- Chimera-users - RBVI Mailing Lists

Question about movie in powerpoint
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Dear Chimera team who is always giving the best support, I have a question regarding movie playing in power point and hope you can help. I'm setting a power point presentation and want to play some movie (.avi MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; however, if I'm in the presenter view mode it does not play and gives me a black screen. I tried to re-insert the movie, change the view size, put everything in the same place...but none of these solved the problem. The funny thing is that other movies bigger in size can play fine in the presenter view mode. These have the same format (avi MSMPEG-4v2) and created using the same program. Do you have any idea how to resolve this issue? Any advice is more than welcome. Also, I noticed that sometimes the movie, that is known to be working fine, does not work for unknown reason. Especially in the case of 2 movies in the same slide. Any tips to have two movies in the same slide to work in a more robust way is really appreciated. Really appreciating your help, thanks; Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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About Amber residue number renumbering
by Francesco Pietra 22 Oct '08

22 Oct '08

Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra

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Error when fetching pdb by ID
by Kenward Vaughan 22 Oct '08

22 Oct '08

Hmm... is this my system or outside it? I'm at home behind a firewall and have never seen such an error before. I'm not sure where I should look for an answer... Fetch by ID. The error log: Opening 1ai2 Error reading 1ai2: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') Done opening 1ai2 It doesn't fail at work, so I'm suspicious of my home network. ??? Both my workstation and gateway/firewall are Debian/Sid boxes. What port is the call made on?? Thanks for any ideas! Kenward -- ."^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Chair, Physical Science Department |,;| Bakersfield College / ', \ 1801 Panorama Drive / o O \ Bakersfield, CA 93305 (oOoOOoOo) http://www2.bc.cc.ca.us/kvaughan ---========--- ???$$MM$$???

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Fwd: Pruning pdb graphically
by Francesco Pietra 21 Oct '08

21 Oct '08

Hi Elaine: LEaP does not understand capping, with a pdb file that Chimera understands perfectly. I have asked for light at both the Amber and Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H to the terminal/beginning and OXT to the terminal/last. Moreover, it tries to join the first ACE with last NME. I have not tried separating the capping residue with TER. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Oct 21, 2008 at 10:34 AM Subject: Re: [Chimera-users] Pruning pdb graphically To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: I had fully protonated histidine and left the chain amino group of lysine in basic form! No excuse for that. Now the charge is 5.0000 so that I expect that dockprep (avoiding add-h!) will work. In my (brief) experience, Chimera is an excellent tool also for capping, especially if Add-H is revised for the cases of capped residues. In some cases (12 residues capped in my case) that is important. Also because I want to run MD under various pH conditions, so that capping will change (constant pH MD is not possible with Amber under explicit medium conditions). That Amber has updated to PDB rules is good news. Perhaps I was so suspicious because a few days ago I found a bug with the latest version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop): the N-hydrogen names for LEU as first residue are written incorrectly. A revised ambpdb is forthcoming. Regards francesco On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > After looking at more parameter files, I now believe that Amber and PDB atom > names in standard residues, including hydrogens, are the same. My previous > information was old (I haven't run Amber for 10 years!), sorry about that. > You would still need to worry about correctly naming any atoms changed or > added with Build Structure, though. > > Besides the Amber *lib files mentioned before, you can also look up the > standard atom names in the links from this PDB page: > http://remediation.wwpdb.org/downloads.html > > Elaine > > > On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote: > >> I forgot to mention that usually you don't need to worry about the atom >> names, as Add Charge knows which PDB names go with which Amber >> names/charges, and AddH uses the standard names. >> >> I think you only have to worry about the names of atoms that were changed >> or added "manually" in Build Structure, and if the nonhydrogen atoms have >> the standard names (PDB = Amber for nonhydrogen atoms in standard residues), >> AddH will use correct names for the hydrogens later added to those atoms. >> If you use hydrogens added by Build Structure, however, you have to fix >> their names. >> >> Elaine >> >> > >

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Residue Accessibility
by Luis Alberto Alvarez 21 Oct '08

21 Oct '08

Hello, I am trying to calculate the relative surface accessibility of residues (It will come to getting the solvent accessibility I guess) and the only information I found is from a post in the mailing list dating to 2005 ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html)I am just wondering if there is anything new in this front or I should just follow the 2005 instructions. Thank you -- Luis Alvarez alvarez(a)lcp.u-psud.fr Laboratoire de Chimie Physique Université Paris-Sud à Orsay microscope: 01 69 15 30 31 (80% du temps) bureau: 01 69 15 56 15

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Presets and multiple structures
by James Nettles 16 Oct '08

16 Oct '08

Something that often comes up is that I have some number of aligned protein structures with nicely color coded secondary features and specific side chains. I then want to fit another molecule in this same space and apply a "preset" graphic mode to the new structure without undoing the previous molecular views. I expect this is possible, but I haven't gotten it to work yet. I've tried making only my molecule of interest "active" in the Model Panel, but the preset still effects everything. I'm using Alpha build 2557 2008/09/13 at the moment. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) ________________________________________________________

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Building ACE, NME (peptide caps)
by Elaine Meng 16 Oct '08

16 Oct '08

On Oct 16, 2008, at 6:22 AM, Francesco Pietra wrote: > Hi Elaine: > Thanks. > Is it possible with Chimera to cap the the protein termini (once the > work below is carried out) with ACE and NMA residues? I have no > experience with such a procedure. > francesco Hi Francesco, I wouldn't recommend doing it in Chimera. If you are using AMBER anyway, do it with that program. In Chimera, you could do it by using Build Structure (under Tools... Structure Editing), Modify Atom section. It would take several cycles of atom modification, being careful to name the residues ACE and NME and to give the atoms the correct types and names as you build out. For the first atom in the new residue you would use "change modified residue's name to ACE" (or NME) and then for the rest of the atoms in the residue, leave the residue name unchanged. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht… > Then, because the names of hydrogens added while building aren't standard for those residues, either delete all the hydrogens and re- add them using AddH, or use Modify Atom to change the hydrogen names to what AMBER expects (shown below), or just write out the file and use a text-editor to change their names. It is easy to make mistakes in this long process. In addition, I just found a bug where addh still thinks the first amino acid has a free N-terminus even though it is capped by ACE, so if you use addh, you would then have to delete the two hydrogens on the first amino acid's nitrogen and then use Build Structure (Modify Atom) on that nitrogen to make it trigonal and get one hydrogen back, and then change the name of that hydrogen to H. THEN you would get correct charges from addcharge. The atom names that AMBER (and addcharge) expect: for ACE: C O CH3 HH31 HH32 HH33 for NME: N H CH3 HH31 HH32 HH33 If you are capping the residues to avoid terminal charges on residues that are not really the termini, there is no need to do this. AddH looks at the SEQRES information in the file to decide what is really a terminal residue. If it is not a real terminus (for example, the structure starts at residue 5 because 1-4 are disordered), the residue will still be treated as an internal residue starting with NH-CA- (etc.) not as NH3+-CA-(etc.). The C-terminus is handled similarly, (...)C(=O) if not a real terminus instead of (...)CO2 minus for the real C-terminus. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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imposing symmetry
by Anindito Sen 16 Oct '08

16 Oct '08

Hi I have a density map with symmetry C8. I have docked the monomer crystal structure. I was wondering if there is any way I can put crystal structures in rest of the 7 monomers without doing it manually. Thanks for your reply in advance. Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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error
by Linnemayr Charlotte 16 Oct '08

16 Oct '08

Hello, I have a problem opening a file, I got it from a friend, who also installed chimera recently. On her computer it works nicly. But I get an errormessage and a white window, with some of the files text. I see the model for about 2 seconds, before the window turns white. Do I need an extra plugin?

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Contact mapping
by Beale, John 16 Oct '08

16 Oct '08

Is there a way in Chimera to generate interresidue contact maps for proteins from MD data? Thanks! John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry and Pharmaceutics St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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