Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra
Hi Francesco, The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this, I believe Chimera is reading the file correctly. Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra
Hi Elaine I had better waited, examining the sequence, before claiming an error. I'll also update chimera. francesco On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this, I believe Chimera is reading the file correctly.
Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra
Hi Elaine: If the deposited sequence for 4i4t is correct, the deposited pdb is wrong (void between 42-45 and 360-369 in chain D). The deposited cif file is correct, however, for reasons that I do not know, chimera follows the error that I said above in extracting pdb. VMD extracts correctly the pdb, at least as far as chain D is concerned (no voids, so that 431 residues, as indicated on RCSB, i.e., missing 442-455). Best regards francesco ---------- Forwarded message --------- From: Francesco Pietra <chiendarret@gmail.com> Date: Sat, Oct 6, 2018 at 9:43 PM Subject: Re: [Chimera-users] error opening .cif file To: chimera <chimera-users@cgl.ucsf.edu> Hi Elaine I had better waited, examining the sequence, before claiming an error. I'll also update chimera. francesco On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this, I believe Chimera is reading the file correctly.
Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra
Hi Francesco, I believe Chimera is using the auth_seq_id (author residue numbering). In mmCIF, there is also another residue numbering value, label_seq_id, and sometimes they are different. Usually there is some reason why the authors numbered differently, but I don’t know in this case. If it bothers you, you can just renumber the chain sequentially (Tools.. Structure Editing… Renumber Residues, or command “resrenumber”). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.h...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2018, at 1:55 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hi Elaine: If the deposited sequence for 4i4t is correct, the deposited pdb is wrong (void between 42-45 and 360-369 in chain D). The deposited cif file is correct, however, for reasons that I do not know, chimera follows the error that I said above in extracting pdb. VMD extracts correctly the pdb, at least as far as chain D is concerned (no voids, so that 431 residues, as indicated on RCSB, i.e., missing 442-455). Best regards francesco
---------- Forwarded message --------- From: Francesco Pietra <chiendarret@gmail.com> Date: Sat, Oct 6, 2018 at 9:43 PM Subject: Re: [Chimera-users] error opening .cif file To: chimera <chimera-users@cgl.ucsf.edu>
Hi Elaine I had better waited, examining the sequence, before claiming an error. I'll also update chimera. francesco
On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Francesco, The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this, I believe Chimera is reading the file correctly.
Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra
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participants (2)
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Elaine Meng -
Francesco Pietra