January 2010 - Chimera-dev - RBVI Mailing Lists

ribbon for circular molecule
by Volodymyr Babin 28 Jan '10

28 Jan '10

Dear Sirs, I am writing to ask for the chimera sources -- I would like to visualize a circular molecule using ribbons. As far as I can tell, with the current code ribbons always have ends (cannot be closed) because of the following snipped from libs/_chimera/Chimera.toolkit/Ribbon.implementation 696 Molecule::updateRibbonData() 697 { 698 clearRibbonData(); 699 700 // 701 // For each residue, find the residues before and after. 702 // Note that only residues with valid guide and plane atoms 703 // may be used as the prev/next residue in a ribbon. 704 // 705 std::map<Residue *, RibbonResidue> rrMap; 706 Residue *prev = NULL; ^^^^^^^^^^^^^^^^^^^^^ Could you please allow me to check out the svn version of the chimera or get (easily compilable) sources of a recent release. Thank you, Volodymyr

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calculate volume major blob
by Jean Didier Pie Marechal 24 Jan '10

24 Jan '10

Dear all, I need to do the work for thousands of structures, so Iam interesting in a scripting solution here. After a surfnet calculation on a given atom selection, my script select the whole surface model and calculates the volume of the all bunch. However, I'd like to have the volume of the major blob only. On the other hand, for a given number of structures, I would like to remove all minor blobs blobs so that only the major one remains on the screen. How could I do this second step? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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

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extensions outside the chimera directory
by Jean Didier Pie Marechal 22 Jan '10

22 Jan '10

Dear All, I am preparing a series of practical for a MSc and I'd like a series of extensions I have to be accessible for students. Unfortunately, I do not have write access to the /usr/local/chimera directory of the pcs of the classrom and the OS images the machines boot on are not upgradable easily. Could I locate extensions in a user directory? Sorry for my ignorance.... Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Gener 20, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. StructureSequence.residues change (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 19 Jan 2010 13:22:31 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] StructureSequence.residues change > Message-ID: <BE4EE11C-A560-4D1D-A08B-5ED3AA052CF5(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > I've made a change in the 1.5 build that could affect > script/extension > writers that use the StructureSequence.residues list. That list > can > now contain None values. This is because now the sequence is the > full > sequence if available in SEQRES records even if some of the > corresponding structure is missing. Such missing structure has > None > for the Residue value. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu >

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StructureSequence.residues change
by Eric Pettersen 19 Jan '10

19 Jan '10

I've made a change in the 1.5 build that could affect script/extension writers that use the StructureSequence.residues list. That list can now contain None values. This is because now the sequence is the full sequence if available in SEQRES records even if some of the corresponding structure is missing. Such missing structure has None for the Residue value. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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(no subject)
by Mojie Duan 19 Jan '10

19 Jan '10

Dear Chimera Developers, I needs to calculate the inter-helical angle for thousands of conformations. We know Chimera can calculate the inter-helical angle for one conformation. We are wondering if Chimera can calculate the inter-helical angle for all these conformations at one time? or would you please point out how to write a script to do this? Thanks. Mojie

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Calculating RMSD
by Victor Muñoz 15 Jan '10

15 Jan '10

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.

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adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Hi everyone, I have obtained cavities for a given atom selection using surfnet and I want to put an atom at the centroid of the main blob. I know how to do this for a selected set of atom but I am struggling with the surfaces. At this point, I splitted it (accelator Sc) and then I can select the blob I am interested in. But how could I create a particular object for this blob? From there, how could I add an atom (i.e. helium) and the centroid of the blob? Thanks for any help, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimarts, Desembre 15, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 71, Issue 4 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > 2. Re: [Chimera-users] Programmer's Guide feedback.... (Tom > Goddard) 3. Re: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 15 Dec 2009 10:55:42 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide > feedback.... > Message-ID: <61EC3E93-8EE5-48E0-AB71-4705D5162EE4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote: > > > 4. The ToolbarButton.py doesn't work unless the "import re" and > > > "import chimera" are in the function body. This is because > Chimera > > deletes all globals after loading a file. This has often been a > > headache for me and Chimera should not delete globals. > > This is a behavior of Python. We load scripts into their own > temporary module to avoid pollution of the Chimera main namespace > (e.g. if the script defined globals named "id" or "sum" or "type" > they > would override built-in functions of the same name for all future > script executions!). When Chimera unloads the temporary module, > Python nulls out it's global namespace (to give garbage collection > a > shot at working). > > Now perhaps Chimera shouldn't unload the module. I think this > would > be a reasonable change. Perhaps it could be discussed at our next > internal Chimera developers' meeting to ensure that I'm not > forgetting > any other ramifications that the change might have. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Chimera-dev January 2010