January 2010 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

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SDF Partial Charges
by Nancy 01 Feb '10

01 Feb '10

Hello, I am performing protein-ligand docking simulations, and the preferred ligand input file format is Mol2. I obtained some of my ligand structures from PubChem in SDF format, and I noticed that the SDF files contain partial charges ("PUBCHEM_MMFF94_PARTIAL_CHARGES"). Is there a way to preserve the charges in Chimera when converting to Mol2 file format? Thanks in advance. Nancy

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Re: [Chimera-users] holle,sir!
by Elaine Meng 30 Jan '10

30 Jan '10

On Jan 29, 2010, at 10:14 PM, gytjyb wrote: > holle,sir! nice to send a letter to you! > (1) about FindHBond .I can find out some HBond between ligand and > receptor,by chimera. I also use Accelrys Discovery Studio to find > out some HBond . but Accelrys Discovery Studio find out HBond to be > more than chimera. why?which one result is ture? > (2)what is meaning about Clashes/Contacts?what is useful for Finding > Clashes/Contacts > (3)how can i find out interaction between ligand and receptor and > classify displaying. > (4)can i use this software to publicate my paper ,directly? > best wishes for you ! (1) FindHBond vs. other programs. Different programs use different methods and cutoffs, and there is no reason to expect exactly the same results. The world of science does not agree on one exact definition of H-bond. Each program should explain its own method, as we have in the FindHBond documentation. Click "Help" on the FindHBond dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > Also, this same question was discussed 2 days ago on the chimera-users list, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004746.html > (2) What are clashes and contacts? This is explained in the Find Clashes/Contacts documentation. Click "Help" on the Find Clashes/Contacts dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas… > (3) use FindHBond and Find Clashes/Contacts. The "Structure Analysis and Comparison" tutorial is one example of using these tools: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> (4) yes, you can use images and calculation results from Chimera in your paper, but please remember to credit Chimera as described here: <http://www.cgl.ucsf.edu/chimera/docs/credits.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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H Bonds in MD simulation
by snoze pa 29 Jan '10

29 Jan '10

Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S

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Re: [Chimera-users] Rename atoms...and chains, residue numbers
by Jonathan Sheehan 28 Jan '10

28 Jan '10

On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > This is actually a little trickier than it really should be in the current > builds. As of tomorrow's daily build the following will work without any > issues to set the name of selected atoms to 'X1': > from chimera import runCommand > runCommand("setattr a name X1 sel") > --or-- > from chimera import selection > for a in selection.currentAtoms(): > a.name = "X1" Hi- Following up on this, I'd like to offer a feature request regarding structure editing. Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-) Would this be difficult to implement? Thanks for considering it, -Jonathan -- Jonathan Sheehan, Ph.D. Comput. Biol. Educ. and Outreach Vanderbilt Univ. Ctr. for Struct. Biol. 5138 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755

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Re: [Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
by Boaz Shaanan 28 Jan '10

28 Jan '10

Hi, The possible reason for the chopped ccp4 maps when they are displayed in Chimera (whereas they're fine Coot) may have to do with the fact that as far as I know Chimera does not apply the crystallographic symmetry operations to the ccp4 map (at least that's how it used to be in v1.3), whereas Coot does. So if the map is defined for the asymmetric unit only, it has to be expanded in order to cover all the region which one wants to display before being read into Chimera. There could of course be other reasons for the chopped maps. Cheers, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Thursday, January 28, 2010 21:11 Subject: Chimera-users Digest, Vol 81, Issue 21 To: chimera-users(a)cgl.ucsf.edu > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Chimera movie question (Tom Goddard) > 2. Contouring ED Map: Sigma versus Chimera > thresholds (Veer Bhatt) > 3. Re: Contouring ED Map: Sigma versus Chimera thresholds > (Elaine Meng) > 4. Contouring ED Maps (Hector Viadiu) > 5. Re: Contouring ED Maps (Tom Goddard) > 6. H Bonds in MD simulation (snoze pa) > 7. Re: H Bonds in MD simulation (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Wed, 27 Jan 2010 12:51:19 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: Bridget Carragher <bcarr(a)scripps.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera movie question > Message-ID: <4B60A747.5030705(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Bridget, > > I put an example animation on the Chimera web site in the > animation > gallery called "Herpes virus slices". There is also a link > to a command > script which makes this movie. You just use File/Open... > in Chimera to > run the command script. > > > http://www.cgl.ucsf.edu/chimera/animations/animations.html > Tom > > > > > > OK, thanks Tom. Any tips on how to do all three planes > at once - or > > > rather keep the others constant while eating though the side > plane. I > > > have sen movies like this but can;t seem to figure out how > to do it in > > > Chimera. > > > Bridget > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 27 Jan 2010 19:12:31 -0500 > From: Veer Bhatt <veer82(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera > thresholds > Message-ID: <C41C6E8E-343B-4FA1-BB71-49BAADB32DF2(a)gmail.com> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Hi, > This in context of using Chimera to view *ccp4 format > electron > density maps. How does Chimera 'Threshold Level' ('Level' in > Volume > viewer) equate or relate to sigma level reported by some > other > programs. For example a 'Level' of 0.4 seems like a map > contoured at > 1.5 sigma or so. > I was wondering if someone could point out how these two are > related, > more precisely. > > Thanks > > Veer Sandeep Bhatt > >

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Contouring ED Map: Sigma versus Chimera thresholds
by Veer Bhatt 27 Jan '10

27 Jan '10

Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely. Thanks Veer Sandeep Bhatt

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lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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running command scripts
by Michael Zimmermann 27 Jan '10

27 Jan '10

Dear Chimera users, I am getting to know Chimera a bit more and was just going through the scripting tutorial here: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Scr… For the command line script 1gfl.com, the tutorial just says "run it" but does not say how. I just typed "run 1gfl.com" in the chimera command line, but I get a syntax error in the script. I can't seem to copy the error text, so a screenshot is attached. Is this an issue with the script or how I am running it? I use chimera v. 1.4 on win XP - 64bit. Thank you, Mike Z

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