- Chimera-users - RBVI Mailing Lists

CHIMERA script for CONSURF
by Fabian Gmail 20 Apr '08

20 Apr '08

Hi all, I am very interested to write a script to deal with the color-coding of CONSURF server (http://consurf.tau.ac.il/index.html) a 9 layer colour from maroon-to-cyan. I basically would like to know how I could translate the code into RGB colors and color the structure accordingly. Any suggestions will be greatly appreciated, Fabian Glaser -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Re: [Chimera-users] [chimera-dev] Chimera in windows: seeing samba mounted disk
by Eric Pettersen 18 Apr '08

18 Apr '08

Hi JD, Under the leftmost column of the file browser there should be a pop- up menu of drives. You should be able to pick F: from that. Let me know if that's not working for you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 18, 2008, at 7:15 AM, Jean-Didier Maréchal wrote: > Dear all, > > I usual use chimera on my linux box, but for some practicities, I need > to use it in windows. > > I realized though that I can not access the disk F: of my windows box > which is a mounted disk from the linux one. Would it be difficult that > the file browser of chimera recognize samba mounted disk? Our is > ther a > trick I miss? > > All the best, > JD

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Command line change active to show models
by Jean-Didier Maréchal 18 Apr '08

18 Apr '08

Hi everyone, I was wondering if it was possible to change the "Active models" list that lays below the command line, to a "showed models" list. I know that I can pilot this through the model panel, however, I think that, for the work I do, a direct access to this option would be more useful. Thanks a lot, JD On Thu, 2008-04-17 at 12:00 -0700, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)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. CHIMERA script for CONSURF (Fabian Gmail) > 2. History feature for command line between sessions (Boaz Shaanan) > 3. Re: CHIMERA script for CONSURF (Elaine Meng) > 4. Re: CHIMERA script for CONSURF (Elaine Meng) > 5. Re: CHIMERA script for CONSURF (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Apr 2008 10:11:42 +0300 > From: Fabian Gmail <fabian.glaser(a)gmail.com> > Subject: [Chimera-users] CHIMERA script for CONSURF > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <4806F82E.7010605(a)gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi all, > > I am very interested to write a script to deal with the color-coding of > CONSURF server (http://consurf.tau.ac.il/index.html) a 9 layer colour > from maroon-to-cyan. I basically would like to know how I could > translate the code into RGB colors and color the structure accordingly. > > Any suggestions will be greatly appreciated, > > Fabian Glaser > > > -- > Fabian Glaser, PhD > > Bioinformatics Knowledge Unit, > The Lorry I. Lokey Interdisciplinary > Center for Life Sciences and Engineering > Technion - Israel Institute of Technology > Haifa 32000, ISRAEL > > Web: http://bku.technion.ac.il > Email: fglaser(a)tx.technion.ac.il > Tel: +972-(0)4-8293701 > Cel: +972-(0)54-4772396 > > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Apr 2008 08:52:31 GMT > From: Boaz Shaanan <bshaanan(a)bgu.ac.il> > Subject: [Chimera-users] History feature for command line between > sessions > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <f652ac011b292.48070fcf(a)bgu.ac.il> > Content-Type: text/plain; charset="utf-8" > > Hi, > > ?The history of commands in the command line mode is retained within a session and is very convenient but I was wondering whether there is a feature that will allow you to recall commands from previous sessions (such as in O for example - it generates an .o-history file which is being constantly updated and is very convenient). If not, is it possible to request the addition of such a feature ? There are many ways to implement this of course and I'm sure you'll find the best way, if it's not already there lurking in Chimera. > > ?? Cheers, > > ????????????? Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > Phone: 972-8-647-2220 ; Fax: 646-1710 > Skype: boaz.shaanan? >

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showing buried pocket
by Eric Pettersen 18 Apr '08

18 Apr '08

On Apr 17, 2008, at 8:59 AM, Gareth Young wrote: > So I've been trying to make an 'inverted surface'. Basically I have > a cavity inside a protein which is almost completely surrounded and > so it is hard to illustrate it to others without removing parts of > the protein (which I could of course do). Does Chimera have a > function to mark the inside of a cavity with a surface, then > allowing the user to remove the protein and just leave the surface > so as to illustrate the size and shape of the cavity in relation to > the protein. > > Have I explained that clearly enough??? Hi Gareth, If this is a standard PDB you can fetch the structure from the CASTp database (File->Fetch By ID...) which will bring up an interface that will allow you to browse the pockets of the structure, with only the browsed pocket being surfaced. If you have a non-standard PDB, you will need to identify some residues near the pocket (let's say they were residues 15 to 19) and then use a command like: ~surf :15-19 z>5 to hide surfaces further than 5 angstroms from those residues, which should hide most of the "outside" surface. Then: ~disp will hide the structure. If you don't know the pocket residues, you might clip through the outside surface with the Side View clip planes and then use the mouse-hovering popup balloons to identify some residues. If your pocket has a channel to the outside, you might want to get a clean cut through the channel by using per-model clipping on the surface and orienting the clip plane so that it cuts the channel. The Per-Model Clipping tool is in the Depiction tools category. I'd like to get Chimera to handle CASTp results for non-standard PDBs, but haven't gotten to that yet. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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History feature for command line between sessions
by Boaz Shaanan 18 Apr '08

18 Apr '08

Hi, The history of commands in the command line mode is retained within a session and is very convenient but I was wondering whether there is a feature that will allow you to recall commands from previous sessions (such as in O for example - it generates an .o-history file which is being constantly updated and is very convenient). If not, is it possible to request the addition of such a feature ? There are many ways to implement this of course and I'm sure you'll find the best way, if it's not already there lurking in Chimera. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Adding arrowheads to protein helix ribbons?
by Peter Knight 15 Apr '08

15 Apr '08

I am dealing with antiparallel alpha helices in helix bundles. It would be very useful to be able to show the polarity of each helix in ribbon display by adding an arrowhead to the C-terminal end. This is the default for beta strands. Is it possible to add such an arrowhead in Chimera? A clunky workaround that occurs to me is to designate the last residue of each helix as beta structure. Has anyone tried this: does it work? Thanks, Peter Knight University of Leeds, UK

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Bouding box dimensions
by Damien Larivière 14 Apr '08

14 Apr '08

Hello Thomas, Thank you very much for your help on this. After opening a PDB file, I would like first to display the bounding box of the macromolecule studied. Then, I wish to know the dimensions of the bounding box along its x,y and z axis (in nm or angstrom). How can I do that ? Is the bounding box optimal (i.e. the smallest bounding box surrounding the macromolecule) or defined by a reference frame in the PDB file ? My best regards, Damien ------------------ Damien Larivière, PhD Fourmentin-Guilbert Scientific Foundation France

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Re: [Chimera-users] Chimera-users Digest, Vol 60, Issue 18
by Ibrahim Moustafa 11 Apr '08

11 Apr '08

Thanks Elaine and thanks for the great support from Chimera developers. I should say that following the Chimera mailing list encouraged me to use Chimera. The example shown in your e-mail was perfect to show how to selectively depict H-bonds. I still hope in the future release of Chimera a full control of the line style can be done in command line. regards, Ibrahim On 4/11/08 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)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: Drawing H-bond (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Apr 2008 10:57:58 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Drawing H-bond > To: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <71A7D18D-2C1B-489A-8099-6410FA6FA3D7(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; > format=flowed > > > On Apr 9, 2008, at 11:59 AM, Ibrahim Moustafa wrote: >> >> Recently I?m switching from my favorite molecular graphics >> software ?Pymol? to Chimera. >> I find chimera very useful in terms of structural analysis and easy >> to drive through the smooth command line. >> I have a question regarding drawing H-bond in figures for >> publications: Is there a way to instruct the program to draw a H-bond >> Between two particular atoms in dotted (dashed) line style? >> >> I know that ?hbond? does a decent job in finding the H-bonds >> represented by solid lines. However, in the cases I tried the H- >> bond network found by ?hbond? >> Is a bit complicated and simplification is necessary for the >> figure. I wonder if the user can have a control over which >> ?psudobond? to draw between what atoms. >> This would make the program very handy for me. > > Hi Ibrahim, > Thanks for your kind words! > > I just wanted to give an example of using PseudoBond Reader. A few > years ago I used it to make a paper figure that shows crosslinks > engineered into rhodopsin. I won't go into the details of all the > colors, but black lines represent disulfide crosslinks that inhibit > activation and gold (actually "goldenrod") lines shows disulfides > that do not inhibit activation. > > The structure is 1f88, and to show just chain A in the figure, I used > commands like: > > open 1f88 > del ~ :.a > chain @ca > focus > ribbon > ribrepr smooth > set bg_color white > color cyan > > Then I started PseudoBond Reader (under Tools... Depiction) and used > it to open a text file listing the atom pairs and the desired > pseudobond colors. In the file-opening dialog you can also specify > the line width (unfortunately not whether the lines are dashed, > however) and pseudobond group name. Contents of the text file are > simply: > > :65@ca :316@ca goldenrod > :110@ca :187@ca goldenrod > :136@ca :222@ca black > :136@ca :225@ca goldenrod > :139@ca :225@ca goldenrod > :140@ca :222@ca black > :140@ca :225@ca goldenrod > :138@ca :251@ca forest green > :139@ca :247@ca black > :139@ca :248@ca black > :139@ca :249@ca black > :139@ca :250@ca black > :139@ca :251@ca black > :140@ca :316@ca yellow > :198@ca :276@ca goldenrod > :200@ca :276@ca goldenrod > :204@ca :276@ca goldenrod > :246@ca :312@ca black > :242@ca :338@ca goldenrod > :245@ca :338@ca goldenrod > > Although not included in this example, you can also specify labels on > the individual pseudobonds in the text file. You would still have to > use PseudoBond Panel, choose the group, and set its attributes to > make the lines dashed, however. I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 60, Issue 18 > ********************************************* >

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Drawing H-bond
by Ibrahim Moustafa 11 Apr '08

11 Apr '08

Hi Chimera users, Recently I¹m switching from my favorite molecular graphics software ³Pymol² to Chimera. I find chimera very useful in terms of structural analysis and easy to drive through the smooth command line. I have a question regarding drawing H-bond in figures for publications: Is there a way to instruct the program to draw a H-bond Between two particular atoms in dotted (dashed) line style? I know that hbond¹ does a decent job in finding the H-bonds represented by solid lines. However, in the cases I tried the H-bond network found by hbond¹ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which ³psudobond² to draw between what atoms. This would make the program very handy for me. Thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Re: [Chimera-users] Drawing H-bond
by Conrad Huang 10 Apr '08

10 Apr '08

As a matter of fact, you _can_ do all this from the command line! The command you're looking for is "setattr", and the following page should provide all the information you need: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html Conrad Ibrahim Moustafa wrote: > Thanks for your reply. My only comment, it would be great if all these steps > could be driven from command line :). > > Thanks, > Ibrahim > > > On 4/9/08 4:29 PM, "Conrad Huang" <conrad(a)cgl.ucsf.edu> wrote: > >> To control the drawing styles for all hydrogen bonds, you should use the >> "PseudoBond Panel", which you can bring up via the menu item "Tools -> >> General Controls -> PseudoBond Panel". From this panel, you can select >> "hydrogen bonds" in the list box on the left, and then click the >> "attributes..." button on the right. This will bring up another panel >> containing all the attributes that you can change, including color, >> dashed line style, etc. (See >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/pbpanel.html for more >> detailed explanation.) >> >> The pseudobond panel changes the attributes of all hydrogen bonds. To >> control the drawing styles for individual hydrogen bonds, you need to >> select the particular bonds using the mouse. Control-left-click to >> select the first bond. Control-shift-left-click to add more bonds. You >> can then bring up the "Selection inspector" by clicking on the green >> button at the bottom-right of the graphics window (the button should be >> labeled something like "2 pbonds" at this point). This will bring up a >> panel similar to the bottom half of the pseudobond attributes panel. >> You can then hide the selected bonds by changing the "displayed" >> attribute from "if atoms shown" to "false". (Note that you can also add >> labels to individual bonds using the selection panel.) >> >> Conrad >> >> Ibrahim Moustafa wrote: >>> Hi Chimera users, >>> >>> Recently I¹m switching from my favorite molecular graphics software >>> ³Pymol² to Chimera. >>> I find chimera very useful in terms of structural analysis and easy to >>> drive through the smooth command line. >>> I have a question regarding drawing H-bond in figures for publications: >>> Is there a way to instruct the program to draw a H-bond >>> Between two particular atoms in dotted (dashed) line style? >>> >>> I know that Œhbond¹ does a decent job in finding the H-bonds >>> represented by solid lines. However, in the cases I tried the H-bond >>> network found by Œhbond¹ >>> Is a bit complicated and simplification is necessary for the figure. I >>> wonder if the user can have a control over which ³psudobond² to draw >>> between what atoms. >>> This would make the program very handy for me. >>> >>> Thanks, >>> Ibrahim >>> -- >>> ------------------------------------------------------------------------ >>> Ibrahim M. Moustafa, Ph.D. >>> Biochemistry and Molecular Biology Dept. >>> 201 Althouse Lab., University Park, >>> Pennsylvania State University >>> PA 16802 >>> >>> Tel. (814) 863-8703 >>> Fax (814) 865-7927 >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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