateNetCharge from OpenSave import osOpen output = osOpen("~/charge-estimates", "w") for m in openModels.list(modelTypes=[Molecule]): print>>output, m, m.name, estimateNetCharge(m.atoms) output.close() If the above code were in a file named "estimate.py", then you could estimate all the charges for all the Mol2 files in a directory with: chimera --nogui *.mol2 estimate.py There's more about programming Chimera in the Programmer's Guide. More info about starting Chimera in nogui/batch mode here: Chimera startup --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From ykarant at csusb.edu Tue Mar 5 21:06:54 2013 From: ykarant at csusb.edu (Yasha Karant) Date: Tue, 05 Mar 2013 21:06:54 -0800 Subject: [Chimera-users] How to fork/specify a web browser Message-ID: <5136CEEE.9050207@csusb.edu> For certain of the tutorials, help files, etc., Chimera linux displays a comment to use a web browser in order to use a URL file://foobar . How does one configure Chimera to automatically use a specified browser to diplay the URL generated by Chimera? I have not been able to find a preferences setting for this, nor an answer on the web or in the Chimera manuals/help. I have not perused the source code for Chimera to find a solution. Yasha Karant From jerome.henin at ibpc.fr Wed Mar 6 08:27:03 2013 From: jerome.henin at ibpc.fr (=?utf-8?B?SsOpcsO0bWUgSMOpbmlu?=) Date: Wed, 6 Mar 2013 17:27:03 +0100 (CET) Subject: [Chimera-users] ViewDock: flexible receptor residues in different chains In-Reply-To: <2080254237.838800.1362586550332.JavaMail.root@raba> Message-ID: <927325315.838974.1362587223338.JavaMail.root@raba> Hi everyone, When viewing Autodock Vina results in ViewDock, I hit a problem that I think is due to insufficient parsing of the PDBQT file. I have flexible receptor residues in two identical chains, say, Leu15 in chain A and Leu15 in chain B - these sidechains are part of the PDBQT file. However, ViewDock apparently ignores chain identifiers in that file, so it is unable to distinguish between these two residues, and it creates mangled bonds linking them while some other bonds are missing. I don't know how much work it would be to parse chain identifiers from the PDBQT file, I would have a go at it if I was more of a Python person, but I really am not. Best, Jerome From gregc at cgl.ucsf.edu Wed Mar 6 11:18:20 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 06 Mar 2013 11:18:20 -0800 Subject: [Chimera-users] How to fork/specify a web browser In-Reply-To: <2a51a722d11f82934d0b22d25a087e80.squirrel@mail.cgl.ucsf.edu> References: <2a51a722d11f82934d0b22d25a087e80.squirrel@mail.cgl.ucsf.edu> Message-ID: <5137967C.3060404@cgl.ucsf.edu> Forgot to include list in reply. -------- Original Message -------- Subject: Re: [Chimera-users] How to fork/specify a web browser Date: Wed, 6 Mar 2013 09:23:11 -0800 From: gregc at cgl.ucsf.edu To: Yasha Karant > For certain of the tutorials, help files, etc., Chimera linux displays a > comment to use a web browser in order to use a URL file://foobar . > How does one configure Chimera to automatically use a specified browser > to diplay the URL generated by Chimera? I have not been able to find a > preferences setting for this, nor an answer on the web or in the Chimera > manuals/help. I have not perused the source code for Chimera to find a > solution. > > Yasha Karant > Chimera uses Python 2.7's webbrowser module to open files in a web browser. For Linux, if you are using a GNOME or KDE desktop environment, then it will use the default browser that is configured for that environment. Otherwise, it looks for firefox (and derivatives), kfm, konqueror, galeon, epiphany, skipstone, opera, mosaic, and grail(!). You can override the the search order with the BROWSER environment variable. You may have noticed that Google's chrome is not on that list. Chrome support is included in Python 3's webbrowser module. But, that support would only be needed if you are not using a GNOME or KDE desktop environment. I will look into how much work it would be to backport Python 3's webbrowser module to Chimera. HTH, Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From scooter at cgl.ucsf.edu Wed Mar 6 14:30:45 2013 From: scooter at cgl.ucsf.edu (Scooter Morris) Date: Wed, 06 Mar 2013 14:30:45 -0800 Subject: [Chimera-users] Chimera Tutorial in Boston area Message-ID: <5137C395.20604@cgl.ucsf.edu> Hi all, I'll be teaching a Chimera tutorial scheduled as part of the VizBI conference in Cambridge, MA. See the Program for information about what we'll be covering, or just bring your favorite structure and we'll explore some of Chimera's new features. -- scooter -------------- next part -------------- An HTML attachment was scrubbed... URL: From chinh.sutranto at gmail.com Fri Mar 8 00:01:35 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Fri, 8 Mar 2013 16:01:35 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera Message-ID: Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. I have bunch of conformations, so I may not use the gui. Thank you. Chinh -------------- next part -------------- An HTML attachment was scrubbed... URL: From ybausty at yahoo.com Fri Mar 8 08:16:12 2013 From: ybausty at yahoo.com (Austin B. Yongye) Date: Fri, 8 Mar 2013 08:16:12 -0800 (PST) Subject: [Chimera-users] Transparency In-Reply-To: Message-ID: <1362759372.2702.YahooMailClassic@web140702.mail.bf1.yahoo.com> Hi everyone,I have chimera-v1.6, and would like to make some residues transparent.I enter: transparency 80,r sel, and I get "Unrecognized command: "transparency"Please is this command available? I checked the updates in chimera-v1.7 and the command was listed.Thanks,Austin- -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 8 08:58:16 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 8 Mar 2013 08:58:16 -0800 Subject: [Chimera-users] Transparency In-Reply-To: <1362759372.2702.YahooMailClassic@web140702.mail.bf1.yahoo.com> References: <1362759372.2702.YahooMailClassic@web140702.mail.bf1.yahoo.com> Message-ID: <8FDE3BBE-055C-4EEB-B2A0-297F72E32E29@cgl.ucsf.edu> Hi Austin, As per the Chimera version 1.7 release notes, ...the transparency command is new in 1.7. In other words, you have to get Chimera 1.7 or newer (1.8 daily build) to use it. 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 Mar 8, 2013, at 8:16 AM, Austin B. Yongye wrote: > Hi everyone, > I have chimera-v1.6, and would like to make some residues transparent. > I enter: transparency 80,r sel, and I get "Unrecognized command: "transparency" > Please is this command available? I checked the updates in chimera-v1.7 and the command was listed. > Thanks, > Austin- From meng at cgl.ucsf.edu Fri Mar 8 09:08:07 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 8 Mar 2013 09:08:07 -0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: References: Message-ID: Hi Chinh, For scripting measurements (distance, angle, torsion) you can use commands: distance, angle These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry. More info on writing Chimera scripts to process multiple data files: 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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote: > Hi, > I have some results after running docking from DOCK. > I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). > > Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. > > I have bunch of conformations, so I may not use the gui. > Thank you. > Chinh From pett at cgl.ucsf.edu Fri Mar 8 10:01:14 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 8 Mar 2013 10:01:14 -0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: References: Message-ID: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> Hi Chinh, If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide to write a script to get the values. There is a programmer's example specifically about atomic-level measurements such as angles and distances: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html Also, Python is reasonably easy to learn, especially if you already know how to program in another language. There are links to Python tutorials in the Programmer's Guide. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote: > Hi Chinh, > For scripting measurements (distance, angle, torsion) you can use commands: distance, angle > > > > These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry. > > More info on writing Chimera scripts to process multiple data files: > > > 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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote: > >> Hi, >> I have some results after running docking from DOCK. >> I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). >> >> Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. >> >> I have bunch of conformations, so I may not use the gui. >> Thank you. >> Chinh > > > _______________________________________________ > 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 ybausty at yahoo.com Fri Mar 8 10:34:35 2013 From: ybausty at yahoo.com (Austin B. Yongye) Date: Fri, 8 Mar 2013 10:34:35 -0800 (PST) Subject: [Chimera-users] Transparency In-Reply-To: <8FDE3BBE-055C-4EEB-B2A0-297F72E32E29@cgl.ucsf.edu> Message-ID: <1362767675.44314.YahooMailClassic@web140703.mail.bf1.yahoo.com> Thank you!Austin- --- On Fri, 3/8/13, Elaine Meng wrote: From: Elaine Meng Subject: Re: [Chimera-users] Transparency To: "Austin B. Yongye" Cc: "UCSF Chimera Mailing List" Date: Friday, March 8, 2013, 8:58 AM Hi Austin, As per the Chimera version 1.7 release notes, ...the transparency command is new in 1.7.? In other words, you have to get Chimera 1.7 or newer (1.8 daily build) to use it. 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 Mar 8, 2013, at 8:16 AM, Austin B. Yongye wrote: > Hi everyone, > I have chimera-v1.6, and would like to make some residues transparent. > I enter: transparency 80,r sel, and I get "Unrecognized command: "transparency" > Please is this command available? I checked the updates in chimera-v1.7 and the command was listed. > Thanks, > Austin- -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Fri Mar 8 13:19:10 2013 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Fri, 08 Mar 2013 13:19:10 -0800 Subject: [Chimera-users] ViewDock: flexible receptor residues in different chains In-Reply-To: <927325315.838974.1362587223338.JavaMail.root@raba> References: <927325315.838974.1362587223338.JavaMail.root@raba> Message-ID: <513A55CE.4000303@cgl.ucsf.edu> This should be fixed in tomorrow's daily build (anything dated March 9 or later). ViewDock will reads chain identifier and insertion code along with residue sequence. Consecutive residues with different chain identifiers will not have a bond between them. The only thing I'm not sure about are the missing bonds. Can you please take a look and see if there are still missing bonds in the new version? Thanks. Conrad On 3/6/2013 8:27 AM, J?r?me H?nin wrote: > Hi everyone, > > When viewing Autodock Vina results in ViewDock, I hit a problem that > I think is due to insufficient parsing of the PDBQT file. I have > flexible receptor residues in two identical chains, say, Leu15 in > chain A and Leu15 in chain B - these sidechains are part of the PDBQT > file. However, ViewDock apparently ignores chain identifiers in that > file, so it is unable to distinguish between these two residues, and > it creates mangled bonds linking them while some other bonds are > missing. > > I don't know how much work it would be to parse chain identifiers > from the PDBQT file, I would have a go at it if I was more of a > Python person, but I really am not. > > Best, Jerome _______________________________________________ > Chimera-users mailing list Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From coyote_v2002 at yahoo.com Fri Mar 8 20:59:09 2013 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Fri, 8 Mar 2013 20:59:09 -0800 (PST) Subject: [Chimera-users] internal coordinates (z-matrix) in chimera (Chinh Su Tran To) In-Reply-To: References: Message-ID: <1362805149.10737.YahooMailNeo@web140806.mail.bf1.yahoo.com> Dear Chinh, I am not sure if you can do multiple (batch) conversions in chimera, but the tool you seek could be openbabel, using command line or openbabel gui. On the command line you can issue, for one molecule (it's for Linux): babel my.mol my.gzmat This creates Gaussian style Bond-Angle-Torsion a.k.a. Z-matrix coordinates. For batch processing, you can use: babel *.mol -ozmat -m Best regards, Vis -------------- next part -------------- An HTML attachment was scrubbed... URL: From chinh.sutranto at gmail.com Sat Mar 9 00:33:34 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Sat, 9 Mar 2013 16:33:34 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> Message-ID: Dear all, Thank you very much for your help. I am coding it in python and will run in batch mode. I think it will work. Chinh On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen wrote: > Hi Chinh, > If you are able to write a Python script, you could use the info in the > Chimera Programmer's Guide > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide > > to write a script to get the values. There is a programmer's example > specifically about atomic-level measurements such as angles and distances: > > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html > > Also, Python is reasonably easy to learn, especially if you already know > how to program in another language. There are links to Python tutorials in > the Programmer's Guide. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote: > > Hi Chinh, > For scripting measurements (distance, angle, torsion) you can use > commands: distance, angle > > > > These measurements are specified individually. Chimera does not have an > option to write out a Z-matrix, sorry. > > More info on writing Chimera scripts to process multiple data files: > > > 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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote: > > Hi, > > I have some results after running docking from DOCK. > > I'd like to obtain information of internal coordinates (bond, angle, > torsion OR z-matrix). > > > Could anyone please give me any suggestion how to do that in Chimera? Or > if possible, please suggest me some references that can help me find it out. > > > I have bunch of conformations, so I may not use the gui. > > Thank you. > > Chinh > > > > _______________________________________________ > 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 tomek.wlodarski at gmail.com Sun Mar 10 14:48:31 2013 From: tomek.wlodarski at gmail.com (Tomek Wlodarski) Date: Sun, 10 Mar 2013 22:48:31 +0100 Subject: [Chimera-users] chimera and modeller Message-ID: Hi! I am trying to run Modeller from Chimera (Model/Refine Loops). I have downloaded the newest version of both, and I can run Modeller as a stand alone software via python. As a location of Modeller exe I put: /usr/lib/modeller9.11/bin/mod9.11 however when I try to run this it does nothing... Status is "completed" while State is "running" and Run time is (-). On the other hand I can run via Modeller server.. When I tried to run /usr/lib/modeller9.11/bin/mod9.11 I got: FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation Any ideas or suggestions? Thanks a lot! Best! tomek -------------- next part -------------- An HTML attachment was scrubbed... URL: From jerome.henin at ibpc.fr Mon Mar 11 02:05:51 2013 From: jerome.henin at ibpc.fr (=?utf-8?B?SsOpcsO0bWUgSMOpbmlu?=) Date: Mon, 11 Mar 2013 10:05:51 +0100 (CET) Subject: [Chimera-users] ViewDock: flexible receptor residues in different chains In-Reply-To: <927325315.838974.1362587223338.JavaMail.root@raba> Message-ID: <270919788.895056.1362992751463.JavaMail.root@raba> Hi Conrad, The daily build works beautifully, with chain identifiers, all the bonds we want, and none of those we don't want. Thanks a lot! Jerome > From: Conrad Huang > Date: March 8, 2013 1:19:10 PM PST > To: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] ViewDock: flexible receptor residues in different chains > > This should be fixed in tomorrow's daily build (anything dated March 9 or later). ViewDock will reads chain identifier and insertion code along with residue sequence. Consecutive residues with different chain identifiers will not have a bond between them. The only thing I'm not sure about are the missing bonds. Can you please take a look and see if there are still missing bonds in the new version? Thanks. > > Conrad From meng at cgl.ucsf.edu Mon Mar 11 09:55:19 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 11 Mar 2013 09:55:19 -0700 Subject: [Chimera-users] chimera and modeller In-Reply-To: References: Message-ID: Hi Tomek, Doublecheck that you chose to use "local installation" in the Chimera-Modeller dialog and browse to make sure that is the correct location of the executable. Is that the same pathname you use to run it via python? If the calculation runs via web service, you don't need your own copy of Modeller, but you do need to also enter the license key in the dialog, as discussed here: However, it sounds like you already knew that. I don't really have other ideas of what to check, sorry... 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 Mar 10, 2013, at 2:48 PM, Tomek Wlodarski wrote: > Hi! > I am trying to run Modeller from Chimera (Model/Refine Loops). > I have downloaded the newest version of both, and I can run Modeller as a stand alone software via python. > As a location of Modeller exe I put: > /usr/lib/modeller9.11/bin/mod9.11 > however when I try to run this it does nothing... > Status is "completed" while State is "running" and Run time is (-). > On the other hand I can run via Modeller server.. > > When I tried to run /usr/lib/modeller9.11/bin/mod9.11 > I got: > FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation > > Any ideas or suggestions? > Thanks a lot! > Best! > > tomek From bshaanan at exchange.bgu.ac.il Mon Mar 11 15:14:41 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Mon, 11 Mar 2013 22:14:41 +0000 Subject: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it? Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F6C03E@hawk3.auth.ad.bgu.ac.il> An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Mar 11 15:41:47 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 11 Mar 2013 15:41:47 -0700 Subject: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it? In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF67F6C03E@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF67F6C03E@hawk3.auth.ad.bgu.ac.il> Message-ID: Hi Boaz, Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS). Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits. After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example. Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog. That option was just provided for convenience because people often like to evaluate pocket hydrophobicity. 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 Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote: > Hi, > I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane? > Thanks for your input. > Boaz From bshaanan at exchange.bgu.ac.il Mon Mar 11 15:51:47 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Mon, 11 Mar 2013 22:51:47 +0000 Subject: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it? In-Reply-To: References: <4B2A491F685D1E4FBBF985E193095AAF67F6C03E@hawk3.auth.ad.bgu.ac.il>, Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F6C0A3@hawk3.auth.ad.bgu.ac.il> Thanks a lot Elaine. That's good to know. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Tuesday, March 12, 2013 12:41 AM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it? Hi Boaz, Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS). Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits. After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example. Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog. That option was just provided for convenience because people often like to evaluate pocket hydrophobicity. 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 Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote: > Hi, > I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane? > Thanks for your input. > Boaz From hakang at postech.ac.kr Tue Mar 12 00:25:49 2013 From: hakang at postech.ac.kr (=?ks_c_5601-1987?B?sK3H9r7G?=) Date: Tue, 12 Mar 2013 16:25:49 +0900 Subject: [Chimera-users] How to change water molecule from triangle stick to folded line stick? Message-ID: <000301ce1ef2$d2b04790$7810d6b0$@postech.ac.kr> Hello, Chimera Users! I am just a beginner and haven?t learned much about Chimera. When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape. Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick) But, they are still triangle. It looks like there is H-H covalent bond in H2O. How can I remove this unwanted bond? Is there any other option for molecule shape? Like licorice? Please let me know how can I draw water with folded line stick shape, not triangle. Thanks in advance. Best regards, Hyeona Kang -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Mar 12 10:17:17 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 12 Mar 2013 10:17:17 -0700 Subject: [Chimera-users] How to change water molecule from triangle stick to folded line stick? In-Reply-To: <000301ce1ef2$d2b04790$7810d6b0$@postech.ac.kr> References: <000301ce1ef2$d2b04790$7810d6b0$@postech.ac.kr> Message-ID: Hello, Hyeona! Water molecules are sometimes defined with the extra H-H bond, to help them hold their shape during simulations. However, in Chimera you can just hide those bonds, for example with command: bonddisplay off :wat&H (show command line using menu: Favorites... Command Line) You could also delete them, although you might not want to do that if you might do energy calculations later or save the file for energy calculations in some other program. If you are sure you won't need the bonds later, you could delete them with command: ~bond :wat&H Whether or not the bond is shown, you can still use any display style for the molecules: stick, ball&stick, sphere ... 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 Mar 12, 2013, at 12:25 AM, ??? wrote: > Hello, Chimera Users! > > I am just a beginner and haven?t learned much about Chimera. > > When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape. > Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick) > But, they are still triangle. It looks like there is H-H covalent bond in H2O. > How can I remove this unwanted bond? > Is there any other option for molecule shape? Like licorice? > Please let me know how can I draw water with folded line stick shape, not triangle. > > Thanks in advance. > > Best regards, > Hyeona Kang From divjak.m at wehi.EDU.AU Tue Mar 12 23:01:31 2013 From: divjak.m at wehi.EDU.AU (Maja Divjak) Date: Wed, 13 Mar 2013 17:01:31 +1100 Subject: [Chimera-users] Reduce mesh density? Message-ID: <1F94C964-28B2-42BF-8233-6681E14FA19C@wehi.edu.au> Hello Chimera, I would like to export some protein models in obj format and I was wondering if there is some way of reducing the mesh complexity when I do that please? I am using the models for animations in Maya and when I use the mesh reduce feature in Maya, Im getting some rather odd results, so was wondering if I can actually simplify the models first in Chimera? Thank you for your time, Maja Divjak Walter and Eliza Hall Institute, 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 goddard at sonic.net Wed Mar 13 10:26:55 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 13 Mar 2013 10:26:55 -0700 Subject: [Chimera-users] Reduce mesh density? In-Reply-To: <1F94C964-28B2-42BF-8233-6681E14FA19C@wehi.edu.au> References: <1F94C964-28B2-42BF-8233-6681E14FA19C@wehi.edu.au> Message-ID: Hi Maja, Chimera OBJ export cannot handle molecular models (ribbons, spheres, sticks?). So I guess you mean surfaces. For a Chimera molecular surface there is a "vertex density" parameter that you can set to a lower value in Favorites / Preferences / New Surfaces? before creating the surface or by selecting the surface and using the selection inspector dialog (Actions / Inspect, MSMS surface). The default vertex density is 2. For density map surfaces you can set the step size in the volume dialog to 2 (use every other data point). For surfaces made with the molmap command you can use the gridSpacing option. Tom On Mar 12, 2013, at 11:01 PM, Maja Divjak wrote: > Hello Chimera, > > I would like to export some protein models in obj format and I was wondering if there is some way of reducing the mesh complexity when I do that please? I am using the models for animations in Maya and when I use the mesh reduce feature in Maya, Im getting some rather odd results, so was wondering if I can actually simplify the models first in Chimera? > > Thank you for your time, > > Maja Divjak > Walter and Eliza Hall Institute, > Melbourne, Australia From Mireya_Gonzalez at URMC.Rochester.edu Thu Mar 14 12:59:29 2013 From: Mireya_Gonzalez at URMC.Rochester.edu (Gonzalez, Mireya) Date: Thu, 14 Mar 2013 15:59:29 -0400 Subject: [Chimera-users] structure Message-ID: <3F27BD44D0C0A043979226900EC0CA7C921D61DE@URMCMS5.urmc-sh.rochester.edu> To whom it should concern I am using your chimera on a specific protein that has/display 8 chains (A,B,C,D,E,F,G,H) with the same sequence. I would like to know how to hide the chains so I can work with one chain at a time in order to see where exactly my compound is binding so I can get the amino acid domain. Any help with this matter will be greatly appreciated. Dr. Mireya Gonzalez-Begne Research Assistant Professor University of Rochester Center for Oral Biology 601 Elmwood Ave. Rochester, NY Telephone: (585)273-1424 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3AIB.pdb Type: application/octet-stream Size: 8714547 bytes Desc: 3AIB.pdb URL: From meng at cgl.ucsf.edu Thu Mar 14 13:36:16 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 14 Mar 2013 13:36:16 -0700 Subject: [Chimera-users] structure In-Reply-To: <3F27BD44D0C0A043979226900EC0CA7C921D61DE@URMCMS5.urmc-sh.rochester.edu> References: <3F27BD44D0C0A043979226900EC0CA7C921D61DE@URMCMS5.urmc-sh.rochester.edu> Message-ID: Hi Mireya, There are several ways to control chain display individually. Here are some simple ways: In the menu you can use Select... Chain to select some chain, then choose something in the Actions menu to act on it, for example Actions... Ribbon... hide, Actions... Atoms/Bonds hide. In the command line (show with menu: Favorites... Command Line), there is a syntax to specify model, chain, residue, atom, ... For example, commands: ~ribbon :.e (hides ribbon for chain E) ~display ~:.e (hides atoms for all chains that are NOT chain E) You might want to take a look at some of the tutorials for learning Chimera, like Getting Started: .... and more, see Chimera menu: Help... Tutorials. 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 Mar 14, 2013, at 12:59 PM, Gonzalez, Mireya wrote: > To whom it should concern > I am using your chimera on a specific protein that has/display 8 chains (A,B,C,D,E,F,G,H) with the same sequence. > I would like to know how to hide the chains so I can work with one chain at a time in order to see where exactly my compound is binding so I can get the amino acid domain. > Any help with this matter will be greatly appreciated. From graham at grahamj.com Fri Mar 15 03:34:41 2013 From: graham at grahamj.com (Graham Johnson (qb3@UCSF)) Date: Fri, 15 Mar 2013 03:34:41 -0700 Subject: [Chimera-users] 3 DAYS! autoPACK Visualization Challenge: HIV in Blood Plasma due March 18 Message-ID: <27EB7817-BF6F-44EE-A0E3-8EE273B968A3@grahamj.com> Autodesk unites with UCSF and TSRI to challenge you to explore the mysterious world of HIV in vivo. We will provide competitors with a cellPACK model of HIV in blood plasma and a powerful open source app, called autoPACK. It is up to you to convey humanity's complex relationships with this virus, be they emotional, political, or intellectual. We need your help to excite general audiences with visuals that will help us spread interest in the search for a cure. We challenge you to use the animation tools available in Chimera, namely the new Animation GUI (Tools>Utilities>Animation), to create a movie and submit it to the challenge. You may submit to any of the following categories: ? Open Video: (grand prize $2,500 cash) competing against professional animators who are 3 months in ? Open Image: (grand prize $1,500 cash) competing against professional artists who are 3 months in ? Newly opened, 3 day long, Molecular-Viewer-Only: ($250, 3D print of HIV model, and AMD graphics card) competing strictly against other Chimera or PMV users only. Critical details on the following pages will help you get started immediately: 1) General challenge site: http://www.autopack.org/cellpackchallenge2012 2) Overview, installation, and animation instructions for Chimera-autoPACK: http://www.autopack.org/documentation/tutorials/molecular-viewers 3) Official autoPACK Visualization Challenge website to register and enter for free: http://autopack.cgsociety.org 4) Full prize details: http://autopack.cgsociety.org/autopack/prizes Please let me know if you have any questions and good luck! Graham Graham Johnson PhD qb3 at UCSF Fellow UCSF Lab: http://mesoscope.org Medical Illustration: http://grahamj.com Enter the autoPACK Visualization Challenge! Ends March 18 http://autopack.cgsociety.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: autoPACKvizChall_18days_1.jpg Type: image/jpeg Size: 22676 bytes Desc: not available URL: From Mireya_Gonzalez at URMC.Rochester.edu Fri Mar 15 07:53:36 2013 From: Mireya_Gonzalez at URMC.Rochester.edu (Gonzalez, Mireya) Date: Fri, 15 Mar 2013 10:53:36 -0400 Subject: [Chimera-users] structure In-Reply-To: References: <3F27BD44D0C0A043979226900EC0CA7C921D61DE@URMCMS5.urmc-sh.rochester.edu> Message-ID: <3F27BD44D0C0A043979226900EC0CA7C921D61E1@URMCMS5.urmc-sh.rochester.edu> Many thanks Elaine -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Thursday, March 14, 2013 4:36 PM To: Gonzalez, Mireya Cc: 'chimera-users at cgl.ucsf.edu' Subject: Re: [Chimera-users] structure Importance: High Hi Mireya, There are several ways to control chain display individually. Here are some simple ways: In the menu you can use Select... Chain to select some chain, then choose something in the Actions menu to act on it, for example Actions... Ribbon... hide, Actions... Atoms/Bonds hide. In the command line (show with menu: Favorites... Command Line), there is a syntax to specify model, chain, residue, atom, ... For example, commands: ~ribbon :.e (hides ribbon for chain E) ~display ~:.e (hides atoms for all chains that are NOT chain E) You might want to take a look at some of the tutorials for learning Chimera, like Getting Started: .... and more, see Chimera menu: Help... Tutorials. 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 Mar 14, 2013, at 12:59 PM, Gonzalez, Mireya wrote: > To whom it should concern > I am using your chimera on a specific protein that has/display 8 chains (A,B,C,D,E,F,G,H) with the same sequence. > I would like to know how to hide the chains so I can work with one chain at a time in order to see where exactly my compound is binding so I can get the amino acid domain. > Any help with this matter will be greatly appreciated. From rosa.miralles at uab.cat Fri Mar 15 09:11:03 2013 From: rosa.miralles at uab.cat (Rosa Miralles) Date: Fri, 15 Mar 2013 17:11:03 +0100 Subject: [Chimera-users] Colors of van der Waals speheres Message-ID: Hi, I would like to create an image with van der Waals radii colored in only one color instead of being colored as the corresponding atoms. Is it possible to choose the color of the van der Waals spheres? Thanks for your help, Rosa. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 15 10:32:05 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Mar 2013 10:32:05 -0700 Subject: [Chimera-users] Colors of van der Waals speheres In-Reply-To: References: Message-ID: <2CBE0B12-F623-42D8-A623-0002FC7ABDEB@cgl.ucsf.edu> Hi Rosa, The spheres are the atoms, just assign the atoms (=spheres) the desired colors with the Actions... Color menu or the "color" command. You might want to take a look at some of the tutorials for learning Chimera, like Getting Started: .... and more, see Chimera menu: Help... Tutorials. 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 Mar 15, 2013, at 9:11 AM, Rosa Miralles wrote: > Hi, > I would like to create an image with van der Waals radii colored in only one color instead of being colored as the corresponding atoms. Is it possible to choose the color of the van der Waals spheres? > Thanks for your help, > Rosa. From waldauer at pci.uzh.ch Fri Mar 15 10:53:25 2013 From: waldauer at pci.uzh.ch (Steven Waldauer) Date: Fri, 15 Mar 2013 18:53:25 +0100 Subject: [Chimera-users] define plane question Message-ID: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> Hi Everyone, Hopefully this isn't a stupid question. I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined? For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation. Thanks, Steve From meng at cgl.ucsf.edu Fri Mar 15 11:25:24 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Mar 2013 11:25:24 -0700 Subject: [Chimera-users] define plane question In-Reply-To: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> References: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> Message-ID: <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> Hi Steven, I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations. Axes/Planes/Centroids: "Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C. The plane is the best-fit plane to the specified points (atoms). Maybe Eric can clarify if more details are needed, however. 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 Mar 15, 2013, at 10:53 AM, Steven Waldauer wrote: > Hi Everyone, > > Hopefully this isn't a stupid question. > > I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined? > > For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation. > > Thanks, > > Steve From meng at cgl.ucsf.edu Fri Mar 15 11:32:13 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Mar 2013 11:32:13 -0700 Subject: [Chimera-users] define plane question In-Reply-To: <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> References: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> Message-ID: <4F7E2231-6552-4FA9-A965-0BD03367CFCB@cgl.ucsf.edu> Forgot to mention the plane center and radius. "The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 ?) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied." On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote: > Hi Steven, > I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations. > > Axes/Planes/Centroids: > > > "Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C. > > The plane is the best-fit plane to the specified points (atoms). > From pett at cgl.ucsf.edu Fri Mar 15 14:42:25 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 15 Mar 2013 14:42:25 -0700 Subject: [Chimera-users] define plane question In-Reply-To: <4F7E2231-6552-4FA9-A965-0BD03367CFCB@cgl.ucsf.edu> References: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> <4F7E2231-6552-4FA9-A965-0BD03367CFCB@cgl.ucsf.edu> Message-ID: <2BAE06B1-7F42-4952-AF4F-E1136B8422CA@cgl.ucsf.edu> On Mar 15, 2013, at 11:32 AM, Elaine Meng wrote: > Forgot to mention the plane center and radius. > > > > "The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 ?) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied." > > On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote: > >> Hi Steven, >> I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations. >> >> Axes/Planes/Centroids: >> >> >> "Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C. >> >> The plane is the best-fit plane to the specified points (atoms). To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jkw at iastate.edu Fri Mar 15 14:49:15 2013 From: jkw at iastate.edu (Jonathan Williams) Date: Fri, 15 Mar 2013 16:49:15 -0500 Subject: [Chimera-users] Import Chimera Modules Message-ID: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> Hello, I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: >>> import chimeraInit >>> chimeraInit.init([]) Traceback (most recent call last): File "", line 1, in File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. Any help or advice would be greatly appreciated, Jon Williams -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Mar 15 17:36:46 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 15 Mar 2013 17:36:46 -0700 Subject: [Chimera-users] chimera and modeller In-Reply-To: References: Message-ID: On Mar 10, 2013, at 2:48 PM, Tomek Wlodarski wrote: > Hi! > > I am trying to run Modeller from Chimera (Model/Refine Loops). > I have downloaded the newest version of both, and I can run Modeller as a stand alone software via python. > As a location of Modeller exe I put: > /usr/lib/modeller9.11/bin/mod9.11 > however when I try to run this it does nothing... > Status is "completed" while State is "running" and Run time is (-). > On the other hand I can run via Modeller server.. > > When I tried to run /usr/lib/modeller9.11/bin/mod9.11 > I got: > FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation This last part: do you mean you tried to run Modeller from outside Chimera and got that error? If so, then you should really ask on the Modeller mailing list: http://salilab.org/modeller/discussion_forum.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Mar 15 17:02:41 2013 From: goddard at sonic.net (Tom Goddard) Date: Fri, 15 Mar 2013 17:02:41 -0700 Subject: [Chimera-users] Import Chimera Modules In-Reply-To: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> References: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> Message-ID: Hi Jon, Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.cpp?rev=36787 and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries." Tom On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: > Hello, > > I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. > > However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: > > >>> import chimeraInit > >>> chimeraInit.init([]) > Traceback (most recent call last): > File "", line 1, in > File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init > import chimera > File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in > from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform > ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen > Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO > Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib > in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO > >>> > > I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. > > Any help or advice would be greatly appreciated, > > Jon Williams > > > > _______________________________________________ > 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 waldauer at pci.uzh.ch Sat Mar 16 07:42:52 2013 From: waldauer at pci.uzh.ch (Steven Waldauer) Date: Sat, 16 Mar 2013 15:42:52 +0100 Subject: [Chimera-users] define plane question In-Reply-To: <2BAE06B1-7F42-4952-AF4F-E1136B8422CA@cgl.ucsf.edu> References: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> <4F7E2231-6552-4FA9-A965-0BD03367CFCB@cgl.ucsf.edu> <2BAE06B1-7F42-4952-AF4F-E1136B8422CA@cgl.ucsf.edu> Message-ID: <78ADB8A8-313D-4525-9A19-330F148F8B1A@pci.uzh.ch> On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote: > To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above. > Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct: The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes. If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices? Thanks again for all the help. ****** Steven Andrew Waldauer Ph.D. Postdoctoral Fellow, Hamm Group Universit?t Z?rich Physikalisch-Chemisches Institut Winterthurerstr. 190, CH-8057 Z?rich Tel: +41 (0)44 635 44 66 Fax: +41 (0)44 635 68 38 E-Mail: waldauer at pci.uzh.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Mar 16 09:14:32 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 16 Mar 2013 09:14:32 -0700 Subject: [Chimera-users] define plane question In-Reply-To: <78ADB8A8-313D-4525-9A19-330F148F8B1A@pci.uzh.ch> References: <953EFF1A-170F-4F78-99C3-707DCA666338@pci.uzh.ch> <29DC3D47-C53A-4242-9D07-DB0E75854CEA@cgl.ucsf.edu> <4F7E2231-6552-4FA9-A965-0BD03367CFCB@cgl.ucsf.edu> <2BAE06B1-7F42-4952-AF4F-E1136B8422CA@cgl.ucsf.edu> <78ADB8A8-313D-4525-9A19-330F148F8B1A@pci.uzh.ch> Message-ID: Hi Steven, The "all helices" (protein) option is the only case where certain atoms are automatically used. All other axis, plane, centroid calculations use whichever atoms you have specified in the define command (or if using GUI, whichever atoms are in the current selection). 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 Mar 16, 2013, at 7:42 AM, Steven Waldauer wrote: > > On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote: > >> To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above. >> > > Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct: > > The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes. > > If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices? > > Thanks again for all the help. > > ****** > Steven Andrew Waldauer Ph.D. > Postdoctoral Fellow, Hamm Group From rswett at chem.wayne.edu Sat Mar 16 18:53:11 2013 From: rswett at chem.wayne.edu (Rebecca Swett) Date: Sat, 16 Mar 2013 21:53:11 -0400 Subject: [Chimera-users] Transparent single atoms when rendering stereoimages Message-ID: <51452207.4040108@chem.wayne.edu> Hi, i'm rendering some peptides structures that have single magnesium and manganese atoms in frame, and when I save the images as a stereopair, the atoms render as transparent, with protein ribbon showing through. I've tried several different colors on this, I think it's just a bug. The tips of sidechains also are transparent where the atoms are showing. I"m using the windows 64 bit build, in 1.7, downloaded today. -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768 From meng at cgl.ucsf.edu Sun Mar 17 10:06:34 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 17 Mar 2013 10:06:34 -0700 Subject: [Chimera-users] Transparent single atoms when rendering stereoimages In-Reply-To: <51452207.4040108@chem.wayne.edu> References: <51452207.4040108@chem.wayne.edu> Message-ID: Hi Rebecca, To report bugs, please use the Chimera menu: Help... Report a Bug. Please attach any files (e.g. session) and describe the steps needed to reproduce the bug, and include your email address if you wish to get feedback. 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 Mar 16, 2013, at 6:53 PM, Rebecca Swett wrote: > Hi, i'm rendering some peptides structures that have single magnesium and manganese atoms in frame, and when I save the images as a stereopair, the atoms > render as transparent, with protein ribbon showing through. I've tried several different colors on this, I think it's just a bug. The tips of sidechains also are transparent where the atoms are showing. I"m using the windows 64 bit build, in 1.7, downloaded today. From goddard at sonic.net Mon Mar 18 10:42:09 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 18 Mar 2013 10:42:09 -0700 Subject: [Chimera-users] Transparent single atoms when rendering stereoimages In-Reply-To: References: <51452207.4040108@chem.wayne.edu> Message-ID: <514751F1.2000604@sonic.net> Hi Rebecca, This is almost certainly a graphics driver bug, and the best chance at fixing it is to update the graphics driver on your system. It also helps us if you report a bug as Elaine suggested because then we know which graphics driver has the problem and can advise others. Tom > Hi Rebecca, > To report bugs, please use the Chimera menu: Help... Report a Bug. Please attach any files (e.g. session) and describe the steps needed to reproduce the bug, and include your email address if you wish to get feedback. > 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 Mar 16, 2013, at 6:53 PM, Rebecca Swett wrote: > >> Hi, i'm rendering some peptides structures that have single magnesium and manganese atoms in frame, and when I save the images as a stereopair, the atoms >> render as transparent, with protein ribbon showing through. I've tried several different colors on this, I think it's just a bug. The tips of sidechains also are transparent where the atoms are showing. I"m using the windows 64 bit build, in 1.7, downloaded today. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Mar 18 10:49:08 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 18 Mar 2013 10:49:08 -0700 Subject: [Chimera-users] Import Chimera Modules In-Reply-To: <47EB7295-9DCE-45B7-BEE2-DF66B6BA7606@iastate.edu> References: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> <47EB7295-9DCE-45B7-BEE2-DF66B6BA7606@iastate.edu> Message-ID: <51475394.9030803@sonic.net> Hi Jon, Chimera includes the version of libfreetype.6.dylib it needs. The error must mean you have another older libfreetype.6.dylib on your system that Chimera is getting instead of its own version. The first thing would be to try to locate where the other libfreetype.6.dylib is. I guess Chimera starts on your machine, so somehow it gets the right library. That suggests that you do not have the environment variables that control library loading setup in the same way as Chimera does. I'd suggest you start Chimera, open the IDLE shell window (Tools / General Controls) and print all the environment variables seen by the running Chimera using for example import os for k,v in os.environ.items(): print k,v and see if those differ from what you are trying outside Chimera. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Import Chimera Modules From: Jonathan Williams To: Tom Goddard Date: 3/18/13 8:05 AM > Hi Tom, > > Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH > variable, and I think this took care of my original problem. However > I have encountered a new error: > > ImportError: > dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, > 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib > Referenced from: > /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib > Reason: Incompatible library version: _chimera.dylib requires > version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 > > This seems like I just need to update my FreeType libraries, but I > have not had a chance to try this yet. If you have any other > suggestions, those would be appreciated, otherwise I'll send an update > when I get a chance. > > Thanks again, > > Jon > > > On Mar 15, 2013, at 7:02 PM, Tom Goddard > wrote: > >> Hi Jon, >> >> Maybe the trick is Chimera uses environment variable >> DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or >> DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that >> sets the environment variables >> >> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.cpp?rev=36787 >> >> and a comment on this code change says "Use >> DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so >> system frameworks will get system versions of shared libraries." >> >> Tom >> >> >> >> On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: >> >>> Hello, >>> >>> I am currently trying to import Chimera modules into a non-Chimera >>> python installation. I have referenced previous messages from this >>> mailing list >>> (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), >>> and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, >>> PYTHONPATH, and CHIMERA environment variables. >>> >>> However when I try to import Chimera, Midas or "import chimeraInit" >>> followed by "chimeraInit.init([])" I receive the following error: >>> >>> >>> import chimeraInit >>> >>> chimeraInit.init([]) >>> Traceback (most recent call last): >>> File "", line 1, in >>> File >>> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", >>> line 594, in init >>> import chimera >>> File >>> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", >>> line 16, in >>> from _chimera import BBox, Camera, Color, ColorGroup, >>> DirectionalLight, LODControl, Lens, LensViewer, Light, Material, >>> MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, >>> OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, >>> PositionalLight, Selectable, SharedState, SpotLight, Sphere, >>> Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >>> ImportError: >>> dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, >>> 2): Symbol not found: __cg_TIFFClientOpen >>> Referenced from: >>> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>> Expected in: >>> /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib >>> in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>> >>> >>> >>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build >>> 38197) for 64bit Mac. >>> >>> Any help or advice would be greatly appreciated, >>> >>> Jon Williams >>> >>> >>> >>> _______________________________________________ >>> 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 jkw at iastate.edu Mon Mar 18 08:05:33 2013 From: jkw at iastate.edu (Jonathan Williams) Date: Mon, 18 Mar 2013 10:05:33 -0500 Subject: [Chimera-users] Import Chimera Modules In-Reply-To: References: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> Message-ID: <47EB7295-9DCE-45B7-BEE2-DF66B6BA7606@iastate.edu> Hi Tom, Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH variable, and I think this took care of my original problem. However I have encountered a new error: ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib Referenced from: /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib Reason: Incompatible library version: _chimera.dylib requires version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 This seems like I just need to update my FreeType libraries, but I have not had a chance to try this yet. If you have any other suggestions, those would be appreciated, otherwise I'll send an update when I get a chance. Thanks again, Jon On Mar 15, 2013, at 7:02 PM, Tom Goddard wrote: > Hi Jon, > > Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables > > http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.cpp?rev=36787 > > and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries." > > Tom > > > > On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: > >> Hello, >> >> I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. >> >> However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: >> >> >>> import chimeraInit >> >>> chimeraInit.init([]) >> Traceback (most recent call last): >> File "", line 1, in >> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init >> import chimera >> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in >> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >> ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen >> Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >> Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib >> in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >> >>> >> >> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. >> >> Any help or advice would be greatly appreciated, >> >> Jon Williams >> >> >> >> _______________________________________________ >> 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 jkw at iastate.edu Mon Mar 18 14:37:31 2013 From: jkw at iastate.edu (Jonathan Williams) Date: Mon, 18 Mar 2013 16:37:31 -0500 Subject: [Chimera-users] Import Chimera Modules In-Reply-To: <51475394.9030803@sonic.net> References: <26619900-6F5D-441F-86AE-52F14AA91231@iastate.edu> <47EB7295-9DCE-45B7-BEE2-DF66B6BA7606@iastate.edu> <51475394.9030803@sonic.net> Message-ID: Hi Tom, Good news: I got the chimera modules to import! I think that you were correct about having an older libfreetype.6.dylib that was being used instead of Chimera's version, probably from my Enthought Python Distribution . Overall I believe that my EPD was making things harder for me. So I removed the EPD from my system, set all of the environment variables per the Chimera IDLE, added ~/Resources/lib and ~/Resources/share to PYTHONPATH, and now I'm in business. Thank you for your help and suggestions! Jon On Mar 18, 2013, at 12:49 PM, Tom Goddard wrote: > Hi Jon, > > Chimera includes the version of libfreetype.6.dylib it needs. The error must mean you have another older libfreetype.6.dylib on your system that Chimera is getting instead of its own version. The first thing would be to try to locate where the other libfreetype.6.dylib is. I guess Chimera starts on your machine, so somehow it gets the right library. That suggests that you do not have the environment variables that control library loading setup in the same way as Chimera does. I'd suggest you start Chimera, open the IDLE shell window (Tools / General Controls) and print all the environment variables seen by the running Chimera using for example > > import os > for k,v in os.environ.items(): > print k,v > > and see if those differ from what you are trying outside Chimera. > > Tom > > > > -------- Original Message -------- > Subject: Re: [Chimera-users] Import Chimera Modules > From: Jonathan Williams > To: Tom Goddard > Date: 3/18/13 8:05 AM >> Hi Tom, >> >> Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH variable, and I think this took care of my original problem. However I have encountered a new error: >> >> ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib >> Referenced from: /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib >> Reason: Incompatible library version: _chimera.dylib requires version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 >> >> This seems like I just need to update my FreeType libraries, but I have not had a chance to try this yet. If you have any other suggestions, those would be appreciated, otherwise I'll send an update when I get a chance. >> >> Thanks again, >> >> Jon >> >> >> On Mar 15, 2013, at 7:02 PM, Tom Goddard wrote: >> >>> Hi Jon, >>> >>> Maybe the trick is Chimera uses environment variable DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that sets the environment variables >>> >>> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.cpp?rev=36787 >>> >>> and a comment on this code change says "Use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so system frameworks will get system versions of shared libraries." >>> >>> Tom >>> >>> >>> >>> On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: >>> >>>> Hello, >>>> >>>> I am currently trying to import Chimera modules into a non-Chimera python installation. I have referenced previous messages from this mailing list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html), and have added the relevant paths to Chimera in the LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. >>>> >>>> However when I try to import Chimera, Midas or "import chimeraInit" followed by "chimeraInit.init([])" I receive the following error: >>>> >>>> >>> import chimeraInit >>>> >>> chimeraInit.init([]) >>>> Traceback (most recent call last): >>>> File "", line 1, in >>>> File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 594, in init >>>> import chimera >>>> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 16, in >>>> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >>>> ImportError: dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, 2): Symbol not found: __cg_TIFFClientOpen >>>> Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>> Expected in: /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib >>>> in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>> >>> >>>> >>>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build 38197) for 64bit Mac. >>>> >>>> Any help or advice would be greatly appreciated, >>>> >>>> Jon Williams >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 Tue Mar 19 09:29:18 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Mar 2013 09:29:18 -0700 Subject: [Chimera-users] show alpha-carbon as sphere in chimera In-Reply-To: References: <30D16A6D-B485-4DDA-B966-CABB88C8CE31@cgl.ucsf.edu> Message-ID: <386867AF-C46C-4518-9587-D9D2AFB56A68@cgl.ucsf.edu> On Mar 18, 2013, at 8:07 PM, Feixia wrote: > Hi Elaine, > Is there a way to show alpha-carbon only in Chimera as sphere? I can show beta-carbon, but always together with alpha-carbon. Alpha-carbon for some reason doesn't show by itself. Thanks a lot. > Best, > Feixia Hi Feixia, Maybe you are also displaying ribbon. By default when the ribbon is shown, the alpha-carbon will not show. You can allow showing both ribbon and alpha-carbon with command: ribbackbone However, you can see the "real" position of the alpha-carbon is not exactly on the ribbon. Sometimes it will seem to float away, and the image might not look good. That is because the default ribbon is a smooth interpolation. Possible ways to handle this issue: (a) don't show ribbon (b) make the alpha-carbon sphere(s) big enough and/or change the viewing angle so it is not obviously floating away from the ribbon. Whether this is possible depends on which positions you are displaying and the specific backbone conformation in those areas. (c) change the ribbon from the default B-spline to cardinal spline, with or without some compromise smoothing, for example with commands: ribspline cardinal ribspline cardinal smooth strand More discussion/explanation of this issue: 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 From y.goudetsidis at mail.cryst.bbk.ac.uk Tue Mar 19 03:56:54 2013 From: y.goudetsidis at mail.cryst.bbk.ac.uk (Yanni) Date: Tue, 19 Mar 2013 10:56:54 +0000 Subject: [Chimera-users] MSI Installer Message-ID: <51484476.4010601@mail.cryst.bbk.ac.uk> Hello Do you have a chimera MSI installer available to download? Many thanks Yanni From rosa.miralles at uab.cat Tue Mar 19 06:38:22 2013 From: rosa.miralles at uab.cat (Rosa Miralles) Date: Tue, 19 Mar 2013 14:38:22 +0100 Subject: [Chimera-users] Colors of van der Waals speheres In-Reply-To: <2CBE0B12-F623-42D8-A623-0002FC7ABDEB@cgl.ucsf.edu> References: <2CBE0B12-F623-42D8-A623-0002FC7ABDEB@cgl.ucsf.edu> Message-ID: Ok, thank you so much! Rosa. 2013/3/15 Elaine Meng > Hi Rosa, > The spheres are the atoms, just assign the atoms (=spheres) the desired > colors with the Actions... Color menu or the "color" command. > > You might want to take a look at some of the tutorials for learning > Chimera, like Getting Started: > > .... and more, see Chimera menu: Help... Tutorials. > > 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 Mar 15, 2013, at 9:11 AM, Rosa Miralles wrote: > > > Hi, > > I would like to create an image with van der Waals radii colored in only > one color instead of being colored as the corresponding atoms. Is it > possible to choose the color of the van der Waals spheres? > > Thanks for your help, > > Rosa. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Tue Mar 19 09:44:57 2013 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Tue, 19 Mar 2013 09:44:57 -0700 Subject: [Chimera-users] MSI Installer In-Reply-To: <51484476.4010601@mail.cryst.bbk.ac.uk> References: <51484476.4010601@mail.cryst.bbk.ac.uk> Message-ID: <51489609.4010802@cgl.ucsf.edu> No, we've stuck with Inno Setup installers because it was the most versatile installer package with a convenient command line interface that we could use as part of our nightly build. Is there a reason the current installer is insufficient? Conrad On 3/19/2013 3:56 AM, Yanni wrote: > Hello > > Do you have a chimera MSI installer available to download? > > Many thanks > Yanni > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From francesco.malatesta at fastwebnet.it Tue Mar 19 11:17:30 2013 From: francesco.malatesta at fastwebnet.it (Francesco Malatesta) Date: Tue, 19 Mar 2013 19:17:30 +0100 Subject: [Chimera-users] simple question Message-ID: Hello I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? thank you very much Francesco Malatesta From meng at cgl.ucsf.edu Tue Mar 19 11:45:32 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Mar 2013 11:45:32 -0700 Subject: [Chimera-users] select by residue type or category In-Reply-To: References: Message-ID: Hi Francesco, You could either just select by residue type and chain ID, for example command select :asp.j,glu.j ... or by amino acid category, for example command select :.j & hydrophobic see command-line atom specification (amino acid category is one of the built-in classifications): These same things can be done with the Actions... Select menu, see submenus "Selection Mode... append" (allows building up a selection instead of always replacing it, or intersecting, as with a specific chain), "Chain...[chain ID]", "Residue... amino acid category" and/or "Residue... [residue name]" but the menu approach is more tedious/longer than commands. The amino acid categories have default assignments taken from a literature reference as shown here, ... but you can change the assignments as you like using the ResProp tool, in menu under Tools... Structure Analysis. 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 Mar 19, 2013, at 11:17 AM, Francesco Malatesta wrote: > Hello > I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? > thank you very much > Francesco Malatesta From francesco.malatesta at fastwebnet.it Tue Mar 19 11:49:59 2013 From: francesco.malatesta at fastwebnet.it (Francesco Malatesta) Date: Tue, 19 Mar 2013 19:49:59 +0100 Subject: [Chimera-users] select by residue type or category In-Reply-To: References: Message-ID: Thank you very much Elaine Francesco Il giorno 19/mar/2013, alle ore 19:45, Elaine Meng ha scritto: > Hi Francesco, > You could either just select by residue type and chain ID, for example command > > select :asp.j,glu.j > > ... or by amino acid category, for example command > > select :.j & hydrophobic > > see command-line atom specification (amino acid category is one of the built-in classifications): > > > These same things can be done with the Actions... Select menu, see submenus "Selection Mode... append" (allows building up a selection instead of always replacing it, or intersecting, as with a specific chain), "Chain...[chain ID]", "Residue... amino acid category" and/or "Residue... [residue name]" but the menu approach is more tedious/longer than commands. > > The amino acid categories have default assignments taken from a literature reference as shown here, > > ... but you can change the assignments as you like using the ResProp tool, in menu under Tools... Structure Analysis. > > 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 Mar 19, 2013, at 11:17 AM, Francesco Malatesta wrote: > >> Hello >> I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both in the say J chain? >> thank you very much >> Francesco Malatesta > From ybausty at yahoo.com Tue Mar 19 12:31:18 2013 From: ybausty at yahoo.com (Austin B. Yongye) Date: Tue, 19 Mar 2013 12:31:18 -0700 (PDT) Subject: [Chimera-users] Version 1.7 on linux In-Reply-To: Message-ID: <1363721478.69178.YahooMailClassic@web140701.mail.bf1.yahoo.com> Hello Chimera users,I just installed version 1.7 on my centos v5.4 machine. When I launch it using an alias, there is a splash across my entire screen and two threads are shown on the bottom panel. This splash persists for long, and I get the usual GUI only after switching between the two threads a couple of times. When I proceed to open a structure, nothing shows up on the GUI though it says a structure has been opened.All these problems go away when I launch chimera directly from the installation directory.Any suggestions? Thanks.Austin- -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Mar 19 12:52:50 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 19 Mar 2013 12:52:50 -0700 Subject: [Chimera-users] Fwd: Re: Version 1.7 on linux In-Reply-To: <5148C1AF.7090705@cgl.ucsf.edu> References: <5148C1AF.7090705@cgl.ucsf.edu> Message-ID: <5148C212.4050507@cgl.ucsf.edu> (Forgot to reply to list as well.) Hi Austin, What's your alias? chimera should *not* be on your PATH, it expects to find its version of various system libraries. Instead put a symbolic link to CHIMERA/bin/chimera in one of the directories on your PATH. Not sure what you mean about two threads, a screenshot would help. HTH, Greg On 03/19/2013 12:31 PM, Austin B. Yongye wrote: > Hello Chimera users, > I just installed version 1.7 on my centos v5.4 machine. When I launch > it using an alias, there is a splash across my entire screen and two > threads are shown on the bottom panel. This splash persists for long, > and I get the usual GUI only after switching between the two threads a > couple of times. When I proceed to open a structure, nothing shows up > on the GUI though it says a structure has been opened. > All these problems go away when I launch chimera directly from the > installation directory. > Any suggestions? Thanks. > Austin- > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chinh.sutranto at gmail.com Wed Mar 20 02:28:35 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Wed, 20 Mar 2013 17:28:35 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> Message-ID: Hello, I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want. With the piece of code: *confor = chimera.openModels.list()* it shows an empty list of models (for mol2 file)??? Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious. Thank you. Chinh On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen wrote: > Hi Chinh, > If you are able to write a Python script, you could use the info in the > Chimera Programmer's Guide > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide > > to write a script to get the values. There is a programmer's example > specifically about atomic-level measurements such as angles and distances: > > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html > > Also, Python is reasonably easy to learn, especially if you already know > how to program in another language. There are links to Python tutorials in > the Programmer's Guide. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote: > > Hi Chinh, > For scripting measurements (distance, angle, torsion) you can use > commands: distance, angle > > > > These measurements are specified individually. Chimera does not have an > option to write out a Z-matrix, sorry. > > More info on writing Chimera scripts to process multiple data files: > > > 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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote: > > Hi, > > I have some results after running docking from DOCK. > > I'd like to obtain information of internal coordinates (bond, angle, > torsion OR z-matrix). > > > Could anyone please give me any suggestion how to do that in Chimera? Or > if possible, please suggest me some references that can help me find it out. > > > I have bunch of conformations, so I may not use the gui. > > Thank you. > > Chinh > > > > _______________________________________________ > 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 pett at cgl.ucsf.edu Wed Mar 20 11:12:13 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 20 Mar 2013 11:12:13 -0700 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> Message-ID: <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote: > Hello, > > I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. > When I ran it for Mol2 input, I could not get the angles I want. > > With the piece of code: > confor = chimera.openModels.list() > > it shows an empty list of models (for mol2 file)??? > > Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? > > I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. > > Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious. As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Wed Mar 20 13:49:51 2013 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 20 Mar 2013 13:49:51 -0700 Subject: [Chimera-users] MSI Installer In-Reply-To: <51489609.4010802@cgl.ucsf.edu> References: <51484476.4010601@mail.cryst.bbk.ac.uk> <51489609.4010802@cgl.ucsf.edu> Message-ID: <514A20EF.5020109@cgl.ucsf.edu> Just as a follow-uy: I don't think we will be generating MSI files any time soon. However, I tried out MSI Wrapper from exemsi.com that seems to work reasonably well. The documentation even specifically mentioned wrapping Inno Setup installers. The program is free and it takes only a few seconds to create the MSI file. Perhaps you can give that a try. (It ends up running the wrapped installer, so if you provide the Inno Setup command line arguments while building the MSI file, you should be able to run the entire Chimera installation in quiet mode.) Conrad On 3/19/2013 9:44 AM, Conrad Huang wrote: > No, we've stuck with Inno Setup installers because it was the most > versatile installer package with a convenient command line interface > that we could use as part of our nightly build. Is there a reason the > current installer is insufficient? > > Conrad > > On 3/19/2013 3:56 AM, Yanni wrote: >> Hello >> >> Do you have a chimera MSI installer available to download? >> >> Many thanks >> Yanni >> _______________________________________________ >> 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 fvy2 at unh.edu Tue Mar 19 17:30:31 2013 From: fvy2 at unh.edu (Feixia) Date: Tue, 19 Mar 2013 20:30:31 -0400 Subject: [Chimera-users] show alpha-carbon as sphere in chimera In-Reply-To: <386867AF-C46C-4518-9587-D9D2AFB56A68@cgl.ucsf.edu> References: <30D16A6D-B485-4DDA-B966-CABB88C8CE31@cgl.ucsf.edu> <386867AF-C46C-4518-9587-D9D2AFB56A68@cgl.ucsf.edu> Message-ID: Yes, very helpful! Thank you so much! Best, Feixia On Tue, 19 Mar 2013 12:29:18 -0400, Elaine Meng wrote: > On Mar 18, 2013, at 8:07 PM, Feixia wrote: > >> Hi Elaine, >> Is there a way to show alpha-carbon only in Chimera as sphere? I can >> show beta-carbon, but always together with alpha-carbon. Alpha-carbon >> for some reason doesn't show by itself. Thanks a lot. >> Best, >> Feixia > > Hi Feixia, > Maybe you are also displaying ribbon. By default when the ribbon is > shown, the alpha-carbon will not show. You can allow showing both > ribbon and alpha-carbon with command: > ribbackbone > > > However, you can see the "real" position of the alpha-carbon is not > exactly on the ribbon. Sometimes it will seem to float away, and the > image might not look good. That is because the default ribbon is a > smooth interpolation. > > Possible ways to handle this issue: > > (a) don't show ribbon > > (b) make the alpha-carbon sphere(s) big enough and/or change the viewing > angle so it is not obviously floating away from the ribbon. Whether > this is possible depends on which positions you are displaying and the > specific backbone conformation in those areas. > > (c) change the ribbon from the default B-spline to cardinal spline, with > or without some compromise smoothing, for example with commands: > ribspline cardinal > ribspline cardinal smooth strand > > > More discussion/explanation of this issue: > > > 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 > > > -- Feixia Chu, Ph.D. Assistant Professor Biochemistry Graduate Program Coordinator Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436 From chinh.sutranto at gmail.com Wed Mar 20 20:12:24 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Thu, 21 Mar 2013 11:12:24 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> Message-ID: Hi, Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []). *import chimera* *confor = chimera.openModels.list()* *print confor* >>> [] """ if I used *print confor[0]* >>> IndexError: list index out of range""" Thank you. Chinh On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen wrote: > On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote: > > Hello, > > I managed to get the torsion angles from scripting, but I encountered one > problem that my code works for pdb file ONLY. > When I ran it for Mol2 input, I could not get the angles I want. > > With the piece of code: > *confor = chimera.openModels.list()* > > it shows an empty list of models (for mol2 file)??? > > Please anyone help show me some hints how to convert Mol2 back to PDB or > anyway that I can directly deal with mol2 format)? > > I greatly appreciate if you please show me references about how chimera > works with Models. I guess I have not understood yet the differences > between pdb and mol2. It seems to me that mol2 contains the same info (in > terms of ATOM and coordinates), but an extra column of charges. > > Does that MODEL here mean conformations? Why the docked_conformer (results > from DOCK with various conformations) contains NO models according to > chimera? I am sorry that I did not mean questioning, but curious. > > > As far as Chimera is concerned, there is very little difference between a > model opened from a PDB file and one opened from a Mol2 file. > chimera.openModels.list() cannot be empty if Chimera is actually showing > any structures. Is it? (when you open the Mol2 file normally)? Maybe you > need to send along your Mol2 file and your script... > > --Eric > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lig_dock_conformers.mol2 Type: application/octet-stream Size: 79991 bytes Desc: not available URL: From chinh.sutranto at gmail.com Wed Mar 20 23:22:50 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Thu, 21 Mar 2013 14:22:50 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> Message-ID: Hi, I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. Thank you very much. Chinh On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To wrote: > Hi, > > Attached is my mol2 file. It is the DOCK result containing 10 > conformations of docked ligand. It does show 10 conformations using GUI > Chimera (they're sub-model, aint they?), but when I run the piece of code > below (just for testing), the result was an empty list (i.e. []). > > *import chimera* > *confor = chimera.openModels.list()* > *print confor* > > >>> [] > > """ if I used *print confor[0]* > > >>> IndexError: list index out of range""" > > Thank you. > > Chinh > > > On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen wrote: > >> On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote: >> >> Hello, >> >> I managed to get the torsion angles from scripting, but I encountered one >> problem that my code works for pdb file ONLY. >> When I ran it for Mol2 input, I could not get the angles I want. >> >> With the piece of code: >> *confor = chimera.openModels.list()* >> >> it shows an empty list of models (for mol2 file)??? >> >> Please anyone help show me some hints how to convert Mol2 back to PDB or >> anyway that I can directly deal with mol2 format)? >> >> I greatly appreciate if you please show me references about how chimera >> works with Models. I guess I have not understood yet the differences >> between pdb and mol2. It seems to me that mol2 contains the same info (in >> terms of ATOM and coordinates), but an extra column of charges. >> >> Does that MODEL here mean conformations? Why the docked_conformer >> (results from DOCK with various conformations) contains NO models according >> to chimera? I am sorry that I did not mean questioning, but curious. >> >> >> As far as Chimera is concerned, there is very little difference between a >> model opened from a PDB file and one opened from a Mol2 file. >> chimera.openModels.list() cannot be empty if Chimera is actually showing >> any structures. Is it? (when you open the Mol2 file normally)? Maybe you >> need to send along your Mol2 file and your script... >> >> --Eric >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hxdon at 126.com Wed Mar 20 22:40:26 2013 From: hxdon at 126.com (han xiaodon) Date: Thu, 21 Mar 2013 13:40:26 +0800 Subject: [Chimera-users] how to make super8.msf. Message-ID: <67C5CDC0-9B3D-421A-A66C-B6CD15FC8C9F@126.com> dear professor. would you share me how to make super8.msf. From meng at cgl.ucsf.edu Thu Mar 21 10:35:55 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Mar 2013 10:35:55 -0700 Subject: [Chimera-users] how to make super8.msf. In-Reply-To: <67C5CDC0-9B3D-421A-A66C-B6CD15FC8C9F@126.com> References: <67C5CDC0-9B3D-421A-A66C-B6CD15FC8C9F@126.com> Message-ID: <8CB27013-65A4-4FAE-A691-72FA30679E9E@cgl.ucsf.edu> Hi Han, The super8.msf file was not made in Chimera. For the other people on the list: that file is a multiple sequence alignment linked to the "Sequences and Structures" tutorial in the Chimera User's Guide. I got it from someone several years ago; I believe it was edited manually in a text-editor after initial creation in some other program. For making multiple sequence alignments, there are far too many programs for me to list. However, I have a web page that lists a sample of databases and web services that can be used as sources of multiple sequence alignments: Chimera focuses more on structure-sequence linkage than on sequence-only data, but here are some related features: (a) MatchMaker can make a pairwise sequence alignment from two related structures (b) Match->Align can make a multiple sequence alignment from multiple structures that are already superimposed (c) Multalign Viewer has some editing features, such as adding a single sequence (with or without a structure) to an existing alignment 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 Mar 20, 2013, at 10:40 PM, han xiaodon wrote: > dear professor. would you share me how to make super8.msf. From pett at cgl.ucsf.edu Thu Mar 21 11:50:51 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 21 Mar 2013 11:50:51 -0700 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> Message-ID: <4AB1DC06-528D-4A6C-B4CA-13DAE24B75F1@cgl.ucsf.edu> Great! --Eric On Mar 20, 2013, at 11:22 PM, Chinh Su Tran To wrote: > Hi, > > I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. > Thank you very much. > > Chinh > > On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To wrote: > Hi, > > Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []). > > import chimera > confor = chimera.openModels.list() > print confor > > >>> [] > > """ if I used print confor[0] > > >>> IndexError: list index out of range""" > > Thank you. > > Chinh > > > On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen wrote: > On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote: > >> Hello, >> >> I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. >> When I ran it for Mol2 input, I could not get the angles I want. >> >> With the piece of code: >> confor = chimera.openModels.list() >> >> it shows an empty list of models (for mol2 file)??? >> >> Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? >> >> I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. >> >> Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious. > > As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script... > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From larrys3255 at gmail.com Thu Mar 21 14:41:59 2013 From: larrys3255 at gmail.com (Larry Simpson) Date: Thu, 21 Mar 2013 14:41:59 -0700 Subject: [Chimera-users] re Message-ID: Hi I have a strange problem with Chimera 1.7. My computer (Windows 7 64 bit) just had Microsoft updates last night and now Chimera does not see any drives but C and D. I usually use files on virtual drives E, etc. I tried rebooting, reinstalling Chimera but it is still the same problem. Any suggestions? Larry -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Mar 21 15:02:47 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 21 Mar 2013 15:02:47 -0700 Subject: [Chimera-users] re In-Reply-To: References: Message-ID: <0CD61170-6E8B-4061-A2AD-8DA6426018B6@cgl.ucsf.edu> On Mar 21, 2013, at 2:41 PM, Larry Simpson wrote: > Hi > > I have a strange problem with Chimera 1.7. My computer (Windows 7 64 bit) just had Microsoft updates last night and now Chimera does not see any drives but C and D. I usually use files on virtual drives E, etc. I tried rebooting, reinstalling Chimera but it is still the same problem. > > Any suggestions? Hi Larry, Chimera determines whether a drive is "useable" simply by trying to go to that's drive's root folder (e.g. "E:"). Can you try this: open IDLE (in General Controls) type "import os" type "os.chdir('E:')" I assume you get some kind of error. What is the error message? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From AARNAOUT1 at PARTNERS.ORG Thu Mar 21 15:25:22 2013 From: AARNAOUT1 at PARTNERS.ORG (Arnaout, M. Amin,M.D.) Date: Thu, 21 Mar 2013 22:25:22 +0000 Subject: [Chimera-users] importing maps into chimera Message-ID: What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From meng at cgl.ucsf.edu Thu Mar 21 17:37:18 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 21 Mar 2013 17:37:18 -0700 Subject: [Chimera-users] importing maps into chimera In-Reply-To: References: Message-ID: <744A7E5B-54D8-44D8-87B3-8EBD9B1D75E6@cgl.ucsf.edu> Hello, The known map formats are listed here ("current" is Chimera 1.7): 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 Mar 21, 2013, at 3:25 PM, Arnaout, M. Amin,M.D. wrote: > What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. > From chinh.sutranto at gmail.com Thu Mar 21 18:06:58 2013 From: chinh.sutranto at gmail.com (Chinh Sutran) Date: Fri, 22 Mar 2013 09:06:58 +0800 Subject: [Chimera-users] internal coordinates (z-matrix) in chimera In-Reply-To: <4AB1DC06-528D-4A6C-B4CA-13DAE24B75F1@cgl.ucsf.edu> References: <50EA37D3-E554-4583-873D-4497579E367B@cgl.ucsf.edu> <1A6ED31D-BE54-416E-8597-9AFB2AA1C829@cgl.ucsf.edu> <4AB1DC06-528D-4A6C-B4CA-13DAE24B75F1@cgl.ucsf.edu> Message-ID: Dear Dr. Pettersen, Greatly thank you for the help from you and Dr. Meng. Regards, Chinh On Mar 22, 2013, at 2:50 AM, Eric Pettersen wrote: > Great! > > --Eric > > On Mar 20, 2013, at 11:22 PM, Chinh Su Tran To wrote: > >> Hi, >> >> I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. >> Thank you very much. >> >> Chinh >> >> On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To wrote: >>> Hi, >>> >>> Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []). >>> >>> import chimera >>> confor = chimera.openModels.list() >>> print confor >>> >>> >>> [] >>> >>> """ if I used print confor[0] >>> >>> >>> IndexError: list index out of range""" >>> >>> Thank you. >>> >>> Chinh >>> >>> >>> On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen wrote: >>>> On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote: >>>> >>>>> Hello, >>>>> >>>>> I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. >>>>> When I ran it for Mol2 input, I could not get the angles I want. >>>>> >>>>> With the piece of code: >>>>> confor = chimera.openModels.list() >>>>> >>>>> it shows an empty list of models (for mol2 file)??? >>>>> >>>>> Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? >>>>> >>>>> I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. >>>>> >>>>> Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious. >>>> >>>> As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script... >>>> >>>> --Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> http://www.cgl.ucsf.edu > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Mar 21 17:42:05 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 21 Mar 2013 17:42:05 -0700 Subject: [Chimera-users] importing maps into chimera In-Reply-To: References: Message-ID: <514BA8DD.8060004@sonic.net> Density map formats read by Chimera are described in the manual. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume MTZ format is x-ray reflection data, not a density map format and Chimera does not read reflection data. Tom > What format does Chimera accept for ED maps? I tried .mtz files but did not work. Thank you. > > From chinh.sutranto at gmail.com Fri Mar 22 00:33:36 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Fri, 22 Mar 2013 15:33:36 +0800 Subject: [Chimera-users] torsion angles to x,y,z coordinate Message-ID: Dear Chimera users, I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations) Is it possible to do that in Chimera? Please help. Thank you. Chinh -------------- next part -------------- An HTML attachment was scrubbed... URL: From prasannavenkatesh1 at gmail.com Fri Mar 22 06:47:19 2013 From: prasannavenkatesh1 at gmail.com (Prasanna Venkatesh) Date: Fri, 22 Mar 2013 22:47:19 +0900 Subject: [Chimera-users] 3D projection of eigen vectors Message-ID: Dear support member, I would like to know the steps or command lines that I should follow to make 3D projection of eigen vectors like Tube representation or porcupine plots in Chimera. Thank you in advance. Regards, Prasanna Ph.D student Ajou university, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 22 10:45:53 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 22 Mar 2013 10:45:53 -0700 Subject: [Chimera-users] 3D projection of eigen vectors In-Reply-To: References: Message-ID: <00F2C0B8-DEE8-4831-B137-33338AB32107@cgl.ucsf.edu> Dear Prasanna, Sorry, there is no easy/automatic function to create porcupine plots in Chimera. You would need to calculate the vectors in some other program, then write out that information and manually convert the data into some input that Chimera understands. Here are some possibilities for that input: (A) the Chimera "Bild" file format; this format describes geometric objects such as the cones you could use to make a porcupine plot, and is fairly simple plain text: (B) the Chimera "shape" command can also create cones (C) other object formats that Chimera can read include VRML 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 Mar 22, 2013, at 6:47 AM, Prasanna Venkatesh wrote: > Dear support member, > > I would like to know the steps or command lines that I should follow to make 3D projection of eigen vectors like Tube representation or porcupine plots in Chimera. Thank you in advance. > > Regards, > Prasanna > Ph.D student > Ajou university, South Korea From meng at cgl.ucsf.edu Fri Mar 22 10:51:08 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 22 Mar 2013 10:51:08 -0700 Subject: [Chimera-users] torsion angles to x,y,z coordinate In-Reply-To: References: Message-ID: Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) ... or the rotation command If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion. 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 Mar 22, 2013, at 12:33 AM, Chinh Su Tran To wrote: > Dear Chimera users, > > I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations) > > Is it possible to do that in Chimera? Please help. > > Thank you. > Chinh From rswett at chem.wayne.edu Fri Mar 22 10:56:05 2013 From: rswett at chem.wayne.edu (Rebecca Swett) Date: Fri, 22 Mar 2013 13:56:05 -0400 Subject: [Chimera-users] 3D projection of eigen vectors In-Reply-To: References: Message-ID: <514C9B35.4050103@chem.wayne.edu> One way you can show those in chimera is a broadened ribbon image, or morphed animation. Generate several pdbs of your protein with per-residue displacement along the eigenvectors in something like R, and then open them all in chimera, displace as backbone trace rounded ribbon. the overlay will show the eigenvectors and eigenvalues as broadened stacks of ribbons in the direction and magnitude of the motion. If you morph between the conformations, you'll get a nice animation of the displacement along any principal component. Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768 On 3/22/2013 9:47 AM, Prasanna Venkatesh wrote: > Dear support member, > > I would like to know the steps or command lines that I should > follow to make 3D projection of eigen vectors like Tube representation > or porcupine plots in Chimera. Thank you in advance. > > Regards, > Prasanna > Ph.D student > Ajou university, South Korea > > > _______________________________________________ > 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 pett at cgl.ucsf.edu Fri Mar 22 11:03:03 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 22 Mar 2013 11:03:03 -0700 Subject: [Chimera-users] torsion angles to x,y,z coordinate In-Reply-To: References: Message-ID: <75E1B4FD-56A1-4A61-9322-5E8A5E319DF4@cgl.ucsf.edu> On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote: > Hi Chinh, > You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) > > > ... or the rotation command > > > If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion. What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees: setattr r phi 90 :14.a --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From chinh.sutranto at gmail.com Fri Mar 22 19:14:57 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Sat, 23 Mar 2013 10:14:57 +0800 Subject: [Chimera-users] torsion angles to x,y,z coordinate In-Reply-To: <75E1B4FD-56A1-4A61-9322-5E8A5E319DF4@cgl.ucsf.edu> References: <75E1B4FD-56A1-4A61-9322-5E8A5E319DF4@cgl.ucsf.edu> Message-ID: Thanks Elaine. I'll have to script it because I have 10 torsions (for each of the 100 ligands) to change. Those 10 are generated from a GA program. I need to use the "rotation" command as you suggested. Do I have to WritePDB for every change of torsions to get the new conformation (new x,y,z coordinates) 'cause I need the new conformations to do DOCK for the next step? Dear Eric, My molecule is a drug (a small molecule). It is not a protein. I was wondering if changing that amount of torsions is too much. We're trying to do some optimizations using GA instead of running MD. Thank you and hope get more your advice. Regards, Chinh On Saturday, March 23, 2013, Eric Pettersen wrote: > On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote: > > Hi Chinh, > You can change torsion angles using the Adjust Torsions GUI (in menu under > Tools... Structure Editing) > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust > > > > ... or the rotation command > > > If you have lots of values, you would probably want to script it, but it > probably wouldn't be that easy/convenient since the commands (or python, if > you do a python script) will need to specify the 4 atoms used to define > each torsion. > > > What Elaine says is absolutely correct. What I would add though is that > if the torsions you are changing are the phi, psi, or chi angles of > standard amino acids, then adjusting them is somewhat easier since they are > attributes of the residue and setting the attribute will change the > torsion. For example, to change the phi angle of residue 14.A to 90 > degrees: > > setattr r phi 90 :14.a > > --Eric > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amitjai20 at gmail.com Sat Mar 23 11:02:04 2013 From: amitjai20 at gmail.com (Amit Jaiswal) Date: Sat, 23 Mar 2013 23:32:04 +0530 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis Message-ID: Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. ~~~~~~~~~~~~~~~~~~~~~~~~~ From meng at cgl.ucsf.edu Sat Mar 23 11:11:22 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 23 Mar 2013 11:11:22 -0700 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: References: Message-ID: <402B67B1-DD16-4925-9178-1F9A31B05A06@cgl.ucsf.edu> Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: > Dear Chimera Users, > I am new to chimera and I have some > protein protein interaction results to be analysed. Most of > the results are from HADDOCK server which gives a > protein protein complex. So, is it possible to visualize > the hydrogen bonds formed between the proteins using > chimera? If yes, how? I am eagerly waiting for the answer. > From meng at cgl.ucsf.edu Sat Mar 23 11:17:06 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 23 Mar 2013 11:17:06 -0700 Subject: [Chimera-users] torsion angles to x,y,z coordinate In-Reply-To: References: <75E1B4FD-56A1-4A61-9322-5E8A5E319DF4@cgl.ucsf.edu> Message-ID: Hi Chinh, If you want a PDB file for each conformation, yes, you would have to use Write PDB (or command "write"). Theoretically no number of rotations is too many. We just meant it would probably be too many to type in each command yourself. Instead you would prefer to script it in either Chimera commands or python, as mentioned in my previous message. Elaine On Mar 22, 2013, at 7:14 PM, Chinh Su Tran To wrote: > Thanks Elaine. I'll have to script it because I have 10 torsions (for each of the 100 ligands) to change. Those 10 are generated from a GA program. I need to use the "rotation" command as you suggested. Do I have to WritePDB for every change of torsions to get the new conformation (new x,y,z coordinates) 'cause I need the new conformations to do DOCK for the next step? > > Dear Eric, > My molecule is a drug (a small molecule). It is not a protein. I was wondering if changing that amount of torsions is too much. We're trying to do some optimizations using GA instead of running MD. > > Thank you and hope get more your advice. > > Regards, > Chinh > > On Saturday, March 23, 2013, Eric Pettersen wrote: > On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote: > >> Hi Chinh, >> You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) >> >> >> ... or the rotation command >> >> >> If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion. > > What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees: > > setattr r phi 90 :14.a > > --Eric > From amitjai20 at gmail.com Sat Mar 23 11:32:09 2013 From: amitjai20 at gmail.com (Amit Jaiswal) Date: Sun, 24 Mar 2013 00:02:09 +0530 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: <402B67B1-DD16-4925-9178-1F9A31B05A06@cgl.ucsf.edu> References: <402B67B1-DD16-4925-9178-1F9A31B05A06@cgl.ucsf.edu> Message-ID: Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists. On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng wrote: > Dear Amit, > Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. > > There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). > > You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. > 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: > >> Dear Chimera Users, >> I am new to chimera and I have some >> protein protein interaction results to be analysed. Most of >> the results are from HADDOCK server which gives a >> protein protein complex. So, is it possible to visualize >> the hydrogen bonds formed between the proteins using >> chimera? If yes, how? I am eagerly waiting for the answer. >> > -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. ~~~~~~~~~~~~~~~~~~~~~~~~~ From chinh.sutranto at gmail.com Sat Mar 23 18:59:26 2013 From: chinh.sutranto at gmail.com (Chinh Su Tran To) Date: Sun, 24 Mar 2013 09:59:26 +0800 Subject: [Chimera-users] torsion angles to x,y,z coordinate In-Reply-To: References: <75E1B4FD-56A1-4A61-9322-5E8A5E319DF4@cgl.ucsf.edu> Message-ID: thank you Elaine. On Sunday, March 24, 2013, Elaine Meng wrote: > Hi Chinh, > If you want a PDB file for each conformation, yes, you would have to use > Write PDB (or command "write"). > > > Theoretically no number of rotations is too many. We just meant it would > probably be too many to type in each command yourself. Instead you would > prefer to script it in either Chimera commands or python, as mentioned in > my previous message. > Elaine > > On Mar 22, 2013, at 7:14 PM, Chinh Su Tran To wrote: > > > Thanks Elaine. I'll have to script it because I have 10 torsions (for > each of the 100 ligands) to change. Those 10 are generated from a GA > program. I need to use the "rotation" command as you suggested. Do I have > to WritePDB for every change of torsions to get the new conformation (new > x,y,z coordinates) 'cause I need the new conformations to do DOCK for the > next step? > > > > Dear Eric, > > My molecule is a drug (a small molecule). It is not a protein. I was > wondering if changing that amount of torsions is too much. We're trying to > do some optimizations using GA instead of running MD. > > > > Thank you and hope get more your advice. > > > > Regards, > > Chinh > > > > On Saturday, March 23, 2013, Eric Pettersen wrote: > > On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote: > > > >> Hi Chinh, > >> You can change torsion angles using the Adjust Torsions GUI (in menu > under Tools... Structure Editing) > >> < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust > > > >> > >> ... or the rotation command > >> > >> > >> If you have lots of values, you would probably want to script it, but > it probably wouldn't be that easy/convenient since the commands (or python, > if you do a python script) will need to specify the 4 atoms used to define > each torsion. > > > > What Elaine says is absolutely correct. What I would add though is that > if the torsions you are changing are the phi, psi, or chi angles of > standard amino acids, then adjusting them is somewhat easier since they are > attributes of the residue and setting the attribute will change the > torsion. For example, to change the phi angle of residue 14.A to 90 > degrees: > > > > setattr r phi 90 :14.a > > > > --Eric > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From berenger at riken.jp Sun Mar 24 18:31:45 2013 From: berenger at riken.jp (Francois Berenger) Date: Mon, 25 Mar 2013 10:31:45 +0900 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: References: <402B67B1-DD16-4925-9178-1F9A31B05A06@cgl.ucsf.edu> Message-ID: <514FA901.2070602@riken.jp> In case you don't get enough from Chimera, I think pisa from CCP4mg is specialized in analyzing protein interfaces. http://www.ccp4.ac.uk/MG/ccp4mg_help/pisa.html On 03/24/2013 03:32 AM, Amit Jaiswal wrote: > Dear Elaine, > Many thanks for the suggestion and reply. I will do as said > and will mail if any problem persists. > > On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng wrote: >> Dear Amit, >> Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. >> >> There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). >> >> You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. >> 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: >> >>> Dear Chimera Users, >>> I am new to chimera and I have some >>> protein protein interaction results to be analysed. Most of >>> the results are from HADDOCK server which gives a >>> protein protein complex. So, is it possible to visualize >>> the hydrogen bonds formed between the proteins using >>> chimera? If yes, how? I am eagerly waiting for the answer. >>> >> > > > From hira.saleem.31 at hotmail.com Sat Mar 23 01:18:10 2013 From: hira.saleem.31 at hotmail.com (Hira Saleem) Date: Sat, 23 Mar 2013 13:18:10 +0500 Subject: [Chimera-users] need help Message-ID: Respected fellows! i need help from you. actually i am working on my project and uses chimera for this . i have a problem because i have a huge data and i have to collect RMSD value of 10000 pdb ids in a 262 by 262 matrix. just wanted to know if there is another procedure to collect value instead of collecting manually. because it takes too much time and very hectic work. waiting for your precious suggestion and will be very thankful to you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadir.mrabet at univ-lorraine.fr Sat Mar 23 12:42:26 2013 From: nadir.mrabet at univ-lorraine.fr (Nadir Mrabet) Date: Sat, 23 Mar 2013 20:42:26 +0100 (CET) Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: Message-ID: <1207888916.1733960.1364067746471.JavaMail.root@univ-lorraine.fr> Hi Elaine, I addressed the question to CCP4BB but il did not seem to interest anyone . I state it again : I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. Ref: "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, and David J. Nesbitt Pure Appl. Chem., Vol. 83, No. 8, pp. 1619?1636, 2011. doi:10.1351/PAC-REP-10-01-01 ? 2011 IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*" Tough job, isn't ? My guess is that Chimera should be involved . Nadir Mrabet ----- Mail original ----- > Dear Elaine, > Many thanks for the suggestion and reply. I will do as said > and will mail if any problem persists. > On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng > wrote: > > Dear Amit, > > Yes, there is a FindHBond tool (in menu under Tools... Structure > > Analysis) and command "findhbond" with the same capabilities. > > Click the Help button on the tool to see its full instructions, or > > enter command "help findhbond" to see the command instructions. > > > > There is an example of using FindHBond in the "Structure Analysis > > and Comparison" tutorial (see Chimera menu, Help... Tutorials). > > > > You can also use Help... Search Documentation in the Chimera menu, > > for example to search for "hydrogen bonds" ... this will give > > several links into the user manual including the things I > > mentioned above. > > 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: > > > >> Dear Chimera Users, > >> I am new to chimera and I have some > >> protein protein interaction results to be analysed. Most of > >> the results are from HADDOCK server which gives a > >> protein protein complex. So, is it possible to visualize > >> the hydrogen bonds formed between the proteins using > >> chimera? If yes, how? I am eagerly waiting for the answer. > >> > > > -- > Yours Sincerely, > ~~~~~~~~~~~~~~~~~~~~~~~~ > Amit Jaiswal, > Department of Bioinformatics, > School of Life Sciences, > Pondicherry Central University, > Kalapet, Pondicherry, > Puducherry - 605 014. > ~~~~~~~~~~~~~~~~~~~~~~~~~ > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Mar 25 15:07:09 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Mar 2013 15:07:09 -0700 Subject: [Chimera-users] calculating NxN RMSDs In-Reply-To: References: Message-ID: <9AA6247E-F00D-4F93-B961-F008B9376323@cgl.ucsf.edu> Hello Hira, If the structures have exactly the same atoms and bonds (same names, same order) then you can open as trajectory and use the RMSD analysis in MD Movie, which will automatically calculate all N x N values and allow you to save the RMSD values to a file. See the MD Movie manual, especially the parts about input and RMSD analysis: If instead they are different proteins and you are using MatchMaker, then you would need to write a script to process the N x N pairs or comparisons, then take the output values from the Reply Log. There is a "matchmaker" command that has the same features as the MatchMaker GUI. See also information about scripting to process multiple PDB files: 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 Mar 23, 2013, at 1:18 AM, Hira Saleem wrote: > Respected fellows! > > i need help from you. actually i am working on my project and uses chimera for this . i have a problem because i have a huge data and i have to collect RMSD value of 10000 pdb ids in a 262 by 262 matrix. just wanted to know if there is another procedure to collect value instead of collecting manually. because it takes too much time and very hectic work. > waiting for your precious suggestion and will be very thankful to you. From meng at cgl.ucsf.edu Mon Mar 25 15:13:29 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Mar 2013 15:13:29 -0700 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: <1207888916.1733960.1364067746471.JavaMail.root@univ-lorraine.fr> References: <1207888916.1733960.1364067746471.JavaMail.root@univ-lorraine.fr> Message-ID: <367A8C83-3F18-4CD5-AEFC-02B04EE954D3@cgl.ucsf.edu> Hi Nadir, Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs. 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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote: > Hi Elaine, > > I addressed the question to CCP4BB but il did not seem to interest anyone. > I state it again : > > I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. > Ref: > "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, > Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, > Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, > Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, > and David J. Nesbitt > Pure Appl. Chem., Vol. 83, No. 8, pp. 1619?1636, 2011. > doi:10.1351/PAC-REP-10-01-01 > ? 2011 IUPAC, Publication date (Web): 8 July 2011 > Defining the hydrogen bond: An account (IUPAC Technical Report)*" > > > Tough job, isn't ? > > My guess is that Chimera should be involved. > > Nadir Mrabet > > > Dear Elaine, > Many thanks for the suggestion and reply. I will do as said > and will mail if any problem persists. > > On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng wrote: > > Dear Amit, > > Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. > > > > There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). > > > > You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. > > 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: > > > >> Dear Chimera Users, > >> I am new to chimera and I have some > >> protein protein interaction results to be analysed. Most of > >> the results are from HADDOCK server which gives a > >> protein protein complex. So, is it possible to visualize > >> the hydrogen bonds formed between the proteins using > >> chimera? If yes, how? I am eagerly waiting for the answer. > >> > > > > > > -- > > Yours Sincerely, > > ~~~~~~~~~~~~~~~~~~~~~~~~ > Amit Jaiswal, > Department of Bioinformatics, > School of Life Sciences, > Pondicherry Central University, > Kalapet, Pondicherry, > Puducherry - 605 014. > > ~~~~~~~~~~~~~~~~~~~~~~~~~ > > _______________________________________________ > 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 Nadir.Mrabet at univ-lorraine.fr Tue Mar 26 07:25:59 2013 From: Nadir.Mrabet at univ-lorraine.fr (Nadir T. Mrabet) Date: Tue, 26 Mar 2013 15:25:59 +0100 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: <367A8C83-3F18-4CD5-AEFC-02B04EE954D3@cgl.ucsf.edu> References: <1207888916.1733960.1364067746471.JavaMail.root@univ-lorraine.fr> <367A8C83-3F18-4CD5-AEFC-02B04EE954D3@cgl.ucsf.edu> Message-ID: <5151AFF7.1050702@univ-lorraine.fr> Hi Elaine, I gave a reference that should be read before initiating a fruitful discussion. I give a second one, which is an (critical) essay and a synthetic summary : Desiraju G.R. (2011) "A Bond by Any Other Name", Angew. Chem. Int. Ed. 50: 52-59. The hydrogen bond is designated X-H???Y-Z (4 atoms; there have been so many articles where only the 3 atoms of a H-bond, C-H???O (3) are considered). X must be more electronegative than H. The H-bond acceptor, Y, is electron rich (either lone electron pair, or pi-bonded pair in Y-Z). The evidence for H-bond may be experimental or theoretical, but better be both. Now, the C atom can be recognized as an H-bond donor (if it fulfills the required criteria). Aromatic rings become H-bond acceptors. For the purpose of optimizing energy, the angle, X-H???Y, must be as close as possible to 180 ? (not new!), but there is no constraint imposed on angle H???Y-Z (a point on which I disagree). Quantum-mechanical calculation is not adamant, but should help (provided one uses an appropriate force field). Therefore, even if force fields attribute partial atomic charges (Note that Amber does not agree "qualitatively" with others on some atoms) they usually mention only NH and OH (and sometimes S) as H-bond donors and N-Z or O-Z, as acceptors. C-H is not considered as an H-bond donor; the pi-electron cloud is not recognized as acceptor. The tough job resides in the choice of an empirical force field that best correlates with experimental data. Redefining H-bond donors and acceptors and their partial charges is also to be done in the molecular modeling program(s). I cannot be exhaustive in a matter of minutes. I just wish to start the discussion and see whether (or not) if it will impact on Chimera. Best regards, Nadir Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 25/03/2013 23:13, Elaine Meng wrote: > Hi Nadir, > > Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs. > > 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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote: > >> Hi Elaine, >> >> I addressed the question to CCP4BB but il did not seem to interest anyone. >> I state it again : >> >> I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. >> Ref: >> "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, >> Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, >> Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, >> Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, >> and David J. Nesbitt >> Pure Appl. Chem., Vol. 83, No. 8, pp. 1619?1636, 2011. >> doi:10.1351/PAC-REP-10-01-01 >> ? 2011 IUPAC, Publication date (Web): 8 July 2011 >> Defining the hydrogen bond: An account (IUPAC Technical Report)*" >> >> >> Tough job, isn't ? >> >> My guess is that Chimera should be involved. >> >> Nadir Mrabet >> >> >> Dear Elaine, >> Many thanks for the suggestion and reply. I will do as said >> and will mail if any problem persists. >> >> On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng wrote: >>> Dear Amit, >>> Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. >>> >>> There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). >>> >>> You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. >>> 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: >>> >>>> Dear Chimera Users, >>>> I am new to chimera and I have some >>>> protein protein interaction results to be analysed. Most of >>>> the results are from HADDOCK server which gives a >>>> protein protein complex. So, is it possible to visualize >>>> the hydrogen bonds formed between the proteins using >>>> chimera? If yes, how? I am eagerly waiting for the answer. >>>> >> >> >> -- >> >> Yours Sincerely, >> >> ~~~~~~~~~~~~~~~~~~~~~~~~ >> Amit Jaiswal, >> Department of Bioinformatics, >> School of Life Sciences, >> Pondicherry Central University, >> Kalapet, Pondicherry, >> Puducherry - 605 014. >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> _______________________________________________ >> 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 > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From xkz3 at wildcats.unh.edu Tue Mar 26 13:46:04 2013 From: xkz3 at wildcats.unh.edu (Xiongzhuo Gao) Date: Tue, 26 Mar 2013 20:46:04 +0000 Subject: [Chimera-users] sphere representation for specific atoms Message-ID: <2C29E2F4D25EE94CA11BCD0FA978511778E8004D@SN2PRD0410MB372.namprd04.prod.outlook.com> Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Mar 26 16:20:11 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 26 Mar 2013 16:20:11 -0700 Subject: [Chimera-users] sphere representation for specific atoms In-Reply-To: <2C29E2F4D25EE94CA11BCD0FA978511778E8004D@SN2PRD0410MB372.namprd04.prod.outlook.com> References: <2C29E2F4D25EE94CA11BCD0FA978511778E8004D@SN2PRD0410MB372.namprd04.prod.outlook.com> Message-ID: <351576D7-AC7C-4D30-BCE0-F039C58240A4@cgl.ucsf.edu> Hi Stephen, I'm not sure what you mean by "didn't work" but I'm guessing you are showing a ribbon. By default, if ribbon is shown you cannot also show CA atoms for the same residues at the same time until after you enter the command "ribbackbone" (show the command line first with menu: Favorites... Command Line). Then you can display whichever CA atoms you like at the same time as the ribbon, for example, command: display :50.A at CA ... to show CA atom of residue 50 in chain A. Since the default ribbon is a smoothed interpolated path, another issue is that the CA atoms may not be on the ribbon but "floating" in space nearby. Possible ways to handle this issue: (1) show the CA atoms as fairly large balls so that it is less obvious that they are not on the ribbon. Maybe you are showing "balls" (default 0.25 of VDW radius) and could instead show "spheres" (equal to VDW radius). You can also change VDW radius with the command "vdwdefine". For example to show CAs as balls and increase their VDW radii by 1.0: repr bs @ca vdwdefine +1.0 @ca The atoms should be represented as balls or spheres (not stick) or else you won't see the difference in size. (2) instead of showing ribbon, just show the CA atom trace as sticks and any specific CA atoms you want to highlight as balls or spheres. I agree this is not as pretty as the ribbon, however. (3) instead of the default B-spline ribbon, instead use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand These things can also be done with menus/GUIs but it would take a lot more typing to describe. 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 Mar 26, 2013, at 1:46 PM, Xiongzhuo Gao wrote: > Hi, > I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. > Best, > Stephen From xkz3 at wildcats.unh.edu Wed Mar 27 12:41:01 2013 From: xkz3 at wildcats.unh.edu (Xiongzhuo Gao) Date: Wed, 27 Mar 2013 19:41:01 +0000 Subject: [Chimera-users] sphere representation for specific atoms In-Reply-To: <351576D7-AC7C-4D30-BCE0-F039C58240A4@cgl.ucsf.edu> References: <2C29E2F4D25EE94CA11BCD0FA978511778E8004D@SN2PRD0410MB372.namprd04.prod.outlook.com>, <351576D7-AC7C-4D30-BCE0-F039C58240A4@cgl.ucsf.edu> Message-ID: <2C29E2F4D25EE94CA11BCD0FA978511778E8006F@SN2PRD0410MB372.namprd04.prod.outlook.com> Hi Elaine, Following your suggestion I can show the CA in the way that I want. Thank you so much for your help. Best Wishes, Stephen ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Tuesday, March 26, 2013 7:20 PM To: Xiongzhuo Gao Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] sphere representation for specific atoms Hi Stephen, I'm not sure what you mean by "didn't work" but I'm guessing you are showing a ribbon. By default, if ribbon is shown you cannot also show CA atoms for the same residues at the same time until after you enter the command "ribbackbone" (show the command line first with menu: Favorites... Command Line). Then you can display whichever CA atoms you like at the same time as the ribbon, for example, command: display :50.A at CA ... to show CA atom of residue 50 in chain A. Since the default ribbon is a smoothed interpolated path, another issue is that the CA atoms may not be on the ribbon but "floating" in space nearby. Possible ways to handle this issue: (1) show the CA atoms as fairly large balls so that it is less obvious that they are not on the ribbon. Maybe you are showing "balls" (default 0.25 of VDW radius) and could instead show "spheres" (equal to VDW radius). You can also change VDW radius with the command "vdwdefine". For example to show CAs as balls and increase their VDW radii by 1.0: repr bs @ca vdwdefine +1.0 @ca The atoms should be represented as balls or spheres (not stick) or else you won't see the difference in size. (2) instead of showing ribbon, just show the CA atom trace as sticks and any specific CA atoms you want to highlight as balls or spheres. I agree this is not as pretty as the ribbon, however. (3) instead of the default B-spline ribbon, instead use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand These things can also be done with menus/GUIs but it would take a lot more typing to describe. 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 Mar 26, 2013, at 1:46 PM, Xiongzhuo Gao wrote: > Hi, > I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. > Best, > Stephen From pett at cgl.ucsf.edu Wed Mar 27 15:20:30 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 27 Mar 2013 15:20:30 -0700 Subject: [Chimera-users] Reg: Hydrogen Bond Analysis In-Reply-To: <5151AFF7.1050702@univ-lorraine.fr> References: <1207888916.1733960.1364067746471.JavaMail.root@univ-lorraine.fr> <367A8C83-3F18-4CD5-AEFC-02B04EE954D3@cgl.ucsf.edu> <5151AFF7.1050702@univ-lorraine.fr> Message-ID: <3D977A2F-8C22-409D-96DD-60AC3F825978@cgl.ucsf.edu> Dear Nadir, I think it's fairly well known that hydrogen bonds are continuous phenomena and not discrete on/off entities as presented by Chimera (and most programs of its ilk). That's why Chimera allows you to loosen its H-bond criteria to explore interactions beyond the default cutoffs. Similarly, weak H-bond interactions can occur between chemical entities other than the ones examined by the Chimera H-bond code, e.g. carbon donors or pi-cloud acceptors. When Chimera's H-bond code was written, Chimera had no capability to assess the energetics of H-bond interactions and therefore simply uses the geometric criteria outlined in the Mills paper cited in Chimera's findhbond documentation to locate obvious H-bond interactions between well known donors and acceptors. C-H hydrogen bonds were excluded in the Mills paper due to their low occurrence and the fact that their geometry was frequently distorted to accommodate stronger H-bond interactions. Chimera isn't really trying to reinvent the wheel here. I think if one needs sophisticated analysis of all types of hydrogen bonding interactions then a dedicated QM or MM program should be used, not a visualization program. Nonetheless, if geometric criteria similar to those in the Mills paper were determined for some of these weaker interactions, I would consider adding them to the code. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 26, 2013, at 7:25 AM, Nadir T. Mrabet wrote: > Hi Elaine, > > I gave a reference that should be read before initiating a fruitful discussion. > I give a second one, which is an (critical) essay and a synthetic summary : > Desiraju G.R. (2011) "A Bond by Any Other Name", Angew. Chem. Int. Ed. 50: 52-59. > > The hydrogen bond is designated X-H???Y-Z (4 atoms; there have been so many articles where only the 3 atoms of a H-bond, C-H???O (3) are considered). > X must be more electronegative than H. > The H-bond acceptor, Y, is electron rich (either lone electron pair, or pi-bonded pair in Y-Z). > The evidence for H-bond may be experimental or theoretical, but better be both. > > Now, the C atom can be recognized as an H-bond donor (if it fulfills the required criteria). > Aromatic rings become H-bond acceptors. > > For the purpose of optimizing energy, the angle, X-H???Y, must be as close as possible to 180 ? (not new!), but there is no constraint imposed on angle H???Y-Z (a point on which I disagree). > > Quantum-mechanical calculation is not adamant, but should help (provided one uses an appropriate force field). > > Therefore, even if force fields attribute partial atomic charges (Note that Amber does not agree "qualitatively" with others on some atoms) they usually mention only NH and OH (and sometimes S) as H-bond donors and N-Z or O-Z, as acceptors. C-H is not considered as an H-bond donor; the pi-electron cloud is not recognized as acceptor. > > The tough job resides in the choice of an empirical force field that best correlates with experimental data. > Redefining H-bond donors and acceptors and their partial charges is also to be done in the molecular modeling program(s). > > I cannot be exhaustive in a matter of minutes. > I just wish to start the discussion and see whether (or not) if it will impact on Chimera. > > Best regards, > > Nadir > > Pr. Nadir T. Mrabet > Structural & Molecular Biochemistry > N-gere - INSERM U-954 > University of Lorraine, Nancy > School of Sciences and Technologies > & School of Medicine > 9, Avenue de la Foret de Haye, BP 184 > 54505 Vandoeuvre-les-Nancy Cedex > France > Phone: +33 (0)3.83.68.32.73 > Fax: +33 (0)3.83.68.32.79 > E-mail: Nadir.Mrabet univ-lorraine.fr > Cell.: +33 (0)6.11.35.69.09 > > LEGAL NOTICE > Unless expressly stated otherwise, this message is confidential and may > be privileged. It is intended for the addressee(s) only. > Access to this E-mail by anyone else is unauthorized. > If you are not an addressee, any disclosure or copying of the contents > of this E-mail, or any action taken (or not taken) in reliance on it, > is unauthorized and may be unlawful. > If you are not an addressee, please inform the sender immediately. > > On 25/03/2013 23:13, Elaine Meng wrote: >> Hi Nadir, >> >> Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs. >> >> 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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote: >> >>> Hi Elaine, >>> >>> I addressed the question to CCP4BB but il did not seem to interest anyone. >>> I state it again : >>> >>> I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. >>> Ref: >>> "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, >>> Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, >>> Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, >>> Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, >>> and David J. Nesbitt >>> Pure Appl. Chem., Vol. 83, No. 8, pp. 1619?1636, 2011. >>> doi:10.1351/PAC-REP-10-01-01 >>> ? 2011 IUPAC, Publication date (Web): 8 July 2011 >>> Defining the hydrogen bond: An account (IUPAC Technical Report)*" >>> >>> >>> Tough job, isn't ? >>> >>> My guess is that Chimera should be involved. >>> >>> Nadir Mrabet >>> >>> >>> Dear Elaine, >>> Many thanks for the suggestion and reply. I will do as said >>> and will mail if any problem persists. >>> >>> On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng wrote: >>>> Dear Amit, >>>> Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions. >>>> >>>> There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials). >>>> >>>> You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. >>>> 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote: >>>> >>>>> Dear Chimera Users, >>>>> I am new to chimera and I have some >>>>> protein protein interaction results to be analysed. Most of >>>>> the results are from HADDOCK server which gives a >>>>> protein protein complex. So, is it possible to visualize >>>>> the hydrogen bonds formed between the proteins using >>>>> chimera? If yes, how? I am eagerly waiting for the answer. >>>>> >>> >>> >>> -- >>> >>> Yours Sincerely, >>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~ >>> Amit Jaiswal, >>> Department of Bioinformatics, >>> School of Life Sciences, >>> Pondicherry Central University, >>> Kalapet, Pondicherry, >>> Puducherry - 605 014. >>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matheus.froeyen at gmail.com Thu Mar 28 02:49:29 2013 From: matheus.froeyen at gmail.com (matheus froeyen) Date: Thu, 28 Mar 2013 10:49:29 +0100 Subject: [Chimera-users] distance label decimal places Message-ID: Hi, does someone know how I can control the number of decimal places shown in a distance label using the command line? thanks! mathy -------------- next part -------------- An HTML attachment was scrubbed... URL: From fugate at hawaii.edu Thu Mar 28 08:05:12 2013 From: fugate at hawaii.edu (Corey Fugate) Date: Thu, 28 Mar 2013 09:05:12 -0600 Subject: [Chimera-users] transparency command unrecognized Message-ID: I am following the Chimera Movie Making tutorial, but when I use the command "transp 80,r" the command line tells me, "Unrecognized command: "transp". I tried replacing "transp" with "transparency" and got the same result. Can someone explain to me why this isn't working? (I'm using build 1.5.3 on my MacBook. Thanks, Corey From meng at cgl.ucsf.edu Thu Mar 28 09:34:58 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Mar 2013 09:34:58 -0700 Subject: [Chimera-users] transparency command unrecognized In-Reply-To: References: Message-ID: Hi Corey, You need to get a newer version of Chimera. 1.5.3 is from a couple years ago. The "transparency" command is new in the Chimera 1.7 production release: When you get an error like that, the first thing to check is whether you have the latest production release. Lack of version synchronization is one problem with using tutorials on the web. Usually I say to use the tutorials in the Help menu if you want them to match your downloaded version. However, some tutorials are only on the website, but in that case we try to note what version is being used. The one I suspect you are using says at the top that it was done with the Chimera 1.7 snapshot from September 2012: 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 Mar 28, 2013, at 8:05 AM, Corey Fugate wrote: > I am following the Chimera Movie Making tutorial, but when I use the command "transp 80,r" the command line tells me, "Unrecognized command: "transp". I tried replacing "transp" with "transparency" and got the same result. Can someone explain to me why this isn't working? (I'm using build 1.5.3 on my MacBook. > > Thanks, > Corey From pett at cgl.ucsf.edu Thu Mar 28 11:13:46 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 28 Mar 2013 11:13:46 -0700 Subject: [Chimera-users] distance label decimal places In-Reply-To: References: Message-ID: <1589ED20-2D30-479A-97F5-11FF6D8EDFA8@cgl.ucsf.edu> On Mar 28, 2013, at 2:49 AM, matheus froeyen wrote: > Hi, > > does someone know how I can control the number of decimal places shown > in a distance label using the command line? Hi Mathy, There isn't such a command, but once you set the precision using the dialog then Chimera remembers that setting. Is there a specific reason you need to use a command for this? If there was, I could add such a command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 28 11:36:57 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 28 Mar 2013 11:36:57 -0700 Subject: [Chimera-users] distance label decimal places In-Reply-To: <1589ED20-2D30-479A-97F5-11FF6D8EDFA8@cgl.ucsf.edu> References: <1589ED20-2D30-479A-97F5-11FF6D8EDFA8@cgl.ucsf.edu> Message-ID: <0F064A73-1AE8-4769-91EB-EB98404078F2@cgl.ucsf.edu> To be more explicit, number of decimal places is a setting in the Distances panel (in menu under under Tools... Structure Analysis). Elaine On Mar 28, 2013, at 11:13 AM, Eric Pettersen wrote: > On Mar 28, 2013, at 2:49 AM, matheus froeyen wrote: > >> Hi, >> does someone know how I can control the number of decimal places shown >> in a distance label using the command line? > > Hi Mathy, > There isn't such a command, but once you set the precision using the dialog then Chimera remembers that setting. Is there a specific reason you need to use a command for this? If there was, I could add such a command. > > --Eric > > From matheus.froeyen at gmail.com Thu Mar 28 15:26:15 2013 From: matheus.froeyen at gmail.com (matheus froeyen) Date: Thu, 28 Mar 2013 23:26:15 +0100 Subject: [Chimera-users] distance label decimal places In-Reply-To: <0F064A73-1AE8-4769-91EB-EB98404078F2@cgl.ucsf.edu> References: <1589ED20-2D30-479A-97F5-11FF6D8EDFA8@cgl.ucsf.edu> <0F064A73-1AE8-4769-91EB-EB98404078F2@cgl.ucsf.edu> Message-ID: I try to generate the graphics by commands, avoiding the use of the menu interface, which works fine in most cases. If chimera will remember the setting, that is a good solution. best regards mathy On Thu, Mar 28, 2013 at 7:36 PM, Elaine Meng wrote: > To be more explicit, number of decimal places is a setting in the > Distances panel (in menu under under Tools... Structure Analysis). > > Elaine > > On Mar 28, 2013, at 11:13 AM, Eric Pettersen wrote: > > > On Mar 28, 2013, at 2:49 AM, matheus froeyen wrote: > > > >> Hi, > >> does someone know how I can control the number of decimal places shown > >> in a distance label using the command line? > > > > Hi Mathy, > > There isn't such a command, but once you set the precision using > the dialog then Chimera remembers that setting. Is there a specific reason > you need to use a command for this? If there was, I could add such a > command. > > > > --Eric > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bshaanan at exchange.bgu.ac.il Fri Mar 29 17:11:38 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sat, 30 Mar 2013 00:11:38 +0000 Subject: [Chimera-users] Weird looking stretch in ribbon presentation Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F95712@hawk3.auth.ad.bgu.ac.il> Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From meng at cgl.ucsf.edu Fri Mar 29 19:05:21 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 29 Mar 2013 19:05:21 -0700 Subject: [Chimera-users] Weird looking stretch in ribbon presentation In-Reply-To: <4B2A491F685D1E4FBBF985E193095AAF67F95712@hawk3.auth.ad.bgu.ac.il> References: <4B2A491F685D1E4FBBF985E193095AAF67F95712@hawk3.auth.ad.bgu.ac.il> Message-ID: <9C6EF9BF-FF12-4343-A9A4-1F0CB206E479@cgl.ucsf.edu> Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand 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 Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote: > Hi , > I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? > Thanks, > Boaz > From bshaanan at exchange.bgu.ac.il Sat Mar 30 04:06:08 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sat, 30 Mar 2013 11:06:08 +0000 Subject: [Chimera-users] Weird looking stretch in ribbon presentation In-Reply-To: <9C6EF9BF-FF12-4343-A9A4-1F0CB206E479@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF67F95712@hawk3.auth.ad.bgu.ac.il>, <9C6EF9BF-FF12-4343-A9A4-1F0CB206E479@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F9683A@hawk3.auth.ad.bgu.ac.il> Thanks Elaine, I'll try your suggestions. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Saturday, March 30, 2013 5:05 AM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Weird looking stretch in ribbon presentation Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand 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 Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote: > Hi , > I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? > Thanks, > Boaz > From bshaanan at exchange.bgu.ac.il Sat Mar 30 08:07:19 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sat, 30 Mar 2013 15:07:19 +0000 Subject: [Chimera-users] Weird looking stretch in ribbon presentation In-Reply-To: <9C6EF9BF-FF12-4343-A9A4-1F0CB206E479@cgl.ucsf.edu> References: <4B2A491F685D1E4FBBF985E193095AAF67F95712@hawk3.auth.ad.bgu.ac.il>, <9C6EF9BF-FF12-4343-A9A4-1F0CB206E479@cgl.ucsf.edu> Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F97863@hawk3.auth.ad.bgu.ac.il> Hi Elaine, Yes, cardinal spline + smooth coil solves my problem. Thanks a lot. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Saturday, March 30, 2013 5:05 AM To: ??? ???? Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Weird looking stretch in ribbon presentation Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand 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 Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote: > Hi , > I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? > Thanks, > Boaz > From bshaanan at exchange.bgu.ac.il Sat Mar 30 14:19:37 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sat, 30 Mar 2013 21:19:37 +0000 Subject: [Chimera-users] deleting entries from the rapid access list Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F97957@hawk3.auth.ad.bgu.ac.il> An HTML attachment was scrubbed... URL: From bshaanan at exchange.bgu.ac.il Sun Mar 31 13:47:09 2013 From: bshaanan at exchange.bgu.ac.il (Boaz Shaanan) Date: Sun, 31 Mar 2013 20:47:09 +0000 Subject: [Chimera-users] deleting entries from rapid access list (plain text format) Message-ID: <4B2A491F685D1E4FBBF985E193095AAF67F98B0B@hawk3.auth.ad.bgu.ac.il> Hi, Is there a way to delete entries from the rapid access list without having to edit the preferences file? If there isn't such a way, is it possible to request to add such feature?? ? Thanks, ? ? ? ? ? ? ?Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan at bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710