- Chimera-users - RBVI Mailing Lists

Distance Lines
by hsosa＠aecom.yu.edu 31 Jul '08

31 Jul '08

Hi , I want to make a solid line (with chosen color) between two atoms. Kind of like the line that appears when measuring distances between atoms, but without the distance legend. Is there an easy way to do that ? Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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PDB morphing
by Dougherty, Matthew T. 28 Jul '08

28 Jul '08

I have a complex structure in two conformations: resting and active. Each structure consists of 24 monomers, corresponding to 24 pdb files. Each monomer file between conformations matches in terms of atom numbers, chain ID, etc. I can morph a single monomer between conformations. I am having no success morphing all the monomers simultaneously between the conformations. Any suggestions on how to organize my data to overcome this? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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Distance between helices
by Thomas Goddard 28 Jul '08

28 Jul '08

HI Tom How do I compute and show the distance between 2 regions (2 alpha helixes) of 2 crystal structures (docked in the density maps), similar portions of each is already highlighted/selected to show the DNA binding region (without showing the atoms). THanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Re: [Chimera-users] BIOMT matrix in Chimera?
by Elaine Meng 28 Jul '08

28 Jul '08

On Jul 27, 2008, at 10:38 AM, Francesco Pietra wrote: > > Hi Elaine: > After a brief playing with Multiscale Models, I was considering your > last suggestion below. I modeled each chain separately, also because > the X-ray diffr data show some conformational differences. Modeling > gave very good DOPE score. Now the problem is appending Chain B to > chain A, etc (each chain opens correctly in Chimera). I have a Python > script (not tried yet) to insert the Chain identifier (which Modeller > did not print), update the Atom serial number, and then append the > files. May I ask, in view of Chimera, if the "Atom number + 1" printed > in Modeller pdb files at column 80 can be left at it is, i.e. not > updated on appending the files? I forgot about that and I have already > problems enough with the script at my minimal level with Python. I > assumed that Python identifies the columns one unity less than PDB > numbering. Finally, do you know what means "1SG" at columns 74-76 of > Modeller pdb files? Hi Francesco, I don't know what MODELLER puts in those columns after "B- factor" (61-66, which may actually contain the "modeller error profile," since a homology model doesn't really have B-factors). Maybe you could ask the modeller people. However, for Chimera purposes they could be omitted (changed to blank). According to the description of ATOM lines: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 67-76 is supposed to be blank, 77-78 element symbol, 79-80 charge. I believe Chimera tolerates lines without the last few columns, as long as the X,Y,Z coords are still there. If your files have stuff in the later columns, it might still be OK, just try opening them in Chimera to see. My suggestion of modeling the multimer from a template multimer would still incorporate the chain differences - you would still use A as the template for A, B for B, etc. However, I don't know how to make modeller do that. > Following the "appending" plan below, is it correct to > append pdb files lacking all hydrogens (as provided by Modeller) and > then rely on Amber's LEAP to complete the multimer? > francesco I don't know what you mean by "complete the multimer" - if just adding hydrogens, you can do that with AddH in Chimera (or addh command). That does not use leap/amber. Best, Elaine

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How to print molecular structures?
by �� 28 Jul '08

28 Jul '08

Hi all, I want to print 1000 molecular structures one by one. I am wondering if it is possible to print molecular structures by Chimera. If it is not, are there some other software can do this? Please kindly advice. Any answer would be appreciated! Best regards, Yolanda Guo Northeast Normal University

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Pointers to writing extensions in chimera
by Mario J. Borgnia 26 Jul '08

26 Jul '08

Hi all, I would like to try and write an extension to chimera. Could anyone give me some pointers on where to find the tools necessary to do so. Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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BIOMT matrix in Chimera?
by Francesco Pietra 25 Jul '08

25 Jul '08

>From a homotrimer pdb template I have created (with Modeler) a homology model, with very good score, using a single subunit. Is it possible with Chimera to create the homology homotrimer, as this is what I need? To this concern, the original pdb for the template includes the BIOMT transformation matrix for both crystallographic and non-crystallographic operation. That is, the pdb includes as many identical chains to open directly the homotrimer for the crystallographic pose. Is that BIOMT matrix usable by Chimera for the homology model? Or the way ti take is another one? I used much technical language, well above - however - my expertise in these affairs. That in view of any help, for which I'll be most grateful. Thanks francesco pietra

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nogui vrml export?
by Paul 25 Jul '08

25 Jul '08

Hello, Is there any way to export .vrml or .wrl in the nogui mode? The idea would be to run a script that would load a .pdb file and transform it into a few different representations and then export them. I saw in previous posts that there is no support for exporting images in this mode. Thanks, Paul

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superimposing active sites
by Elaine Meng 24 Jul '08

24 Jul '08

On Jul 23, 2008, at 6:18 PM, Maria wrote: > Elaine, > I have created active sites by using the zone in > chimera for 72 proteins. Is there a way I can > do structural superimposition of the active > sites using chimera? > Thanks, > Maria Hi Maria, Sure, there are many, many ways to superimpose structures in Chimera. If the structures are homologous (have the same fold, usually also some sequence similarity), probably the easiest are these two methods: (A) MatchMaker tool (or the "matchmaker" command, which acts exactly the same way) - it creates a sequence alignment and then uses those alignment columns to superimpose the structures (B) if you already have a sequence alignment, you can open that in Chimera and use it to superimpose the structures With both (A) and (B) you would use the whole structures - it is OK if you are only displaying a zone as long as the other atoms are still there (are merely hidden, not deleted). Some other approaches can be used for either homologous or nonhomologous proteins: (C) "match" command - you specifically name the atoms you want to use for fitting in the command; for example, atoms from a few active site residues and/or from the ligand (D) interactive fitting "by hand" Links to more detailed information... Discussion and examples of more than one method: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#s… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#com… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match… MatchMaker man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… "matchmaker" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html "match" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Using a pre-existing sequence alignment: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/fr… (see "Structural Superposition" section) Best, 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

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making MD movie
by bala 24 Jul '08

24 Jul '08

Hello freinds, While recording a MD movie or saving an image, chimera considers full screen ares. Is there any way that i can select a particular area in the screen and ouput the image or the MD movie accordingly. Thanks, Bala

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