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
> longe
