- Chimera-users - RBVI Mailing Lists

Input from Avogadro, solvation.
by Paul Buscemi 23 May '17

23 May '17

Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB

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ImportError: libGL.so.1: cannot open shared object file: No such file or directory - Error shown when trying to run xdg-setup or chimera (Linus Ubuntu)
by Hannah Goldberg 23 May '17

23 May '17

Hello, I have installed the 32 bit version of Chimera-1.11.2, and I am having difficulty getting the icon on the desktop and launching. I get the following error: ImportError: libGL.so.1: cannot open shared object file: No such file or directory I have tried installing the libgl1-mesa-glx package and have even tried Idconfig. I can't find any errors similar to this anywhere. Please help! I can give more info if needed - I will be at my desk all day trying to install this Icon! -Cheers, Hannah -- *Hannah Goldberg* Case Western Reserve University Class of 2019 Physics B.S. Geological Sciences B.S. Undergraduate Research Assistant- Theoretical Biophysics

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FW: chimera download
by Williams, Joanne 23 May '17

23 May '17

Here is another inquiry for user help. From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 18, 2017 at 10:53 PM To: Joanne Williams <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download Hello Sir will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format??? What format I can take of my ligand to load in Chimera?? On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> wrote: My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN. is that OK Regards On Thu, May 18, 2017 at 7:41 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Apologies, I was waiting to hear back from you. Please send me the following information: 1. Full Name: 2. School Name or company name that you are affiliated with: Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Wednesday, May 17, 2017 at 10:35 PM To: "Williams, Joanne" <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: FW: chimera download Hello Sir I know I am disturbing you, but I asked for Chimera free trial (if possible). waiting for your kind response On Thu, May 11, 2017 at 8:12 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Ok, let me know which school you are affiliated with and I will see about getting you access. Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 11, 2017 at 2:28 AM To: "Williams, Joanne" <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download I am associated with a school and need for my project (that small work that I am left with. Any chance? On Wed, May 10, 2017 at 8:23 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Thank you for your inquiry. I am sorry, we do not offer a free trial period. Are you affiliated with a school or company? Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Monday, May 8, 2017 at 1:22 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: chimera download Hello Sir Can I download chimera as free trial on my laptop. windows 7, 500GB, 32bits???

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Re: [Chimera-users] question about report of hydrogen bonds that Chimera produces
by Elaine Meng 22 May '17

22 May '17

> On May 22, 2017, at 2:43 PM, Roberto Garza-Lopez <RAGL4747(a)pomona.edu> wrote: > > Hi Elaine, I saw your name in the chimera group in a conversation on line and I was wondering if I can ask you a very simple question. > > I used FindHBond under Structure Analysis to generate the document with all the hydrogen bonds for protein PDB# 1aac (amicyanin). See attached. > > I noticed that for some H bond distances the report includes both A---B and B---A like in the cases below which of course have the same distance. > > <image001.png> > <image002.png> > > <image003.png> > <image004.png> > > However for other cases like the one below, I do not find the reverse, meaning LEU 80.A O à VAL 43.A N. WHY IS THAT? > > VAL 43.A N LEU 80.A O no hydrogen 2.815 N/A > > Thanks, > Roberto Hi Roberto (CC-ing chimera-users(a)cgl.ucsf.edu , recommended address for Chimera questions) It is because the lines list H-bond donor before H-bond acceptor. Some groups can be both donor and acceptor, but some groups (like carbonyl O) can only be acceptors, and some can only be donors. The results include a title row which explains what the columns mean. For example, opening 1aac and running findhbond gives: #0, chain A: amicyanin 1aac opened Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: #0 1aac H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ASP 1.A N HOH 297.A O.1 no hydrogen 3.132 N/A ASP 1.A N HOH 297.A O.2 no hydrogen 3.093 N/A ASP 1.A N HOH 297.A O.3 no hydrogen 3.360 N/A LYS 2.A N LEU 62.A O no hydrogen 2.776 N/A [… etc. …] 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

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Some questions about the software
by Lizar wang 22 May '17

22 May '17

Good morning, When I open Chimera11.1.2, it shows that" Chimera existed abnormally; the exit code is 1. Use the -- debug command line option for the full error message." What should I do? I cannot see the interface, just this error window.Thank you. User 发自我的 iPhone

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FW: UCSF CHIMERA
by Williams, Joanne 22 May '17

22 May '17

Hello, I am not sure if you already responded to this email below or if I forwarded it even. Just in case, please read below. Thank you, JoAnne From: Manjunath gl <glmanjunath.iitm(a)gmail.com<mailto:glmanjunath.iitm@gmail.com>> Date: Monday, May 15, 2017 at 11:02 PM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: UCSF CHIMERA Hi Please let me know can I use this software for geomaterial modeling? Thanks Dr. Manjunath

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Using vop to cover a whole molecule
by Pradeep Pallan 22 May '17

22 May '17

Hi All, I would like to know how to extend an e-density map in y or z direction. Here is my case: The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis? Thank you! -- ------------------------------------------------------------------- Pradeep Pallan

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Open a file with Windows 10 Command Prompt
by Mark F Rosenberg 20 May '17

20 May '17

For Mac in Terminal I can type Chimera and the file name to open a volume etc which is very useful. In Windows 10 for Command Prompt Terminal I cannot seem to achieve this. I thought if I added "open" after the executable I could achieve this but it does not appear to work. Please can you advise? Many thanks. Mark

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Re: [Chimera-users] Help in docking with Chimera
by m_uddin 19 May '17

19 May '17

Hi Dr. Elaine, Got it. It worked. Thanks a lot. Zahir -------- Original message --------From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: 5/19/17 1:01 PM (GMT-08:00) To: Md Zahir Uddin <m_uddin(a)u.pacific.edu> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Help in docking with Chimera Hi Zahir, Based on the error message, all I can suggest is to make sure that the location for output files is somewhere you have permission to write and read files. I.e in the Autodock Vina dialog, there is an “Output file” box. Next to it is a button “Browse” which you should click and then navigate in the resulting dialog to set the location to some folder in which you are sure that you have permission to read and write files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> 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 May 19, 2017, at 11:46 AM, Md Zahir Uddin <m_uddin(a)u.pacific.edu> wrote: > > Hi, > My name is Zahir. I am a Ph.D. student of Pharmaceutics at University of the Pacific. Recently in our lab we were trying to do some docking of our peptide ligands on the human Aminopeptidase N (CD13) receptor using the Autodock vina option in the Chimera. But everytime we are getting an error message and the docking stops. I am attaching the error message here. We did dockprep of the receptor and ligands. And we tried to do the docking with both pdb and mol2 files. > > We would really appreciate your help in this regard. > Thanks, > Md Zahir Uddin

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Help in docking with Chimera
by Md Zahir Uddin 19 May '17

19 May '17

Hi, My name is Zahir. I am a Ph.D. student of Pharmaceutics at University of the Pacific. Recently in our lab we were trying to do some docking of our peptide ligands on the human Aminopeptidase N (CD13) receptor using the Autodock vina option in the Chimera. But everytime we are getting an error message and the docking stops. I am attaching the error message here. We did dockprep of the receptor and ligands. And we tried to do the docking with both pdb and mol2 files. We would really appreciate your help in this regard. Thanks, Md Zahir Uddin <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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saving rotated volume
by Reginald McNulty 18 May '17

18 May '17

Dear Users, I have two objects open in Chimera. One is a .bild file that shows axes x,y,z. The other is a volume of a virus with a tail. I used “activate only” to manipulate the volume relative to the axis.bild object. After rotating the virus to align the tail to the Z-axis, I try to save the map but it’s always back in the original position when I re-open it in Chimera. Is there a way to save this transformed map? -Reggie

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morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

For this one, I found a solution: >Also is there a commandline version to access the conformations and to re-run >kdssp on each interpolated conformation? I read you need the perframe command >for that. Does anyone have a working example ? There is a good example (and several more) in http://www.cgl.ucsf.edu/chimera/animations/animations.html (for instance leucyl-tRNA.cmd ) However, I still don't know how to re-open a morphing menu that disappeared and the per-frame kdssp is not yet clear to me yet. Thanks, Lothar

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morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

Hi, I used Tools->Structure Comparison->Morph Conformations and it worked well. However, I somehow lost the menu that opens up after the morph is complete. Well, I cannot find it. How can you re-open it to run through the morphed conformations again ? Also is there a commandline version to access the conformations and to re-run kdssp on each interpolated conformation? I read you need the perframe command for that. Does anyone have a working example ? Thanks, Lothar

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reading in electron density map H32 vs R32
by Christine Gee 17 May '17

17 May '17

Hi, I have a structure in the space group H32. I wrote out a map, which lists it as space group 155. I was wondering if chimera would read that in as space group H32 (R32:h) or as R32 (R32:r). Regards Christine

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Open file interface suggestion
by Dan Kool 15 May '17

15 May '17

Hello, I have been using your software for a while. I love the features and general user interface. There is one thing that drives me nuts, though. The side-by-side list interface when I go to open files.A window-based one would be much easier. Is there an option for that that I am not seeing? If not, I suggest adding the option. Thank you for your software! Best, Dan ---------------------------------------------------- Daniel Kool Graduate Research Assistant, Jernigan Lab Bioinformatics and Computational Biology Iowa State University *kool(a)iastate.edu <kool(a)iastate.edu>*

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error or bug
by Arthur Szabo 15 May '17

15 May '17

Continuing my earlier question. I tried the suggestions sent to me neither split nor surfcat seemed to work. After some attempts I received this window and reported the bug [cid:image001.png@01D2CD74.26A7D780] I then tried to use molmap and I did get a surface and saw how by moving the cursor in the molmap window I could get the surface to progressively disappear leaving the selected domains that were colored previously. The surface was for the entire protein, one of the models #0. I could also change the surface color. Then I went looking at some of the tabs on the molmap window and cannot describe the sequence, but ended up with another window that I eventually found out was for visualizing Cryo EM maps. Now I have a surface that is multicolored and looks like jelly beans. Somehow perhaps by selecting one of the models from the command lines, (#0) I was able to pull out a surface of the entire molecule, rotate it etc, and progressively remove the surface, til the selected domains remained. Stuck!!! This is one model: [cid:image003.png@01D2CD79.3D09E040] [cid:image004.jpg@01D2CD79.3D09E040] HERE IS ANOTHER which is #1 or #2 [cid:image005.jpg@01D2CD79.3D09E040] [cid:image006.png@01D2CD79.3D09E040] Arthur Szabo

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Visualizing specific atoms in autodock-vina output
by Francesco Pietra 15 May '17

15 May '17

I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand. With command sel #1.1@N z<5 I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1. How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra

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Saving multiscale models only?
by Healey, Joe 12 May '17

12 May '17

Hi Chimera team, Is it possible to save a multiscale model without the atomic coordinates that generated it in the first place? I've seen that the multiscale models can be saved within Scenes, but I'd like to save it as a 'structure' such that I can continue to use it in subsequent sessions. At present, when I close the PDB model that generated the MultiScale map, the map also closes. Thanks, Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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surface transparency animation
by esserlo＠helix.nih.gov 12 May '17

12 May '17

Hi, I am trying to animate a transition of a surface from 100% transparent to opaque. In a test (the real case is more complicated) I did this: open 1hen.pdb # Lysozyme test # Chimera shows a blue ribbon model on gray background surface #0 scolor #0 color green # chimera shows a green surface over a (now invisible) blue ribbon model # According to the manual the following (I think) should work: transparency 80,s #0 # I expected to see the green surface to become 80% transparent and the blue ribbon model to shine through. # No luck. What am I missing ? BTW the page https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/transparency… seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar

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scripting & density
by Dougherty, Matthew T 12 May '17

12 May '17

Hi, I have a dataset, its values are 1-255. I would like to modify the density values using a script. Specifically, I would like to set density values 50-74 & 90-110 to the value of zero. Is there a way to do that using scripting, or do I need to do that using python? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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surfaces
by Arthur Szabo 12 May '17

12 May '17

Working with a structure that has many domains. I would like to show the surface of three of the domains. I have hidden the ribbon residues of all but the ribbons of three domains. I receive the following error message [cid:image001.png@01D2CB26.2CA19B30] The domains are not contiguous in the structure, but even if I try to show the surface of only one domain I get the same message. And going to the Selection inspector is not helpful since it is not obvious as to how that option assists the surface representation. Over to you Thanks Arthur G. Szabo

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vop scale and vop morph (maybe chimeraX?)
by Oliver Clarke 11 May '17

11 May '17

Hi, When I morph two maps, if they have different mean/sd, I always have to scale the mean and sd of the second map to that of the first, otherwise the morph looks very non-linear - nothing happens until fraction 0.9, and then the morphing happens increasingly fast (so not ideal for visualization). If I normalize one map to the other I get a beautiful, smooth, linear morph. Would it be possible in either chimera or chimeraX to automate this? Either to add an option to vop scale to scale one map directly to the parameters of another (rather than having to use vop measure mapstats) or to have an option for vop morph to put both maps on the same scale? Cheers Oli

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suggestion: if clip planes cross, swap them?
by Oliver Clarke 11 May '17

11 May '17

Hi, Quite often, in aliases and scripts where I am adjusting the clip planes, I get the error “far clip plane placed in front of near clip plane”, or words to that effect. I’ve tried various ways to remedy this but it has to be done on a case by case basis and sometimes I just can’t figure it out. Would there be any possibility for Chimera to rather than triggering an error in such a case, just swap the clip planes when this happens, so the near plane becomes the far plane, and vice-versa? Or is there some other foolproof way to avoid this? I get this error when I want to adjust the hither and yon planes successively - would it be possible to add a command that adjusts them both at the same time, like `section` but with simultaneous independent control over both clip planes? Cheers Oli

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morph map fails with solid representation
by Oliver Clarke 10 May '17

10 May '17

Hi, When I create (using the latest nightly build) a morph between two maps using the “Morph map” GUI, and then I change the representation of the resultant volume to solid, the morph no longer runs, or rather, it appears to run, but the solid volume does not update. This used to work - I used it to create quite a few movies - so I guess it is a bug? Cheers Oli

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symmetrical fit of maps
by Oleksiy Kovtun 10 May '17

10 May '17

Hi all, is there is a way to do symmetrical fit and add symmetrical copies for map to map fitting? The standard symmetrical fitting protocol (measure symmetry. #0...; sym #1 group #0 update true; fitmap...) only works for molecule to map fit. Thank you, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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