Pdb saved in Chimera not displaying upon opening
Hi, I have opened a pdb structure of a ribosome, hidden parts of it and then saved a new pdb of the displayed atoms through “File->Save pdb” ticking “save displayed atoms only”. When I try to open this saved pdb file, Chimera states “Opened ….pdb”, however, it does not display. The model panel is empty etc. Checking the pdb file in textedit, it does contain the secondary structure information and all the amino acids but it seems to lack coordinate information, see pictures below of parts of it. I’ve also tried to save the pdb through “Actions-> write pdb”. Do you know how I can solve this issue? Is it a saving issue or a displaying issue? Thanks, Magdalena [cid:image001.png@01D8C371.3C765B60][cid:image002.png@01D8C371.3C765B60] När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
Hi Magdalena, It is not possible to answer with certainty since I don't know exactly what atoms you had displayed when you tried to the save the PDB. However, most likely the problem is that you displayed ribbons only. Displaying ribbons is not the same as displaying the atoms (e.g. as sticks or wire). For example, to show atoms, menu: Presets... interactive 2 (all atoms). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2022, at 1:53 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I have opened a pdb structure of a ribosome, hidden parts of it and then saved a new pdb of the displayed atoms through “File->Save pdb” ticking “save displayed atoms only”. When I try to open this saved pdb file, Chimera states “Opened ….pdb”, however, it does not display. The model panel is empty etc. Checking the pdb file in textedit, it does contain the secondary structure information and all the amino acids but it seems to lack coordinate information, see pictures below of parts of it. I’ve also tried to save the pdb through “Actions-> write pdb”.
Do you know how I can solve this issue? Is it a saving issue or a displaying issue?
Thanks, Magdalena
Hi Elaine, That was indeed the problem. Thanks a lot! Cheers, Magdalena Hämta Outlook för iOS<https://aka.ms/o0ukef> ________________________________ Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: Thursday, September 8, 2022 6:04:00 PM Till: Magdalena Riad <magdalena.riad@ki.se> Kopia: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Ämne: Re: [Chimera-users] Pdb saved in Chimera not displaying upon opening [Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt på https://aka.ms/LearnAboutSenderIdentification ] Hi Magdalena, It is not possible to answer with certainty since I don't know exactly what atoms you had displayed when you tried to the save the PDB. However, most likely the problem is that you displayed ribbons only. Displaying ribbons is not the same as displaying the atoms (e.g. as sticks or wire). For example, to show atoms, menu: Presets... interactive 2 (all atoms). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2022, at 1:53 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I have opened a pdb structure of a ribosome, hidden parts of it and then saved a new pdb of the displayed atoms through “File->Save pdb” ticking “save displayed atoms only”. When I try to open this saved pdb file, Chimera states “Opened ….pdb”, however, it does not display. The model panel is empty etc. Checking the pdb file in textedit, it does contain the secondary structure information and all the amino acids but it seems to lack coordinate information, see pictures below of parts of it. I’ve also tried to save the pdb through “Actions-> write pdb”.
Do you know how I can solve this issue? Is it a saving issue or a displaying issue?
Thanks, Magdalena
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
participants (2)
-
Elaine Meng -
Magdalena Riad