- Chimera-users - RBVI Mailing Lists

presets criteria
by Roberta King 17 Jul '07

17 Jul '07

Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 16 Jul '07

16 Jul '07

Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine

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ValueError: More than 2 coplanar positions specified!
by Mike Gretes 13 Jul '07

13 Jul '07

Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________

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Forward of moderated message
by mailman-bounces＠cgl.ucsf.edu 13 Jul '07

13 Jul '07

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 11 Jul '07

11 Jul '07

Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @<TRIPOS>ATOM section and then a corresponding @<TRIPOS>SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370) > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono

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memory usage
by jean-francois menetret 11 Jul '07

11 Jul '07

It seems that Chimera is not releasing memory easily on our linux PC. Is this a know problem for Chimera ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Chimera and Debian
by Arkadiusz Czader 11 Jul '07

11 Jul '07

Hi, I have a problem running 32 bit linux version of Chimera on Debian64. When I run it, it complains about some libraries. Below I pasted what I get when I type chimera in a terminal window arek@teton:~$ chimera Traceback (most recent call last): File "/home/arek/progs/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "/home/arek/progs/chimera/share/chimeraInit.py", line 231, in init import chimera File "/home/arek/progs/chimera/lib/python2.4/site-packages/PIL/__init__.py", l ine 15, in ? ImportError: libGL.so.1: cannot open shared object file: No such file or directory The library libGL.so.1 is only in /usr/lib. Should it be in a different place? Any help appreciated. cheers, Arek ____________________________________________________ | | __ __ | | Arkadiusz Czader | | | _| | __ | | Department of Chemistry | | | | | | | | | | University of Houston | | | | | | | | | | Houston, TX 77204-5003 | | | | |_|_| | | | Phone: (713)-743-5101 | \ \_| ___ | | | E-mail: aczader(a)uh.edu | \___| |/ | | | | | | | | | | | | |__| |__| | |____________________________|_______________________| ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/

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Re: [Chimera-users] pdb-l: Selecting phytols in Chimera?
by Eric Pettersen 09 Jul '07

09 Jul '07

On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote: > Is it possible to write a selection string that will select all the > phytol substituents in a model? I'm looking at photosystem II. I > would like to select all the phytol side chains of the many > chlorophyll molecules and hide them, so that only the porphyrin-like > chlorin ring structures are visible. Can that be done? Thanks! Morgan Hi Morgan, I think the only direct way is to use the command line (Favorites- >Command Line). This command should do it: ~disp :cla@c=; disp :cla@c?a,c?b,c?c,c?d It undisplays all the carbons in the chlorophyll (:cla@c=) and then redisplays the carbons involved in the porphyrin ring (all of which have 3-letter names that end in A-D). You might want to consider posing Chimera-specific questions to the Chimera users mailing list (chimera-users(a)cgl.ucsf.edu) since there will be more people able to answer there. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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clobbered chimera, can't start from fresh install (help)
by William Jeffrey Triffo 09 Jul '07

09 Jul '07

hello, I changed some of the preferences for the IDLE shell, which produced errors that would not allow IDLE to run (tried to remap a couple of keys). This problem persisted when restarting Chimera. so, I deleted that install (Mac OS X) and re-installed the most recent release, but still produced the errors, and cannot launch IDLE. I went ahead and deleted the files in ~/.chimera, but the errors still occur. Are there any other user-specific files that I can delete that might be causing the problem? I am assuming this is the case, because even a fresh install has the same problem. I submitted a bug report about the IDLE preferences issue I experienced, but am hoping a simple fix might allow me to launch IDLE again. thanks, -Jeff

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occupancy calculation
by bala 09 Jul '07

09 Jul '07

Hello, 1) I want to calculate the occupancy of water around few base pairs in a RNA duplex. I had one query while i was going through the "calculate atomic occupancy" documentation. "For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group" In the options give for this particular calculation, nowhere there is an option to select whether i am interested in WATER or ION occupany. How then chimera calculates the occupancy. 2)I presume that chimera calculates the occupany of say water as follows, if i select a residue, it puts the residue in a grid and calculated the density of water molecule in the grid points in frame. Is this the way it calculates the occupancy. I am not getting how i should differentiate occupancy and density. thanks, Bala

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