- Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] [Chimera-users] associating multiple structures and sequences
by Eric Pettersen 07 Feb '12

07 Feb '12

On Feb 6, 2012, at 7:01 PM, Uppal, Karan wrote: > Hi, > > I am writing a custom extension based on MultiAlign Viewer that > highlights regions in a multiple sequence alignment based on > numerical values stored in an external file. I modified the > RegionBrowser.py script, and added a function that works just like > "showSS". There may be ways to accomplish what you modification does without changing the MAV code. Just using an imported MAV rather than your custom mod has the advantage of gaining any additional functionality and bug fixes that MAV gets in later releases. One possibility is for you to use "sequence coloring files" that MAV already reads (they can also optionally color associated structures). The format is documented here: JEvTrace File Formats Such files can be read programatically with the MAViewer.loadScfFile method. Another possibility is to directly create the new regions you want with the MAViewer.newRegion method. The 'blocks' argument to that method is a series of 4-tuples describing the rectangles composing the region: (top-seq, bottom-seq, left, right) where left/right are zero- based sequence indices. > It works fine for one structure and sequence combination. However, I > am trying to associate multiple copies of the same protein structure > and its sequence. So, the structures are identical and so are the > sequences in the sequence alignment, but each copy represents > different information. My problem is that the sequences in the > alignment viewer dialog box are highlighted in a random fashion. > And, I want the sequences to be highlighted in an ordered fashion > starting from first sequence to last sequence since we want to be > able to map the highlighted regions back to the external file. > > Is there a way to control the order in which the sequences are > highlighted in the alignment viewer dialog? Or is there a way to get > the model # associated with a particular sequence and using the > model # to highlight the alignment viewer? I'm not 100% sure what "highlighted" means here, but I presume the problem is that your first structure isn't necessarily associating with your first sequence, since the structure and alignment sequences are all identical? If that's the issue, then you need to explicitly control the structure association rather than allowing automatic association to occur. You do that by providing the argument 'autoAssociate=False' to the MAViewer constructor. Then you need to call the MAViewer's 'associate' method for every structure association you want to set up. Now, there's a big doc string for that method, but briefly you want to call associate like so: mav.associate(mseq, seq=aseq) where mseq is the Sequence from the structure you want to associate and aseq is the Sequence in alignment you want to associate with. You get the Sequences from a model with: mol.sequences() or, if you know the chain ID you want (e.g. 'A'): mol.sequence('A') --Eric P.S. I cc'ed this to chimera-dev and set replies to go there since this seems like much more a developer topic than a user topic. Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 1

IDE
by ELNAZ REZAEI 06 Feb '12

06 Feb '12

Hello, Is it possible to use other python IDE (e.g. komodo) with Chimera? Thanks, ELnaz

3 2

non-natural sidechains
by david gfeller 18 Nov '11

18 Nov '11

Dear Chimera developer, I've been working recently on a database on non-natural sidechains ( http://www.swisssidechain.ch) Among else, we've developed a novel approach to accurately predict rotamers and our paper will be submitted within a few days. I'd be very interested to develop a Chimera extension to visualize them (so far, we only have a PyMOL plug-in). I have rotamer library files in the same format as the Dunbrack 2002 rotamer library for each of the >200 sidechains included in my database. However, it appears that rotamer files (dependentRotamerData.zip) are encrypted in Chimera and I could not figure out how this encryption is done. I was wondering if you could advise me something to help me (especially whether there are some hard-coded part that would need to be modified to include new sidechains in Chimera) and if you'd be interested in such an extension. best David -- David Gfeller, PhD Molecular Modeling Swiss Institute of Bioinformatics http://ludwig-sun1.unil.ch/~dgfeller/homepage/

3 3

(no subject)
by Shujian Cun 16 Nov '11

16 Nov '11

Very frequently, I need to view and analyze multiple structures at the same time. But now, all I can do is to open and close different sessions all the time. Does the Chimera team have any plan to add a tab-like feature so that the user can do multiple tasks? Best, Shujian

2 1

hardware requirements for Chimer software
by Whitney_Roessler＠Dell.com 15 Nov '11

15 Nov '11

Chimera Team, One of my customers at IUPUI will be utilizing the Chimera software and is looking to purchase a 3-D capable system. I was wondering if you could provide to me the minimum or recommended hardware requirements to run this software. Thanks, Whitney Roessler -Account Manager Major Public Accounts ESL PH: 512-513-9351/ Toll Free 877-671-3355, ext 5139351 PO Fax: 512-283-7082 Email: whitney_roessler(a)dell.com<mailto:whitney_roessler@dell.com>

2 1

Fwd: SASA calculation in Chimera
by Elaine Meng 15 Nov '11

15 Nov '11

Hi Edu, I don't do any of the Chimera programming (I do testing, documentation, web content), so I can only forward your question to the developers/programmers. It may be possible to have your surface calculation as a separate extension instead of integrated into the Chimera core, but I'm guessing integration has some advantages... perhaps computational efficiency? Programmers who have worked on surface calculations in Chimera should have better or more complete answers for you. However, please bear with us, as this week is especially busy for our group. Best, Elaien ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco Begin forwarded message: > From: Eduardo José Cepas Quiñonero <ecepasqui(a)gmail.com> > Date: November 15, 2011 3:19:17 AM PST > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: SASA calculation in Chimera > > Hi Elaine, > > I'm Edu, colleague of Horacio. I would like to ask you several things related to the previous question he asked. > > As Horacio said before, we have developed a new SASA calculation method. Our intention is to integrate it into Chimera, as another way to calculate the data Chimera needs to show molecular solid surfaces (instead of using msms). > > Since Chimera doesn't call msms executable, but it has msms integrated into it, we assume that whe have to adapt our method to Chimera, and compile both together, right?¿ If not, Is there another simple way to change the method Chimera uses to calculate molecular surfaces?¿ > > Then, after reading the link > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > we realize that this can be a really complex purpose...: > > "Compiling Chimera requires building over 40 third-party packages and is not recommended" > > " creating a full build-from-source copy of Chimera is a lot of work and depends on getting a bunch of things in the build environment set up just right for your particular platform. Currently we do not have any documentation describing the build environment or procedure." > > > Could we have some help on this¿? Could you advice us? > > Thanks in advance, > Edu. > > > >> From: Elaine Meng <meng(a)cgl.ucsf.edu> >> Subject: Re: SASA calculation in Chimera >> Date: 21 September , 2011 7:13:29 PM GMT+02:00 >> To: Horacio Pérez-Sánchez <horacio(a)um.es> >> Cc: chimera-users(a)cgl.ucsf.edu >> Reply-To: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> >> >> Hi Horacio, >> Chimera is using MSMS to generate the surface and give surface area values per atom. There is more information and an MSMS reference here: >> >> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Sep 21, 2011, at 9:01 AM, Horacio Pérez-Sánchez wrote: >> >>> We have developed a fast and accurate new GPU based SASA calculation method. It can bring information about SASA per atom and also grid per atom necessary to graphically render the molecular surface. We are new to Chimera but we would like to know: >>> >>> a) where could we find information about the SASA method Chimera uses so we can test with our own method >>> b) same question for the method Chimera uses to graphically render the molecular surface >>> >>> Thanks in advance, >>> Horacio >>> >>> >> > > =============================================================================================== > Horacio Pérez-Sánchez, PhD > Grupo de Arquitectura y Computación Paralela | Parallel Computer Architecture Group > Departamento de Ingeniería y Tecnología de Computadores | Computer Engineering and Technology Department > Facultad de Informática | School of Computer Science > Universidad de Murcia | University of Murcia > Campus de Espinardo - 30080 Murcia (Spain) > Email: horacio(a)um.es > Tel: + 34 868 88 8509 > =============================================================================================== > > > > > > > >

2 1

chimera version
by ERIK.LAURINI＠phd.units.it 11 Oct '11

11 Oct '11

Dear Chimera developers, I'm dr. Erik Laurini, researcher for the University of Triest (Italy) in the field of computational chemist for biosystems. I have a tricky question: to date, I'm using a chimera-alpha-win64 version downloaded as a daily builds in 27 march 2011. Is it possible to obtain the same version but for 32 bit platform? I'm having a problem that it's very hard to explain now but I think that I can solve quickly by this way. Otherwise, I'll try to find with you another solution. Many thanks in advance. Best, -erik laurini- Dr. Erik Laurini Dipartimento di Ingegneria Industriale e dell'Informazione Università degli Studi di Trieste Via Valerio 10, 34127, Trieste (Italy) Tel. 0405583757

2 1

(no subject)
by Kristen Eisenberg 10 Sep '11

10 Sep '11

[chimera-dev] Calculating RMSD Hi, I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong? Thanks for your help. Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

2 1

Using Pmw widgets
by Mateusz Dobrychłop 01 Sep '11

01 Sep '11

Dear Chimera Dev Team, I am writing a Chimera extension and I use the Pmw toolkit in my GUI. I had no problems testing it and it worked great until I decided to reinstall my OS (Windows 7). After that, I installed Chimera 1.5.3, imported my extension and didn't face any problems at first. But then, after closing the viewer and running it again, an error occured right after importing the extension's gui: Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> b=Pmw.EntryField(a,labelpos="w",label_text="asd") File "C:\Program Files (x86)\Chimera 1.5\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwEntryField.py", line 73, in __init__ sequences = root.bind_class(tag) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 1012, in bind_class return self._bind(('bind', className), sequence, func, add, 0) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 947, in _bind return self.tk.splitlist(self.tk.call(what)) TclError: bad window path name ".94327912.94328912" I didn't change anything since the last succesful testing of my extension - something happened after closing Chimera for the first time, and I have no idea what it is. After that, I tried reinstalling Chimera, installing older versions - it's always the same story; everything works great on the first run, but after I close the viewer for the first time, I am not ever able to use Pmw anymore. The code that causes this error is simple: a=Tkinter.Tk() b=Pmw.EntryField(a,labelpos="w",labeltext="c") I tried to type the same thing in IDLE and I got the exact same error. Thank you for any help, best, Mateusz

4 4

Re: [chimera-dev] Chimera-dev Digest, Vol 90, Issue 1
by Jean Didier Pie Marechal 29 Aug '11

29 Aug '11

HI everyone, just a small suggestion. When opening the match ->aling tool. All the models present in the session are selected. Could we have a pushing button somewhere for select all/none action? or that mouse sliding would select or unselect series of models. Thanks a lot JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimarts, Agost 16, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 90, Issue 1 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Residue.uniprotIndex (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 16 Aug 2011 11:42:15 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [chimera-dev] Residue.uniprotIndex > To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu>, > chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <1235B56D-4D54-4ED8-9F5A-BD981304D475(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > I thought some of the script writers out there might want to know > that > in the latest daily builds residues have a "uniprotIndex" attribute > > which gives the position of the residues relative to their UniProt > sequence, if the correspondence can be determined. To determine > the > correspondence the structure must have valid PDB HEADER and SEQRES > records, and the PDB web site must be reachable (to use their > UniProt > mapping service). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

2 1

Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

numpy library compiled to run with other libraries inside Chimera
by Terry Lang 15 Jul '11

15 Jul '11

Hey Guys! I use Chimera as a back end library for a bunch of my code. I occasionally run into a function that an external library, scipy for example, has already implemented. I have found the chimera flag that allows me to import python libraries for use. However, because numpy is already distributed with Chimera, importing libraries that depend on numpy is almost _impossible_. We run into a variety of version and compiler issues that are very difficult to work around. Would it be possible to get more transparent documentation on how the numpy library is compiled and when it will be upgraded in a particular release? (NOTE: We actually have this problem right now, so even an email with a description of the current nightly build set up would be SUPER helpful!). Thanks in advance, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

5 4

RMSD map, urgent help please
by Jean Didier Pie Marechal 22 Jun '11

22 Jun '11

Hi guys, Sorry to ask you that but I urgently need to recover the matrix from an RMSD map obtained from a MD movie. Basically, that would be the same as the graphic of the map but in a file with the numbers. I only have 40 structures but doint it by hands is just painful. Could you please tell me how to catch the rmsd map, I guess we can do it from the script section of the MD movie, but can't figure it out. Sorry to bother you, Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Juny 10, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 88, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: Protofibril model (Elaine Meng) > 2. Re: Protofibril model (lihong huang) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 9 Jun 2011 13:30:22 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, UCSF Chimera Mailing List > <chimera-users(a)cgl.ucsf.edu>, "Susan T. Lord Ph.D." > <susan(a)sucofa.com>, lihong huang <lihonghuang1980(a)gmail.com> > Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Lihong and others, > The Multiscale Models tool in Chimera is meant for this purpose --- > it shows low-resolution surfaces, which are often preferred for > large complexes. > > In Chimera I tried opening 1ei3, then started Multiscale Models (in > menu under Tools... Higher-Order Structure), then clicked the "Make > models" button at the bottom of the multiscale dialog. This shows > the structure with low-resolution surfaces and automatically uses > different colors for the different chains. You can adjust the > colors, surface resolution, etc. in the dialog. Click the dialog's > Help button to see its manual page. There is also a copy here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu…> > > I also tried it with 1m1j, which also worked fine on my computer. > > 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, 2011, at 12:13 PM, Russell M. Taylor II wrote: > > > Dear Lihong, > > I am glad to hear that Chimera let you start down this path. > > I'm CCing the Chimera developer mailing list in case they > know of a better solution. > > You can also join the chimera users list at > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html > and then post a query there. > > > > The following is a somewhat convoluted path to get where you want > to go. Hopefully someone on one of the above mailing lists will > know a better one. If you need to go down this path, we should > probably set a time for us to sit down together and go through this. > > > > Download MGLTools from > http://mgltools.scripps.edu/downloads. I ran the Windows installer. > > This launched the Python Molecule Viewer. > > Select Compute/Coarse Molecular Surface. Kept the default > parameters. This produced a surface that was near the outside of > the molecule. > > Clicked to turn off the red dot under the CPK label so > that we only see the surface. > > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL > file.> > > I was able to load the resulting .wrl file back into > Chimera. This should provide you with a simplified model. You > should be able to adjust the parameters for the coarse saving to > get different model quality. > > > > I attach the resulting coarse model (inside a Zip file) to > this email. > > Russ > > > > [Things below I tried that didn't work] > > > > (Fine surface) > > Select File/Read Molecule. Opened 1EI3.pdb (when I used > 1M1J.pdb, it crashed trying to make the surface). > > Compute/Molecular Surface/Compute Molecular Surface. Used > the default parameters (other parameters caused it to crash). This > produced a fine molecular surface. This could be used directly or > simplified.> > > VMD uses a program called MSMS, but can't run it. When I go to > the MSMS home page, it eventually redirects me to MGLTools from > Scripps.> > > NOPE: > > > > You can load the PDB file into the VMD program (File/New, > select the file name and click Load on the Molecule File Browser). > Then select Graphics/Representations from the VMD Main menu. Then > pull down Drawing Method and select Surf. Turn off the "Apply > Changes Automatically" control and then set the Probe Radius to 4.0 > and click Apply. > > To turn off the little axes display, select Display/Axes/Off > > To save the resulting geometry, select File/Render from > the main menu. Pull down "Render using" and select Wavefront. > Change the .obj file name to one that is useful to you (I named id > protofibril.obj). Click the "Start Rendering" button. > > > > Open Blender (available from blender.org) Press delete > to get rid of the cube that is created by default. > > Select File/Import/Wavefront to load the model. Pick the > file name and then click "Import a Wavefront OBJ" > > > > At 10:18 AM 6/7/2011, lihong huang wrote: > >> Dear Dr. Taylor, > >> > >> I am postdoc working in Dr. Susan Lord's lab. According to your > suggestion, we set up the protofibril model using UCSF Chimera > program which is very nice. Now we want to move on to make small > fiber model, however, the program run very slowly when we add more > fibrinogen molecules. We are thinking if we could make the > fibrinogen molecule lose more details, maybe the program could run > easily. Do you know which program could do this? We just want to > show the basic shape of fibrinogen, no needs to show very detailed > part, such as alpha, beta and gamma chains. Thanks a lot for your > help.>> > >> Lihong Huang, > >> Postdco > >> Pathology and lab medicine > > > > --- > > Russell M. Taylor II, Ph.D. > taylorr(a)cs.unc.edu> CB #3175, Sitterson Hall > www.cs.unc.edu/~taylorr> University of North Carolina, > Voice: (919) 962-1701 > > Chapel Hill, NC 27599-3175 FAX: (919) > 962-1799 > <protofibril.zip>_______________________________________________> > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Jun 2011 09:32:02 -0400 > From: lihong huang <lihonghuang1980(a)gmail.com> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: meng(a)cgl.ucsf.edu, chimera-dev(a)cgl.ucsf.edu, susan(a)sucofa.com > Message-ID: <BANLkTinJsiLgAiE9ghyTyP-0TUZT_YP_Nw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Russ, Elaine and Tom, > > Thank you very much for your help. We will try what you suggested > and let > you know how it works. > > Best, > Lihong > > On Thu, Jun 9, 2011 at 3:13 PM, Russell M. Taylor II > <taylorr(a)cs.unc.edu>wrote: > > Dear Lihong, > > I am glad to hear that Chimera let you start down this path. > > I'm CCing the Chimera developer mailing list in case they > know of a > > better solution. > > You can also join the chimera users list at > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera- > users/index.html and > > then post a query there. > > > > The following is a somewhat convoluted path to get where you want > to go. > > Hopefully someone on one of the above mailing lists will know a > better one. > > If you need to go down this path, we should probably set a time > for us to > > sit down together and go through this. > > > > Download MGLTools from > http://mgltools.scripps.edu/downloads. I > > ran the Windows installer. > > This launched the Python Molecule Viewer. > > Select Compute/Coarse Molecular Surface. Kept the default > > parameters. This produced a surface that was near the outside of > the> molecule. > > Clicked to turn off the red dot under the CPK label so > that we only > > see the surface. > > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL > file.> > > I was able to load the resulting .wrl file back into > Chimera. This > > should provide you with a simplified model. You should be able > to adjust > > the parameters for the coarse saving to get different model quality. > > > > I attach the resulting coarse model (inside a Zip file) to > this> email. > > Russ > > > > [Things below I tried that didn't work] > > > > (Fine surface) > > Select File/Read Molecule. Opened 1EI3.pdb (when I used > 1M1J.pdb,> it crashed trying to make the surface). > > Compute/Molecular Surface/Compute Molecular Surface. Used > the> default parameters (other parameters caused it to crash). > This produced a > > fine molecular surface. This could be used directly or simplified. > > > > VMD uses a program called MSMS, but can't run it. When I go to > the MSMS > > home page, it eventually redirects me to MGLTools from Scripps. > > > > NOPE: > > > > You can load the PDB file into the VMD program (File/New, > select the > > file name and click Load on the Molecule File Browser). Then select > > Graphics/Representations from the VMD Main menu. Then pull down > Drawing> Method and select Surf. Turn off the "Apply Changes > Automatically" control > > and then set the Probe Radius to 4.0 and click Apply. > > To turn off the little axes display, select Display/Axes/Off > > To save the resulting geometry, select File/Render from > the main > > menu. Pull down "Render using" and select Wavefront. Change the > .obj file > > name to one that is useful to you (I named id protofibril.obj). > Click the > > "Start Rendering" button. > > > > Open Blender (available from blender.org) Press delete > to get rid > > of the cube that is created by default. > > Select File/Import/Wavefront to load the model. Pick the > file name > > and then click "Import a Wavefront OBJ" > > > > > > At 10:18 AM 6/7/2011, lihong huang wrote: > > > >> Dear Dr. Taylor, > >> > >> I am postdoc working in Dr. Susan Lord's lab. According to your > >> suggestion, we set up the protofibril model using UCSF Chimera > program which > >> is very nice. Now we want to move on to make small fiber model, > however, the > >> program run very slowly when we add more fibrinogen molecules. > We are > >> thinking if we could make the fibrinogen molecule lose more > details, maybe > >> the program could run easily. Do you know which program could do > this? We > >> just want to show the basic shape of fibrinogen, no needs to > show very > >> detailed part, such as alpha, beta and gamma chains. Thanks a > lot for your > >> help. > >> > >> Lihong Huang, > >> Postdco > >> Pathology and lab medicine > >> > > > > --- > > Russell M. Taylor II, Ph.D. > taylorr(a)cs.unc.edu> CB #3175, Sitterson Hall > www.cs.unc.edu/~taylorr<http://www.cs.unc.edu/%7Etaylorr>> > University of North Carolina, Voice: (919) 962- > 1701> Chapel Hill, NC 27599-3175 FAX: > (919) 962-1799 >

2 1

Re: [chimera-dev] Protofibril model
by Russell M. Taylor II 10 Jun '11

10 Jun '11

Dear Lihong, I am glad to hear that Chimera let you start down this path. I'm CCing the Chimera developer mailing list in case they know of a better solution. You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. This launched the Python Molecule Viewer. Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. Clicked to turn off the red dot under the CPK label so that we only see the surface. Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. I attach the resulting coarse model (inside a Zip file) to this email. Russ [Things below I tried that didn't work] (Fine surface) Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. NOPE: You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. To turn off the little axes display, select Display/Axes/Off To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. Open Blender (available from blender.org) Press delete to get rid of the cube that is created by default. Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" At 10:18 AM 6/7/2011, lihong huang wrote: >Dear Dr. Taylor, > >I am postdoc working in Dr. Susan Lord's lab. According to your >suggestion, we set up the protofibril model using UCSF Chimera >program which is very nice. Now we want to move on to make small >fiber model, however, the program run very slowly when we add more >fibrinogen molecules. We are thinking if we could make the >fibrinogen molecule lose more details, maybe the program could run >easily. Do you know which program could do this? We just want to >show the basic shape of fibrinogen, no needs to show very detailed >part, such as alpha, beta and gamma chains. Thanks a lot for your help. > >Lihong Huang, >Postdco >Pathology and lab medicine --- Russell M. Taylor II, Ph.D. taylorr(a)cs.unc.edu CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr University of North Carolina, Voice: (919) 962-1701 Chapel Hill, NC 27599-3175 FAX: (919) 962-1799

3 2

Biopython paths
by Mateusz Dobrychłop 19 May '11

19 May '11

Hi, I've got another problem, that also revolves around "paths". In my extension I use BioPython libraries. Unfortunately, in every file I have to determine the path to my Python installation (sys.path.append("C:\Python27\Lib\site-packages"), because otherwise, Chimera isn't able to import Biopython. Is there any way to fix that? Mateusz

4 3

Extensions - problem with paths
by Mateusz Dobrychłop 10 May '11

10 May '11

Hello, I'm trying to write my own Chimera extension. First of all, I'd like to thank you for providing so much useful information and so many examples on your site, it's extremely helpful. But there's one problem that might be a serious issue once I try to share this extension with other people. I don't know why, every time I need the extension to write a file, I have to determine an exact path to the localisation where I want the file to be placed. Otherwise it always creates the file on the desktop (I use Windows 7). Is there any way to make Chimera create new files in the extension's directory without giving it an accurate path? Thank you in advance for your help, Mateusz

2 1

Monitor lines
by moneal＠notes.cc.sunysb.edu 19 Apr '11

19 Apr '11

Hello, We just purchased a Zcorp 650, http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx and would like to begin building models of proteins. As you probably know, when you print a physical model of a protein @ 100,000x scale on one of these printers, it is very fragile. To help support the model, one must place "Struts" in key locations. We currently use Jmol because it has a strut algorithm built into the software. The algorithm is open source, written originally by George Phillips and adapted by Bob Hanson (see email below). But Stony Brook faculty are begging us to train our students on Chimera and not JMol because (not surprisingly) most faculty at SBU use Chimera and not JMol. My question: would you be willing to incorporate this algorithm into Chimera (or does it already exist)? This would allow Chimera to output pdb files that are ready for rapid prototyping, a blossoming field: http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFT… I look forward to your response, Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology 108 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 Sure, why not! It's not my algorithm, though. See http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelse… 125 // 126 // Struts calculation (for rapid prototyping) 127 // 128 /////////////////////////////////////////////////////////// 129 /** 130 * 131 * Algorithm of George Phillips phillips(a)biochem.wisc.edu 132 * 133 * originally a contribution to pyMol as struts.py; 134 * adapted here by Bob Hanson for Jmol 1/2010 135 * 136 * Return a vector of support posts for rapid prototyping models 137 * along the lines of George Phillips for Pymol except on actual molecular 138 * segments (biopolymers), not PDB chains (which may or may not be 139 * continuous). Bob On Thu, Apr 14, 2011 at 9:57 AM, <moneal(a)notes.cc.sunysb.edu> wrote: Bob, I teach introductory biology labs at Stony Brook and use physical models to introduce students to research. I have used Ras-Mol but recently switched to Chimera. I would like to share your strut algorithm with the Chimera group in hopes that they will incorporate it into the software. Would you be willing to work with me on this? Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 -----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM ----- To: "moneal(a)notes.cc.sunysb.edu" <moneal(a)notes.cc.sunysb.edu> From: "Franzen, Margaret" <franzen(a)msoe.edu> Date: 04/13/2011 01:56PM Subject: RE: strut algorithm (See attached file: Bob Hansen.vcf) Hi, Marvin! Your earlier question now makes sense! Bob Hansen is the Jmol guru who teaches Chemistry at St. Olaf – and breathes life into all things Jmol. His contact is below: Margaret From: moneal(a)notes.cc.sunysb.edu [mailto:moneal@notes.cc.sunysb.edu] Sent: Wednesday, April 13, 2011 12:51 PM To: Franzen, Margaret Subject: RE: strut algorithm Hey Margaret, My question about the Strut command in Jmol was specific to the math of the algorithm. I was looking for the equation that runs in the background when a student types this command. I couldn't find it in the documentation guide. Do you have Bob's email? There seem to be several Bob Hanson's on the internet. Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680

5 5

minimize in IDLE and command line
by Elisabeth Ortega 07 Apr '11

07 Apr '11

Dear Chimera Dev. Team, I have a problem when I'm trying to launch "minimize" in the Python IDLE. If I write in the IDLE: >>> import MMMD >>> MMMD.base.Minimizer(chimera.openModels.list(modelTypes=[chimera.Molecule]),nsteps=0) I get (in the IDLE): <MMMD.base.Minimizer instance at 0x9e0978c> But if I write in the command line: minimize nsteps 0 I get (in the IDLE and in the message bar): >>> Initial energy: 475.211926 Anybody has any idea about that? Kind regards. Elisabeth Ortega - Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona

2 1

Molecular energy
by Elisabeth Ortega 05 Apr '11

05 Apr '11

Dear Chimera Dev. Team, I'm trying to add energy calculations in my script. To do so, I started with the class Minimize, defining nsteps as 0 but I think that it is not so tidy. In chimera/share/MMMD/MMTKinter.py I found the function minimize and a line that says: msg = "Initial energy: %f" % self.universe.energy() . My question is... How can I invoke this self.universe.energy() in order to get the energy? I tried to write a new class in MMMD/base.py and a new function in MMMD/MMTKinter.py in order to obtain a function like "MMMD.base.energy()" to write in my script but I think that I am doing it more complex that it is... Anyone has any idea for doing it successfully? Thanks, Elisabeth Ortega-Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona.

2 1

Re: [chimera-dev] [Chimera-users] Energy Minimisation Citation
by Konrad Hinsen 28 Mar '11

28 Mar '11

On 28 Mar, 2011, at 5:26 , Nancy wrote: > I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? The minimization code used by Chimera comes from MMTK, whose reference is this paper: http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2 The force field is some dialect of Amber, though I don't know which one exactly is used by Chimera. I hope someone else can provide that information. Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------

3 2

minimizer
by Elisabeth Ortega 17 Mar '11

17 Mar '11

Dear Chimera Dev. Team, I have a question about the Minimizer. I want to use it in the Python/IDLE to calculate the initial energy of a system during the execution of one of my scripts, but I don't found any way to call the function Minimizer and obtain the numeric result without show the addCharge window if I have a metallic system. What can I do to call this function correctly? Thank You Elisabeth Ortega Universitat Autònoma de Barcelona

2 1

Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

3 2

Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 15 Mar '11

15 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

1 0

clashes and contacts with hidden models
by Elisabeth Ortega 28 Feb '11

28 Feb '11

Dear Chimera dev. Team, I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? Thank you for your time. Elisabeth Ortega-Carrasco Universitat Autònoma de Barcelona Spain

3 2

Re: [chimera-dev] [Chimera-users] Surface electrostatic and hydrophobicity.
by Miguel Ortiz Lombardia 29 Jan '11

29 Jan '11

Le 28/01/2011 20:37, Elaine Meng a écrit : > and there is nothing like a "hydrophobic potential" Dear Elaine, In fact, such a thing does exist, have a look here: http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html and here: http://www.moldiscovery.com/docs/vsplus/grid.html I tried long ago to import GRID maps to Chimera but faced two problems: 1/ GRID did not provide a real "volume object", but one that would actually have non-zero values only on grid points corresponding to the solvent accessible surface, which is not implemented in Chimera (and the vdwdefine +1.4 trick is not good enough here) 2/ Eventually, GRID became part of a big package that needed a big licence fee... How this potential is calculated was published long ago (see the second web page above and Goodford's cite in the first one) It would be truly useful if it was implemented in Chimera (if you still have slots in your wish-list) I can enter a feature request if you want... Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1