March 2014 - Chimera-users - RBVI Mailing Lists

stereo3D
by Dougherty, Matthew T 26 Mar '14

26 Mar '14

I have a toshiba qosmio x875-7390 S3D laptop, which is based on the NVidia NVision 3D. Toshiba structured the device to be user unfriendly, limiting stereo3D for bluray and youtube 3d via adobe flash. coming across a pymol S3D post I see there is a workaround, for a different Toshiba model. http://nanonan.wordpress.com/2012/03/28/pymol-and-coot-3d-stereo-on-qosmio-… http://coxcoppes.nl/3DScreenActivator/index.php?pagina=1 Any comments about chimera using S3D on NVidia NVision 3D? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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(no subject)
by Francesco Pietra 23 Mar '14

23 Mar '14

Hello: About stereo drawings with chimera (GNU Linux), I received from the editorial staff: All stereoview illustrations have been drawn in the cross-eye mode, i.e. the > picture for the right eye is on the left and vice versa. > Has this been chosen deliberately? In our opinion, the parallel-eye mode > seems to be used more often. > Please let us know whether we should switch the figures (you would not need > to send new ones) or not. They did the job of transformation to parallel-eye. Next time, I would like to be able to do that myself, while I don't see the parallel-eye mode in chimera. Which is the equivalent? thanks francesco pietra

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Detection of Internal water along MD trajectory
by James Starlight 20 Mar '14

20 Mar '14

Dear Chimera users! I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Chimera tools suitable for such task. Many thanks for help, James

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Chimera Sequence alignment window
by meginir urestal 20 Mar '14

20 Mar '14

Hi, I was wondering if there was a way of printing the contents of the chimera alignment window. If not, could anyone suggest something for printing saved aligned fasta sequences. Thanks

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Morph conformation - conformation collapsing
by Helge.Paternoga＠bzh.uni-heidelberg.de 18 Mar '14

18 Mar '14

Hello, I'm trying to morph two structures which have two chains each. The problem is that if I just add the two confirmations one chain will turn the wrong way, because it is taking the shortest distance to the final position. What i did now is I used this initial morphing to extract 4 frames of the movement of the other chain and inserted the movement of the smaller chain in each of these structures by hand (so the movement is in the right direction and happening at the same time as the other chain). But when I now add these 4 structures in my morph confirmation list like this: Start confirmation frame 1 frame 2 frame 3 frame 4 End confirmation It nicely starts moving in the right way but then at a transition to a new frame the whole structre collapses, bonds get distorted, it somehow shrinks and then extends again later to end up at the final confirmation... I think this is independent of which frame i use (I tried to simplify it by using only 2 intermediates) Do you have any idea what is causing this collapse? The initial confirmation has the same number of chains as the end confirmation (with the same names) but they have a different number of atoms (which i don't quite understand because they are the same macromolecules...) Could this be part of the problem? best regards, Helge

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Recording movie with simultaneous map morph and PDB morph conformation
by Joel Meyerson 17 Mar '14

17 Mar '14

Hi, Is it possible to record a movie that shows both an MRC map morph and PDB conformation morph happening simultaneously? Joel

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residue number in Gromacs tpr file
by Mario Dejung 17 Mar '14

17 Mar '14

Hi all, I am experimenting with Gromacs a little bit and try to open the tpr file and the corresponding trajectory in chimera. Works fine, but the numbering is completely wrong. The residues get numbered continuous and not starting at 1 for the next chain. Not sure if the problem is in the tpr file or in chimera. I have 4 chains in my pdb file and all have a chain identifier, O P g and h and they are separated by TER I have also 4 .itp files with names like “topol_Protein_chain_O.itp” My topol.top file say 4 molecules [ molecules ] ; Compound #mols Protein_chain_O 1 Protein_chain_P 1 Protein_chain_g 1 Protein_chain_h 1 and ; Include chain topologies #include "topol_Protein_chain_O.itp" #include "topol_Protein_chain_P.itp" #include "topol_Protein_chain_g.itp" #include “topol_Protein_chain_h.itp" I create my tpr file with grompp Has anybody experience with this kind of issue? Kind regards Mario

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Chimera and XP?
by Boaz Shaanan 13 Mar '14

13 Mar '14

Hi, For some reason, I couldn't get Chimera (1.8.1 and the 12/3 daily build) to work today on my laptop running XP (32bit). It gets stuck in 'initializing graphics'. See attached screen shot of run with --debug. Chimera worked for years on this machine. Other programs work fine (spdbv, Coot, etc.). I can't imagine it has to do with the imminent downfall of XP support, or maybe it does? Please advise. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Wednesday, March 12, 2014 9:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 131, Issue 13 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.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. match-align using just selected protein areas ? (Marek Maly) 2. Re: match-align using just selected protein areas ? (Elaine Meng) 3. Re: surface failures (Elaine Meng) 4. Re: match-align using just selected protein areas ? (Marek Maly) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Mar 2014 02:53:47 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xck57xhvlc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ Message: 2 Date: Wed, 12 Mar 2014 09:35:39 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "Marek Maly" <marek.maly(a)ujep.cz> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <67EFA59C-7032-4F2A-8517-6D32E11C4F2D(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Marek, Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made). In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> In the matchmaker (mmaker) command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> ... it is similar but you instead specify the residues directly instead of selecting them: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> 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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote: > Hello, > I would like to know if it is possible in Chimera > align two proteins let say protein A and protein B, > but just using selected subsequences A_sel, B_sel > (i.e. just the selected subsequences are going to be > optimally matched and the rest of both proteins is not involved > in the matching process/calculation) ? > Thank you in advance ! > Best wishes, > Marek ------------------------------ Message: 3 Date: Wed, 12 Mar 2014 09:51:04 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Julian Marzi <julian.marzi(a)googlemail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] surface failures Message-ID: <91C53A76-7F10-4123-9752-0AE5F5C58689(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote: > Dear Eric, > I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. > Thank you so much > Regards > Julian Hi Julian, The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction). Color Zone is mentioned along with molmap in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu. I hope this helps! P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco ------------------------------ Message: 4 Date: Wed, 12 Mar 2014 19:44:27 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xcmg0dxylc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Dear Elaine, thank you very much for your help ! Best wishes, Marek Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <meng(a)cgl.ucsf.edu> napsal/-a: > Hi Marek, > Yes, if you mean MatchMaker (Match->Align does not align the structures, > it just makes a sequence alignment from a structural alignment you > already made). > > In the MatchMaker GUI, there is a "Further restrict matching to current > selection" setting: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> > > In the matchmaker (mmaker) command, > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> > ... it is similar but you instead specify the residues directly instead > of selecting them: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> > > 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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote: > >> Hello, >> I would like to know if it is possible in Chimera >> align two proteins let say protein A and protein B, >> but just using selected subsequences A_sel, B_sel >> (i.e. just the selected subsequences are going to be >> optimally matched and the rest of both proteins is not involved >> in the matching process/calculation) ? >> Thank you in advance ! >> Best wishes, >> Marek > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 9532 > (20140312) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 131, Issue 13 **********************************************

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'Old-style' silhouette edges?
by Thomas Mitterfellner 13 Mar '14

13 Mar '14

Hello! It seems that somewhere between 1.6.2 and 1.7, the way silhouette edges are drawn has changed. Most of the silhouette edges are now drawn in white regardless of the color I set (presumably due to some smart algorithm?). In my opinion, the old way gave a much clearer appearance of the molecule on different backgrounds and it gave it a 'cartoonish' flavor which made it look quite distinguished from the images other software produces and I really loved that. So my question is: is there any way to get back the 'old-style' (pre 1.7) silhouette edges in 1.7+ releases? Kind regards, Thomas

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editing selected dihedral angles
by Francesco Pietra 13 Mar '14

13 Mar '14

Hello: I would appreciate receiving instructions on changing selected dihedral angles in a peptide. Imagine that the initial and final stretches are alpha-helices, while in the middle, dihedral angles are such that two alpha-helix coiled portions make an angle different from 180 degrees. In all that, all dihedrals in the alpha-helix portions should not be modified. Thanks francesco pietra

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