December 2021 - Chimera-users - RBVI Mailing Lists

Chimera on RDS Servers farm
by ROTH Stephane (DNUM) 09 Dec '21

09 Dec '21

Hi, We want to use Chimera on RDS Windows Server (Windows Server 2012). Its possible to use it on this environment ? What is the system recommendation to windows platform ? Best Regards, -- Cordialement, Stephane Roth 03 68 85 11 94 Chef de Projet / Ingénieur Systèmes Direction du Numérique Université de Strasbourg

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aPNG
by Frank Irby 07 Dec '21

07 Dec '21

I produce high quality Animated PNG files and it takes a lot of juggling different computers to accomplish.Is there a way to simply chose APNG from the movie recorder output pulldown menue?Would there be a plug in for that? My animations can be found at:https://www.deviantart.com/mandelscape/gallery/24158715/molecular Thank you Sent from Yahoo Mail on Android

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Re: [Chimera-users] Question about Chimera Fit in Map
by Tom Goddard 06 Dec '21

06 Dec '21

Hi Rakesh, Chimera Fit in Map and also the measure correlation command by default only compute the cross-correlation within the displayed envelope of the first map. So it should give the masked value you are looking for, although the actual value will depend sensitively on the surface level of the first map that you choose since that will control which grid points near the boundary of your fragment are included. There is no right answer about how tightly to mask and since the correlation value is so sensitive to that it is not too meaningful to try to compare correlation values although people do it anyways. Check out the measure correlation and fit in map docs for more details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correla… https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.h… Tom On 12/6/2021 5:09 PM, Rakesh Ramachandran wrote: > Sorry, what I meant was say I am fitting a fragment into a large map, > the cross correlation should be calculated only around the fitted > region of the fragment, that is any voxels outside the fragment > location should not be taken into account in the cross-correlation score. > > I need this because I am fitting fragments of different sizes into a > map and I tend to get quite similar cross correlation scores even > though principally it should. > > On Mon, Dec 6, 2021 at 5:03 PM Tom Goddard <goddard(a)sonic.net > <mailto:goddard@sonic.net>> wrote: > > Hi Rakesh, > > I don't understand what you mean by "length normalized by > masking". Chimera can compute cross-correlation using the Fit in > Map panel. If you are fitting an atomic model to the map it needs > to simulate a map from the atomic model since correlation is > between two maps. You do that using the "Use map simulated from > atoms" option in the Fit in Map panel Options pane. > > Tom > > > On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote: >> Hi Tom, >> I am using Chimera Fit in Map for EM fitting. Though it does >> fit well, I want to calculate a cross correlation score based on >> the model map size, that is the cross correlation should be >> length normalized by masking the rest of the map. >> >> -- >> Regards >> Rakesh Ramachandran > > > > -- > Regards > Rakesh Ramachandran

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Re: [Chimera-users] Question about Chimera Fit in Map
by Tom Goddard 06 Dec '21

06 Dec '21

Hi Rakesh, I don't understand what you mean by "length normalized by masking". Chimera can compute cross-correlation using the Fit in Map panel. If you are fitting an atomic model to the map it needs to simulate a map from the atomic model since correlation is between two maps. You do that using the "Use map simulated from atoms" option in the Fit in Map panel Options pane. Tom On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote: > Hi Tom, > I am using Chimera Fit in Map for EM fitting. Though it does fit > well, I want to calculate a cross correlation score based on the model > map size, that is the cross correlation should be length normalized by > masking the rest of the map. > > -- > Regards > Rakesh Ramachandran

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Error when starting Chimera
by vaishnavy chaurasia 03 Dec '21

03 Dec '21

How I fix it.... Please help... Please it's urgent

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Re: [Chimera-users] mRNA Structure
by Elaine Meng 03 Dec '21

03 Dec '21

> On Dec 3, 2021, at 6:44 AM, SANDOVAL, KENNETH <K.SANDOVAL1(a)nuigalway.ie> wrote: > > Hello, > I have a predicted secondary structure of an mRNA molecule. I am interested in trying to visualize this with UCSF Chimera. But I'm unsure what file format the program accepts for this? Does it need some sort of mRNA equivalent of a .pdb file? > Thank you, > Kenneth Hello Kenneth, The recommended address for Chimera questions is chimera-users(a)cgl.ucsf.edu CC'd here. By secondary structure I'm guessing that you mean the base-pairing pattern, and not actually 3D atomic coordinates. For Chimera you would generally need 3D atomic coordinates, most commonly in PDB format. If that is really what you have (base-pairing information only), then here are two ideas for building a 3D structure in Chimera using that information: (1) The RNArtist plugin to Chimera - quite extensive, has a lot of nice features, needs to be downloaded separately: <https://github.com/fjossinet/RNArtist> <https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html> (2) The "rna" command in Chimera can also build models but much more roughly. See "rna model": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

Hi Byrne, I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html Tom Model from gltf export from linked ChimeraX example > On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello Tom, > > Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. > > But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. > > The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! > > Thanks again, > > Byrne > > >> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >> >> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >> >> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >> >> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >> >> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >> >> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >> >> Tom >> >>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>> >>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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UCSF software cannot be opened normally
by 免孑 02 Dec '21

02 Dec '21

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.dae export for ChimeraX
by Byrne Pedit 02 Dec '21

02 Dec '21

ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.)

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Curiosity regarding amino acid category in UCSF chimera
by Prathvi Singh 01 Dec '21

01 Dec '21

Hi, In UCSF chimera, when I go to Select > Residue > Amino Acid Category > Hydrophobic, the LYSINE residues also get selected. However, according to the Kyte-Dolittle scale, LYSINE is a fairly hydrophilic residue. Is there any specific reason why chimera lists them as hydrophobic residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Chimera-users December 2021