- 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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