- Chimera-users - RBVI Mailing Lists

Calculating SAS and SES with Chimera-MSMS wrap
by Jaime Rodríguez-Guerra 07 Apr '14

07 Apr '14

Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime.

2 1

Re: [Chimera-users] Reaction Mechanism Movie
by Eric Pettersen 07 Apr '14

07 Apr '14

On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote: > Dear Dr. Pettersen, > I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. Hi Moses, It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do. The simplest method is to decide which frame# you want the bond to start existing and use the "Define script…" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame. For example, if you wanted a bond between :337.A@P and :338.A@O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script: #53 bond :337.A@P :338.A@O3' There is also a hidden capability in Chimera to compute all bonds on a per-frame basis. I can tell you how to access that if it turns out you really need it. However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you. I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file…" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other. There are some values at the top of the script that you can edit to make it work best in your situation. There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0). There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames). Let me know if you need more help than this. Hmmm, this all assumes you have a trajectory of the reaction. You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

presets-interactive 3-hydrophobicity surface- those water molecules stay!
by Ying-Chieh Sun 06 Apr '14

06 Apr '14

Hi, I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine 'crystal (or say, ordered) water molecules'. This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. Thank you for your help. Ying-chieh Ying-Chieh Sun, Professor of Computational Chemistry Chemistry Department National Taiwan Normal University Taipei, Taiwan 11617 Tel: +886-2-7734-6215 Fax: +886-2-2932-4249

3 2

Resolution of .stl file of ribbon representatiom
by Gavin Whittaker 04 Apr '14

04 Apr '14

Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I /can/ now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin

3 7

query
by Bhaskar Bagchi 04 Apr '14

04 Apr '14

Respected Sir I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. Thanking you Yours faithfully, Bhaskar Bagchi Research Scholar Raiganj University College Email: bhaskarbagchi(a)gmail.com

2 1

ellipsoid main axis alignment ?
by Hugo J Bohorquez 03 Apr '14

03 Apr '14

Hi, I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. Every ellipsoid should be positioned at a specific location *P* = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-*A*, *B*, *C*. However, when I create an ellipsoid with shape_command it gets located correctly at *P* but it is aligned with the global axis. I can't find a general way to reorient an object so its original axes point along the vectors *A*, *B*, and *C*. I will appreciate any suggestion how to do it. -- Hugo J Bohórquez <https://sites.google.com/site/hugojbohorquez/home>, PhD *Investigador* Grupo de Biofísica Fundación Instituto de Inmunología de Colombia TEL. +57 +1 -3158920 Ext. 122 CEL. +57 315-6169069 *The Pauli energy grows exponentially with the electronic localisation <http://dx.doi.org/10.1080/00268976.2013.836605>*

3 3

resampling maps
by Jason Kaelber 03 Apr '14

03 Apr '14

Hi all, I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. Thanks, Jason <type 'exceptions.TypeError'> Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x276b2d88>> (type: <type 'instancemethod'>) Args: (<Tkinter.Event instance at 0x276a2ea8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand midas_text.makeCommand(cmdText) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd vop_command(cmdname, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command doExtensionFunc(func, fargs, specInfo = spec) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op boundingGrid, False, None, modelId) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation scale = scale[i]) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values <type 'exceptions.TypeError'>: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' ================================================ Event contents: char: delta: 36 height: ?? keycode: 36 keysym: Return keysym_num: 65293 num: ?? send_event: False serial: 39103 state: 16 time: 139539396 type: 2 widget: .59791048.661335648.802317088.802317376.802317448 width: ?? x: 159 x_root: 524 y: 9 y_root: 988 TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values See reply log for Python traceback. -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA

2 3

Is there a way to save animation editing process?
by Li, Leon 03 Apr '14

03 Apr '14

Dear all, I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. Thanks, Leon

2 2

combining different chains
by faeze mohajer 01 Apr '14

01 Apr '14

good day I have modeled heavy and light chains of myosin now I want to combine them through chimera, would you plz help me on that your faithfully *FAEZE SADAT MOHAJERPhD Student * *Faculty of Bioscience and Medical Engineering (FBME)* *Universiti Teknologi Malaysia (UTM)* Buzzdock ads <http://www.buzzdock.com/setting/V2hpbG9raWk=> Search ResultsFaculty of Biosciences & Medical Engineering<http://fbme.utm.my/>

2 1

Re: [Chimera-users] Chimera Shutting Down
by Tom Goddard 31 Mar '14

31 Mar '14

Hi Joshua, Glad to hear that the new graphics driver fixed the Chimera side view crash on your Ubuntu 12.04 system. Maybe this will help some other Chimera users. Tom On Mar 31, 2014, at 12:33 PM, Joshua Broyde wrote: > Dear Tom, > I installed a new graphics driver, so now it works. In case anybody else has this same problem, I installed the Gallium Radeon driver and it worked fine. I followed step 2 from this link: > http://arstechnica.com/civis/viewtopic.php?f=16&t=1137372 > > Thanks for the tip. > Sincerely, > Joshua Broyde > ----- Original Message ----- > From: "Tom Goddard" <goddard(a)sonic.net> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, March 27, 2014 12:58:50 AM > Subject: Re: [Chimera-users] Chimera Shutting Down > > The crash is due to a buggy graphics driver and the only fix is likely to be installing a working graphics driver. Sometimes some trick like starting the side view before opening models as described in the post you referenced avoids the problem, but usually there is no way to avoid a graphics driver crash other than replace the driver with one that doesn’t have the bug. > > Tom > > > On Mar 26, 2014, at 6:05 AM, Joshua Broyde wrote: > >> Hi, >> I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. >> >> OS: Ubuntu 12.04 >> Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) >> >> >> For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. >> Is there another workaround that I could do to open the side view? >> >> Thanks! >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

1 0

Binding pocket surface command script not working
by Markus Heller 28 Mar '14

28 Mar '14

Hello, I'm trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file. I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z. Running latest Chimera. Steps to reproduce: open 2v5z delete :.b split atoms :sag surface measure contactArea #0.2 #0.1 3 slab -.1,0 color tan gives an error: error: Array must be 2-dimensional, got 1-dimensional File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area area = surface_area(varray, tarray) See reply log for Python traceback. Why, and would it be helpful to file a bug report? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CF49BD.0097D1F0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

3 4

Chimera surface error
by Elaine Meng 28 Mar '14

28 Mar '14

On Mar 28, 2014, at 4:27 AM, Uzma Saqib wrote: > Hi Elaine, > Chimera is not showing me the surface of my protein file and gives the attached eror. > i tried what it suggested, but no improvement. > plz help. > attashed , is the pdb. This is a common problem in Chimera. Some explanation and all of our ideas for possible solutions are in this page (no use for me just to repeat that information here): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> #3 and #4 in that page will always work because they use different methods instead of the standard molecular surface calculation. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send chimera questions to chimera-users(a)cgl.ucsf.edu, unless including private data

1 0

Measuring surface area of region
by Anindito Sen 27 Mar '14

27 Mar '14

Dear all, I was wondering if there is any way one can measure the surface area with a threshold higher than its neighbouring region in a TEM micrograph ? Thanks Andy Dr. Anindito Sen (Ph.D) >

2 1

Chimera Shutting Down
by Joshua Broyde 26 Mar '14

26 Mar '14

Hi, I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. OS: Ubuntu 12.04 Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. Is there another workaround that I could do to open the side view? Thanks! Sincerely, Joshua Broyde

3 2

Viewing Gromacs 4.6.5 trajectories
by William McDonald 26 Mar '14

26 Mar '14

Hello Chimera users, I recently upgraded my gromacs simulation software from 4.5.5 to 4.6.5; however, when I attempt to load a new simulation trajectory (either a .xtc or .trr file), Chimera allocates ~13GB RAM causing my machine to swap, and Chimera never loads the trajectory. The old trajectories from gromacs 4.5.5 load with out any problems. Has anyone else experienced this? I am using 64 bit Chimera 1.8.1 on a dual quad-core Mac Pro running OS 10.6.8. The simulation has ~50000 atoms of protein, lipid, and water and is 1ns long. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

2 1

selection color
by George Tzotzos 26 Mar '14

26 Mar '14

Hi everybody, I’ve conducted Principal Component Analysis on a trajectory and generated an ensemble of structures (see attachment, pc2.pdb). There should be a way of coloring (occupancy?) the most mobile regions of the protein (e.g. residues 67 - 72). I haven’t found a way to do this. Any help would be much appreciated. Best regards George

2 3

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

2 1

(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

2 1

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

3 4

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

3 2

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

2 1

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

2 1

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

2 1

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 **********************************************

2 1

'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

2 2