Thank you, Dr. Ali Kusay and Dr. Blaine Mooers I will try this. With Warm Regards *Dr. Vijay H. Masand* Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/
On Sun, Jun 21, 2020 at 10:08 PM Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > 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= > > > > >
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