- Chimera-users - RBVI Mailing Lists

by solomon 15 Oct '03

15 Oct '03

Hi, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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how to edit pdb file
by solomon 15 Oct '03

15 Oct '03

dear sir, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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Re: bug? (HETATMs)
by Eric Pettersen 06 Oct '03

06 Oct '03

On Saturday, October 4, 2003, at 10:21 AM, solomon wrote: > when i open a pdb format file like below: > HETATM ................................. > HETATM ................................. > HETATM ................................. > ... > ... > ... > HETATM ................................. > > then I find that all the HETATM type atoms are bonding each other. All > the HETATM need a ter card to split them. As for HETATM type, I think > maybe there is some wrong with chimera. > best regards > gaokeng xiao Dear Gaokeng, As far as know, Chimera will connect HETATM segments of all standard PDB files (i.e. those distributed by the RCSB) correctly. That being said, Chimera has to do a lot of guessing when it comes to connecting non-standard PDB files (which I'm pretty sure is the kind of file you're talking about here). One thing to keep in mind with HETATMs is that they don't necessarily imply a chain break. Also, they are supposed to have CONECT records detailing their connectivity. So for instance, part of PDB entry 1f1j looks like this: ATOM 3688 OG SER B 602 58.714 25.290 29.976 1.00 66.81 O TER 3689 SER B 602 HETATM 3690 C ACE C 701 29.751 29.860 -0.650 1.00 52.20 C HETATM 3691 O ACE C 701 28.552 30.100 -0.812 1.00 55.72 O HETATM 3692 CH3 ACE C 701 30.801 30.183 -1.675 1.00 52.54 C ATOM 3693 N ASP C 702 30.252 29.308 0.427 1.00 51.48 N The ACE residue in the HETATM records is connected to residue 702 (as detailed in the CONECT records for the file). So in summary, you can have sequences like these where the HETATM residues are connected: ATOM ATOM HETATM HETATM HETATM ATOM ATOM -or- HETATM HETATM HETATM ATOM ATOM Now the really big problem is that the SCOP web site returns "PDB" files with just these kinds of sequences but with _no_ CONECT records! So, Chimera guesses as best it can in this situation. The rule of thumb that it uses is that HETATMs are connected unless they occur somewhere after a TER card with no intervening ATOM record. Explicit CONECT records can add connectivity. So for your file of all HETATMs where nothing should be connected, there is a silver lining: in order to get nothing connected you just have to add a _single_ TER card at the beginning of the file, like this: TER HETATM ................................. HETATM ................................. HETATM ................................. --Eric

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graphics accelorator choice of chip
by David Griffiths 02 Oct '03

02 Oct '03

Since Fire GL2 is now discontinued does anybody have experience of latest graphics acceloratots for use on chimera It has been suggested to me that the following should be OK but does anybody have experience of using them ? NVidia Geforce FX 5600/5900 ATI 9700/9500. david griffiths d.g.griffiths(a)herts.ac.uk

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Re: [Chimera-users] how to color ribbons?
by Elaine Meng 20 Aug '03

20 Aug '03

Hi Mario, I'll include two different ways you could do this in Chimera 1.1700: ---------------- with menu ---------------- Actions... Atoms/Bonds... hide Actions... Ribbon... show Actions... Ribbon... edged Actions... Color... white Select... Structure... secondary structure... helix Actions... Color... red Select... Structure... secondary structure... sheet Actions... Color... cyan Select... Clear selection ---------------- with commands ---------------- ~display ribbon ribrepr edged ribcolor white ribcolor red :/isHelix ribcolor cyan :/isSheet ---------------- In both approaches, first the atoms are undisplayed, then the ribbon is turned on. The step setting the ribbon type to "edged" is optional; you could use whichever ribbon type you want. Then, I make everything white before making helices red and strands cyan. The reason I don't use the turn descriptor is that it only applies to explicit PDB TURN records, whereas in most cases, the PDB only contains HELIX and SHEET records. You could just put the commands in a plain text file, for example named "sscolor.com," and then use the command "source sscolor.com" to execute all the commands in the file. (The file must be in the working directory; otherwise you will have to include the whole path in the source command.) I hope this helps! Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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how to color ribbons?
by Mario Albrecht 20 Aug '03

20 Aug '03

Hi, I'm new to Chimera but I'm missing a simple script in the menu for the normal display of ribbons. Helices in ribbons should be colored in red, strands in cyan, and the rest in white. May you provide such a script? Thank you much, Mario Albrecht

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background manipulation
by Jacob Schmidt 18 Aug '03

18 Aug '03

Greetings: Can you tell me how to completely get rid of the black background on which structures appear? As you probably know printer ink is not cheap. Thanks - Jakob Schmidt, Dept . Biochem and Cell Biol. SUNY Stony Brook

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saving partial coordinates
by Elaine Meng 21 Jul '03

21 Jul '03

Hi Mark, In the current release of Chimera: if you are on a non-Windows system, you can use the command "pdbrun" to save just the atoms that are displayed. You can see the manual page for this command by typing "help pdbrun" in the Chimera Command Line (by default, Favorites... Command Line). example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." All the atoms should be in view (i.e. if you are zoomed in and the atoms around the periphery cannot be seen in the Chimera window, they won't be in your output file either). The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on Windows, I am not aware of a solution in the current release. In our working version and thus the next release (late summer or early fall, I believe) there is a delete action. This would allow you to select the atoms/bonds outside a zone, for example, and then actually delete them. (Actions... Atoms/Bonds... delete). Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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I Need Help!
by Mark Cunningham 21 Jul '03

21 Jul '03

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Re: ribbons, chimera, and collagen
by Eric Pettersen 18 Jul '03

18 Jul '03

Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric > I'm trying to make a ribbon plot of collagen using chimera, but it > doesn't > recognize collagen's secondary structure. > Can I just tell it to make a ribbon with the backbone atoms (or peptide > bonds), and not worry about what kind of secondary structure it really > is? > If so, how? > Have a nice day, > Randy

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