- Chimera-dev - RBVI Mailing Lists

Invitation to connect on LinkedIn
by Christopher Lau 16 Apr '12

16 Apr '12

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Christopher Christopher Lau ODP Associate at Baxter Healthcare United States Confirm that you know Christopher Lau: https://www.linkedin.com/e/qmxwak-h14gpxie-1a/isd/6709452220/_Ma-PXTx/?hs=f… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/qmxwak-h14gpxie-1a/q4TF6l0mGNnJlSZF-zGBU1EDXRtE03… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Fwd: Chimera (any version) + Nvidia GeForce GT 430 1GB + OpenSuse (11.0 or 12.1)
by Elisabeth Ortega 28 Mar '12

28 Mar '12

Dear Chimera development team, I have a little problem when I use Chimera with my new Video card Nvidia geforce GT 430. Chimera runs well the firsts 2 minutes but, then, it gets stucked and I can't move whatever I had open in these moment (even if I had a little model of less than 50 atoms!). I've been updated the drivers of the video card twice and also I re-installed the operating System but Chimera remains getting stucked. Before change the Video Card (first I had a ATI Radeon (I don't remember the model) of 1GB) Chimera runs perfectly. Anyone has any idea of how can I fix it without change the video card? (the best solution is using back the ATI video card... but I want to use NVidia in my computer) I'm running Chimera over Linux (Opensuse 11.0 32 bits and Opensuse 12.1 64 bits) in a Intel Dual core CPU E8400 @ 3.00 GHz with 2 GB of RAM. Thank you in advance. Elisabeth Ortega-Carrasco Ph.D. Student. Universitat Autònoma de Barcelona (Spain)

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Re: [chimera-dev] IDE
by Eric Pettersen 07 Feb '12

07 Feb '12

On Feb 6, 2012, at 6:33 PM, Elnaz Rezaei wrote: > I need to know what are the functions and properties of "atom > object" do in chemira. > I searched but I could not find! Hi Elnaz, In IDLE you can type "dir(chimera.Atom)" to see the names of all methods/attrs of Atom, or "help(chimera.Atom)" to get a longer but somewhat more readable listing. We do have some information in the Chimera Programmer's Guide: Chimera Programmer's Guide but an encyclopedic listing of Atom attrs/methods isn't part of it. If you said what you were looking to accomplish I could probably offer better advice. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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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

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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

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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/

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(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

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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>

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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 > =============================================================================================== > > > > > > > >

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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

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