pseudobond problem while writing mol2 format
Hi All, I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred. PS: I send you the molecule in PDB format as an example case. Thanks in advance, Kiruba ________________________________ This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.
Hi Kiruba, For each of those pseudobonds, there is a hidden “real” bond. To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted. I have attached a simple Python script that does that. So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2. Keep in mind that deleting those hidden bonds will change the corresponding atom types. So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide). —Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 6, 2019, at 7:43 AM, Palani, Kirubakaran <Kirubakaran.Palani@fccc.edu> wrote:
Hi All,
I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred.
PS: I send you the molecule in PDB format as an example case.
Thanks in advance, Kiruba
This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message. <test.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Eric, That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes. Best regards, Kiruba From: Eric Pettersen <pett@cgl.ucsf.edu> Reply-To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Date: Friday, December 6, 2019 at 2:28 PM To: "Palani, Kirubakaran" <Kirubakaran.Palani@fccc.edu> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] pseudobond problem while writing mol2 format EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails. ________________________________ Hi Kiruba, For each of those pseudobonds, there is a hidden “real” bond. To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted. I have attached a simple Python script that does that. So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2. Keep in mind that deleting those hidden bonds will change the corresponding atom types. So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide). —Eric Eric Pettersen UCSF Computer Graphics Lab ________________________________ This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.
Happy to help! —Eric
On Dec 6, 2019, at 12:03 PM, Palani, Kirubakaran <Kirubakaran.Palani@fccc.edu> wrote:
Hi Eric,
That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes.
Best regards, Kiruba
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Date: Friday, December 6, 2019 at 2:28 PM To: "Palani, Kirubakaran" <Kirubakaran.Palani@fccc.edu <mailto:Kirubakaran.Palani@fccc.edu>> Cc: "chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] pseudobond problem while writing mol2 format
EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails.
Hi Kiruba, For each of those pseudobonds, there is a hidden “real” bond. To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted. I have attached a simple Python script that does that. So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2. Keep in mind that deleting those hidden bonds will change the corresponding atom types. So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (2)
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Eric Pettersen -
Palani, Kirubakaran