- Chimera-users - RBVI Mailing Lists

Questions about IMOD files in Chimera software.
by 박시훈 09 Dec '21

09 Dec '21

Dear chimera-users community, I have questions about opening IMOD files in Chimera software. Can I open the IMOD files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover, the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera? Best regards Si Hoon Park

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Selecting residues from one chain
by Joao M.C. Teixeira 09 Dec '21

09 Dec '21

Hi, I am a bit confused on how to select residues from a chain. This is the command I am trying:

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Chimera error at start-up
by Hernando J Sosa 09 Dec '21

09 Dec '21

Dear Chimera, I cannot open Chimer anymore in a computer (Windos10 64) where it was running until yesterday. I tried with no success reinstalling the program and installing the latestChimera daily release. The error that I get at startup says: [cid:cfb0a3aa-9306-42f0-bfd0-328d433ceb1e] If I start in debug mode I get the following error in a command window: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 How can I resolve this issue? Thanks Hernando ___________________________________

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Mismatch between display and saved image
by Visvaldas K. 09 Dec '21

09 Dec '21

Dear all, I get a very odd mismatch between what is displayed and what is saved as a png image. I am attaching two figures, and you can probably guess what I want. Of course I will try this in ChimeraX if I am not able to fix the figure, but the image took quite some work, so I'd hate redoing it... Or I could use screenshot I guess... But certainly this is some sort of bug. I'm using Chimera 1.15 on MacOS 12.0.1. Thank you, Vis

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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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Minimization on complex
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 29 Nov '21

29 Nov '21

Hi, I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results. So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?). Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand. Hope someone can help me, thanks.

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Get Minimization Energy
by Leonard Zhao 26 Nov '21

26 Nov '21

Hello, I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? Thanks, Leonard Zhao

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question regarding UCSF Chimera FindHBond feature
by Aditi Laddha 25 Nov '21

25 Nov '21

Hello, I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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how to rectify error No MMTK name for atom
by Smriti Singh 2018RBT01 24 Nov '21

24 Nov '21

hello administrator, I am trying to minimize the Nucleotide sequence (DNA aptamer) through chimera. While performing energy minimisation steps, Chimera error "No MMTK name for atom 'HO5' in standard residue 'DA' showed. Please let me know how to rectify this issue. With warm regards Smriti Singh Research Scholar Department of Biotechnology MNNIT Allahabad

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Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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Chimera compatibility with Window 11
by HK Haris 23 Nov '21

23 Nov '21

Hi, Please confirm can I download the following version of Chimera on my laptop which is operating on Windows 11. Microsoft Windows 64-bit chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 152310162 bytes MD5: 6a68ab33f35a298059b9ef89f6372cfc Dec 18, 2020 Instructions <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html> Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/> Runs on Windows 7 or later. *Best Regards,Dr. HIRA KHALID* Associate Professor Chemistry Forman Christian College University (A Chartered University) Lahore, Pakistan.54600 Ph: 042-99231581-88 x: 562 www.fccollege.edu.pk ........................ HEC APPROVED Supervisor Advisor ACS Punjab Associate member RSC Member & Ambassador Chemistry ACS Member AOCS Life-time CSP Member IUPAC Young Fellow

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FAD Topology/Parameter Files
by Zehra GÜNEŞ 22 Nov '21

22 Nov '21

Dear all, I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have? Thanks in advance, Zehra Güneş

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chimera, H-bonds
by Rio Aquarius 19 Nov '21

19 Nov '21

Dear Developer, I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want?

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How to smooth trajectory?
by Saikat Pal 15 Nov '21

15 Nov '21

Dear all, I want to make a movie using chimera. So, what are the steps to smooth the trajectory? Thanks and Regards, Saikat Pal

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Chimera Launch Error
by Cassidy Terrell 12 Nov '21

12 Nov '21

Hello, A student in my course (cced here) is trying to open Chimera 1.15 and this is the error message that appears: "chimera exited abnormally; the exit code was -1073741819. Use the --debug command line option for the full error message." We cannot open the program, which mean we cannot get to the command line. Thoughts about how to proceed? We have already removed/uninstalled previous version and re-downloaded new one. The same messages appears each time. Best Cassidy -- Cassidy R. Terrell, Ph.D. (she/her/hers) Assistant Professor, Biochemistry Center for Learning Innovation | University of Minnesota | Rochester 300 University Square | Rochester, MN 55904 *Always believe something wonderful is about to happen*

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Regarding publication using Chimera.
by Kavya Pandya 11 Nov '21

11 Nov '21

Dear Sir/Ma'am, I am a PhD scholar at the Institute of Advanced Research, India. I have been using the free version of Chimera for the last few days. I wanted to ask if I could publish the images created in Chimera using that free version by citing it appropriately using the citation provided on the website or do I need to buy the license to publish? Would you please guide me for the same. Thank You Kavya PhD Scholar -- Disclaimer : This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) /addressee and may contain confidential and privileged information. If you are not the intended recipient/addressee, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email or any action taken in reliance on this email is strictly prohibited and may be unlawful. The recipient /addressee acknowledges that Institute of Advanced Research (IAR) are unable to exercise control or ensure or guarantee the integrity of/over the contents of the information contained in e-mail transmissions and further acknowledges that any views expressed in this message are those of the individual sender and no binding nature of the message shall be implied or assumed unless the sender does so expressly with due authority of Institute of Advanced Research (IAR). Internet communications cannot be guaranteed to be timely, secure, error or virus-free, thus the sender does not accept liability for any errors or omissions. Before opening any attachments please check them for viruses and defects.

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