November 2016 - Chimera-users - RBVI Mailing Lists

Question: Dock Prep
by wang_q＠tib.cas.cn 14 Nov '16

14 Nov '16

Dear Colleagues, I am a beginner in docking(using DOCK 6.7). I learned from DOCK6 tutorial that I could use UCSF chimera to prepare my inputs file for DOCK6 and I prepared the inputs mol2 format file ( converting from PDB to mol2) successfully indeed. And now I have a question, is there a way that I can use in commend line to convert PDB to mol2 format file in chimera, because I want to use this format conversion function in server. I would be very grateful if someone could help me solve the puzzle. Thanks very much! Aaran 发送自 Windows 10 版邮件应用

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Ribbon outline
by George Tzotzos 14 Nov '16

14 Nov '16

I’m attaching an image generated with Chimera for easy reference. The image was generated using the following commands colordef transblue 0 0 1 .2 color transblue,r :1-125 I’m looking for ways to remove the ribbon black outline which somehow I generated inadvertently. I’m also looking for ways to either (a) change the color of the grid lines or (b) the density of grid lines Any help would be greatly appreciated Regards George

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Chimera/auto dock vina
by Maketansky, Grace M 10 Nov '16

10 Nov '16

Hello, I am contacting you due to an error message that repeatedly gets displayed upon attempt to use auto dock vina through chimera. I have had no issues with running chimera on my mac, however I cannot get auto dock vina to work properly (I attempted to install and input the proper commands but cannot seem to get it to work). Attached is a screen shot of the error that keeps occurring. Any help would be greatly appreciated! Thank you! [cid:BD8D0978-A4C1-41ED-BDAA-54FFB6EA5958@res.enc.edu]

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Surface calculations difficulties
by Sarah Piper 10 Nov '16

10 Nov '16

Hi everyone, I’ve been struggling with getting the structure surface of my molecule shown (actions surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html ), I can’t get all needed surfaces displayed. Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes. A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? Or do the .pdb files have to be in a certain format? I usually get the following errors: "Surface calculation failed, mscalc returned code 2. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html” My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation). I'd appreciate any feedback or reply! Many thanks for your help, Sarah ………………………………………………………………….. Sarah Piper, PhD student University of Queensland, St Lucia, 4072 QLD, Australia Phone: +61 7 3346 2325 Email: sarah.piper(a)uq.edu.au<mailto:sarah.piper@uq.edu.au>

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Measuring SASA of ligand
by George Tzotzos 09 Nov '16

09 Nov '16

I’m dealing with two separate trajectories involving: 1. Ligand A in complex with the monomeric subunit of a given protein A 2. the same ligand in complex with the dimer of protein A I would like to measure the buried (or solvent accessible) surface area of ligand A in both cases. I referred to a relevant posting in the list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012472.html) but I’m not sure how this could apply in the above case. I’d be grateful for any suggestion on how to deal with this type of measurement. Many thanks in advance for any suggestions George

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Help for downloading UCSFchimera
by Rosaura Padilla 07 Nov '16

07 Nov '16

Hello, I am unable to down chimera onto my mac book pro. I get the following message: “Chimera” can’t be opened because the identity of the developer cannot be confirmed. Can you please help me Thank you so much. Rosaura -- *Rosaura Padilla-Salinas, PhD* Research Associate, Yin Lab University of Colorado BioFrontiers Institute Boulder, Colorado Rosaura.Padilla(a)Colorado.edu

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I need SSEBuilder and SSEHunter plug in
by b.behkamal＠mail.um.ac.ir 07 Nov '16

07 Nov '16

> Hello, > > I am a Ph.D. candidate of computer engineering in structural bioinformatic from Ferdowsi University of Mashhad, Iran. I'm working on cryo-em modeling. I necessary need the "SSEBuilder and SSEHunter plug in" in chimera to build the SSEs and continue my work. Would you mind please help me about this matter. > > Thank you very much in advanced. > > _Sincerely,_ -- Bahareh Behkamal Ph. D. Candidate of Computer Engineering Researcher in Structural Bioinformatics Dept. of Computer Engineering Ferdowsi University of Mashhad, Mashhad, Iran

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FW: request for operating delete option
by Williams, Joanne 07 Nov '16

07 Nov '16

Mr. Rama needs help. Please read below. Thanks! jo From: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Reply-To: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Date: Monday, November 7, 2016 at 2:09 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: request for operating delete option Good day, I have two same molecules saved in pdb file. I want to delete one molecule from the saved pdb file. How to do it when i open in chimera software. Iam attaching the concerned file. Please help me how to delete one molecule. Thanking you, G.Rama Devi.

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Upgrade chimera?
by Michał Kadlof 07 Nov '16

07 Nov '16

Hello, is it possible to upgrade built-in numpy in chimera python from version 1.7.0b2 to current version 1.11.2 in close future? This week preferably? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Depiction of backbone CA atoms as spheres
by George Tzotzos 05 Nov '16

05 Nov '16

I’m trying to depict selected backbone atoms as spheres with a smaller vdw radius. Residue side chains should not been shown. I checked the list and found an option that appears to do the job, e.g sel :77-80, 91-94 repr bs @ca vdwdefine +1.0 @ca But this didn’t work for me. Grateful for any suggestions Thanks in advance George

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Chimera-users November 2016