- Chimera-users - RBVI Mailing Lists

Axis Of Symmetry
by Catherine Jenifer Rajam Rajendran 06 Jun '17

06 Jun '17

Hi Eric, I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: I am using chimera version 1.11.2. Can you please help me with this? Thanks, Catherine

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measure surface area
by 陈柳青 06 Jun '17

06 Jun '17

Hi! i want measure several selected residues surface area and volume, but in the reply log, it always give the total surface area and volume of the protein, how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate. in addition, the castP server can't give me the pocket i wanted, because it give a bigger pocket than i wanted. thanks in advance！ liuqing chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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extracting real numerical values for steric energies
by Fenton Heirtzler 05 Jun '17

05 Jun '17

Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers. I 've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log". For example, the potential energy values which are returned can be either < 0 or > 0 (!!) If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense. Some advice and instruction would be appreciated. Thanks *Dr. Fenton Heirtzler* ------------------------------- Phone: +1-301-312-5145 LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>

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Chimera files to be read in Pymol?
by Tuli Mukhopadhyay 05 Jun '17

05 Jun '17

Hello, Is there a (simple) way to read Chimera session in Pymol or vice versa? Tuli -- -- Tuli Mukhopadhyay Department of Biology Indiana University Simon Hall MSBI, Room 220C 212 S. Hawthorne Drive Bloomington, IN 47405-7003 Phone 812.856.3686 Fax 812.856.5710 sumukhop(a)indiana.edu | Tuli Lab Webpage <http://www.bio.indiana.edu/~tulilab/> | @TuliLab <https://twitter.com/TuliLab>

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Re: [Chimera-users] Chimera how to question
by Elaine Meng 05 Jun '17

05 Jun '17

> On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok(a)ualberta.ca> wrote: > > Hello, > Is there a way to delete a set of residues in the beginning of the sequence, so these residues disappear from the sequence in the pdb file? > I am working on the structure-base alignment and the exogneous residues in the protein sequence (eg. affinity-tag) interfere with the nubmering of the endigenous residues. > Thank you > Egor Hi Egor, Of course you can delete atoms. You can select them and then use menu: Actions… Atoms/Bonds… delete, or you can use the “delete” command ...either with selection (delete sel) or with some other kind of specification of what you wanted to delete, e.g. delete :1-20.A ...to delete residues 1-20 of chain A. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> Maybe in your case it would be easiest to use the sequence window (Favories… Sequence) to select the set of residues you want to delete by dragging a box around them, and then using the menu or command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> However, this will not change any sequence numbering. Chimera just uses the numbers that are in the input file. Sometimes but not always, affinity-tag residues are given negative residue numbers in the input file. If you want to renumber residues, see menu: Tools.. Structure Editing… Renumber Residues, or the command “resrenumber”: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html> Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure that they will be answered. 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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failure to add-H to quaternary C
by Francesco Pietra 05 Jun '17

05 Jun '17

pdbqt from autodock-vina -> pdb with chimera -> addH with chimera. Chimera fails (systematically) to add one H to a quaternary carbon of the diterpenoid. avogadro (which does not understand pdbqt) does the addH job correctly from chimera-savedpdb. Should Eric be interested, I could send (privately) the file best regards francesco pietra

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surfaces
by P. Buscemi 01 Jun '17

01 Jun '17

Elaine, A conceptual question. I'm trying to work with surfaces - large flat surfaces that proteins and polymers might adsorb. Think fibrinogen on medical devices. Chimera does not seem to like large surfaces in box. IF a portion of the surface slips outside the box, it goes to the other ( abnormal side). Constraining a portion of the surface does not help. Constraining all of the surface has not been tried. I'd like to use a box to keep the solvent and protein local. Any suggestions on how to handle this, or point me to a URL ? Can I constrain only in two directions perhaps ? or use a box size 30,30, infinite ? Best Paul Buscemi, Ph.D.

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addaa
by ‪farial tavakoli‬ ‪ 31 May '17

31 May '17

hi I am new chimera user. I wanna add an amino acid before the lys 12 in N-ter of my protein sequence but i dont know how should i type its command. I read the tutorial but just found adding an amino acid in C-ter. is there anyone who ca help me? I would be grateful if anybody helps me in the new residue's conformation ? thanks alotF.T

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membership
by P. Buscemi 31 May '17

31 May '17

Dear Chimera, I had registered as a member, but when I send or even return emails, I get placed on "hold till approved" waiting list. Can this be corrected ? Regards, Paul Buscemi, Ph.D. UMN

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Re: [Chimera-users] Help in docking with Chimera
by Elaine Meng 30 May '17

30 May '17

Hi Zahir, It might just be display (like one bond not shown) without any affect on the calculations because of the format of the file output by Autodock Vina. Autodock Vina is not our program, so we cannot control the output format. However, impossible for us to tell if that is the issue unless you send us an example file or files. You could use menu: Help… Report a Bug and include brief explanation and your email address and attach the example file or session that shows the problem. Keep in mind it might not be a Chimera bug. Best, 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 25, 2017, at 1:13 PM, Md Zahir Uddin <m_uddin(a)u.pacific.edu> wrote: > > Hi, > We are seeing a new problem in the docking of our peptides. After docking of our peptides using Autodock Vina function in Chimera, we are seeing in the output that the peptides are broken (splitting into two parts) at the protein's binding site. Our peptides are 8 amino acid long (one is 5 amino acid cyclic peptide by disulfide bond) and we prepared the peptides using the Build Structure function in Chimera and then dockprep & minimize structure. > Can you please help me in this? We would really appreciate your help. > Thanks, > Zahir >

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it might be nice to have the code on github
by Francois BERENGER 30 May '17

30 May '17

Hello, Sometimes, I want to dig into the source code of chimera, to know the implementation details of something. For projects hosted on github, this is easy. Also, in my experience, github fosters contributions from users. That being said, I did not use chimera for 2/3 years. I am glad to see that it is even more powerful and easy to use than before. The tutorials are also excellent (like: Preparing Molecules for DOCKing) and the .bild format that chimera can read in is extremely programmer friendly (it is so easy to generate). My love for chimera (over pymol) is renewed. Regards, Francois.

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high resolution animation in chimera
by Gangwar, Shanti P. 26 May '17

26 May '17

Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal ******************************************** Shanti Pal Gangwar, Ph.D Dept of Pharmacology and Toxicology University of Texas Medical Branch Galveston, Texas-77555 Mobile: +1-409-256-8400 Email: spgangwa(a)utmb.edu

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custom presets not appearing
by Healey, Joe 26 May '17

26 May '17

Hi Chimera Team, I've defined a custom preset (implemented in both python and 'chimera language'), and I've placed in a folder which I have directed the custom preset dialogue to. E.g, in /Users/joehealey/Documents/Warwick/PhD/Structural_Work/Scripts/Presets/ I have the following script (chimera implemented one): # Goodsell.cmd ############################################################# # # # Chimera syntax commands for use as a preset. Sets the # # depiction in the style of David Goodsell. # # (The PDB Molecule-of-the-Month style). # # # ############################################################# # Create lower resolution surface models: sym surfaces all resolution 2 # Hide dashed bonds that may appear though the surface setattr g display false # Apply silhouette edging and colouring set silhouetteWidth 3.5 set silhouetteColor black set silhouette # Set depth cueing depth and colour set dcColor black set dcStart 0.5 set dcEnd 1.5 # Set background transparency set bgTransparency # Set lighting mode for flat rendering lighting mode ambient # Hide ribbons ~ribbon # Set surface colour color red ,s # Make sure molecule is in focus focus However, as per the documentation ( http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets ) the preset doesn't appear in the presets menu. I can execute the script as normal with exec, and it works and has the desired effect, but I'd like it to be in the preset menu if possible? I suspect I'm missing something? Thanks, 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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Non-canonical H-bonds
by Markus Heller 25 May '17

25 May '17

Hi, Are there any plans to extend the H-bond detection functionality to include non-canonical H-bonds, e.g. C―H...A (A = N, O, S), D―H...π (D = N, O) and C―H...π varieties? Thanks Markus

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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 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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