- Chimera-users - RBVI Mailing Lists

drawing axes of rotational symmetry
by Arvind SHARMA 15 Mar '19

15 Mar '19

Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share. Have a lovely weekend, arvind.

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32-bit release
by Marwa Elnaiem 14 Mar '19

14 Mar '19

Dear UCSF Chimera team, I highly need to use the software Chimera, but unfortunately, my operating system is 32-bit which is no longer supported. I would like to ask if any old release of chimera that I could download on my 32-bit operating system. Could you please help? Regards, Marwa

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Re: [Chimera-users] CASTp to Chimera
by Elaine Meng 13 Mar '19

13 Mar '19

> On Mar 13, 2019, at 9:57 AM, Chakraborty, Joydeep <jc323(a)njit.edu> wrote: > > Hi Elaine > I am trying to show the active site space fill model as depicted by the CASTp. However I am having difficulty to generate the same file using chimera. I was wondering if there is any special way we could depict a ribbon diagram of the protein with a space filled active site pocket. > Thanks, > Joydeep. Hi Joydeep, A picture would have been helpful, but I’m guessing you mean how it looks at the CASTp website. I looked at the website and see it shows some transparent spheres filling the pocket. However, these spheres are not described in any of the files Chimera gets from CASTp (which are the same as the files you get if you choose “Download” on their website), so we don’t have any way of showing them, sorry. I didn’t see any way to get the spheres from the website… I agree it would be useful! Just to help explain it to everybody else, I attached an image showing left to right: the Chimera CASTp dialog, Chimera window showing PDB structure 3TRG ribbon with molecular surface of biggest pocket from CASTp, and image of the same structure and pocket at the CASTp website <http://sts.bioe.uic.edu/castp/index.html?3trg>, including the transparent spheres: For future reference, it is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d on this message) to ensure you get an answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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MD simulation fails with barostat
by Simon Wheeler 13 Mar '19

13 Mar '19

Hi everyone. I'm trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I've applied periodic boundary conditions and specified the box size. Does anyone know what I'm doing wrong? Thanks, Simon

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CHIMERA ISSUES
by Acco . 13 Mar '19

13 Mar '19

Hello, I am a beginner with Chimera and I am looking for how to "bring to front" the residues that I have selected displaying the remaining structure of the protein in kind of blurred view. Is it possible to do this? Thank you in advance for your help Sincerely, Andrea

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how to load pseudobonds from command line?
by Michał Kadlof 12 Mar '19

12 Mar '19

Hello, I'd like to display my psudobond in chimera script. How can I do it? -- regards Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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membrane boundaries
by Anaswara Ashok 12 Mar '19

12 Mar '19

Hi I would like to know if we could add membrane boundaries of proteins with chimera? -- Regards Anaswara Ashok

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OS differences in Chimera
by Marco J. Müller 11 Mar '19

11 Mar '19

Dear Chimera team, I do have a question regarding differences between OSes. Our group recently encountered a problem in the surface creation of proteins, which might be related to the OS. Recently, for some structures, directly obtained from the PDB (e.g. 6GB5, 1H97, 4YLJ) or prepared single-chain structures for docking runs, the surface creation of the proteins resulted in error 5 from mscalc.exe. This, however, seems to be an isolated problem of the Windows versions of ucsf chimera 1.12-1.13.1, as the same versions of chimera on macOS or Linux (Lubuntu) could successfully create these surfaces. Even more strangely, we are pretty sure that we could show surfaces of the very same files about half a year ago with these versions (1.12 and 1.13rc1). Did a recent update of Windows change the behavior of chimera? ChimeraX could actually show these surfaces on Windows, but gave us some other troubles. We did have a look at http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012874.html which did solve our problem for now, but we would like to know whether we can improve the reliability of chimera's functions, aside from tips mentioned in http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. An older post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005805.html) indicates that it is a numerical problem, is this still the case and means that it is indeed OS-dependent? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

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font problem
by 管泓翔 11 Mar '19

11 Mar '19

When I started chimera, it showed "Cannot find a usable font Aborted (core dumped)". How to fix the problem? Thank you HH

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Deterministic traversal of a chemical graph
by Jaime Rodríguez-Guerra Pedregal 08 Mar '19

08 Mar '19

Dear Chimera team, I have two questions regarding the same idea. I am trying to develop a script to find topologically equivalent residues in a structure (e.g. MOF, cages, and so on). To do this, I am using SplitMolecule.split.split_connected and then comparing the resulting pieces by number of atoms, empirical formula and, ultimately, I would like to compare the chemical graph (i.e. test for graph isomorphism). Is there any built-in function/object for that in Chimera? Since I didn't want to overcomplicate the algorithm, for now I am trusting that there won't be isomers in the structure and the empirical formula (actually a collections.Counter applied to atom.element.name<http://atom.element.name>) is enough of a test.This is working ok but, in some cases, the resulting pieces have totally different atom names because they come from a unified generic residue that encompasses all the pieces. As a result, I want to rename them in the same way consistently. My first attempt at this consists of finding the chimera.Root atom of each piece and then using chimera.Molecule.traverseAtoms to iterate over the piece. However, I've found that the Root is not always the same (topologically speaking) atom, so the naming scheme differs from piece to piece. Is there anyway to guarantee topologically equivalent traversals? I guess that both questions would lead to the same result, because it seems that I will need a chemical graph anyway. Thank you in advance, Jaime.

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