May 2017 - Chimera-users - RBVI Mailing Lists

Surface function question
by Frances Shepherd 25 May '17

25 May '17

Hi, I am modeling a rotavirus VP7 protein using Chimera (PDB 3fmg), and I’m having trouble with the surface function. This protein is modeled with a monoclonal antibody conjugated to it, which I am able to hide. But when I show the surface for just the VP7 protein, there are gaps in the surface. The gaps appear to be in the areas where the VP7 protein comes into contact with the antibody. Is there a way to fill in these gaps? I’ve seen other publications that have used this protein (same PDB number), but the surface is complete. If you have any suggestions, I’d appreciate it. Thanks! -Frances

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Input from Avogadro, solvation.
by Paul Buscemi 24 May '17

24 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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