October 2016 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Fwd: chimera minimize option
by Jacqueline Vitali 07 Dec '16

07 Dec '16

It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only) How do you fix this? And can you run it with the whole protein selected?

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how to select atom within a rectangular region
by Cherry Dons 01 Nov '16

01 Nov '16

Hi Chimera Developers, This is Dengpan, one of chimera users. I have a question about how to select atoms within a region? For example, I I want to select atoms within a rectangular region x0 to x1, y0 to y1, z0 to z1. Could you please give me a hint how to do it? Thanks. Dengpan Dong -- Department of Materials Science and Engineering, University of Utah

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Headless Chimera Registration Notification
by Healey, Joe 01 Nov '16

01 Nov '16

Hi Chimera Team, For some reason the install I have of headless Chimera as recently started warning me that I'm using an unregistered copy (I have actually registered before via the GUI version installed on my Mac (local machine)). Is there some way I can suppress this message (only purely because it's cluttering the STDOUT in my pipelines and I sometimes want to parse this). Or is there a chimera env variable I can modify to tell it that I am registered? Obviously I can't register in the manner the warning describes, as I'm unable to launch a GUI variant of Chimera on the server I'm using. Thanks! Joe Healey M.Sc. B.Sc. (Hons) 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>

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How I can use extension in chimera
by b.behkamal＠stu-mail.um.ac.ir 27 Oct '16

27 Oct '16

Hello, I need to work with the extension files which is attached. The attached files is related to SSETracer. I didn't know how I can use them in chimera. Would you mind please help me about this matter and say to me the details of work step by step. Thank you very much in advanced. Regards, -- 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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problem regarding saving a file
by gutta ramadevi 26 Oct '16

26 Oct '16

Good day, I am using chimera following tutorials. I saved the processed receptor and ligand files in pdb format.But the files are not being saved.when i open the saved files i am getting the unprocessed receptor and ligand files. please help me to save the files.

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Definition of residues involved in binding ligand
by Maarten Schledorn 26 Oct '16

26 Oct '16

Dear reader, I have a pdb file of a protein with bound ADP and the file contains nothing but atomic coordinates and a few CONECT lines. If I open the file, the residues involved in binding ADP are shown, but I would like to know how Chimera knows this. I assume it is some VdW vicinity/overlap perhaps, or all residues within a certain distance from the ADP molecule, but I would like to know exactly how it is defined. I have tried to look for it in the documentation but haven't been successful so far. Does someone know the answer or a link to where it has been discussed previously? Many thanks in advance! Maarten

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pythonic version of fitmap tool
by Michał Kadlof 25 Oct '16

25 Oct '16

Is there any pythonic way of running fitmap tool? I would like to use it as a function that return parameters that I can assign to variable without parsing the output. I didn't find anything similar in Midas module. -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Re: [Chimera-users] chimera minimization querry
by Elaine Meng 21 Oct '16

21 Oct '16

On Oct 21, 2016, at 2:42 AM, Shumaila Khan <shumailakhan432(a)yahoo.com> wrote: > > Hello, > I am shumaila khan , M.phil student at Quaid-i-Azam University Islamabad, Pakistan. Attached File is my structure and I want to minimize it. But there occurs an error that "Residue #0.1:165.A (ALA/ alanine) should have either atom HN or H, but not both. Kindly please reply me asap and help me out. > Thanks Dear Shumaila, For future reference, you should use the chimera-users(a)cgl.ucsf.edu email address for questions. For the minimization error, it is probably what the message says! I can only repeat the message: the residue should not have both of those atoms that it mentions, so you would need to delete one of them. 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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Chimera-users October 2016