Hi Ali, Thank you for the follow-up explanation!
I forgot that you can specify valence in a sdf file. This is something that you cannot do in a pdb file. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Ali Kusay [akus8...@uni.sydney.edu.au] Sent: Sunday, June 21, 2020 7:41 AM To: Mooers, Blaine H.M. (HSC); Vijay Masand Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] [EXTERNAL] Valence_Mode issue Hi Vijar and Blaine, >>> Had to send this message again since it was flagged by the image size >>> restriction <<< Thank you for showing me all these possibilities, I am convinced that PyMOL is excellent for 2D molecules! I have found similar similar Blaine as far as manually setting bonds: I have managed to change delocalised bonds to “bonds inside” by directly setting the bond order between 2 atoms using the “bond” command and “valence” commands. Both are not perfect solutions, documentation in https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Valence&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=sV8ovzxIsDWSl0uoHo1BUdChLeAdw_h5R5-BeBtHkN0&e= . Its perhaps easiest to edit the bonds from the files itself (or load one with the right bonds order), see attached images of file difference between left (valence between atoms 5-6 and 5-7 bond set to 4 delocalised) and right (valence between atoms 5-6 and 5-7 bond set to 1 and 2 bonds inside), PyMOL image in the same order. BTW this is aspirin from https://urldefense.proofpoint.com/v2/url?u=https-3A__www.drugbank.ca_drugs_DB00945&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=fe5TrhAFsg6zZY9iAHu1aINfqUuQ91KvQFo8gQiSa8o&e= , in the downloaded sdf file it already has the non-delocalised bond and I made delocalised using the valence command with the guess option, its just hard to go the other way around! Kind regards, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au On 21/6/20, 10:32 pm, "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu> wrote: Hi Vijay, It is unlikely that PyMOL can correctly interpret the atom names in your ligand. I suspect that you have to manually unbound and then bond each pair of atoms of interest in your ligand. You can do so by pasting a pair of commands like the following on the command line at the PyMOL> prompt below the command history window. unbond name CBE, name CBF;bond name CBE, name CBF, 2 See the attached images for a ligand after applying the above two commands. The Ball-and-Stick representation is found in the Presets under the A menu in the internal gui on the right. You can get the atom names printed to the command history window by switching the selection mode in the lower right hand corner to 'Atoms' and then left-click on the atom of interest. Explanation: One would hope that the following command would work: set valence, 1, ligand; set valence_mode, 1, ligamd See https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_fNQtC2xMQzin5pN4UnwJ-5FQ-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=II8Q6vB36GagQ-ygUFTK6ybIZsN6DIfSjl0ytoVurhU&e= A work around would be to add the ligand atoms of interest the wonderful script by Andreas Warnecke: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_KbvGC3QNPBiLDp5PSqeXG3-3Fdomain-3Draw.githubusercontent.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=S_bEV5e15l4ZTM263lAHuxIKRG4onVuWMeGlvXD_YF4&e= This will require edits in several locations, but it would provide a longer term solution. See https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_jWHFC4QOPEiL4BpnSBL3lk-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=55G8zMnSza8lxpwMY204KzRDFduU4QYBr1_vVMVB_S8&e= Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Dr. Vijay Masand [vijaymas...@gmail.com] Sent: Sunday, June 21, 2020 2:53 AM To: pymol-users Subject: [EXTERNAL] [PyMOL] Valence_Mode issue Dear All I am trying to get a nice 2D- like representation for a small molecule using PyMOL. I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands: set valence, 1 set valence_mode, 1 Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode? [Pymol-Issue-Valence-Mode.jpg] With Warm Regards Dr. Vijay H. Masand Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5UqYC5QPXJiqkZVzs2DXxq-3Fdomain-3Dsites.google.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=BC3gq6JqpYp36Fvo1wYIKytH83HmQiOliRmJKAA_XxY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Mh47C6XQ4LfQLrngTxJNJp-3Fdomain-3Durldefense.proofpoint.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=bX1f_BrDYaN_2GLjXqmyl3JC_xv8khukhFxEwiSCYdU&e= > _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
