From leonqli at gmail.com Fri Sep 2 12:02:46 2016 From: leonqli at gmail.com (Li, Leon) Date: Fri, 02 Sep 2016 19:02:46 +0000 Subject: [Chimera-users] Command line doesn't work properly on Mac Message-ID: Hello All, The command line in Chimera seems not working properly on my Mac. Any input in the command line will not show unless you select them. Does anybody experience this problem? Or any idea about this? Both versions of 1.11 and 1.11.1 have been tried. My mac is iMac (Retina 5K, 27-inch) OS X EI Capitan. Thanks, Leon -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Sep 2 12:24:05 2016 From: goddard at sonic.net (Tom Goddard) Date: Fri, 2 Sep 2016 12:24:05 -0700 Subject: [Chimera-users] Command line doesn't work properly on Mac In-Reply-To: References: Message-ID: <684504A9-C60A-4335-8BCD-67AC7C24C373@sonic.net> Hi Leon, We?ve seen this before where enabling the ?multisampling? graphics quality option (Chimera menu Tools / Viewing Controls / Effects) causes typed text in the command-line to not appear. Graphics drivers, especially on Mac, often have bugs in multisampling. So try turning that off if it is enable (the default is off), save that preference (Save button on Effects dialog), and restart Chimera. If that doesn?t work try renaming your Chimera preferences file ~/.chimera/preferences so Chimera uses a new one, because possibly some other preference setting is causing this bug. Tom > On Sep 2, 2016, at 12:02 PM, Li, Leon wrote: > > Hello All, > > The command line in Chimera seems not working properly on my Mac. Any input in the command line will not show unless you select them. Does anybody experience this problem? Or any idea about this? > > Both versions of 1.11 and 1.11.1 have been tried. My mac is iMac (Retina 5K, 27-inch) OS X EI Capitan. > > Thanks, > Leon > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From ddgae at ucdavis.edu Fri Sep 2 13:43:06 2016 From: ddgae at ucdavis.edu (david gae) Date: Fri, 2 Sep 2016 13:43:06 -0700 Subject: [Chimera-users] disabling previous state Message-ID: <4D32D439-CE20-49EB-A9DC-05277E78AB8E@ucdavis.edu> Dear Chimera Users, I am wondering if anyone can help me with this question: Whenever I start up CHIMERA. My previous settings and panels show up. Is there a way to prevent my previous preferences being saved? Thanks, David From meng at cgl.ucsf.edu Fri Sep 2 14:54:36 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Sep 2016 14:54:36 -0700 Subject: [Chimera-users] disabling previous state In-Reply-To: <4D32D439-CE20-49EB-A9DC-05277E78AB8E@ucdavis.edu> References: <4D32D439-CE20-49EB-A9DC-05277E78AB8E@ucdavis.edu> Message-ID: Hi David, Most preferences (the ones that show up in the Preferences dialog) don?t save unless you actually click Save on the Preferences dialog. However, there are some other things like recent files/directories, ribbon styles, and Multalign Viewer settings that save instantly. In that case, some ways to prevent saving are: (1) have an unwriteable preferences file (on mac or linux, ?chmod? the preferences file to be unwriteable). In that case you will always get a (possibly annoying) message upon startup that the preferences are not writeable. (2) have a file of the preferences you want to keep ?forever? and automatically copy it to the working preferences file whenever you start up Chimera. I do this with aliased commands on mac (and you could do something similar on linux) because I have different sets of preferences that I use for different situations. So on my system I could alias ?start1? to copy a particular file to another filename and then start up Chimera using that copy (not the original) as the preferences. In that case, you are not actually preventing saving, but whenever you start up, it wipes out the copy that had been changed and restores it to the pristine state. An example of such an alias in my mac .tcshrc file (all one line): alias demo1 "cd ~/Desktop/demo1; \cp -f prefs.demo1 preferences; ~/Desktop/Chimera.app/Contents/MacOS/chimera" These are both unix-y approaches. I am not adept with windows so I can?t speak to how you would handle it on that system. You can totally wipe out everything in the preferences file by deleting that file (when you are not running Chimera). You can see filename/location of the file that is being used as the preferences and reset the settings that appear in the Preferences dialog with Chimera menu: Favorites? Preferences, category Preferences. ? remember to Save after resetting. You can specify using a particular file as the preferences at the time of startup with a startup option I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 2, 2016, at 1:43 PM, david gae wrote: > Dear Chimera Users, > > I am wondering if anyone can help me with this question: > > Whenever I start up CHIMERA. My previous settings and panels show up. Is there a way to prevent my previous preferences being saved? > > Thanks, > David From ddgae at ucdavis.edu Fri Sep 2 16:44:15 2016 From: ddgae at ucdavis.edu (david gae) Date: Fri, 2 Sep 2016 16:44:15 -0700 Subject: [Chimera-users] disabling previous state In-Reply-To: References: <4D32D439-CE20-49EB-A9DC-05277E78AB8E@ucdavis.edu> Message-ID: I like the second option. just did this in my bash environment: chimera=$chimera/Applications/Chimera.app/Contents/MacOS export chimera export PATH=$PATH:$chimera alias chimera='chimera --preferences' thanks Elaine. > On Sep 2, 2016, at 2:54 PM, Elaine Meng wrote: > > Hi David, > Most preferences (the ones that show up in the Preferences dialog) don?t save unless you actually click Save on the Preferences dialog. However, there are some other things like recent files/directories, ribbon styles, and Multalign Viewer settings that save instantly. In that case, some ways to prevent saving are: > > (1) have an unwriteable preferences file (on mac or linux, ?chmod? the preferences file to be unwriteable). In that case you will always get a (possibly annoying) message upon startup that the preferences are not writeable. > > (2) have a file of the preferences you want to keep ?forever? and automatically copy it to the working preferences file whenever you start up Chimera. I do this with aliased commands on mac (and you could do something similar on linux) because I have different sets of preferences that I use for different situations. So on my system I could alias ?start1? to copy a particular file to another filename and then start up Chimera using that copy (not the original) as the preferences. In that case, you are not actually preventing saving, but whenever you start up, it wipes out the copy that had been changed and restores it to the pristine state. > > An example of such an alias in my mac .tcshrc file (all one line): > > alias demo1 "cd ~/Desktop/demo1; \cp -f prefs.demo1 preferences; ~/Desktop/Chimera.app/Contents/MacOS/chimera" > > These are both unix-y approaches. I am not adept with windows so I can?t speak to how you would handle it on that system. > > You can totally wipe out everything in the preferences file by deleting that file (when you are not running Chimera). > You can see filename/location of the file that is being used as the preferences and reset the settings that appear in the Preferences dialog with Chimera menu: Favorites? Preferences, category Preferences. > > > ? remember to Save after resetting. > > You can specify using a particular file as the preferences at the time of startup with a startup option > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 2, 2016, at 1:43 PM, david gae wrote: > >> Dear Chimera Users, >> >> I am wondering if anyone can help me with this question: >> >> Whenever I start up CHIMERA. My previous settings and panels show up. Is there a way to prevent my previous preferences being saved? >> >> Thanks, >> David > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjurica at ucsc.edu Fri Sep 2 13:23:30 2016 From: mjurica at ucsc.edu (Melissa Jurica) Date: Fri, 2 Sep 2016 13:23:30 -0700 Subject: [Chimera-users] extracting chaing colors from session file? Message-ID: I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? For example: color #6168c8fb41bc #0.17 Also- How do I get that color to apply to the little square that shows up on the model panel? Melissa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 2 17:11:32 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Sep 2016 17:11:32 -0700 Subject: [Chimera-users] extracting chaing colors from session file? In-Reply-To: References: Message-ID: Hi Melissa, At first I was going to suggest ?mcopy? but from your description, it sounds like you have each chain as a separate model. ?mcopy? is only for copying settings within one model to other models. You can get the current atom-color RGB definitions or hex codes by Ctrl-click to select an atom (or ribbon segment to select the whole residue, if all of its atoms are the same color), showing the Selection Inspector, Inspect: atom, and then clicking the square color well to get the Color Editor. Then in the Color Editor you can see the hex code starting with # in the ?Color name? field. The square in the Model Panel shows the model-level color. Chimera has a coloring hierarchy, where if the atoms are individually assigned colors (such as with your color command), in the 3D display those colors mask the model-level color, which may be different. You can use the modelcolor command, for example ?modelcolor #6168c8fb41bc #0.17? or click the color square in the Model Panel to make the Color Editor dialog appear, and then enter the hex code in the ?Color name? field of the Color Editor: There is only one model-level color per model, as the name suggests, even though the atoms and per-residue ribbon segments might be all different colors. More about color hierarchy: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 2, 2016, at 1:23 PM, Melissa Jurica wrote: > I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? > > For example: > > color #6168c8fb41bc #0.17 > > Also- > How do I get that color to apply to the little square that shows up on the model panel? > > Melissa From meng at cgl.ucsf.edu Fri Sep 2 17:17:30 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Sep 2016 17:17:30 -0700 Subject: [Chimera-users] extracting chaing colors from session file? In-Reply-To: References: Message-ID: <4CBAFA5E-00CC-4830-A899-05271C52F177@cgl.ucsf.edu> Just a bit more detail on this step: On Sep 2, 2016, at 5:11 PM, Elaine Meng wrote: > showing the Selection Inspector, After making a selection, you can show the Inspector by clicking the green magnifying glass near the lower right of the Chimera window, or choosing Actions? Inspect from the menu. Best, Elaine From leonqli at gmail.com Sun Sep 4 08:06:16 2016 From: leonqli at gmail.com (Li, Leon) Date: Sun, 4 Sep 2016 11:06:16 -0400 Subject: [Chimera-users] Command line doesn't work properly on Mac In-Reply-To: <684504A9-C60A-4335-8BCD-67AC7C24C373@sonic.net> References: <684504A9-C60A-4335-8BCD-67AC7C24C373@sonic.net> Message-ID: Thanks, Tom! I didn't get a chance to test it, but I guess that should be the reason because I do use the "multisampling". :) Best, Leon On Fri, Sep 2, 2016 at 3:24 PM, Tom Goddard wrote: > Hi Leon, > > We?ve seen this before where enabling the ?multisampling? graphics > quality option (Chimera menu Tools / Viewing Controls / Effects) causes > typed text in the command-line to not appear. Graphics drivers, especially > on Mac, often have bugs in multisampling. So try turning that off if it is > enable (the default is off), save that preference (Save button on Effects > dialog), and restart Chimera. If that doesn?t work try renaming your > Chimera preferences file ~/.chimera/preferences so Chimera uses a new one, > because possibly some other preference setting is causing this bug. > > Tom > > > > On Sep 2, 2016, at 12:02 PM, Li, Leon wrote: > > > > Hello All, > > > > The command line in Chimera seems not working properly on my Mac. Any > input in the command line will not show unless you select them. Does > anybody experience this problem? Or any idea about this? > > > > Both versions of 1.11 and 1.11.1 have been tried. My mac is iMac (Retina > 5K, 27-inch) OS X EI Capitan. > > > > Thanks, > > Leon > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjurica at ucsc.edu Sat Sep 3 11:23:15 2016 From: mjurica at ucsc.edu (Melissa Jurica) Date: Sat, 3 Sep 2016 11:23:15 -0700 Subject: [Chimera-users] extracting chaing colors from session file? In-Reply-To: References: Message-ID: <571AE5B5-02D7-4E2D-9E07-7F5C4F6E710F@ucsc.edu> Thanks Elaine- My structures have more than 20 individual components (recent spliceosome cryo-EM models- example PDB 5GMK). They came as 1 model, which I split to have more control over for analysis. I can go through each component by hand and copy/paste the color for each model into a text file and then turn then this into a command file to color another structure with the same components in another conformation. (Thanks for turning me on to the ?modelcolor? command. That will be helpful!) However, I was hoping there was a way to use something like grep to extract this information from the .py session file. Melissa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ On Sep 2, 2016, at 5:11 PM, Elaine Meng wrote: > Hi Melissa, > At first I was going to suggest ?mcopy? but from your description, it sounds like you have each chain as a separate model. ?mcopy? is only for copying settings within one model to other models. > > > You can get the current atom-color RGB definitions or hex codes by Ctrl-click to select an atom (or ribbon segment to select the whole residue, if all of its atoms are the same color), showing the Selection Inspector, Inspect: atom, and then clicking the square color well to get the Color Editor. Then in the Color Editor you can see the hex code starting with # in the ?Color name? field. > > The square in the Model Panel shows the model-level color. Chimera has a coloring hierarchy, where if the atoms are individually assigned colors (such as with your color command), in the 3D display those colors mask the model-level color, which may be different. You can use the modelcolor command, for example ?modelcolor #6168c8fb41bc #0.17? or click the color square in the Model Panel to make the Color Editor dialog appear, and then enter the hex code in the ?Color name? field of the Color Editor: > > There is only one model-level color per model, as the name suggests, even though the atoms and per-residue ribbon segments might be all different colors. > > More about color hierarchy: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 2, 2016, at 1:23 PM, Melissa Jurica wrote: > >> I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? >> >> For example: >> >> color #6168c8fb41bc #0.17 >> >> Also- >> How do I get that color to apply to the little square that shows up on the model panel? >> >> Melissa > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dongming618 at gmail.com Sun Sep 4 19:52:09 2016 From: dongming618 at gmail.com (Ming) Date: Sun, 4 Sep 2016 22:52:09 -0400 Subject: [Chimera-users] secondary structure incomplete Message-ID: Dear Chimera team, I was using chimera to do some pdb editing and exporting the file for pymol printing. However after the editing with chimera the pdb file won't show secondary cartoon in pymol (It still shows perfect secondary structure in chimera). I used the file--export function in chimera and I have checked the pdb file and the secondary structure description in the pdb file is intact. Do you think if I export the file in a wrong way that caused the incomplete cartoon? If not what do you think could be the reason causing the issue? Thank you, Ming -------------- next part -------------- An HTML attachment was scrubbed... URL: From igorl.kjuru at hotmail.com Mon Sep 5 07:13:16 2016 From: igorl.kjuru at hotmail.com (Igor Peixoto Rodrigues) Date: Mon, 5 Sep 2016 11:13:16 -0300 Subject: [Chimera-users] Bonds Message-ID: Hi my name is Igor Peixoto, and I have a question. There is some way to count the number of bonds in molecule? Like how much bonds of kind B-C, C-C, B-N.... for example? -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.kadlof at cent.uw.edu.pl Tue Sep 6 06:48:49 2016 From: m.kadlof at cent.uw.edu.pl (=?UTF-8?Q?Micha=C5=82_Kadlof?=) Date: Tue, 6 Sep 2016 15:48:49 +0200 Subject: [Chimera-users] Mesh points from volume data Message-ID: Hello, I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. How can I do that? -- pozdrawiam serdecznie Micha? Kadlof -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Sep 6 10:28:24 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 6 Sep 2016 10:28:24 -0700 Subject: [Chimera-users] Mesh points from volume data In-Reply-To: References: Message-ID: <5FDE3495-DBC7-4F50-ADFA-C6A7D02684E8@cgl.ucsf.edu> Hi Michal, You can use the ?meshmol? command to make the isosurface mesh into a fake molecule, where the the points are ?atoms? and the mesh lines are ?bonds? shown as sticks. Although the new ?molecule model? is suppressed from appearing in the File? Save PDB dialog, you can still save it to PDB from the command line with ?write? ? or save it as a marker set using the File menu of the Volume Tracer tool. Either of those formats will contain the coordinates. The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 6, 2016, at 6:48 AM, Micha? Kadlof wrote: > > Hello, > > I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. > > How can I do that? > -- > pozdrawiam serdecznie > Micha? Kadlof From pett at cgl.ucsf.edu Tue Sep 6 10:42:16 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 6 Sep 2016 10:42:16 -0700 Subject: [Chimera-users] secondary structure incomplete In-Reply-To: References: Message-ID: Hi Ming, I don?t really know why PyMOL wouldn?t show the secondary structure. Chimera outputs legal HELIX/SHEET records. I guess my suggestion is to ask on the PyMOL mailing list why PyMOL doesn?t show secondary structure for your molecule, and attach the PDB file so that they can figure out what the problem is. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 4, 2016, at 7:52 PM, Ming wrote: > > Dear Chimera team, > > I was using chimera to do some pdb editing and exporting the file for pymol printing. However after the editing with chimera the pdb file won't show secondary cartoon in pymol (It still shows perfect secondary structure in chimera). I used the file--export function in chimera and I have checked the pdb file and the secondary structure description in the pdb file is intact. Do you think if I export the file in a wrong way that caused the incomplete cartoon? If not what do you think could be the reason causing the issue? > > Thank you, > > Ming > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 6 10:59:33 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 6 Sep 2016 10:59:33 -0700 Subject: [Chimera-users] Bonds In-Reply-To: References: Message-ID: <22A15704-C295-4C37-B85C-42FEF4DB843A@cgl.ucsf.edu> > On Sep 5, 2016, at 7:13 AM, Igor Peixoto Rodrigues wrote: > > Hi my name is Igor Peixoto, and I have a question. There is some way to count the number of bonds in molecule? Like how much bonds of kind B-C, C-C, B-N.... for example? Hi Igor, There is. If you are only doing this for a few structures, then the easiest way is probably to use the commands to select the endpoint atoms, which will also select the bonds. The number of selected atoms and bonds will be reported on the right side of the command line. If the endpoint atoms are of different elements (say C and B) you will then have to do two additional selections to find the bonds between the identical elements (C-C and B-B in this example) and subtract those off, since those were also selected by the first command. So, for example, to find the number of C-N bonds in 3fx2: sel @/element=C @/element=N (reports 905 bonds) sel C (can use this simpler form if there?s only one element; reports 556 bonds) sel N (reports 0 bonds) 905 - 556 - 0 = 349 For a large number of structures you would probably want to use a Python script to do this more automatically. If so, let me know and I?ll provide some pointers. ?Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 6 11:13:42 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 6 Sep 2016 11:13:42 -0700 Subject: [Chimera-users] extracting chaing colors from session file? In-Reply-To: <571AE5B5-02D7-4E2D-9E07-7F5C4F6E710F@ucsc.edu> References: <571AE5B5-02D7-4E2D-9E07-7F5C4F6E710F@ucsc.edu> Message-ID: Hi Melissa, Here?s a little Python script that will go through your molecular models and print out the ?modelcolor? command that would give them their current color. You can run the script simply by opening it with the ?open? command or with the File->Open dialog. The commands will appear in the Reply Log. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 3, 2016, at 11:23 AM, Melissa Jurica wrote: > > Thanks Elaine- > > My structures have more than 20 individual components (recent spliceosome cryo-EM models- example PDB 5GMK). They came as 1 model, which I split to have more control over for analysis. I can go through each component by hand and copy/paste the color for each model into a text file and then turn then this into a command file to color another structure with the same components in another conformation. (Thanks for turning me on to the ?modelcolor? command. That will be helpful!) However, I was hoping there was a way to use something like grep to extract this information from the .py session file. > > Melissa > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Melissa S. Jurica, Ph.D. > Professor, Molecular, Cell & Developmental Biology > Center for Molecular Biology of RNA > University of California, Santa Cruz > 1156 High Street > Santa Cruz, CA 95064 > > Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs > Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 > http://www.mcd.ucsc.edu/faculty/jurica.html > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > On Sep 2, 2016, at 5:11 PM, Elaine Meng > wrote: > >> Hi Melissa, >> At first I was going to suggest ?mcopy? but from your description, it sounds like you have each chain as a separate model. ?mcopy? is only for copying settings within one model to other models. >> > >> >> You can get the current atom-color RGB definitions or hex codes by Ctrl-click to select an atom (or ribbon segment to select the whole residue, if all of its atoms are the same color), showing the Selection Inspector, Inspect: atom, and then clicking the square color well to get the Color Editor. Then in the Color Editor you can see the hex code starting with # in the ?Color name? field. >> >> The square in the Model Panel shows the model-level color. Chimera has a coloring hierarchy, where if the atoms are individually assigned colors (such as with your color command), in the 3D display those colors mask the model-level color, which may be different. You can use the modelcolor command, for example ?modelcolor #6168c8fb41bc #0.17? or click the color square in the Model Panel to make the Color Editor dialog appear, and then enter the hex code in the ?Color name? field of the Color Editor: >> > >> There is only one model-level color per model, as the name suggests, even though the atoms and per-residue ribbon segments might be all different colors. >> >> More about color hierarchy: >> > >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Sep 2, 2016, at 1:23 PM, Melissa Jurica > wrote: >> >>> I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? >>> >>> For example: >>> >>> color #6168c8fb41bc #0.17 >>> >>> Also- >>> How do I get that color to apply to the little square that shows up on the model panel? >>> >>> Melissa >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: getcolors.py Type: text/x-python-script Size: 170 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.kadlof at cent.uw.edu.pl Tue Sep 6 12:36:41 2016 From: m.kadlof at cent.uw.edu.pl (=?UTF-8?Q?Micha=C5=82_Kadlof?=) Date: Tue, 6 Sep 2016 21:36:41 +0200 Subject: [Chimera-users] Mesh points from volume data In-Reply-To: <5FDE3495-DBC7-4F50-ADFA-C6A7D02684E8@cgl.ucsf.edu> References: <5FDE3495-DBC7-4F50-ADFA-C6A7D02684E8@cgl.ucsf.edu> Message-ID: Works like a charm! :) -- pozdrawiam serdecznie Micha? Kadlof 2016-09-06 19:28 GMT+02:00 Elaine Meng : > Hi Michal, > You can use the ?meshmol? command to make the isosurface mesh into a fake > molecule, where the the points are ?atoms? and the mesh lines are ?bonds? > shown as sticks. > > > Although the new ?molecule model? is suppressed from appearing in the > File? Save PDB dialog, you can still save it to PDB from the command line > with ?write? ? or save it as a marker set using the File menu of the Volume > Tracer tool. > > volumepathtracer/framevolpath.html> > > Either of those formats will contain the coordinates. The marker format > will do a better job of preserving the stick bonds and their radii, if that > matters to you. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Sep 6, 2016, at 6:48 AM, Micha? Kadlof > wrote: > > > > Hello, > > > > I have density data in .cmap file format. I want to save a coordinates > for points that are on the surface for given cutoff. I need exactly that > points which are visible in mesh representation. > > > > How can I do that? > > -- > > pozdrawiam serdecznie > > Micha? Kadlof > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Wed Sep 7 07:36:27 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Wed, 7 Sep 2016 14:36:27 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> References: , <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> Message-ID: Hi Eric, That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. Do you have any advice about how best to proceed? Many thanks, Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 31 August 2016 18:23 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe, This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ".bin" extension but it's really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs... http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html -Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Sep 7 11:49:19 2016 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 7 Sep 2016 11:49:19 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> Message-ID: Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ, https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, and came up with pychimera, https://pypi.python.org/pypi/pychimera. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. HTH, Greg On 09/07/2016 07:36 AM, Healey, Joe wrote: > > Hi Eric, > > > That looks good thank you. I think I'm going about this slightly the > wrong way after some investigation however. > > > Am I right in thinking that chimera can't be imported in to python > inside a normal bash shell, and rather it must be done the other way > round? So file manipulation and such must be done by calls to the > system from within the chimera python shell, rather than a python > interpreter calling chimera modules in? > > > It certainly makes the chimera steps I plan to do much easier, but I > was going to include it in a pipeline with some other programs and it > makes that a little more taxing (though not insurmountable!). > > > Additionally, I plan to invoke this inside a script on a headless > linux box (hence why running it through a python script was ideal), so > whatever solution I use will need to be 'command line friendly'. > > > In effect all I need is the actual algorithm for the matching process > to be accessed somehow from a python script. > > > Do you have any advice about how best to proceed? > > > Many thanks, > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab > > (WMS Microbiology and Infection Unit) > and the Gibson Lab > (Warwick > Chemistry) > > Twitter: @JRJHealey | Website: MOAC > Page > > > > ------------------------------------------------------------------------ > *From:* Eric Pettersen > *Sent:* 31 August 2016 18:23 > *To:* Healey, Joe > *Cc:* chimera-users at cgl.ucsf.edu > *Subject:* Re: [Chimera-users] Recursive structure matching and > acquisition of descriptive numbers > Hi Joe, > This old chimera-users post has a Python script attachment that > demonstrates how to call the underlying MatchMaker function to get the > RMSD value programmatically. The mailing list gives the attachment a > ?.bin? extension but it?s really a .py file. Just change the > extension if you need to. Let me know if you have any questions about > how to adapt the script to your needs? > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Aug 31, 2016, at 3:02 AM, Healey, Joe > > wrote: >> >> Hi, >> >> I have several hundred structure simulations that were performed on >> our HPC resource. Each simulation has approximately 5 models >> associated with it. I also have HMM model homologies for each of >> these proteins. >> >> I would like to use chimera's matchmaker function to compare the >> simulated structured to their nearest 'real' counterpart with a >> resolved structure. In order to do this I plan to script chimera to >> pull in the simulated models as well as the near homolog and then run >> the matchmaker algorithm. >> >> My question is: can the RMSD value that is returned in the reply log >> be 'accessed directly' such that for each match that is performed, I >> can obtain the RMSD and thus a ranking for the best fitting >> structures - or will it require parsing the reply log? >> >> Thanks >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email:J.R.J.Healey at warwick.ac.uk >> >> >> Jointly working in: >> Waterfield Lab >> (WMS >> Microbiology and Infection Unit) >> and the Gibson Lab >> (Warwick >> Chemistry) >> >> Twitter:@JRJHealey | Website:MOAC >> Page >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu >> >> Manage >> subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 7 16:29:50 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 7 Sep 2016 16:29:50 -0700 Subject: [Chimera-users] Mesh points from volume data In-Reply-To: References: <5FDE3495-DBC7-4F50-ADFA-C6A7D02684E8@cgl.ucsf.edu> <88DDB111-B05F-4A00-940C-F4FF6AEE40D3@cgl.ucsf.edu> Message-ID: <6788BC84-B0A6-43B5-BF7A-24FECD4B1E19@cgl.ucsf.edu> Hello, Sorry, I can?t help on this one, so I?m forwarding to the list! Best, Elaine On Sep 7, 2016, at 6:24 AM, Micha? Kadlof wrote: > Hello, > > I'm almost home. There are several issues: > 1. I need not only points but also planes -> point triples from surface triangulation. > 2. I have quite a lot of points (more than 30 000). PDB file format fails in the CONNECT records: > > In the end of file they looks like this: > CONECT3051230171301923050530506 > CONECT3051230511 > CONECT3051330165301663018830508 > CONECT3051330514 > CONECT3051430188302133050830509 > CONECT305143051330515 > CONECT3051530213302163050930510 > CONECT305153051430516 > CONECT3051630193302163021830510 > CONECT305163051130515 > END > > Is there any walkaround? Preferably it would be best solution for me if I could access both points and planes (faces) programatically with python. Is it possible? > > -- > pozdrawiam serdecznie > Micha? Kadlof > > > On Sep 6, 2016, at 12:36 PM, Micha? Kadlof wrote: > > > > Works like a charm! :) > > > > -- > > pozdrawiam serdecznie > > Micha? Kadlof > > > > 2016-09-06 19:28 GMT+02:00 Elaine Meng : > > Hi Michal, > > You can use the ?meshmol? command to make the isosurface mesh into a fake molecule, where the the points are ?atoms? and the mesh lines are ?bonds? shown as sticks. > > > > > > Although the new ?molecule model? is suppressed from appearing in the File? Save PDB dialog, you can still save it to PDB from the command line with ?write? ? or save it as a marker set using the File menu of the Volume Tracer tool. > > > > > > > > Either of those formats will contain the coordinates. The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you. > > I hope this helps, > > Elaine > > ---------- > > Elaine C. Meng, Ph.D. > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > > > On Sep 6, 2016, at 6:48 AM, Micha? Kadlof wrote: > > > > > > Hello, > > > > > > I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. > > > > > > How can I do that? > > > -- > > > pozdrawiam serdecznie > > > Micha? Kadlof > > > > From goddard at sonic.net Wed Sep 7 16:53:46 2016 From: goddard at sonic.net (Tom Goddard) Date: Wed, 7 Sep 2016 16:53:46 -0700 Subject: [Chimera-users] Mesh points from volume data In-Reply-To: <6788BC84-B0A6-43B5-BF7A-24FECD4B1E19@cgl.ucsf.edu> References: <5FDE3495-DBC7-4F50-ADFA-C6A7D02684E8@cgl.ucsf.edu> <88DDB111-B05F-4A00-940C-F4FF6AEE40D3@cgl.ucsf.edu> <6788BC84-B0A6-43B5-BF7A-24FECD4B1E19@cgl.ucsf.edu> Message-ID: It is easy to access the Chimera density map surface vertices and triangles in Python. I?ve attached a bit of Python code triangles.py that illustrates this, just open a map, then open this script in Chimera. Below is example output. More Python Chimera script examples are on the Chimera developer wiki. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom emd_1080.map map, 21656 vertices, 43200 triangles vertex coordinates: -22.218 -43.2 -64.8 -20.904 -43.2 -64.8 -21.6 -43.508 -64.8 -21.6 -42.459 -64.8 -21.6 -43.2 -64.871 ... triangle vertex indices: 0 4 2 3 4 0 1 2 4 3 1 4 5 9 7 ? -------------- next part -------------- A non-text attachment was scrubbed... Name: triangles.py Type: text/x-python-script Size: 763 bytes Desc: not available URL: -------------- next part -------------- > On Sep 7, 2016, at 4:29 PM, Elaine Meng wrote: > > Hello, > Sorry, I can?t help on this one, so I?m forwarding to the list! > Best, > Elaine > > On Sep 7, 2016, at 6:24 AM, Micha? Kadlof wrote: > >> Hello, >> >> I'm almost home. There are several issues: >> 1. I need not only points but also planes -> point triples from surface triangulation. >> 2. I have quite a lot of points (more than 30 000). PDB file format fails in the CONNECT records: >> >> In the end of file they looks like this: >> CONECT3051230171301923050530506 >> CONECT3051230511 >> CONECT3051330165301663018830508 >> CONECT3051330514 >> CONECT3051430188302133050830509 >> CONECT305143051330515 >> CONECT3051530213302163050930510 >> CONECT305153051430516 >> CONECT3051630193302163021830510 >> CONECT305163051130515 >> END >> >> Is there any walkaround? Preferably it would be best solution for me if I could access both points and planes (faces) programatically with python. Is it possible? >> >> -- >> pozdrawiam serdecznie >> Micha? Kadlof >> >>> On Sep 6, 2016, at 12:36 PM, Micha? Kadlof wrote: >>> >>> Works like a charm! :) >>> >>> -- >>> pozdrawiam serdecznie >>> Micha? Kadlof >>> >>> 2016-09-06 19:28 GMT+02:00 Elaine Meng : >>> Hi Michal, >>> You can use the ?meshmol? command to make the isosurface mesh into a fake molecule, where the the points are ?atoms? and the mesh lines are ?bonds? shown as sticks. >>> >>> >>> Although the new ?molecule model? is suppressed from appearing in the File? Save PDB dialog, you can still save it to PDB from the command line with ?write? ? or save it as a marker set using the File menu of the Volume Tracer tool. >>> >>> >>> >>> Either of those formats will contain the coordinates. The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you. >>> I hope this helps, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Sep 6, 2016, at 6:48 AM, Micha? Kadlof wrote: >>>> >>>> Hello, >>>> >>>> I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. >>>> >>>> How can I do that? >>>> -- >>>> pozdrawiam serdecznie >>>> Micha? Kadlof >>> >>> > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jaime.rogue at gmail.com Thu Sep 8 05:38:15 2016 From: jaime.rogue at gmail.com (=?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?=) Date: Thu, 8 Sep 2016 14:38:15 +0200 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: Hi! Such an honor to see my name listed here! Yes, with pychimera you should be able to do it! All you need to do is to patch the environment so that Chimera can find its libraries and dependencies, and then initialize it. In practice, this means importing pychimera and calling pychimera.patch_environ() and pychimera.load_chimera() at module level. Then you can proceed as you'd do with a standard Python distribution. If you don't want (or are not able) to modify the script, pychimera also installs a binary that will patch and load Chimera for you, so you can just do "pychimera myscript.py" However, it's a bit buggy when it comes to parsing additional arguments for your script. That said, the binary is very useful to fiddle with Chimera internals from the command line, since it provides a patched python in which you can import chimera, and also hooks for ipython and jupyter notebook (with magic calls to render inline!). pychimera will do its best to locate your Chimera installation, but if it doesn't succeed, you can always provide it manually with the envvar CHIMERADIR, which is what you would probably need to load the headless edition of Chimera. Additionally, it will load your current Python distribution sys.path, which means it will be able to import already installed packages in such distribution. As a result, you don't need to install the packages again for Chimera. This is particularly useful if you are using virtual envs or conda envs! I think that's all. If further questions arise or something is not working as you'd expect, please report that in the issues page of GH ( https://github.com/insilichem/pychimera), or write to me directly. Cheers, Jaime. -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Thu Sep 8 11:53:54 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Thu, 8 Sep 2016 18:53:54 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> , Message-ID: Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Greg Couch Sent: 07 September 2016 19:49:19 To: Healey, Joe; chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ, https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, and came up with pychimera, https://pypi.python.org/pypi/pychimera. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. HTH, Greg On 09/07/2016 07:36 AM, Healey, Joe wrote: Hi Eric, That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. Do you have any advice about how best to proceed? Many thanks, Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 31 August 2016 18:23 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe, This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html ?Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Thu Sep 8 14:43:55 2016 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 8 Sep 2016 14:43:55 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> Message-ID: chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. -- Greg On 09/08/2016 11:53 AM, Healey, Joe wrote: > > Brilliant, that sounds like the most likely option. I had stumbled > across pychimera a couple of days ago while trying to find out if > chimera could simply be imported as a module. I initially steered away > from it as I don't have sudo rights for the server where I'm trying to > set all this up (couldnt run pip), but I've since sorted it with our > sysadmin. > > > On a related point, is running chimera with --nogui equivalent to > running headless chimera? I'm just wondering if pychimera is happy > with either > > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab > > (WMS Microbiology and Infection Unit) > and the Gibson Lab > (Warwick > Chemistry) > > Twitter: @JRJHealey | Website: MOAC > Page > > ------------------------------------------------------------------------ > *From:* Greg Couch > *Sent:* 07 September 2016 19:49:19 > *To:* Healey, Joe; chimera-users at cgl.ucsf.edu BB > *Subject:* Re: [Chimera-users] Recursive structure matching and > acquisition of descriptive numbers > > Yes, Chimera's Python code is only "warrantied" to work with its own > Python. See question 3b of the Chimera Programming FAQ, > https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, > for how to install other software into Chimera. Other parts of the > FAQ may help you too. > > > That said, Jaime Rodr?guez-Guerra took my previous comments on this > subject, > http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, > and came up with pychimera, https://pypi.python.org/pypi/pychimera. I > haven't checked to see how it handles all of my caveats, and it can't > completely without using a modified Python, but I suspect that it > would be good enough for you. > > > HTH, > > > Greg > > > On 09/07/2016 07:36 AM, Healey, Joe wrote: >> >> Hi Eric, >> >> >> That looks good thank you. I think I'm going about this slightly the >> wrong way after some investigation however. >> >> >> Am I right in thinking that chimera can't be imported in to python >> inside a normal bash shell, and rather it must be done the other way >> round? So file manipulation and such must be done by calls to the >> system from within the chimera python shell, rather than a python >> interpreter calling chimera modules in? >> >> >> It certainly makes the chimera steps I plan to do much easier, but I >> was going to include it in a pipeline with some other programs and it >> makes that a little more taxing (though not insurmountable!). >> >> >> Additionally, I plan to invoke this inside a script on a headless >> linux box (hence why running it through a python script was ideal), >> so whatever solution I use will need to be 'command line friendly'. >> >> >> In effect all I need is the actual algorithm for the matching process >> to be accessed somehow from a python script. >> >> >> Do you have any advice about how best to proceed? >> >> >> Many thanks, >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab >> >> (WMS Microbiology and Infection Unit) >> and the Gibson Lab >> (Warwick >> Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC >> Page >> >> >> >> ------------------------------------------------------------------------ >> *From:* Eric Pettersen >> *Sent:* 31 August 2016 18:23 >> *To:* Healey, Joe >> *Cc:* chimera-users at cgl.ucsf.edu >> *Subject:* Re: [Chimera-users] Recursive structure matching and >> acquisition of descriptive numbers >> Hi Joe, >> This old chimera-users post has a Python script attachment that >> demonstrates how to call the underlying MatchMaker function to get >> the RMSD value programmatically. The mailing list gives the >> attachment a ?.bin? extension but it?s really a .py file. Just >> change the extension if you need to. Let me know if you have any >> questions about how to adapt the script to your needs? >> >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >> >> ?Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Aug 31, 2016, at 3:02 AM, Healey, Joe >> > wrote: >>> >>> Hi, >>> >>> I have several hundred structure simulations that were performed on >>> our HPC resource. Each simulation has approximately 5 models >>> associated with it. I also have HMM model homologies for each of >>> these proteins. >>> >>> I would like to use chimera's matchmaker function to compare the >>> simulated structured to their nearest 'real' counterpart with a >>> resolved structure. In order to do this I plan to script chimera to >>> pull in the simulated models as well as the near homolog and then >>> run the matchmaker algorithm. >>> >>> My question is: can the RMSD value that is returned in the reply log >>> be 'accessed directly' such that for each match that is performed, I >>> can obtain the RMSD and thus a ranking for the best fitting >>> structures - or will it require parsing the reply log? >>> >>> Thanks >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email:J.R.J.Healey at warwick.ac.uk >>> >>> >>> Jointly working in: >>> Waterfield Lab >>> (WMS >>> Microbiology and Infection Unit) >>> and the Gibson Lab >>> (Warwick >>> Chemistry) >>> >>> Twitter:@JRJHealey | Website:MOAC >>> Page >>> >>> _______________________________________________ >>> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu >>> >>> Manage >>> subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu >> Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.rodriguezguerra at uab.cat Fri Sep 9 01:10:51 2016 From: jaime.rodriguezguerra at uab.cat (=?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?=) Date: Fri, 9 Sep 2016 10:10:51 +0200 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: Message-ID: Joe, If admin permissions are an issue, you can always install the Miniconda 2.7 distribution, which will install all packages in your user folder, virtualenvs included. I cannot recommend it enough! Greg, I have not come across any problems without that windowsize command, so I guess it just works? I posted a gist which shows how to render images programatically for a bunch of pdb files. Let me know if it works! https://gist.github.com/jaimergp/09104ca2bbccb81ff430374f9c2522a7 Cheers! From J.R.J.Healey at warwick.ac.uk Mon Sep 12 04:47:44 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Mon, 12 Sep 2016 11:47:44 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> , Message-ID: That sounds very promising, I'll rework the script for pychimera and see how I get on. Many thanks for all the help. Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Greg Couch Sent: 07 September 2016 19:49:19 To: Healey, Joe; chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ, https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, and came up with pychimera, https://pypi.python.org/pypi/pychimera. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. HTH, Greg On 09/07/2016 07:36 AM, Healey, Joe wrote: Hi Eric, That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. Do you have any advice about how best to proceed? Many thanks, Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 31 August 2016 18:23 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe, This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html ?Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.gcp.almeida at gmail.com Sat Sep 10 18:45:17 2016 From: jose.gcp.almeida at gmail.com (=?UTF-8?Q?Jos=C3=A9_Almeida?=) Date: Sun, 11 Sep 2016 02:45:17 +0100 Subject: [Chimera-users] Chimera input from command line Message-ID: Hello, I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so. Already thanking any attention given to this problem, Best regards, Jos? Guilherme de Almeida -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ilan.Chemmama at ucsf.edu Mon Sep 12 14:24:52 2016 From: Ilan.Chemmama at ucsf.edu (Chemmama, Ilan) Date: Mon, 12 Sep 2016 21:24:52 +0000 Subject: [Chimera-users] RMF Viewer and Resolution Selection Message-ID: Dear developers, I am trying to select hierarchical features based on resolutions (for example to show or hide). Using the resolution sliders does not seems to work however. I could not find anything in the documentation page though. Is there an easy way (command line would be the best) to select a given resolution? Thanks, Ilan From dinhchauphi at gmail.com Tue Sep 13 01:27:05 2016 From: dinhchauphi at gmail.com (Chau Phi DINh) Date: Tue, 13 Sep 2016 10:27:05 +0200 Subject: [Chimera-users] Problem in installing Chimera in Linux Message-ID: Dear my friends, I tried to install Chimera on Ubuntu. I followed the instruction in Release Note of UCSF. I typed in Terminal command the following: chmod +x chimera-installer.bin chimera-installer.bin but it shows me : chimera-installer.bin: command not found Can you tell me how I can do to install it ? Regards, Phi Sent with Mailtrack -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 14 10:46:16 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 14 Sep 2016 10:46:16 -0700 Subject: [Chimera-users] Problem in installing Chimera in Linux In-Reply-To: References: Message-ID: <99A81543-127C-4007-8154-DD2C9715699F@cgl.ucsf.edu> Hi Phi, Assuming you are in the right place (the directory or folder where the bin file is), instead of chimera-installer.bin try this: ./chimera-installer.bin ? which just says to use the file in the directory you?re currently in, instead of searching your paths, which might not include that directory. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2016, at 1:27 AM, Chau Phi DINh wrote: > Dear my friends, > > I tried to install Chimera on Ubuntu. I followed the instruction in Release Note of UCSF. I typed in Terminal command the following: > > chmod +x chimera-installer.bin > chimera-installer.bin > > but it shows me : chimera-installer.bin: command not found > > Can you tell me how I can do to install it ? > > Regards, > > Phi From conrad at cgl.ucsf.edu Wed Sep 14 10:48:45 2016 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 14 Sep 2016 10:48:45 -0700 Subject: [Chimera-users] RMF Viewer and Resolution Selection In-Reply-To: References: Message-ID: <6f670655-f59a-46bf-08c9-f45ae0596a1f@cgl.ucsf.edu> Resolution in RMF has been a moving target, so the current code probably handles a different aspect of resolution than what your data file contains. Can you please send me an example file and a short description of how you'd like the resolution slider to work (or perhaps a completely different interface for selecting resolution)? Thanks. Conrad On 9/12/2016 2:24 PM, Chemmama, Ilan wrote: > Dear developers, > > I am trying to select hierarchical features based on resolutions (for example to show or hide). > Using the resolution sliders does not seems to work however. > I could not find anything in the documentation page though. > Is there an easy way (command line would be the best) to select a given resolution? > > > Thanks, > Ilan > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Wed Sep 14 11:02:08 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 14 Sep 2016 11:02:08 -0700 Subject: [Chimera-users] Chimera input from command line In-Reply-To: References: Message-ID: <281E6F75-402B-4276-80D9-4FB460B4874D@cgl.ucsf.edu> Hi Jose, You can create an input test file that is a script with a series of instructions in either Chimera commands or Python, and then from the command line, start Chimera in nogui mode and specify that input file. Startup from system command line, see also - -nogui startup option: Input file types including Chimera command files and Python scripts: Basic primer on Python scripting for Chimera: Some possible reasons to use Python instead of Chimera command scripts are if you need looping, or some function that is not available as a Chimera command. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 10, 2016, at 6:45 PM, Jos? Almeida wrote: > Hello, > I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so. > > Already thanking any attention given to this problem, > Best regards, > Jos? Guilherme de Almeida From pett at cgl.ucsf.edu Wed Sep 14 13:05:14 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 14 Sep 2016 13:05:14 -0700 Subject: [Chimera-users] Chimera input from command line In-Reply-To: <281E6F75-402B-4276-80D9-4FB460B4874D@cgl.ucsf.edu> References: <281E6F75-402B-4276-80D9-4FB460B4874D@cgl.ucsf.edu> Message-ID: <0C88633B-6208-471B-9BC5-F26E35523830@cgl.ucsf.edu> Hi Jose, All Elaine?s info is correct. In case your question was about using Chimera functions from your own Python interpreter, see this recent chimera-users thread: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012704.html ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 14, 2016, at 11:02 AM, Elaine Meng wrote: > > Hi Jose, > You can create an input test file that is a script with a series of instructions in either Chimera commands or Python, and then from the command line, start Chimera in nogui mode and specify that input file. > > Startup from system command line, see also - -nogui startup option: > > > > Input file types including Chimera command files and Python scripts: > > > Basic primer on Python scripting for Chimera: > > > Some possible reasons to use Python instead of Chimera command scripts are if you need looping, or some function that is not available as a Chimera command. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 10, 2016, at 6:45 PM, Jos? Almeida wrote: > >> Hello, >> I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so. >> >> Already thanking any attention given to this problem, >> Best regards, >> Jos? Guilherme de Almeida > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dinhchauphi at gmail.com Wed Sep 14 13:02:50 2016 From: dinhchauphi at gmail.com (Chau Phi DINh) Date: Wed, 14 Sep 2016 22:02:50 +0200 Subject: [Chimera-users] Problem in installing Chimera in Linux In-Reply-To: <99A81543-127C-4007-8154-DD2C9715699F@cgl.ucsf.edu> References: <99A81543-127C-4007-8154-DD2C9715699F@cgl.ucsf.edu> Message-ID: Thank you for your advice, I try as you told me but when I typed ./chimera-installer.bin , it showed that bash: ./chimera-installer.bin: No such file or directory. My working folder is Downloads and when I typed ls, I saw chimera-installer.bin in the list. I took a snapshot to show you. Please, help me!!! Thank you so much, Phi Sent with Mailtrack 2016-09-14 19:46 GMT+02:00 Elaine Meng : > Hi Phi, > Assuming you are in the right place (the directory or folder where the bin > file is), instead of > > chimera-installer.bin > > try this: > > ./chimera-installer.bin > > ? which just says to use the file in the directory you?re currently in, > instead of searching your paths, which might not include that directory. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 13, 2016, at 1:27 AM, Chau Phi DINh wrote: > > > Dear my friends, > > > > I tried to install Chimera on Ubuntu. I followed the instruction in > Release Note of UCSF. I typed in Terminal command the following: > > > > chmod +x chimera-installer.bin > > chimera-installer.bin > > > > but it shows me : chimera-installer.bin: command not found > > > > Can you tell me how I can do to install it ? > > > > Regards, > > > > Phi > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-09-14 21-59-01.png Type: image/png Size: 176040 bytes Desc: not available URL: From gregc at cgl.ucsf.edu Wed Sep 14 15:58:03 2016 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 14 Sep 2016 15:58:03 -0700 Subject: [Chimera-users] Problem in installing Chimera in Linux In-Reply-To: References: <99A81543-127C-4007-8154-DD2C9715699F@cgl.ucsf.edu> Message-ID: <2d7183c9-00ca-53c3-156d-c9cc1d10693c@cgl.ucsf.edu> In the bash shell, double check that the chimera-installer is executable with: ls -l chimera-installer.bin I would expect the output to be: -rwxr-xr-x chimera-installer.bin If the x's are missing: chmod +x chimera-installer.bin If the x's are still missing, then change your umask with: umask 0002 and do the chmod again. Then run: ./chimera-installer.bin And everything should be wonderful :-) HTH, Greg On 09/14/2016 01:02 PM, Chau Phi DINh wrote: > > Thank you for your advice, > > I try as you told me but when I typed ./chimera-installer.bin , it > showed that bash: ./chimera-installer.bin: No such file or directory. > > My working folder is Downloads and when I typed ls, I saw > chimera-installer.bin in the list. > I took a snapshot to show you. Please, help me!!! > > Thank you so much, > > Phi > > > > > Sent with Mailtrack > > > 2016-09-14 19:46 GMT+02:00 Elaine Meng >: > > Hi Phi, > Assuming you are in the right place (the directory or folder where > the bin file is), instead of > > chimera-installer.bin > > try this: > > ./chimera-installer.bin > > ? which just says to use the file in the directory you?re > currently in, instead of searching your paths, which might not > include that directory. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 13, 2016, at 1:27 AM, Chau Phi DINh > wrote: > > > Dear my friends, > > > > I tried to install Chimera on Ubuntu. I followed the > instruction in Release Note of UCSF. I typed in Terminal command > the following: > > > > chmod +x chimera-installer.bin > > chimera-installer.bin > > > > but it shows me : chimera-installer.bin: command not found > > > > Can you tell me how I can do to install it ? > > > > Regards, > > > > Phi > > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.gcp.almeida at gmail.com Thu Sep 15 07:10:53 2016 From: jose.gcp.almeida at gmail.com (=?UTF-8?Q?Jos=C3=A9_Almeida?=) Date: Thu, 15 Sep 2016 15:10:53 +0100 Subject: [Chimera-users] Chimera input from command line In-Reply-To: <0C88633B-6208-471B-9BC5-F26E35523830@cgl.ucsf.edu> References: <281E6F75-402B-4276-80D9-4FB460B4874D@cgl.ucsf.edu> <0C88633B-6208-471B-9BC5-F26E35523830@cgl.ucsf.edu> Message-ID: Hello all, I am much obliged for the information, I will try it as soon as possible. The information seems to be just what I needed. The problem was that I was trying to work around the creation of a new file, but if it is the only way I will give it a try. Thank you very much for the time, All the best, Jos? On Wed, Sep 14, 2016 at 9:05 PM, Eric Pettersen wrote: > Hi Jose, > All Elaine?s info is correct. In case your question was about using > Chimera functions from your own Python interpreter, see this recent > chimera-users thread: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016- > September/012704.html > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Sep 14, 2016, at 11:02 AM, Elaine Meng wrote: > > Hi Jose, > You can create an input test file that is a script with a series of > instructions in either Chimera commands or Python, and then from the > command line, start Chimera in nogui mode and specify that input file. > > Startup from system command line, see also - -nogui startup option: > > > > Input file types including Chimera command files and Python scripts: > > > Basic primer on Python scripting for Chimera: > > > Some possible reasons to use Python instead of Chimera command scripts are > if you need looping, or some function that is not available as a Chimera > command. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Sep 10, 2016, at 6:45 PM, Jos? Almeida > wrote: > > Hello, > I am a beggining Chimera user and was wondering if it was possible to run, > all in the same command, something that enabled me to use a function (e.g. > hbonds) without utilizing the console or the gui. I am trying to include > this into a program so that I can calculate H-Bond data on several proteins > in order to automatize the procedure, but I haven't been able to do so. > > Already thanking any attention given to this problem, > Best regards, > Jos? Guilherme de Almeida > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Tue Sep 20 05:07:14 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Tue, 20 Sep 2016 12:07:14 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> , Message-ID: Hi again, I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. Is there are resource with more information on the commandline implementation of match anywhere other than the link below? https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html But I can't quite unwrap the options specified in the command for my uses. Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. Many thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Greg Couch Sent: 08 September 2016 22:43:55 To: Healey, Joe; chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. -- Greg On 09/08/2016 11:53 AM, Healey, Joe wrote: Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Greg Couch Sent: 07 September 2016 19:49:19 To: Healey, Joe; chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ, https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html, and came up with pychimera, https://pypi.python.org/pypi/pychimera. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. HTH, Greg On 09/07/2016 07:36 AM, Healey, Joe wrote: Hi Eric, That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. Do you have any advice about how best to proceed? Many thanks, Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 31 August 2016 18:23 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe, This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html ?Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 20 11:30:38 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 20 Sep 2016 11:30:38 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <4A416758-3538-409E-8CB8-502417B9B486@cgl.ucsf.edu> Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42@cgl.ucsf.edu> Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Greg Couch > > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Greg Couch >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b , for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html , and came up with pychimera, https://pypi.python.org/pypi/pychimera . I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: Eric Pettersen >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users at cgl.ucsf.edu >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>>> >>>> Jointly working in: >>>> Waterfield Lab (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Tue Sep 20 15:16:02 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Tue, 20 Sep 2016 22:16:02 +0000 Subject: [Chimera-users] Chimera-users Digest, Vol 161, Issue 19 In-Reply-To: References: Message-ID: Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: chimera-users-bounces at cgl.ucsf.edu on behalf of chimera-users-request at cgl.ucsf.edu Sent: 20 September 2016 19:30 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen To: "Healey, Joe" Cc: "chimera-users at cgl.ucsf.edu BB" Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Greg Couch > > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Greg Couch >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b , for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html , and came up with pychimera, https://pypi.python.org/pypi/pychimera . I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: Eric Pettersen >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users at cgl.ucsf.edu >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>>> >>>> Jointly working in: >>>> Waterfield Lab (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 161, Issue 19 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Sep 20 16:20:41 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 20 Sep 2016 16:20:41 -0700 Subject: [Chimera-users] Chimera-users Digest, Vol 161, Issue 19 In-Reply-To: References: Message-ID: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. ?Eric > On Sep 20, 2016, at 3:16 PM, Healey, Joe wrote: > > Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. > > In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: > > > chimera.openModels.open(top_hit, type="PDB") > > # Open model structures > for model_path in model_list: > chimera.openModels.open(model_path,type="PDB") > print("Opened: " + model_path) > > rmsd_file = '{0}.tsv'.format(rmsd) > with open(rmsd_file, "a") as rmsd_output_file: > for j in len(model_list): > match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) > runCommand(match_cmd) > > # > > or the other option would be to do the above but avoiding the string synthesis step with something like: > chimera.module.mmaker() > > If the module can be accessed directly? If so which module is the mmaker function within? > > > Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? > > Looking at your Match script the rmsd was the 3rd value of the tuple in the line: > atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] > > Would the same be true for mmaker? > > > (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) > > Thanks again for all your help > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > > From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > > Sent: 20 September 2016 19:30 > To: chimera-users at cgl.ucsf.edu > Subject: Chimera-users Digest, Vol 161, Issue 19 > > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Recursive structure matching and acquisition of > descriptive numbers (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 20 Sep 2016 11:30:38 -0700 > From: Eric Pettersen > > To: "Healey, Joe" > > Cc: "chimera-users at cgl.ucsf.edu BB" > > Subject: Re: [Chimera-users] Recursive structure matching and > acquisition of descriptive numbers > Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu > > Content-Type: text/plain; charset="windows-1252" > > Hi Joe, > I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options > > > I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. > > ?Eric > > > > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: > > > > Hi again, > > > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > > > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > > > > But I can't quite unwrap the options specified in the command for my uses. > > > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 > incase it gives you some indication of what I'm attempting to do. > > > > Many thanks > > > > > > Joe Healey > > > > > > M.Sc. B.Sc. (Hons) > > PhD Student > > MOAC CDT, Senate House > > University of Warwick > > Coventry > > CV47AL > > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > > > > Jointly working in: > > Waterfield Lab > (WMS Microbiology and Infection Unit) > > and the Gibson Lab > (Warwick Chemistry) > > > > Twitter: @JRJHealey > | Website: MOAC Page > > > From: Greg Couch >> > > Sent: 08 September 2016 22:43:55 > > To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB > > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > > > -- Greg > > > > On 09/08/2016 11:53 AM, Healey, Joe wrote: > >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. > >> > >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either > >> > >> > >> Joe Healey > >> > >> > >> M.Sc. B.Sc. (Hons) > >> PhD Student > >> MOAC CDT, Senate House > >> University of Warwick > >> Coventry > >> CV47AL > >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > >> > >> Jointly working in: > >> Waterfield Lab > (WMS Microbiology and Infection Unit) > >> and the Gibson Lab > (Warwick Chemistry) > >> > >> Twitter: @JRJHealey > | Website: MOAC Page > > >> From: Greg Couch > > > >> Sent: 07 September 2016 19:49:19 > >> To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB > >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > >> > >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b >, for how to install other software into Chimera. Other parts of the FAQ may help you too. > >> > >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html >, and came up with pychimera, https://pypi.python.org/pypi/pychimera >. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. > >> > >> HTH, > >> > >> Greg > >> > >> On 09/07/2016 07:36 AM, Healey, Joe wrote: > >>> Hi Eric, > >>> > >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. > >>> > >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? > >>> > >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). > >>> > >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. > >>> > >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. > >>> > >>> Do you have any advice about how best to proceed? > >>> > >>> Many thanks, > >>> > >>> Joe Healey > >>> > >>> > >>> M.Sc. B.Sc. (Hons) > >>> PhD Student > >>> MOAC CDT, Senate House > >>> University of Warwick > >>> Coventry > >>> CV47AL > >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > >>> > >>> Jointly working in: > >>> Waterfield Lab > (WMS Microbiology and Infection Unit) > >>> and the Gibson Lab > (Warwick Chemistry) > >>> > >>> Twitter: @JRJHealey > | Website: MOAC Page > > >>> > >>> From: Eric Pettersen > > > >>> Sent: 31 August 2016 18:23 > >>> To: Healey, Joe > >>> Cc: chimera-users at cgl.ucsf.edu > > >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > >>> > >>> Hi Joe, > >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? > >>> > >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > >>> > >>> ?Eric > >>> > >>> Eric Pettersen > >>> UCSF Computer Graphics Lab > >>> > >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe >> wrote: > >>>> > >>>> Hi, > >>>> > >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. > >>>> > >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. > >>>> > >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? > >>>> > >>>> Thanks > >>>> > >>>> Joe Healey > >>>> > >>>> > >>>> M.Sc. B.Sc. (Hons) > >>>> PhD Student > >>>> MOAC CDT, Senate House > >>>> University of Warwick > >>>> Coventry > >>>> CV47AL > >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > >>>> > >>>> Jointly working in: > >>>> Waterfield Lab > (WMS Microbiology and Infection Unit) > >>>> and the Gibson Lab > (Warwick Chemistry) > >>>> > >>>> Twitter: @JRJHealey > | Website: MOAC Page >_______________________________________________ > >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >>> > >>> > >>> _______________________________________________ > >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >> > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 161, Issue 19 > ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Wed Sep 21 08:01:45 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Wed, 21 Sep 2016 15:01:45 +0000 Subject: [Chimera-users] Chimera-users Digest, Vol 161, Issue 19 In-Reply-To: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> References: , <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> Message-ID: Thanks Eric, I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do. I'm now getting errors from it such as: return proteinMatrix == chain.hasProtein() AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein' Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python. This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing: result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)') leaves "result" as None. I was hoping it would behave like your multiple variable assignment in: "atoms1, atoms2, rmsd = match(......)" Allowing me to then pull out the number. All help much appreciated, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 21 September 2016 00:20:41 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: Chimera-users Digest, Vol 161, Issue 19 As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. ?Eric On Sep 20, 2016, at 3:16 PM, Healey, Joe > wrote: Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > Sent: 20 September 2016 19:30 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen > To: "Healey, Joe" > Cc: "chimera-users at cgl.ucsf.edu BB" > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Greg Couch > > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Greg Couch > >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html , and came up with pychimera, https://pypi.python.org/pypi/pychimera . I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: Eric Pettersen > >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users at cgl.ucsf.edu >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>>> >>>> Jointly working in: >>>> Waterfield Lab (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 161, Issue 19 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Sep 21 10:54:26 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 21 Sep 2016 10:54:26 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> Message-ID: <236B3496-3DA4-4177-97CC-47059A55D7BC@cgl.ucsf.edu> When the matching is CP_SPECIFIC_SPECIFIC, the arguments have to be chains, not structures. This is what this part of the original commented-out code was doing: s1, s2 = openModels.list(modelTypes=[Molecule]) c1, c2 = s1.sequence('A'), s2.sequence('A?) c1/c2 were the specific chains (namely, the ?A? chains) that would be used in the ?match? call: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], iterate=defaults[ITER_CUTOFF])[0] Maybe if you sent me the part of your script that was trying to make the ?match? call I could help you sort this out. ?runCommand? is a generic command that just treats the string as if it were typed at the command line (and therefore it could contain multiple commands strung together with ?;?) and does not return any value. ?Eric > On Sep 21, 2016, at 8:01 AM, Healey, Joe wrote: > > Thanks Eric, > > I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do. > > I'm now getting errors from it such as: > return proteinMatrix == chain.hasProtein() > AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein' > > Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python. > > This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing: > > result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)') > > leaves "result" as None. I was hoping it would behave like your multiple variable assignment in: > > "atoms1, atoms2, rmsd = match(......)" > > Allowing me to then pull out the number. > > All help much appreciated, > > Joe > > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Eric Pettersen > Sent: 21 September 2016 00:20:41 > To: Healey, Joe > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: Chimera-users Digest, Vol 161, Issue 19 > > As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. > > ?Eric > >> On Sep 20, 2016, at 3:16 PM, Healey, Joe > wrote: >> >> Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. >> >> In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: >> >> >> chimera.openModels.open(top_hit, type="PDB") >> >> # Open model structures >> for model_path in model_list: >> chimera.openModels.open(model_path,type="PDB") >> print("Opened: " + model_path) >> >> rmsd_file = '{0}.tsv'.format(rmsd) >> with open(rmsd_file, "a") as rmsd_output_file: >> for j in len(model_list): >> match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) >> runCommand(match_cmd) >> >> # >> >> or the other option would be to do the above but avoiding the string synthesis step with something like: >> chimera.module.mmaker() >> >> If the module can be accessed directly? If so which module is the mmaker function within? >> >> >> Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? >> >> Looking at your Match script the rmsd was the 3rd value of the tuple in the line: >> atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] >> >> Would the same be true for mmaker? >> >> >> (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) >> >> Thanks again for all your help >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> >> From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > >> Sent: 20 September 2016 19:30 >> To: chimera-users at cgl.ucsf.edu >> Subject: Chimera-users Digest, Vol 161, Issue 19 >> >> Send Chimera-users mailing list submissions to >> chimera-users at cgl.ucsf.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> or, via email, send a message with subject or body 'help' to >> chimera-users-request at cgl.ucsf.edu >> >> You can reach the person managing the list at >> chimera-users-owner at cgl.ucsf.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Chimera-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Recursive structure matching and acquisition of >> descriptive numbers (Eric Pettersen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 20 Sep 2016 11:30:38 -0700 >> From: Eric Pettersen > >> To: "Healey, Joe" > >> Cc: "chimera-users at cgl.ucsf.edu BB" > >> Subject: Re: [Chimera-users] Recursive structure matching and >> acquisition of descriptive numbers >> Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu > >> Content-Type: text/plain; charset="windows-1252" >> >> Hi Joe, >> I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: >> >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options > >> >> I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. >> >> ?Eric >> >> >> > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: >> > >> > Hi again, >> > >> > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. >> > >> > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? >> > >> > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > >> > >> > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > >> > >> > But I can't quite unwrap the options specified in the command for my uses. >> > >> > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? >> > >> > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 > incase it gives you some indication of what I'm attempting to do. >> > >> > Many thanks >> > >> > >> > Joe Healey >> > >> > >> > M.Sc. B.Sc. (Hons) >> > PhD Student >> > MOAC CDT, Senate House >> > University of Warwick >> > Coventry >> > CV47AL >> > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >> > >> > Jointly working in: >> > Waterfield Lab > (WMS Microbiology and Infection Unit) >> > and the Gibson Lab > (Warwick Chemistry) >> > >> > Twitter: @JRJHealey > | Website: MOAC Page > >> > From: Greg Couch >> >> > Sent: 08 September 2016 22:43:55 >> > To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB >> > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> > >> > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. >> > >> > -- Greg >> > >> > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> >> >> >> Joe Healey >> >> >> >> >> >> M.Sc. B.Sc. (Hons) >> >> PhD Student >> >> MOAC CDT, Senate House >> >> University of Warwick >> >> Coventry >> >> CV47AL >> >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >> >> >> >> Jointly working in: >> >> Waterfield Lab > (WMS Microbiology and Infection Unit) >> >> and the Gibson Lab > (Warwick Chemistry) >> >> >> >> Twitter: @JRJHealey > | Website: MOAC Page > >> >> From: Greg Couch > > >> >> Sent: 07 September 2016 19:49:19 >> >> To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB >> >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b >, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html >, and came up with pychimera, https://pypi.python.org/pypi/pychimera >. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> >> >> HTH, >> >> >> >> Greg >> >> >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >> >>> Hi Eric, >> >>> >> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >> >>> >> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >> >>> >> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >> >>> >> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >> >>> >> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >> >>> >> >>> Do you have any advice about how best to proceed? >> >>> >> >>> Many thanks, >> >>> >> >>> Joe Healey >> >>> >> >>> >> >>> M.Sc. B.Sc. (Hons) >> >>> PhD Student >> >>> MOAC CDT, Senate House >> >>> University of Warwick >> >>> Coventry >> >>> CV47AL >> >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >> >>> >> >>> Jointly working in: >> >>> Waterfield Lab > (WMS Microbiology and Infection Unit) >> >>> and the Gibson Lab > (Warwick Chemistry) >> >>> >> >>> Twitter: @JRJHealey > | Website: MOAC Page > >> >>> >> >>> From: Eric Pettersen > > >> >>> Sent: 31 August 2016 18:23 >> >>> To: Healey, Joe >> >>> Cc: chimera-users at cgl.ucsf.edu > >> >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >>> >> >>> Hi Joe, >> >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >> >>> >> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > >> >>> >> >>> ?Eric >> >>> >> >>> Eric Pettersen >> >>> UCSF Computer Graphics Lab >> >>> >> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe >> wrote: >> >>>> >> >>>> Hi, >> >>>> >> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >> >>>> >> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >> >>>> >> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >> >>>> >> >>>> Thanks >> >>>> >> >>>> Joe Healey >> >>>> >> >>>> >> >>>> M.Sc. B.Sc. (Hons) >> >>>> PhD Student >> >>>> MOAC CDT, Senate House >> >>>> University of Warwick >> >>>> Coventry >> >>>> CV47AL >> >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >> >>>> >> >>>> Jointly working in: >> >>>> Waterfield Lab > (WMS Microbiology and Infection Unit) >> >>>> and the Gibson Lab > (Warwick Chemistry) >> >>>> >> >>>> Twitter: @JRJHealey > | Website: MOAC Page >_______________________________________________ >> >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > >> >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >> >>> >> >>> >> >>> _______________________________________________ >> >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > >> >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >> >> >> > >> > >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: > >> >> ------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> End of Chimera-users Digest, Vol 161, Issue 19 >> ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Wed Sep 21 11:47:04 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Wed, 21 Sep 2016 18:47:04 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: <236B3496-3DA4-4177-97CC-47059A55D7BC@cgl.ucsf.edu> References: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> , <236B3496-3DA4-4177-97CC-47059A55D7BC@cgl.ucsf.edu> Message-ID: Thanks for clarifying Eric. That is what I had assumed the code to be doing, but I guess I'm trying to be a bit more naive than that in not having to specify the chains/atoms. I'll explain a little more of what I'm trying to do in the hope that makes it a bit more understandable: As per the original question, I have several hundred protein simulation models. I'm running the HHSuite of tools to identify their nearest published structures, and then I want to get the RMSDs of the 'reference' structure, vs each of my simulations (for any given protein, there are up to 5 simulated PDBs). So far everything works, I parse in the top hit no problem, and can retrieve my models and open everything in chimera programmatically. ------ If we assume in the preceeding code, a variable is populated with the PDB ID of the nearest hit and stored in "top_hit". Next the script trawls my folders of all the simulations, finds them based on a "basename" which is just the locus tag for the corresponding gene (also defined earlier in the code): # Acquire the protein simulations model_list = [] for root, dirnames, filenames in os.walk(directory): for filename in fnmatch.filter(filenames, '*.pdb'): if filename.startswith(basename): model_list.append(os.path.join(root, filename)) print("---------------------------") print("Found the following models:") for model_path in model_list: print(model_path) locus_dir = os.path.dirname(model_path) # Get reference structure from PDB reference = chimera.openModels.open(top_hit,type="PDB") print("Opened reference structure: " + top_hit) # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): # For every model retrieved above, match it to the reference structure and obtain an RMSD for it rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) < capture RMSD somehow > rmsd_output_file.write(reference + "\t" + j + "\t" + rmsd) So where I'm still stuck is that when I execute the mmaker command within chimera in it's own syntax, I can specify the models and not the atoms with the #0 #1 notations. The command runs and chimera picks the best atoms for me (this is also desirable because when I run this unattended on many structures, I don't know which chain within those chimera might match best). I want to emulate that behaviour exactly. So unless I'm very much mistaken, chimera should take the 2 models, fit them as best it can, and return the RMSD. In short, whatever the MatchMaker.match() equivalent syntax of the relatively 'naive' rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) command is what I need I think? Hope that's clear, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 21 September 2016 18:54:26 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers When the matching is CP_SPECIFIC_SPECIFIC, the arguments have to be chains, not structures. This is what this part of the original commented-out code was doing: s1, s2 = openModels.list(modelTypes=[Molecule]) c1, c2 = s1.sequence('A'), s2.sequence('A?) c1/c2 were the specific chains (namely, the ?A? chains) that would be used in the ?match? call: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], iterate=defaults[ITER_CUTOFF])[0] Maybe if you sent me the part of your script that was trying to make the ?match? call I could help you sort this out. ?runCommand? is a generic command that just treats the string as if it were typed at the command line (and therefore it could contain multiple commands strung together with ?;?) and does not return any value. ?Eric On Sep 21, 2016, at 8:01 AM, Healey, Joe > wrote: Thanks Eric, I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do. I'm now getting errors from it such as: return proteinMatrix == chain.hasProtein() AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein' Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python. This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing: result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)') leaves "result" as None. I was hoping it would behave like your multiple variable assignment in: "atoms1, atoms2, rmsd = match(......)" Allowing me to then pull out the number. All help much appreciated, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen > Sent: 21 September 2016 00:20:41 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: Chimera-users Digest, Vol 161, Issue 19 As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. ?Eric On Sep 20, 2016, at 3:16 PM, Healey, Joe > wrote: Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > Sent: 20 September 2016 19:30 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen > To: "Healey, Joe" > Cc: "chimera-users at cgl.ucsf.edu BB" > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Greg Couch > > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Greg Couch > >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html , and came up with pychimera, https://pypi.python.org/pypi/pychimera . I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: Eric Pettersen > >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users at cgl.ucsf.edu >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>>> >>>> Jointly working in: >>>> Waterfield Lab (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 161, Issue 19 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Sep 21 13:47:20 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 21 Sep 2016 13:47:20 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> <236B3496-3DA4-4177-97CC-47059A55D7BC@cgl.ucsf.edu> Message-ID: <8B21293D-F64E-4FB7-AF54-083F0EC796FA@cgl.ucsf.edu> Hi Joe, I guess the first thing is that since you are using the default chain pairing (i.e. best pair in both) you want to call match() with CP_BEST rather than CP_SPECIFIC_SPECIFIC. Then you can pass in structures instead of chains. Of course, you still need to get the structures (rather than just their ID numbers). Assuming the ref structure is opened first, the following code will get the structures: models = chimera.openModels.list(modelTypes=[chimera.Molecule]) ref = models[0] sims = models[1:] # No iteration is the default, so just omit the ?iterate? keyword. ?rmsd? and ?fullRmsd? will be the same when there's no iteration. for simAtoms, refAtoms, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): # One set of simAtoms/refAtoms/rmsds per sim structure ?output RMSD? ?Eric P.S. You?ll need to import CP_BEST instead of CP_SPECIFIC_SPECIFIC > On Sep 21, 2016, at 11:47 AM, Healey, Joe wrote: > > Thanks for clarifying Eric. That is what I had assumed the code to be doing, but I guess I'm trying to be a bit more naive than that in not having to specify the chains/atoms. I'll explain a little more of what I'm trying to do in the hope that makes it a bit more understandable: > > As per the original question, I have several hundred protein simulation models. I'm running the HHSuite of tools to identify their nearest published structures, and then I want to get the RMSDs of the 'reference' structure, vs each of my simulations (for any given protein, there are up to 5 simulated PDBs). So far everything works, I parse in the top hit no problem, and can retrieve my models and open everything in chimera programmatically. > > ------ > > If we assume in the preceeding code, a variable is populated with the PDB ID of the nearest hit and stored in "top_hit". Next the script trawls my folders of all the simulations, finds them based on a "basename" which is just the locus tag for the corresponding gene (also defined earlier in the code): > > # Acquire the protein simulations > > model_list = [] > for root, dirnames, filenames in os.walk(directory): > for filename in fnmatch.filter(filenames, '*.pdb'): > if filename.startswith(basename): > model_list.append(os.path.join(root, filename)) > > print("---------------------------") > print("Found the following models:") > for model_path in model_list: > print(model_path) > > locus_dir = os.path.dirname(model_path) > > # Get reference structure from PDB > reference = chimera.openModels.open(top_hit,type="PDB") > print("Opened reference structure: " + top_hit) > > # Open model structures > for model_path in model_list: > chimera.openModels.open(model_path,type="PDB") > print("Opened: " + model_path) > > > rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename) > > with open(rmsd_file, "a") as rmsd_output_file: > for j in len(model_list): # For every model retrieved above, match it to the reference structure and obtain an RMSD for it > rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) > < capture RMSD somehow > > rmsd_output_file.write(reference + "\t" + j + "\t" + rmsd) > > > So where I'm still stuck is that when I execute the mmaker command within chimera in it's own syntax, I can specify the models and not the atoms with the #0 #1 notations. The command runs and chimera picks the best atoms for me (this is also desirable because when I run this unattended on many structures, I don't know which chain within those chimera might match best). I want to emulate that behaviour exactly. So unless I'm very much mistaken, chimera should take the 2 models, fit them as best it can, and return the RMSD. > > In short, whatever the MatchMaker.match() equivalent syntax of the relatively 'naive' rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) command is what I need I think? > > Hope that's clear, > > Joe > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Eric Pettersen > Sent: 21 September 2016 18:54:26 > To: Healey, Joe > Cc: chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > When the matching is CP_SPECIFIC_SPECIFIC, the arguments have to be chains, not structures. This is what this part of the original commented-out code was doing: > > s1, s2 = openModels.list(modelTypes=[Molecule]) > c1, c2 = s1.sequence('A'), s2.sequence('A?) > > c1/c2 were the specific chains (namely, the ?A? chains) that would be used in the ?match? call: > > atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], > "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], > iterate=defaults[ITER_CUTOFF])[0] > > Maybe if you sent me the part of your script that was trying to make the ?match? call I could help you sort this out. ?runCommand? is a generic command that just treats the string as if it were typed at the command line (and therefore it could contain multiple commands strung together with ?;?) and does not return any value. > > ?Eric > >> On Sep 21, 2016, at 8:01 AM, Healey, Joe > wrote: >> >> Thanks Eric, >> >> I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do. >> >> I'm now getting errors from it such as: >> return proteinMatrix == chain.hasProtein() >> AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein' >> >> Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python. >> >> This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing: >> >> result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)') >> >> leaves "result" as None. I was hoping it would behave like your multiple variable assignment in: >> >> "atoms1, atoms2, rmsd = match(......)" >> >> Allowing me to then pull out the number. >> >> All help much appreciated, >> >> Joe >> >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Eric Pettersen > >> Sent: 21 September 2016 00:20:41 >> To: Healey, Joe >> Cc: chimera-users at cgl.ucsf.edu >> Subject: Re: Chimera-users Digest, Vol 161, Issue 19 >> >> As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. >> >> ?Eric >> >>> On Sep 20, 2016, at 3:16 PM, Healey, Joe > wrote: >>> >>> Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. >>> >>> In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: >>> >>> >>> chimera.openModels.open(top_hit, type="PDB") >>> >>> # Open model structures >>> for model_path in model_list: >>> chimera.openModels.open(model_path,type="PDB") >>> print("Opened: " + model_path) >>> >>> rmsd_file = '{0}.tsv'.format(rmsd) >>> with open(rmsd_file, "a") as rmsd_output_file: >>> for j in len(model_list): >>> match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) >>> runCommand(match_cmd) >>> >>> # >>> >>> or the other option would be to do the above but avoiding the string synthesis step with something like: >>> chimera.module.mmaker() >>> >>> If the module can be accessed directly? If so which module is the mmaker function within? >>> >>> >>> Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? >>> >>> Looking at your Match script the rmsd was the 3rd value of the tuple in the line: >>> atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] >>> >>> Would the same be true for mmaker? >>> >>> >>> (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) >>> >>> Thanks again for all your help >>> >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > >>> Sent: 20 September 2016 19:30 >>> To: chimera-users at cgl.ucsf.edu >>> Subject: Chimera-users Digest, Vol 161, Issue 19 >>> >>> Send Chimera-users mailing list submissions to >>> chimera-users at cgl.ucsf.edu >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> or, via email, send a message with subject or body 'help' to >>> chimera-users-request at cgl.ucsf.edu >>> >>> You can reach the person managing the list at >>> chimera-users-owner at cgl.ucsf.edu >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Chimera-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: Recursive structure matching and acquisition of >>> descriptive numbers (Eric Pettersen) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 20 Sep 2016 11:30:38 -0700 >>> From: Eric Pettersen > >>> To: "Healey, Joe" > >>> Cc: "chimera-users at cgl.ucsf.edu BB" > >>> Subject: Re: [Chimera-users] Recursive structure matching and >>> acquisition of descriptive numbers >>> Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu > >>> Content-Type: text/plain; charset="windows-1252" >>> >>> Hi Joe, >>> I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: >>> >>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options > >>> >>> I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. >>> >>> ?Eric >>> >>> >>> > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: >>> > >>> > Hi again, >>> > >>> > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. >>> > >>> > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? >>> > >>> > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > >>> > >>> > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > >>> > >>> > But I can't quite unwrap the options specified in the command for my uses. >>> > >>> > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? >>> > >>> > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 > incase it gives you some indication of what I'm attempting to do. >>> > >>> > Many thanks >>> > >>> > >>> > Joe Healey >>> > >>> > >>> > M.Sc. B.Sc. (Hons) >>> > PhD Student >>> > MOAC CDT, Senate House >>> > University of Warwick >>> > Coventry >>> > CV47AL >>> > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >>> > >>> > Jointly working in: >>> > Waterfield Lab > (WMS Microbiology and Infection Unit) >>> > and the Gibson Lab > (Warwick Chemistry) >>> > >>> > Twitter: @JRJHealey > | Website: MOAC Page > >>> > From: Greg Couch >> >>> > Sent: 08 September 2016 22:43:55 >>> > To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB >>> > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> > >>> > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. >>> > >>> > -- Greg >>> > >>> > On 09/08/2016 11:53 AM, Healey, Joe wrote: >>> >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >>> >> >>> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >>> >> >>> >> >>> >> Joe Healey >>> >> >>> >> >>> >> M.Sc. B.Sc. (Hons) >>> >> PhD Student >>> >> MOAC CDT, Senate House >>> >> University of Warwick >>> >> Coventry >>> >> CV47AL >>> >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >>> >> >>> >> Jointly working in: >>> >> Waterfield Lab > (WMS Microbiology and Infection Unit) >>> >> and the Gibson Lab > (Warwick Chemistry) >>> >> >>> >> Twitter: @JRJHealey > | Website: MOAC Page > >>> >> From: Greg Couch > > >>> >> Sent: 07 September 2016 19:49:19 >>> >> To: Healey, Joe; chimera-users at cgl.ucsf.edu > BB >>> >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >> >>> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b >, for how to install other software into Chimera. Other parts of the FAQ may help you too. >>> >> >>> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html >, and came up with pychimera, https://pypi.python.org/pypi/pychimera >. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >>> >> >>> >> HTH, >>> >> >>> >> Greg >>> >> >>> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> >>> Hi Eric, >>> >>> >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> >>> >>> Do you have any advice about how best to proceed? >>> >>> >>> >>> Many thanks, >>> >>> >>> >>> Joe Healey >>> >>> >>> >>> >>> >>> M.Sc. B.Sc. (Hons) >>> >>> PhD Student >>> >>> MOAC CDT, Senate House >>> >>> University of Warwick >>> >>> Coventry >>> >>> CV47AL >>> >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >>> >>> >>> >>> Jointly working in: >>> >>> Waterfield Lab > (WMS Microbiology and Infection Unit) >>> >>> and the Gibson Lab > (Warwick Chemistry) >>> >>> >>> >>> Twitter: @JRJHealey > | Website: MOAC Page > >>> >>> >>> >>> From: Eric Pettersen > > >>> >>> Sent: 31 August 2016 18:23 >>> >>> To: Healey, Joe >>> >>> Cc: chimera-users at cgl.ucsf.edu > >>> >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> >>> >>> Hi Joe, >>> >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > >>> >>> >>> >>> ?Eric >>> >>> >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe >> wrote: >>> >>>> >>> >>>> Hi, >>> >>>> >>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>> >>>> >>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>> >>>> >>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>> >>>> >>> >>>> Thanks >>> >>>> >>> >>>> Joe Healey >>> >>>> >>> >>>> >>> >>>> M.Sc. B.Sc. (Hons) >>> >>>> PhD Student >>> >>>> MOAC CDT, Senate House >>> >>>> University of Warwick >>> >>>> Coventry >>> >>>> CV47AL >>> >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > >>> >>>> >>> >>>> Jointly working in: >>> >>>> Waterfield Lab > (WMS Microbiology and Infection Unit) >>> >>>> and the Gibson Lab > (Warwick Chemistry) >>> >>>> >>> >>>> Twitter: @JRJHealey > | Website: MOAC Page >_______________________________________________ >>> >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > >>> >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > >>> >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >>> >> >>> > >>> > >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: > >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> End of Chimera-users Digest, Vol 161, Issue 19 >>> ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From J.R.J.Healey at warwick.ac.uk Thu Sep 22 07:29:58 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Thu, 22 Sep 2016 14:29:58 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: <8B21293D-F64E-4FB7-AF54-083F0EC796FA@cgl.ucsf.edu> References: <1C216F2B-9727-46B3-9B58-790A6A7E0DC6@cgl.ucsf.edu> <236B3496-3DA4-4177-97CC-47059A55D7BC@cgl.ucsf.edu> , <8B21293D-F64E-4FB7-AF54-083F0EC796FA@cgl.ucsf.edu> Message-ID: Hi Eric, That is perfect thanks very much. I think I'm at the last hurdle now more or less. I can pull the RMSD out of the loop, having ended up with the code below: # Get reference structure from PDB chimera.openModels.open(top_hit,type="PDB") print("Opened reference structure: " + top_hit) # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + os.path.basename(model_path)) if args.rmsd is not None: rmsd_file = args.rmsd else: rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename) with open(rmsd_file, "a") as rmsd_output_file: all_models = chimera.openModels.list(modelTypes=[chimera.Molecule]) ref = all_models[0] sims = all_models[1:] for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST,[ref, sims],defaults[MATRIX],\ "nw",defaults[GAP_OPEN],defaults[GAP_EXTEND]): print(str(atoms1) + "\t" + str(atoms2) + "\t" + str(rmsd)) rmsd_output_file.write(str(atoms1) + "\t" + str(atoms2) + "\t" + str(rmsd)) rmsd_output_file.close() The final hurdle seems to be can I access the model name rather than the atomspec for the output of each iteration of match? My current output looks like this: .....(abridged)... <_molecule.Atom object at 0x3a9c288> <_molecule.Atom object at 0x3a9c3c8> <_molecule.Atom object at 0x3a9c530> <_molecule.Atom object at 0x3a9c620> <_molecule.Atom object at 0x3a9c6e8>] 3.06267824307 Which is pretty close. I assume I'd need something like: chimera.Atom.name() or Molecule.name() to access that element of the class , but that's just throwing me back this error: File "strucfit.py", line 198, in main ref_name = chimera.Atom.name(atoms1) TypeError: 'getset_descriptor' object is not callable I'm hoping to get the final output to be a tab separated list of: referenceName \t modelName \t RMSD Final step then I promise I'll leave you be!! Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 21 September 2016 21:47:20 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe, I guess the first thing is that since you are using the default chain pairing (i.e. best pair in both) you want to call match() with CP_BEST rather than CP_SPECIFIC_SPECIFIC. Then you can pass in structures instead of chains. Of course, you still need to get the structures (rather than just their ID numbers). Assuming the ref structure is opened first, the following code will get the structures: models = chimera.openModels.list(modelTypes=[chimera.Molecule]) ref = models[0] sims = models[1:] # No iteration is the default, so just omit the ?iterate? keyword. ?rmsd? and ?fullRmsd? will be the same when there's no iteration. for simAtoms, refAtoms, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): # One set of simAtoms/refAtoms/rmsds per sim structure ?output RMSD? ?Eric P.S. You?ll need to import CP_BEST instead of CP_SPECIFIC_SPECIFIC On Sep 21, 2016, at 11:47 AM, Healey, Joe > wrote: Thanks for clarifying Eric. That is what I had assumed the code to be doing, but I guess I'm trying to be a bit more naive than that in not having to specify the chains/atoms. I'll explain a little more of what I'm trying to do in the hope that makes it a bit more understandable: As per the original question, I have several hundred protein simulation models. I'm running the HHSuite of tools to identify their nearest published structures, and then I want to get the RMSDs of the 'reference' structure, vs each of my simulations (for any given protein, there are up to 5 simulated PDBs). So far everything works, I parse in the top hit no problem, and can retrieve my models and open everything in chimera programmatically. ------ If we assume in the preceeding code, a variable is populated with the PDB ID of the nearest hit and stored in "top_hit". Next the script trawls my folders of all the simulations, finds them based on a "basename" which is just the locus tag for the corresponding gene (also defined earlier in the code): # Acquire the protein simulations model_list = [] for root, dirnames, filenames in os.walk(directory): for filename in fnmatch.filter(filenames, '*.pdb'): if filename.startswith(basename): model_list.append(os.path.join(root, filename)) print("---------------------------") print("Found the following models:") for model_path in model_list: print(model_path) locus_dir = os.path.dirname(model_path) # Get reference structure from PDB reference = chimera.openModels.open(top_hit,type="PDB") print("Opened reference structure: " + top_hit) # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): # For every model retrieved above, match it to the reference structure and obtain an RMSD for it rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) < capture RMSD somehow > rmsd_output_file.write(reference + "\t" + j + "\t" + rmsd) So where I'm still stuck is that when I execute the mmaker command within chimera in it's own syntax, I can specify the models and not the atoms with the #0 #1 notations. The command runs and chimera picks the best atoms for me (this is also desirable because when I run this unattended on many structures, I don't know which chain within those chimera might match best). I want to emulate that behaviour exactly. So unless I'm very much mistaken, chimera should take the 2 models, fit them as best it can, and return the RMSD. In short, whatever the MatchMaker.match() equivalent syntax of the relatively 'naive' rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j)) command is what I need I think? Hope that's clear, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen > Sent: 21 September 2016 18:54:26 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers When the matching is CP_SPECIFIC_SPECIFIC, the arguments have to be chains, not structures. This is what this part of the original commented-out code was doing: s1, s2 = openModels.list(modelTypes=[Molecule]) c1, c2 = s1.sequence('A'), s2.sequence('A?) c1/c2 were the specific chains (namely, the ?A? chains) that would be used in the ?match? call: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], iterate=defaults[ITER_CUTOFF])[0] Maybe if you sent me the part of your script that was trying to make the ?match? call I could help you sort this out. ?runCommand? is a generic command that just treats the string as if it were typed at the command line (and therefore it could contain multiple commands strung together with ?;?) and does not return any value. ?Eric On Sep 21, 2016, at 8:01 AM, Healey, Joe > wrote: Thanks Eric, I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do. I'm now getting errors from it such as: return proteinMatrix == chain.hasProtein() AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein' Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python. This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing: result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)') leaves "result" as None. I was hoping it would behave like your multiple variable assignment in: "atoms1, atoms2, rmsd = match(......)" Allowing me to then pull out the number. All help much appreciated, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen > Sent: 21 September 2016 00:20:41 To: Healey, Joe Cc: chimera-users at cgl.ucsf.edu Subject: Re: Chimera-users Digest, Vol 161, Issue 19 As you?ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there?s an intermediate ?cmdMatch? function that does some argument parsing). You already do the correct imports at the top of your script (?from MatchMaker import match, ??). I think you just need to adapt the commented-out code into the script?s workflow. ?Eric On Sep 20, 2016, at 3:16 PM, Healey, Joe > wrote: Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: chimera-users-bounces at cgl.ucsf.edu > on behalf of chimera-users-request at cgl.ucsf.edu > Sent: 20 September 2016 19:30 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen > To: "Healey, Joe" > Cc: "chimera-users at cgl.ucsf.edu BB" > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42 at cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe > wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > From: Greg Couch > > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >> >> Jointly working in: >> Waterfield Lab (WMS Microbiology and Infection Unit) >> and the Gibson Lab (Warwick Chemistry) >> >> Twitter: @JRJHealey | Website: MOAC Page >> From: Greg Couch > >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users at cgl.ucsf.edu BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html , and came up with pychimera, https://pypi.python.org/pypi/pychimera . I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>> >>> Jointly working in: >>> Waterfield Lab (WMS Microbiology and Infection Unit) >>> and the Gibson Lab (Warwick Chemistry) >>> >>> Twitter: @JRJHealey | Website: MOAC Page >>> >>> From: Eric Pettersen > >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users at cgl.ucsf.edu >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe > wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk >>>> >>>> Jointly working in: >>>> Waterfield Lab (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey | Website: MOAC Page _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 161, Issue 19 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Sep 22 09:44:02 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 22 Sep 2016 09:44:02 -0700 Subject: [Chimera-users] Saving scenes In-Reply-To: References: Message-ID: Hi Josh, Chimera session files (menu File / Save Session) save the data, views, colors, display styles, what is hidden and shown. The savepos and reset commands save and restore the positions of models and clip planes and view direction and zoom, just in memory (e.g. ?savepos view1?, ?reset view1?). Positions saved this way are also saved in sessions so after reloading a session you can use the reset command to get those positions back. Savepos does not save the colors, display styles, or what is hidden and shown. ?Scenes? are created by the ?Animation? tool (menu Tools / Utilities / Animation) and the ?scene? command and include positions, camera view, colors, display styles, what is hidden and shown. Scenes try to capture exactly how the scene looks so they are like sessions but no file is used (although the are preserved in session files). So to save the current scene use command ?scene s1 save? and to restore it ?scene s1 reset?. Like savepos/reset you can save as many scenes as you want with different names. Scenes are a more recent feature and are not completely reliable ? they don?t record everything and sometimes the cause errors saving sessions. Tom > On Sep 22, 2016, at 5:38 AM, Broyde, Joshua E. wrote: > > Dear Tom, > I hope you are well. I was wondering how to save a particular view (i.e. with specified zoom, atoms displayed and angle of view) in Chimera? Currently, I simply save this as a different session, but I was wondering if there is a better or easier way? > > Josh > -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From baaden at smplinux.de Wed Sep 21 16:02:18 2016 From: baaden at smplinux.de (baaden at smplinux.de) Date: Thu, 22 Sep 2016 01:02:18 +0200 Subject: [Chimera-users] Two open positions on molecule visualization and virtual reality in Paris Message-ID: <20160921230218.ACA8E3181A53@raba.ibpc.fr> Dear Colleague, It's already 2,5 years since Faraday discussion #169. I hope this message finds you well. Because of your interest for molecular visualization, I thought I share the following in the hope you can circulate it, or even direct candidates towards me :) Thanks in advance! We have two open positions in Paris, France, both relating to molecule and network visualization developments in Unity3D, and one specifically to VR. We are looking to hire ASAP and funds are available. The first position is for a postdoc on Development and Application of a Virtual Reality Immersive Modelling Platform for Enabling Drug Discovery. You can find an html version at [1] and PDF at [2]. The second position is for an engineer (or postdoc) on Computational Analysis, Visualization and Modeling of Redox Signaling Networks. You can find an html version at [3] and PDF at [4]. Thank you, Marc [1] http://www.baaden.ibpc.fr/ns16/pdoc1.html [2] http://www.baaden.ibpc.fr/ns16/pdoc1.pdf [3] http://www.baaden.ibpc.fr/ns16/inge1.html [4] http://www.baaden.ibpc.fr/ns16/inge1.pdf -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From jaime.rodriguezguerra at uab.cat Thu Sep 22 11:45:04 2016 From: jaime.rodriguezguerra at uab.cat (=?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?=) Date: Thu, 22 Sep 2016 20:45:04 +0200 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: Hi! Since you are getting lists of atoms back, you only need to do some attribute access (rather than method calling)! Every chimera.Atom object has an attribute called molecule: a reference to its parent chimera.Molecule. chimera.Molecule objects have an attribute called 'name', but sometimes this is not very informative (depends on your input), so you need to resort to the pdb filename, stored in the first element of the openedAs tuple. In code, this looks like this: for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): molecule1 = atoms1[0].molecule # any atom from the list will do molecule2 = atoms2[0].molecule print molecule1.name, "\t", molecule2.name, "\t", rmsd # molecule1.openedAs[0] will also work here I don't know if atoms1 comes consistently from the reference molecule, but I'd guess it does. Hope it helps! From pett at cgl.ucsf.edu Thu Sep 22 12:54:35 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 22 Sep 2016 12:54:35 -0700 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: Message-ID: <121336DD-F53D-4178-84C0-9AF332AC2C0C@cgl.ucsf.edu> Thanks Jaime ? exactly right. I realized that the ?atoms1, atoms2? in my original example didn?t really give any indication of which atoms were which, which is why in my later examples I changed to "simAtoms, refAtoms?, so it?s actually ?atoms2? that are the reference atoms. ?Eric > On Sep 22, 2016, at 11:45 AM, Jaime Rodr?guez-Guerra wrote: > > Hi! > > Since you are getting lists of atoms back, you only need to do some > attribute access (rather than method calling)! > > Every chimera.Atom object has an attribute called molecule: a > reference to its parent chimera.Molecule. chimera.Molecule objects > have an attribute called 'name', but sometimes this is not very > informative (depends on your input), so you need to resort to the pdb > filename, stored in the first element of the openedAs tuple. > > In code, this looks like this: > > for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], > defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): > molecule1 = atoms1[0].molecule # any atom from the list will do > molecule2 = atoms2[0].molecule > print molecule1.name, "\t", molecule2.name, "\t", rmsd # > molecule1.openedAs[0] will also work here > > I don't know if atoms1 comes consistently from the reference molecule, > but I'd guess it does. > > Hope it helps! > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From J.R.J.Healey at warwick.ac.uk Fri Sep 23 02:27:35 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Fri, 23 Sep 2016 09:27:35 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: <121336DD-F53D-4178-84C0-9AF332AC2C0C@cgl.ucsf.edu> References: , <121336DD-F53D-4178-84C0-9AF332AC2C0C@cgl.ucsf.edu> Message-ID: That was exactly what I was after thanks! I figured the object orientation should provide that somewhere but was barking up slightly the wrong tree! Thank you all for all your help - definitely wouldn't have been able to do it without you! If it's of any interest, or it helps for any future questions where you might want to refer back to code segments, I've put the more-or-less-finished script in this paste: http://pastebin.com/xJNSWJGq Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Eric Pettersen Sent: 22 September 2016 20:54:35 To: Jaime Rodr?guez-Guerra Cc: chimera-users at cgl.ucsf.edu; Healey, Joe Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Thanks Jaime ? exactly right. I realized that the ?atoms1, atoms2? in my original example didn?t really give any indication of which atoms were which, which is why in my later examples I changed to "simAtoms, refAtoms?, so it?s actually ?atoms2? that are the reference atoms. ?Eric > On Sep 22, 2016, at 11:45 AM, Jaime Rodr?guez-Guerra wrote: > > Hi! > > Since you are getting lists of atoms back, you only need to do some > attribute access (rather than method calling)! > > Every chimera.Atom object has an attribute called molecule: a > reference to its parent chimera.Molecule. chimera.Molecule objects > have an attribute called 'name', but sometimes this is not very > informative (depends on your input), so you need to resort to the pdb > filename, stored in the first element of the openedAs tuple. > > In code, this looks like this: > > for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], > defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): > molecule1 = atoms1[0].molecule # any atom from the list will do > molecule2 = atoms2[0].molecule > print molecule1.name, "\t", molecule2.name, "\t", rmsd # > molecule1.openedAs[0] will also work here > > I don't know if atoms1 comes consistently from the reference molecule, > but I'd guess it does. > > Hope it helps! > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.rodriguezguerra at uab.cat Fri Sep 23 02:56:38 2016 From: jaime.rodriguezguerra at uab.cat (=?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?=) Date: Fri, 23 Sep 2016 11:56:38 +0200 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <121336DD-F53D-4178-84C0-9AF332AC2C0C@cgl.ucsf.edu> Message-ID: Hi Joe! You're welcome! Glad to see you got it working. I've reviewed your code and would want to point out some details that might be helpful to you in the future, though. These are mostly style-related things, but those will contribute to a cleaner reading experience! 1. You don't need backslashes if you're inside parenthesis. So, in all those parse_argument lines, you can safely delete them. Related to this, you can wrap imports with parenthesis, so that backslashes are not needed. 2. Tuple unpacking does not need parenthesis in you're dealing with 1D-tuples. Only needed if you are dealing with more than one dimension (ie, (animal, fruit), sport = [['tiger', 'pear'], 'soccer'] 3. Since you are opening files with the "with" context manager, you don't need to manually close the file later. It's closed automatically as soon as you leave that with block. 4. Lines 166-170 could be replaced with a (cleaner, but not necessarily more performant) glob.glob() call. Check it out to see if it satisfies your requirements. 5. While you are at it, take a look at the PEP8 docs and the Google Python style guide. You don't need to follow all the rules, but they are really helpful in bringing consistency to your own style! That's it! Hope you don't mind these pieces of advice :) Cheers, Jaime. 2016-09-23 11:27 GMT+02:00 Healey, Joe : > That was exactly what I was after thanks! I figured the object orientation > should provide that somewhere but was barking up slightly the wrong tree! > > > Thank you all for all your help - definitely wouldn't have been able to do > it without you! > > > If it's of any interest, or it helps for any future questions where you > might want to refer back to code segments, I've put the > more-or-less-finished script in this paste: > > > http://pastebin.com/xJNSWJGq > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > ________________________________ > From: Eric Pettersen > Sent: 22 September 2016 20:54:35 > To: Jaime Rodr?guez-Guerra > Cc: chimera-users at cgl.ucsf.edu; Healey, Joe > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of > descriptive numbers > > Thanks Jaime ? exactly right. I realized that the ?atoms1, atoms2? in my > original example didn?t really give any indication of which atoms were > which, which is why in my later examples I changed to "simAtoms, refAtoms?, > so it?s actually ?atoms2? that are the reference atoms. > > ?Eric > >> On Sep 22, 2016, at 11:45 AM, Jaime Rodr?guez-Guerra >> wrote: >> >> Hi! >> >> Since you are getting lists of atoms back, you only need to do some >> attribute access (rather than method calling)! >> >> Every chimera.Atom object has an attribute called molecule: a >> reference to its parent chimera.Molecule. chimera.Molecule objects >> have an attribute called 'name', but sometimes this is not very >> informative (depends on your input), so you need to resort to the pdb >> filename, stored in the first element of the openedAs tuple. >> >> In code, this looks like this: >> >> for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], >> defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): >> molecule1 = atoms1[0].molecule # any atom from the list will do >> molecule2 = atoms2[0].molecule >> print molecule1.name, "\t", molecule2.name, "\t", rmsd # >> molecule1.openedAs[0] will also work here >> >> I don't know if atoms1 comes consistently from the reference molecule, >> but I'd guess it does. >> >> Hope it helps! >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From J.R.J.Healey at warwick.ac.uk Fri Sep 23 03:51:40 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Fri, 23 Sep 2016 10:51:40 +0000 Subject: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers In-Reply-To: References: <121336DD-F53D-4178-84C0-9AF332AC2C0C@cgl.ucsf.edu> , Message-ID: Not at all! Much appreciated, as I think I mentioned, this is my first go at writing anything remotely complex in python (and not a bad turn out for about a week I don't think...) A lot of the mess comes from copying functional bits from StackOverflow in the interests of just getting it working first, and making it pretty second as I'm sure you can appreciate (you'd hate to see my LaTeX preamble)! Not needed to close the file with 'with' is useful to know (takes some of the headache out of knowing where to place the close). I'll certainly make the tidy ups you've suggested, for my own learning. Thanks again, Joe :) Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page ________________________________ From: Jaime Rodr?guez-Guerra Sent: 23 September 2016 10:56:38 To: Healey, Joe Cc: Eric Pettersen; Jaime Rodr?guez-Guerra; chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe! You're welcome! Glad to see you got it working. I've reviewed your code and would want to point out some details that might be helpful to you in the future, though. These are mostly style-related things, but those will contribute to a cleaner reading experience! 1. You don't need backslashes if you're inside parenthesis. So, in all those parse_argument lines, you can safely delete them. Related to this, you can wrap imports with parenthesis, so that backslashes are not needed. 2. Tuple unpacking does not need parenthesis in you're dealing with 1D-tuples. Only needed if you are dealing with more than one dimension (ie, (animal, fruit), sport = [['tiger', 'pear'], 'soccer'] 3. Since you are opening files with the "with" context manager, you don't need to manually close the file later. It's closed automatically as soon as you leave that with block. 4. Lines 166-170 could be replaced with a (cleaner, but not necessarily more performant) glob.glob() call. Check it out to see if it satisfies your requirements. 5. While you are at it, take a look at the PEP8 docs and the Google Python style guide. You don't need to follow all the rules, but they are really helpful in bringing consistency to your own style! That's it! Hope you don't mind these pieces of advice :) Cheers, Jaime. 2016-09-23 11:27 GMT+02:00 Healey, Joe : > That was exactly what I was after thanks! I figured the object orientation > should provide that somewhere but was barking up slightly the wrong tree! > > > Thank you all for all your help - definitely wouldn't have been able to do > it without you! > > > If it's of any interest, or it helps for any future questions where you > might want to refer back to code segments, I've put the > more-or-less-finished script in this paste: > > > http://pastebin.com/xJNSWJGq > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > ________________________________ > From: Eric Pettersen > Sent: 22 September 2016 20:54:35 > To: Jaime Rodr?guez-Guerra > Cc: chimera-users at cgl.ucsf.edu; Healey, Joe > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of > descriptive numbers > > Thanks Jaime ? exactly right. I realized that the ?atoms1, atoms2? in my > original example didn?t really give any indication of which atoms were > which, which is why in my later examples I changed to "simAtoms, refAtoms?, > so it?s actually ?atoms2? that are the reference atoms. > > ?Eric > >> On Sep 22, 2016, at 11:45 AM, Jaime Rodr?guez-Guerra >> wrote: >> >> Hi! >> >> Since you are getting lists of atoms back, you only need to do some >> attribute access (rather than method calling)! >> >> Every chimera.Atom object has an attribute called molecule: a >> reference to its parent chimera.Molecule. chimera.Molecule objects >> have an attribute called 'name', but sometimes this is not very >> informative (depends on your input), so you need to resort to the pdb >> filename, stored in the first element of the openedAs tuple. >> >> In code, this looks like this: >> >> for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], >> defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): >> molecule1 = atoms1[0].molecule # any atom from the list will do >> molecule2 = atoms2[0].molecule >> print molecule1.name, "\t", molecule2.name, "\t", rmsd # >> molecule1.openedAs[0] will also work here >> >> I don't know if atoms1 comes consistently from the reference molecule, >> but I'd guess it does. >> >> Hope it helps! >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kparent at msu.edu Fri Sep 23 07:52:47 2016 From: kparent at msu.edu (Kristin Parent) Date: Fri, 23 Sep 2016 10:52:47 -0400 Subject: [Chimera-users] segmentation and resolution Message-ID: To whom it may concern, I am currently working on segmenting a high resolution cryo-EM map (~4? by the ?gold standard FSC?) to phase crystallography data. After the segmentation, my colleague doing the phasing tells me that map appears more like 12? resolution and I am worried I am doing something wrong during the process and somehow distorting my original data. I believe the 4? of the original map based on structural features that I can clearly see. And the segmented density does not appear as defined. Therefore it appears that there has been some changes. In order to begin the process, I did some manipulations before I started. This is an icosahedral virus map created through Auto3dem. I am only using an small quadrant of the original map, and since it was in pif format originally, I used proc3d to convert to mrc and invert the contrast to be compatible with segger. Before segmentation the map visually looked the same as the original pif map when both were displayed in chimera. The procedure I followed after segmentation was: "Save selected regions to .mrc file... save density map masked by the selected segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)?. I have made sure that the correct binning has been applied during segmentation. Any help would be much appreciated. Kristin -- Kristin N. Parent, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology Michigan State University 603 Wilson Road Room 519 Biochemistry Building East Lansing, MI 48824 Office phone: (517) 432-8434 https://kparentlab.natsci.msu.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Sep 23 10:53:28 2016 From: goddard at sonic.net (Tom Goddard) Date: Fri, 23 Sep 2016 10:53:28 -0700 Subject: [Chimera-users] segmentation and resolution In-Reply-To: References: Message-ID: <667D72D3-FA84-4D94-A77A-2EC81EFC6BBE@sonic.net> Hi Kristin, Here is my guess about why your segmented map looks lower resolution. When the Chimera Segment Map (Segger) tool writes a selected region to an MRC file it simply sets to zero all the map values outside the region surface. This creates a jagged boundary in the resulting saved map that looks horrible when you view the surface of the saved map. It will be especially bad in your case because the segmentation region surface has hundreds of tiny protrusions. A better approach is to first smooth the map, say Gaussian filter with standard deviation 5 Angstroms, segment that smooth map, giving smooth regions without all the little protrusions, then save the desired region to an MRC using the original full resolution map. This makes jagged boundary only on the outside smooth surface of the region instead of around hundreds of little protrusions. There is a trick to this procedure. To extract the full resolution density using the smoothed map regions, choose the high resolution map in the Segment Map dialog and use its menu entry File / Associate Selected to associate the smoothed map segmentation with the full resolution map. I?ve attached images showing the problem and suggested approach applied to beta-galactosidase EMDB 2984 at about 3A resolution. You still have sharp drops in the density to 0 and you may want to roll those off using the ?vop falloff? command described here http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html Tom 3A beta-galactosidase map Segmentation with Segment Map / Segger is too detailed. Smoothed map with Gaussian filter, 5A standard deviation: Segmentation surfaces using smoothed map Region extracted from full resolution map using segmentation from smoothed map > On Sep 23, 2016, at 7:52 AM, Kristin Parent wrote: > > To whom it may concern, > > I am currently working on segmenting a high resolution cryo-EM map (~4? by the ?gold standard FSC?) to phase crystallography data. After the segmentation, my colleague doing the phasing tells me that map appears more like 12? resolution and I am worried I am doing something wrong during the process and somehow distorting my original data. I believe the 4? of the original map based on structural features that I can clearly see. And the segmented density does not appear as defined. Therefore it appears that there has been some changes. > > In order to begin the process, I did some manipulations before I started. This is an icosahedral virus map created through Auto3dem. I am only using an small quadrant of the original map, and since it was in pif format originally, I used proc3d to convert to mrc and invert the contrast to be compatible with segger. Before segmentation the map visually looked the same as the original pif map when both were displayed in chimera. > > The procedure I followed after segmentation was: "Save selected regions to .mrc file... save density map masked by the selected segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)?. I have made sure that the correct binning has been applied during segmentation. > > Any help would be much appreciated. Kristin > > -- > Kristin N. Parent, Ph.D. > Assistant Professor > Dept. of Biochemistry and Molecular Biology > Michigan State University > 603 Wilson Road > Room 519 Biochemistry Building > East Lansing, MI 48824 > Office phone: (517) 432-8434 > https://kparentlab.natsci.msu.edu / > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd2984.png Type: image/png Size: 71774 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd2984_seg.png Type: image/png Size: 208345 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd2984_g5.png Type: image/png Size: 40835 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd2984_g5_seg.png Type: image/png Size: 85207 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd2984_reg.png Type: image/png Size: 84631 bytes Desc: not available URL: From david.haselbach at mpibpc.mpg.de Mon Sep 26 02:00:42 2016 From: david.haselbach at mpibpc.mpg.de (Haselbach, David) Date: Mon, 26 Sep 2016 09:00:42 +0000 Subject: [Chimera-users] Interpolate colors in Morph after Color zone Message-ID: Hi everyone, Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don't really like the edge that is created by the segmentation. Kind regards David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 26 08:56:19 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 26 Sep 2016 08:56:19 -0700 Subject: [Chimera-users] Interpolate colors in Morph after Color zone In-Reply-To: References: Message-ID: <413E14B0-B518-476B-9BEE-82B9071CD5E1@cgl.ucsf.edu> Hi David, It may be that you need to color-zone the morph map (not just the input maps), and there is an example in this previous post: See the first attachment, which is just a short Chimera command script (plain text) despite the mail-system changing its name to something.obj. The second attachment is the resulting movie. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 26, 2016, at 2:00 AM, Haselbach, David wrote: > > Hi everyone, > > Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don?t really like the edge that is created by the segmentation. > > Kind regards > David From patriciatran93 at gmail.com Sun Sep 25 21:40:47 2016 From: patriciatran93 at gmail.com (Patty Tran) Date: Sun, 25 Sep 2016 21:40:47 -0700 Subject: [Chimera-users] Problem with running Chimera Message-ID: Hello! I installed two versions of Chimera (Microsoft Windows 64-bit chimera-1.11.2-win64.exe and Microsoft Windows 64-bit chimera-1.11-win64.exe) I have only been able to run the program once and that was when I clicked "start program" after installing the 1.11 version. I have been unable to find the Chimera desktop icons and the program itself in the list of programs. I thought I could find the programs under my C:/Program Files/Chimera but there are no folders. Could someone provide instruction on how to uninstall the programs and install them so I could find and use the program easily? Thank you. Patricia -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Sep 26 10:41:34 2016 From: goddard at sonic.net (Tom Goddard) Date: Mon, 26 Sep 2016 10:41:34 -0700 Subject: [Chimera-users] Interpolate colors in Morph after Color zone In-Reply-To: <413E14B0-B518-476B-9BEE-82B9071CD5E1@cgl.ucsf.edu> References: <413E14B0-B518-476B-9BEE-82B9071CD5E1@cgl.ucsf.edu> Message-ID: <95E20895-EFB2-456F-90BA-1BA54847F282@sonic.net> Elaine is right. The morph map ?interpolate colors? option only handles the case where the maps have a single color. If the maps have multiple colors the morphing is not smart enough to know how the color should be applied to interpolated maps since the interpolation is just linear interpolation of the density values point-wise followed by computing a new contour surface. If you have a structure fit into the maps you can morph the structure with the ?Morph Confomations? tool. Then morph both the atomic structure and map at the same time, and color the map to match the structure using color zone to get your domain coloring ? the structure does not need to be shown. Tom > On Sep 26, 2016, at 8:56 AM, Elaine Meng wrote: > > Hi David, > It may be that you need to color-zone the morph map (not just the input maps), and there is an example in this previous post: > > > > See the first attachment, which is just a short Chimera command script (plain text) despite the mail-system changing its name to something.obj. The second attachment is the resulting movie. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 26, 2016, at 2:00 AM, Haselbach, David wrote: >> >> Hi everyone, >> >> Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don?t really like the edge that is created by the segmentation. >> >> Kind regards >> David > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From gtzotzos at me.com Mon Sep 26 09:49:55 2016 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 26 Sep 2016 18:49:55 +0200 Subject: [Chimera-users] Measuring angles and distances between planes defined by two aromatic rings In-Reply-To: <9B21D00A-277C-4B2E-A7F6-D8DE270D304E@cgl.ucsf.edu> References: <9B21D00A-277C-4B2E-A7F6-D8DE270D304E@cgl.ucsf.edu> Message-ID: Hi Elaine, I?m writing as a follow up of our earlier exchange of emails (see below). I followed your suggestion and I generated the requisite ?markers?. Model # 6 corresponds to marker of Phe123. Model #5 corresponds to the marker of the ligand. distance #5 #6 throws the following error ?Exactly two atoms/axes/planes must be selected. You selected 6?. See attached snapshot. When I select #6, I get ?1 atom selected?. When I select #5, I get ?5 atoms selected?. Any help on this one would be most welcome. Best regards George > On 09 Jun 2016, at 18:13, Elaine Meng wrote: > > Hi George, > You cannot show a dotted line between two centroids. Instead you would have to use different commands to make ?markers? (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms. > > Here are some example commands: > > measure center :1 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 > measure center :4 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 > distance #5 #6 > > ? this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools? Structure Analysis? Distances, then change ?depiction options? within that dialog. > > Another difference to note between ?measure center? and ?define centroid? is that ?measure center? always uses mass weighting, whereas with ?define centroid? you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn?t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations. > > > > > 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 Jun 9, 2016, at 7:15 AM, George Tzotzos wrote: >> >> Hi Elaine, >> >> Sorry to bother you again on the same subject. >> >> As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I?d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I?m sure there?s a way to do this but I haven?t been able to work it out. >> >> Any help would be most welcome. >> >> Regards >> >> George >> >>> On 27 May 2016, at 19:02, Elaine Meng wrote: >>> >>> Hi George, >>> You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log. >>> >>> In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame? Define script), Chimera commands: >>> >>> echo frame: >>> define centroid number 1 radius 0.5 :1 at cg,cd1,cd2,ce1,ce2,cz >>> define plane number 1 :1 at cg,cd1,cd2,ce1,ce2,cz >>> define centroid number 2 radius 0.5 :4 at cg,cd1,cd2,ce1,ce2,cz >>> define plane number 2 :4 at cg,cd1,cd2,ce1,ce2,cz >>> distance c1 c2 >>> angle p1 p2 >>> >>> ? which gave output like this in the Reply Log: >>> >>> [?] >>> frame: 09 >>> centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) >>> plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 >>> centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) >>> plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 >>> Distance from c1 to c2 is 6.541 >>> Angle between p1 and p2 is 50.860 >>> frame: 10 >>> centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) >>> plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 >>> centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) >>> plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 >>> Distance from c1 to c2 is 6.548 >>> Angle between p1 and p2 is 69.698 >>> [?] >>> >>> You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar. >>> >>> I also attached an image of my example system with the centroids and planes shown. >>> >>> 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 >>> >>> <1plx-image.png> >>> >>> On May 27, 2016, at 1:30 AM, George Tzotzos wrote: >>> >>>> Having generated a 100ns trajectory, I?m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I?m dealing with pi-pi stacking interactions. >>>> >>>> I?ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven?t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. >>>> >>>> I?d appreciate any suggestions on possible solutions to the problem described above. I?m attaching a snapshot of measuring distances between two atoms (not really a good solution). >>>> >>>> Thanks in advance >>>> >>>> George >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.tiff Type: image/tiff Size: 118544 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Sep 26 11:47:12 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 26 Sep 2016 11:47:12 -0700 Subject: [Chimera-users] Measuring angles and distances between planes defined by two aromatic rings In-Reply-To: References: <9B21D00A-277C-4B2E-A7F6-D8DE270D304E@cgl.ucsf.edu> Message-ID: <9EF53990-C0A9-4C4A-918C-6840DC719A5A@cgl.ucsf.edu> Hi George, I can only guess that maybe you accidentally made 5 ligand markers in the same place. You could try closing #5 and then starting over to make the ligand marker, being careful to make it only once. I hope this helps, Elaine > On Sep 26, 2016, at 9:49 AM, George Tzotzos wrote: > > Hi Elaine, > > I?m writing as a follow up of our earlier exchange of emails (see below). I followed your suggestion and I generated the requisite ?markers?. > > Model # 6 corresponds to marker of Phe123. Model #5 corresponds to the marker of the ligand. > > distance #5 #6 throws the following error ?Exactly two atoms/axes/planes must be selected. You selected 6?. See attached snapshot. > > When I select #6, I get ?1 atom selected?. When I select #5, I get ?5 atoms selected?. > > Any help on this one would be most welcome. > > Best regards > > George > > > >> On 09 Jun 2016, at 18:13, Elaine Meng wrote: >> >> Hi George, >> You cannot show a dotted line between two centroids. Instead you would have to use different commands to make ?markers? (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms. >> >> Here are some example commands: >> >> measure center :1 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 >> measure center :4 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 >> distance #5 #6 >> >> ? this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools? Structure Analysis? Distances, then change ?depiction options? within that dialog. >> >> Another difference to note between ?measure center? and ?define centroid? is that ?measure center? always uses mass weighting, whereas with ?define centroid? you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn?t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations. >> >> >> >> >> 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 Jun 9, 2016, at 7:15 AM, George Tzotzos wrote: >>> >>> Hi Elaine, >>> >>> Sorry to bother you again on the same subject. >>> >>> As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I?d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I?m sure there?s a way to do this but I haven?t been able to work it out. >>> >>> Any help would be most welcome. >>> >>> Regards >>> >>> George >>> >>>> On 27 May 2016, at 19:02, Elaine Meng wrote: >>>> >>>> Hi George, >>>> You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log. >>>> >>>> In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame? Define script), Chimera commands: >>>> >>>> echo frame: >>>> define centroid number 1 radius 0.5 :1 at cg,cd1,cd2,ce1,ce2,cz >>>> define plane number 1 :1 at cg,cd1,cd2,ce1,ce2,cz >>>> define centroid number 2 radius 0.5 :4 at cg,cd1,cd2,ce1,ce2,cz >>>> define plane number 2 :4 at cg,cd1,cd2,ce1,ce2,cz >>>> distance c1 c2 >>>> angle p1 p2 >>>> >>>> ? which gave output like this in the Reply Log: >>>> >>>> [?] >>>> frame: 09 >>>> centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) >>>> plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 >>>> centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) >>>> plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 >>>> Distance from c1 to c2 is 6.541 >>>> Angle between p1 and p2 is 50.860 >>>> frame: 10 >>>> centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) >>>> plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 >>>> centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) >>>> plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 >>>> Distance from c1 to c2 is 6.548 >>>> Angle between p1 and p2 is 69.698 >>>> [?] >>>> >>>> You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar. >>>> >>>> I also attached an image of my example system with the centroids and planes shown. >>>> >>>> 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 >>>> >>>> <1plx-image.png> >>>> >>>> On May 27, 2016, at 1:30 AM, George Tzotzos wrote: >>>> >>>>> Having generated a 100ns trajectory, I?m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I?m dealing with pi-pi stacking interactions. >>>>> >>>>> I?ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven?t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. >>>>> >>>>> I?d appreciate any suggestions on possible solutions to the problem described above. I?m attaching a snapshot of measuring distances between two atoms (not really a good solution). >>>>> >>>>> Thanks in advance >>>>> >>>>> George >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From gtzotzos at me.com Mon Sep 26 13:30:41 2016 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 26 Sep 2016 22:30:41 +0200 Subject: [Chimera-users] Measuring angles and distances between planes defined by two aromatic rings In-Reply-To: <9EF53990-C0A9-4C4A-918C-6840DC719A5A@cgl.ucsf.edu> References: <9B21D00A-277C-4B2E-A7F6-D8DE270D304E@cgl.ucsf.edu> <9EF53990-C0A9-4C4A-918C-6840DC719A5A@cgl.ucsf.edu> Message-ID: <6BFF20B8-E66F-4C9B-B936-EAEE76517DAB@me.com> Thank you Elaine, I don?t know how I goofed in the first place but with your help the problem is resolved. All the best George > On 26 Sep 2016, at 20:47, Elaine Meng wrote: > > Hi George, > I can only guess that maybe you accidentally made 5 ligand markers in the same place. You could try closing #5 and then starting over to make the ligand marker, being careful to make it only once. > I hope this helps, > Elaine > >> On Sep 26, 2016, at 9:49 AM, George Tzotzos wrote: >> >> Hi Elaine, >> >> I?m writing as a follow up of our earlier exchange of emails (see below). I followed your suggestion and I generated the requisite ?markers?. >> >> Model # 6 corresponds to marker of Phe123. Model #5 corresponds to the marker of the ligand. >> >> distance #5 #6 throws the following error ?Exactly two atoms/axes/planes must be selected. You selected 6?. See attached snapshot. >> >> When I select #6, I get ?1 atom selected?. When I select #5, I get ?5 atoms selected?. >> >> Any help on this one would be most welcome. >> >> Best regards >> >> George >> >> >> >>> On 09 Jun 2016, at 18:13, Elaine Meng wrote: >>> >>> Hi George, >>> You cannot show a dotted line between two centroids. Instead you would have to use different commands to make ?markers? (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms. >>> >>> Here are some example commands: >>> >>> measure center :1 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 >>> measure center :4 at cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 >>> distance #5 #6 >>> >>> ? this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools? Structure Analysis? Distances, then change ?depiction options? within that dialog. >>> >>> Another difference to note between ?measure center? and ?define centroid? is that ?measure center? always uses mass weighting, whereas with ?define centroid? you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn?t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations. >>> >>> >>> >>> >>> 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 Jun 9, 2016, at 7:15 AM, George Tzotzos wrote: >>>> >>>> Hi Elaine, >>>> >>>> Sorry to bother you again on the same subject. >>>> >>>> As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I?d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I?m sure there?s a way to do this but I haven?t been able to work it out. >>>> >>>> Any help would be most welcome. >>>> >>>> Regards >>>> >>>> George >>>> >>>>> On 27 May 2016, at 19:02, Elaine Meng wrote: >>>>> >>>>> Hi George, >>>>> You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log. >>>>> >>>>> In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame? Define script), Chimera commands: >>>>> >>>>> echo frame: >>>>> define centroid number 1 radius 0.5 :1 at cg,cd1,cd2,ce1,ce2,cz >>>>> define plane number 1 :1 at cg,cd1,cd2,ce1,ce2,cz >>>>> define centroid number 2 radius 0.5 :4 at cg,cd1,cd2,ce1,ce2,cz >>>>> define plane number 2 :4 at cg,cd1,cd2,ce1,ce2,cz >>>>> distance c1 c2 >>>>> angle p1 p2 >>>>> >>>>> ? which gave output like this in the Reply Log: >>>>> >>>>> [?] >>>>> frame: 09 >>>>> centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) >>>>> plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 >>>>> centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) >>>>> plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 >>>>> Distance from c1 to c2 is 6.541 >>>>> Angle between p1 and p2 is 50.860 >>>>> frame: 10 >>>>> centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) >>>>> plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 >>>>> centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) >>>>> plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 >>>>> Distance from c1 to c2 is 6.548 >>>>> Angle between p1 and p2 is 69.698 >>>>> [?] >>>>> >>>>> You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar. >>>>> >>>>> I also attached an image of my example system with the centroids and planes shown. >>>>> >>>>> 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 >>>>> >>>>> <1plx-image.png> >>>>> >>>>> On May 27, 2016, at 1:30 AM, George Tzotzos wrote: >>>>> >>>>>> Having generated a 100ns trajectory, I?m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I?m dealing with pi-pi stacking interactions. >>>>>> >>>>>> I?ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven?t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. >>>>>> >>>>>> I?d appreciate any suggestions on possible solutions to the problem described above. I?m attaching a snapshot of measuring distances between two atoms (not really a good solution). >>>>>> >>>>>> Thanks in advance >>>>>> >>>>>> George >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gregc at cgl.ucsf.edu Tue Sep 27 13:19:33 2016 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 27 Sep 2016 13:19:33 -0700 Subject: [Chimera-users] Problem with running Chimera In-Reply-To: References: Message-ID: <9c08c74d-6747-15d1-116b-f699205db1da@cgl.ucsf.edu> Hi Patricia, We'll need more information about your computer to start to figure out what's going wrong. Please run the "dxdiag" program (without the quotes), click on the "Save All Information" button to save the information about your computer into a text file. Then email that text file as an attachment to chimera-bugs at cgl.ucsf.edu with a description of the problem (a copy of your original email will do). Either I or another one of the chimera programmers will look at that information and get back to you. FYI, we only want the information from the System and Display tabs, so you can edit the text file to only have those sections if you wish. HTH, Greg On 09/25/2016 09:40 PM, Patty Tran wrote: > Hello! > > I installed two versions of Chimera (Microsoft Windows 64-bit > chimera-1.11.2-win64.exe > > and Microsoft Windows 64-bit chimera-1.11-win64.exe) > > > I have only been able to run the program once and that was when I > clicked "start program" after installing the 1.11 version. > > I have been unable to find the Chimera desktop icons and the program > itself in the list of programs. I thought I could find the programs > under my C:/Program Files/Chimera but there are no folders. > > Could someone provide instruction on how to uninstall the programs and > install them so I could find and use the program easily? > > Thank you. > Patricia > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Sep 27 18:49:44 2016 From: goddard at sonic.net (Tom Goddard) Date: Tue, 27 Sep 2016 18:49:44 -0700 Subject: [Chimera-users] Chimera crashes on Mac OS Sierra (10.12) Message-ID: <37142D4B-890C-4B54-B25B-2D52B3D8B73B@sonic.net> The Chimera developers have received 8 Chimera crash reports on the new Mac OS Sierra (10.12) somehow related to scrollbars. You may want to hold off updating to Sierra if you make heavy use of Chimera. We have not yet been able to reproduce the crash. It is very likely a bug in the Mac Tk window toolkit that Chimera uses, so even when we figure out how to reproduce it it may take time to figure out a fix since the problem is not in our code. Tom -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From esserlo at helix.nih.gov Wed Sep 28 09:09:24 2016 From: esserlo at helix.nih.gov (esserlo at helix.nih.gov) Date: Wed, 28 Sep 2016 12:09:24 -0400 Subject: [Chimera-users] Surface area list Message-ID: Hi, with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand. Thanks for any advice. Lothar From meng at cgl.ucsf.edu Wed Sep 28 09:28:15 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 28 Sep 2016 09:28:15 -0700 Subject: [Chimera-users] Surface area list In-Reply-To: References: Message-ID: Hi Lothar, You can use a script with commands and then save the results from the Reply Log. More details... As soon as you calculate and show molecular surfaces, for example with the ?surface? command, the analytical surface areas are reported in the Reply Log (open from Favorites menu). Similarly, if you use ?measure area? and ?measure volume? commands, the values will be in the Reply Log. The surface areas from ?measure area? will be a little different than from the ?surface? command, because the former just sums up the flat surface triangle areas rather than figuring out the analytical (curved) surface area like the latter. If you had used ?split?, the surfaces would be in separate submodels but with the same main model number, e.g. #0.1, #0.2, etc., but you could just measure them en masse, e.g. command measure volume #0 They would still be listed separately in the Reply Log. Now, to loop through multiple structures, you may want to embed the Chimera commands in a Python script instead of just making a Chimera command script. How to do that is outlined here: Saving the Reply Log contents to file: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 28, 2016, at 9:09 AM, esserlo at helix.nih.gov wrote: > > Hi, > > with the help of "split #0" I created 10 segments of my protein and > calculated the surface of each fragment. I can go to tools and measure > volume and area but I'd prefer to write out the results as a file. Can > Chimera do this ? > I am asking because I intend to do more complex things than just 10 surfaces > and it would be rather tedious if not impossible to do all this by hand. > > Thanks for any advice. > > Lothar From mjurica at ucsc.edu Tue Sep 27 16:24:36 2016 From: mjurica at ucsc.edu (Melissa Jurica) Date: Tue, 27 Sep 2016 16:24:36 -0700 Subject: [Chimera-users] differentiating lower and upper case chain ID's Message-ID: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> Hi- Is it possible to differentiate between chain ID?s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa From meng at cgl.ucsf.edu Wed Sep 28 09:43:03 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 28 Sep 2016 09:43:03 -0700 Subject: [Chimera-users] differentiating lower and upper case chain ID's In-Reply-To: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> References: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> Message-ID: Hi Melissa, This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results: sel :.a sel :.A Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 27, 2016, at 4:24 PM, Melissa Jurica wrote: > > Hi- > Is it possible to differentiate between chain ID?s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). > Thanks, > Melissa From pett at cgl.ucsf.edu Wed Sep 28 10:47:18 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 28 Sep 2016 10:47:18 -0700 Subject: [Chimera-users] Surface area list In-Reply-To: References: Message-ID: <0DA2EA8F-0DD7-4B26-8600-2410CEA7A054@cgl.ucsf.edu> > On Sep 28, 2016, at 9:28 AM, Elaine Meng wrote: > > Saving the Reply Log contents to file: > > > > Saving the Reply Log is actually a little simpler now than it was when those messages were written: from chimera.tkgui import saveReplyLog saveReplyLog(?file name?) Note that ?file name? should be a full path to a file unless you know what folder the script is executing in. Also, you can use an initial ?~? character to indicate your home folder, so e.g. ?~/Desktop/reply_log.txt?. ?Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjurica at ucsc.edu Wed Sep 28 09:53:03 2016 From: mjurica at ucsc.edu (Melissa Jurica) Date: Wed, 28 Sep 2016 09:53:03 -0700 Subject: [Chimera-users] differentiating lower and upper case chain ID's In-Reply-To: References: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> Message-ID: <27BBFDB7-FA12-45CC-AB8A-65A4E8D14468@ucsc.edu> Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the ?split? command to separate the chains into sub-models. setattr m name Brr2_B #0:.B setattr m name smb1_b #0:.b Melissa On Sep 28, 2016, at 9:43 AM, Elaine Meng wrote: > Hi Melissa, > This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results: > > sel :.a > sel :.A > > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 27, 2016, at 4:24 PM, Melissa Jurica wrote: >> >> Hi- >> Is it possible to differentiate between chain ID?s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). >> Thanks, >> Melissa > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 28 14:12:20 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 28 Sep 2016 14:12:20 -0700 Subject: [Chimera-users] differentiating lower and upper case chain ID's In-Reply-To: <27BBFDB7-FA12-45CC-AB8A-65A4E8D14468@ucsc.edu> References: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> <27BBFDB7-FA12-45CC-AB8A-65A4E8D14468@ucsc.edu> Message-ID: <2C16013D-B131-4C2C-8F1D-9B9BDF79A435@cgl.ucsf.edu> Hi Melissa, After you use split, there is no a longer a model with both upper- and lower-case chain IDs (since each model is now only one chain) and so the case is ignored. After splitting you would have to specify by model number instead, e.g. #0.25. It is only in models with both upper- and lower-case chain IDs that the case you type matters. Elaine > On Sep 28, 2016, at 9:53 AM, Melissa Jurica wrote: > > Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the ?split? command to separate the chains into sub-models. > > setattr m name Brr2_B #0:.B > setattr m name smb1_b #0:.b > > Melissa > > On Sep 28, 2016, at 9:43 AM, Elaine Meng wrote: > >> Hi Melissa, >> This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results: >> >> sel :.a >> sel :.A >> >> Best, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Sep 27, 2016, at 4:24 PM, Melissa Jurica wrote: >>> >>> Hi- >>> Is it possible to differentiate between chain ID?s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). >>> Thanks, >>> Melissa >> From esserlo at helix.nih.gov Wed Sep 28 14:59:08 2016 From: esserlo at helix.nih.gov (esserlo at helix.nih.gov) Date: Wed, 28 Sep 2016 17:59:08 -0400 Subject: [Chimera-users] Surface area list In-Reply-To: References: Message-ID: Hi Elaine, > Hi Lothar, > You can use a script with commands and then save the results from the Reply > Log. > > More details... > As soon as you calculate and show molecular surfaces, for example with the > ???surface??? command, the analytical surface areas are reported in the Reply > Log (open from Favorites menu). Similarly, if you use ???measure area??? and > ???measure volume??? commands, the values will be in the Reply Log. The > surface areas from ???measure area??? will be a little different than from the > ???surface??? command, because the former just sums up the flat surface > triangle areas rather than figuring out the analytical (curved) surface area > like the latter. If you had used ???split???, the surfaces would be in > separate submodels but with the same main model number, e.g. #0.1, #0.2, etc., > but you could just measure them en masse, e.g. command > > measure volume #0 > > They would still be listed separately in the Reply Log. This is very helpfu. I did not realize that there is a Reply Log as such. > Now, to loop through multiple structures, you may want to embed the Chimera > commands in a Python script instead of just making a Chimera command script. > How to do that is outlined here: > Well, I am very fuzzy with Python - I am more tcl guy. But I think with simple command scripts I can do it followed copy and paste of the log file, I can in the end write a program to sort the log file for the entries and values I need. Thanks! Have a great day. Lothar > Saving the Reply Log contents to file: > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 28, 2016, at 9:09 AM, esserlo at helix.nih.gov wrote: >> >> Hi, >> >> with the help of "split #0" I created 10 segments of my protein and >> calculated the surface of each fragment. I can go to tools and measure >> volume and area but I'd prefer to write out the results as a file. Can >> Chimera do this ? >> I am asking because I intend to do more complex things than just 10 surfaces >> and it would be rather tedious if not impossible to do all this by hand. >> >> Thanks for any advice. >> >> Lothar > From mjurica at ucsc.edu Thu Sep 29 10:53:22 2016 From: mjurica at ucsc.edu (Melissa Jurica) Date: Thu, 29 Sep 2016 10:53:22 -0700 Subject: [Chimera-users] differentiating lower and upper case chain ID's In-Reply-To: <2C16013D-B131-4C2C-8F1D-9B9BDF79A435@cgl.ucsf.edu> References: <9405BBD7-E390-4065-AC17-EE7E30C29EC9@ucsc.edu> <27BBFDB7-FA12-45CC-AB8A-65A4E8D14468@ucsc.edu> <2C16013D-B131-4C2C-8F1D-9B9BDF79A435@cgl.ucsf.edu> Message-ID: <465CC7E2-F48C-49B6-A7D1-F1BB11D0A958@ucsc.edu> OK- thanks. M ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ On Sep 28, 2016, at 2:12 PM, Elaine Meng wrote: > Hi Melissa, > After you use split, there is no a longer a model with both upper- and lower-case chain IDs (since each model is now only one chain) and so the case is ignored. After splitting you would have to specify by model number instead, e.g. #0.25. It is only in models with both upper- and lower-case chain IDs that the case you type matters. > Elaine > >> On Sep 28, 2016, at 9:53 AM, Melissa Jurica wrote: >> >> Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the ?split? command to separate the chains into sub-models. >> >> setattr m name Brr2_B #0:.B >> setattr m name smb1_b #0:.b >> >> Melissa >> >> On Sep 28, 2016, at 9:43 AM, Elaine Meng wrote: >> >>> Hi Melissa, >>> This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results: >>> >>> sel :.a >>> sel :.A >>> >>> Best, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Sep 27, 2016, at 4:24 PM, Melissa Jurica wrote: >>>> >>>> Hi- >>>> Is it possible to differentiate between chain ID?s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). >>>> Thanks, >>>> Melissa >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sameer.singh at einstein.yu.edu Thu Sep 29 17:50:37 2016 From: sameer.singh at einstein.yu.edu (Sameer K Singh) Date: Fri, 30 Sep 2016 00:50:37 +0000 Subject: [Chimera-users] 3D to 2D Message-ID: Hi, I was wondering if it's possible to extract information from 3D plots in Chimera and render them as 2d plots.Specifically I'm trying to extract information from a .bild file displayed in chimera and display it as a 2D plot of some kind in an external program (eg: excel) Thank you very much. Best, Sameer ________________ Sameer Singh, PhD Albert Einstein College of Medicine 1300 Morris Park Avenue New York, NY - 10461 Phone: 718-430-2048 Cell: 917-848-9319 -------------- next part -------------- An HTML attachment was scrubbed... URL: From SHuo at clarku.edu Thu Sep 29 20:05:04 2016 From: SHuo at clarku.edu (Shuanghong Huo) Date: Fri, 30 Sep 2016 03:05:04 +0000 Subject: [Chimera-users] build a homotetramer based on crystallographic symmetry Message-ID: Dear All, Can UCSF Chimera build a homotetramer from a dimer based on crystallographic symmetry? Thanks, Sharon Huo Clark University -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 30 10:14:21 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Sep 2016 10:14:21 -0700 Subject: [Chimera-users] 3D to 2D In-Reply-To: References: Message-ID: <9D797AB0-81FA-48B3-9D56-387F0FB682FB@cgl.ucsf.edu> Hi Sameer, You would have to be more specific about what you mean by ?information,? but since you mention bild objects, I suspect the answer is no. Of course Chimera has quite a few ways for measuring all kinds of things on atomic structures (distances, angles, RMSDs, residue-residue distance matrices, etc.) and density maps, and then reporting or writing out the values. However, bild objects are just geometrical objects so there aren?t really commands to measure things about them. Presumably if you had the bild file in the first place the object coordinates and dimensions would already be in there. Maybe you want the coordinates as projected into 2D, as if you saved an image. My only guess would be to save such an image file and then trace outlines in the image with some general mage-processing software. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 29, 2016, at 5:50 PM, Sameer K Singh wrote: > Hi, > I was wondering if it's possible to extract information from 3D plots in Chimera and render them as 2d plots.Specifically I'm trying to extract information from a .bild file displayed in chimera and display it as a 2D plot of some kind in an external program (eg: excel) > Thank you very much. > Best, > Sameer From meng at cgl.ucsf.edu Fri Sep 30 10:26:06 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Sep 2016 10:26:06 -0700 Subject: [Chimera-users] build a homotetramer based on crystallographic symmetry In-Reply-To: References: Message-ID: <1B8DBD56-2F8A-4FD6-B296-C31267801B34@cgl.ucsf.edu> Hi Sharon, Chimera has lots of different ways for building multimers using crystallographic symmetry information. If the symmetry information is already in the file, it is quite easy. Otherwise, you would have to specify the symmetry yourself in a command. Possibilities include: ?sym? command (which also allows you to enter the symmetry yourself if needed) ? and two graphical interfaces, Unit Cell tool Multiscale Models tool I would probably try ?sym? first just to see what happens, i.e. if your dimer is open as model #0 and you think the input file has the symmetry information in it already as BIOMT matrices, try: sym #0 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you can also fetch predicted biounit from PDB, see menu: File? Fetch by ID On Sep 29, 2016, at 8:05 PM, Shuanghong Huo wrote: > Dear All, > Can UCSF Chimera build a homotetramer from a dimer based on crystallographic symmetry? > Thanks, > Sharon Huo > Clark University From mheller at cdrd.ca Fri Sep 30 22:41:32 2016 From: mheller at cdrd.ca (Markus Heller) Date: Sat, 1 Oct 2016 05:41:32 +0000 Subject: [Chimera-users] Split view feature Message-ID: <1BBC8C44802DFA4FBF69CC371B45149B1D6E8266@MERCURY.cdrd.ca> Hi all, Not sure split view is the proper term for what I'm looking for but here goes: I want to compare to structures of two proteins bound to their respective ligands, and I do NOT want to do this as overlay. What I want is a split screen or split view in the Chimera main window, where one structure is displayed on the left, and the other on the right. Movements (rotation, translation etc.) would be synchronized between both windows, whereas other functionality such as Zone select, find Hbonds etc. would not. Is such a feature available for the current release, or is it planned for ChimeraX? Thanks and Cheers Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: