Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation. I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand. 2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon. Is there any solution?
Hi Francesco, It is difficult to try anything without the files. Here are some generalities. Usually bonds can be specified correctly in PDB by following the format rules and using CONECT lines if needed. However, the format rules might not include the situation of a circular biopolymer. Similarly, I believe the ribbon code is not designed to consider a circular chain (tested on 2kux, cyclic peptide). Any extra bonds can just be deleted in Chimera, say using the "Adjust Bonds" tab in the "Build Structure" tool, or the command ~bond, but this would not fix the ribbon problem. 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 Sep 23, 2010, at 6:33 AM, Francesco Oteri wrote:
Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation.
I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand. 2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon.
Is there any solution? _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Sep 23, 2010, at 6:33 AM, Francesco Oteri wrote:
Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation.
I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand.
I would need the PDB file in order to see exactly what you mean here, and to fix the problem.
2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon.
This problem is marked as "fixed" in our bug database, but some simple testing shows that it is not. I have reopened that entry and will add you to the recipient list so that you will get notified when we fix it (hopefully for real!) again. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I've attached the file Il 23/09/2010 19:38, Eric Pettersen ha scritto:
On Sep 23, 2010, at 6:33 AM, Francesco Oteri wrote:
Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation.
I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand.
I would need the PDB file in order to see exactly what you mean here, and to fix the problem.
2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon.
This problem is marked as "fixed" in our bug database, but some simple testing shows that it is not. I have reopened that entry and will add you to the recipient list so that you will get notified when we fix it (hopefully for real!) again.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems. In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc. If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened. Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks. Conrad On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I've downloaded the latest alpha version, and i saw that for 2kux pdb the problem was solves, unfortunately the same is not for my molecule. I tryed with the amber files and I still see uncorrect viualization. Moreover, when I active the ribbon visualizaton, the stick bonds are displayed in a wrong way: it semms that the ribbon change the connectivity of the first atom and last atom of the circular structure!!!! I checked the connectivity with vmd, and it is ok. I attached the amber files, as a tgz archive, so you can experiance by yourself the problem. In each case, thanks for the speed of your answer. PS: Is it possible to add the possibility to open topology directly from the menu File->Open? On 28/09/2010 02:39, Conrad Huang wrote:
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks.
Conrad
On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Francesco, An MD Movie "metafile" can be opened with File... Open or the command "open." It is a simple text file that has the same things you would normally enter into the MD Movie input dialog, for example: amber 500 1000 prmtop mdcrd ... if my AMBER input files are named prmtop and mdcrd, and I want to view only frames 500-1000. The reasoning is that most trajectory formats require more than one file and/or some other parameters to be entered. Also, in the case of a single PDB file (with MODEL/ENDMDL around each frame), the behavior is different if you open it as a trajectory (allows play-through) than if you just opened it as a regular PDB file (shows all frames together at the same time). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile> Maybe this metafile approach will be helpful. 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 Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
PS: Is it possible to add the possibility to open topology directly from the menu File->Open?
Hi Francesco, It seems that the new ribbon code for handling circular structures doesn't properly handle models containing multiple circular structures, like yours does. We'll keep working on it and keep you in the "loop" so to speak. --Eric On Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
I've downloaded the latest alpha version, and i saw that for 2kux pdb the problem was solves, unfortunately the same is not for my molecule. I tryed with the amber files and I still see uncorrect viualization. Moreover, when I active the ribbon visualizaton, the stick bonds are displayed in a wrong way: it semms that the ribbon change the connectivity of the first atom and last atom of the circular structure!!!! I checked the connectivity with vmd, and it is ok.
I attached the amber files, as a tgz archive, so you can experiance by yourself the problem.
In each case, thanks for the speed of your answer.
PS: Is it possible to add the possibility to open topology directly from the menu File->Open?
On 28/09/2010 02:39, Conrad Huang wrote:
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks.
Conrad
On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Yup. My updated code was only updating the last residue ribbon information properly. I've committed some more changes, and your trajectory file displays properly now with the new code. These changes should be incorporated in tomorrow's daily build, so can you please give it another try tomorrow? Thanks. Conrad On 9/28/2010 2:29 PM, Eric Pettersen wrote:
Hi Francesco, It seems that the new ribbon code for handling circular structures doesn't properly handle models containing multiple circular structures, like yours does. We'll keep working on it and keep you in the "loop" so to speak.
--Eric
On Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
I've downloaded the latest alpha version, and i saw that for 2kux pdb the problem was solves, unfortunately the same is not for my molecule. I tryed with the amber files and I still see uncorrect viualization. Moreover, when I active the ribbon visualizaton, the stick bonds are displayed in a wrong way: it semms that the ribbon change the connectivity of the first atom and last atom of the circular structure!!!! I checked the connectivity with vmd, and it is ok.
I attached the amber files, as a tgz archive, so you can experiance by yourself the problem.
In each case, thanks for the speed of your answer.
PS: Is it possible to add the possibility to open topology directly from the menu File->Open?
On 28/09/2010 02:39, Conrad Huang wrote:
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks.
Conrad
On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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OK, I will try and I will report on mailing-list the result!!! Il 29/09/2010 21:04, Conrad Huang ha scritto:
Yup. My updated code was only updating the last residue ribbon information properly. I've committed some more changes, and your trajectory file displays properly now with the new code. These changes should be incorporated in tomorrow's daily build, so can you please give it another try tomorrow? Thanks.
Conrad
On 9/28/2010 2:29 PM, Eric Pettersen wrote:
Hi Francesco, It seems that the new ribbon code for handling circular structures doesn't properly handle models containing multiple circular structures, like yours does. We'll keep working on it and keep you in the "loop" so to speak.
--Eric
On Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
I've downloaded the latest alpha version, and i saw that for 2kux pdb the problem was solves, unfortunately the same is not for my molecule. I tryed with the amber files and I still see uncorrect viualization. Moreover, when I active the ribbon visualizaton, the stick bonds are displayed in a wrong way: it semms that the ribbon change the connectivity of the first atom and last atom of the circular structure!!!! I checked the connectivity with vmd, and it is ok.
I attached the amber files, as a tgz archive, so you can experiance by yourself the problem.
In each case, thanks for the speed of your answer.
PS: Is it possible to add the possibility to open topology directly from the menu File->Open?
On 28/09/2010 02:39, Conrad Huang wrote:
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks.
Conrad
On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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I've tested the last daily build and it works fine for both AMBER files and pdb. In the latter case i've corrected the pdb and chimera read it with the correct connectivity. On 29/09/2010 21:04, Conrad Huang wrote:
Yup. My updated code was only updating the last residue ribbon information properly. I've committed some more changes, and your trajectory file displays properly now with the new code. These changes should be incorporated in tomorrow's daily build, so can you please give it another try tomorrow? Thanks.
Conrad
On 9/28/2010 2:29 PM, Eric Pettersen wrote:
Hi Francesco, It seems that the new ribbon code for handling circular structures doesn't properly handle models containing multiple circular structures, like yours does. We'll keep working on it and keep you in the "loop" so to speak.
--Eric
On Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
I've downloaded the latest alpha version, and i saw that for 2kux pdb the problem was solves, unfortunately the same is not for my molecule. I tryed with the amber files and I still see uncorrect viualization. Moreover, when I active the ribbon visualizaton, the stick bonds are displayed in a wrong way: it semms that the ribbon change the connectivity of the first atom and last atom of the circular structure!!!! I checked the connectivity with vmd, and it is ok.
I attached the amber files, as a tgz archive, so you can experiance by yourself the problem.
In each case, thanks for the speed of your answer.
PS: Is it possible to add the possibility to open topology directly from the menu File->Open?
On 28/09/2010 02:39, Conrad Huang wrote:
I've added some ribbon code to handle circular structures. Both the original "cycle.pdb" file from bug report #2777 and pdb:2kux are now displayed properly. I tried your frames2.pdb, but that still showed two ends. I'm not sure if that is due to the incorrect connectivity in the file. Can you download the latest daily build and see if it works any better with your trajectory input file? Thanks.
Conrad
On 9/23/2010 12:30 PM, Francesco Oteri wrote:
I've supposed the problem resides in the pdb, for this reason i tested the amber topology as input. Using amber, in fact, the correct bonds are displayed. Nevertheless, the ribbon is still cutted. I saw that it is a bug and that a new entry in the bugzilla has been opened.
Il 23/09/2010 20:31, Elaine Meng ha scritto:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Francesco, As Elaine mentions, as per the PDB standard the chain connectivity of standard residues (i.e. residues in ATOM records) is implied by their order in the file, barring TER records between the residues. This is why Chimera is producing those longs bonds. For example, your file has residues 300 and 301 one after the other in the PDB file without a TER card, so Chimera connects them despite them being >50A apart. What you really need to do is reorder the file so that it is in connectivity order. Also, the file was seemingly made by trjconv, which AFAIK is a program for converting Gromacs trajectories to PDB format. I thought you were using an Amber trajectory. Why aren't you using ambpdb, which directly converts Amber trajectories to PDB files? Lastly, trjconv is doing a bad job with justification of hydrogen names in the 4 columns alloted to the atom name. It does well with some names, like "1H2*" and " H3*" (so Chimera can deduce the element type from the first two columns) but then outputs some stinkers like " 1H7" and " 2H7". Sigh. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 23, 2010, at 11:31 AM, Elaine Meng wrote:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
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As I told to Elaine, i know the problem about pdb file, for me is not a problem reordering it. Nevertheless, the problem remains: using amber topology I don't see a continue ribbon. I'll wait for the fixing of this bug. Thanks for your help Il 23/09/2010 21:47, Eric Pettersen ha scritto:
Hi Francesco, As Elaine mentions, as per the PDB standard the chain connectivity of standard residues (i.e. residues in ATOM records) is implied by their order in the file, barring TER records between the residues. This is why Chimera is producing those longs bonds. For example, your file has residues 300 and 301 one after the other in the PDB file without a TER card, so Chimera connects them despite them being >50A apart. What you really need to do is reorder the file so that it is in connectivity order. Also, the file was seemingly made by trjconv, which AFAIK is a program for converting Gromacs trajectories to PDB format. I thought you were using an Amber trajectory. Why aren't you using ambpdb, which directly converts Amber trajectories to PDB files? Lastly, trjconv is doing a bad job with justification of hydrogen names in the 4 columns alloted to the atom name. It does well with some names, like "1H2*" and " H3*" (so Chimera can deduce the element type from the first two columns) but then outputs some stinkers like " 1H7" and " 2H7". Sigh.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Sep 23, 2010, at 11:31 AM, Elaine Meng wrote:
Hi Francesco, Wow, this is a very pretty structure! However, the PDB looks somewhat messed up. Perhaps using the AMBER files solves most of these problems.
In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER. However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity. Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions. I tried just putting TER after every 75 residues, which does eliminate the very long bonds. However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity. For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.
If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand. If this DNA is all one big circular strand, there should be only one break in the ribbon. 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
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participants (4)
-
Conrad Huang -
Elaine Meng -
Eric Pettersen -
Francesco Oteri