Hi Elaine, Hope you're well! I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research Phone +61 3 8559 5961 Email maja.divjak@petermac.org 305 Grattan Street Melbourne Victoria 3000 www.petermac.org Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
Hi Maja, 3eyv chain H has multiple residues that each contain C1,C2,C3. So to specify three atoms named C1,C2,C3 in 3eyv, you also have to specify in which residue (GUC 223 or GAL 224 or NDG 225 or FUC 226). Here is an image of these 4 residues in 3eyv with residue labels in green and atom labels on their carbons in tan, and another image of the pubchem molecule (hydrogens hidden for simplicity) with atom labels on its carbons in light blue. I don't know which atoms you want to match with which atoms, but for example if 3eyv was #0 and the pubchem molecule #1, then to match pubchem molecule atoms C1,C2,C3 with 3eyv chain H residue 225 atoms C3,C2,C1 (in that order) you would use command: match #1@c1,c2,c3 #0:225.h@c3,c2,c1 I am pretty sure those are not the right atoms to match, however. You would need to substitute the model numbers that you have (check in the Model Panel, opened from Favorites menu), as well as the residue number in 3eyv and the atom names that you actually want to match in the order in which you want them to be matched. If the oligosaccharides are not in a similar conformation, however, the overall match probably won't look that good. Match command and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> How to specify atoms in the command line: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 5, 2020, at 6:53 PM, Divjak Maja <Maja.Divjak@petermac.org> wrote:
Hi Elaine,
Hope you're well! I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please?
Thanks so much and best wishes,
Maja
Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research
Phone +61 3 8559 5961 Email maja.divjak@petermac.org 305 Grattan Street Melbourne Victoria 3000 www.petermac.org
Hi Elaine, Thank you so much, worked perfectly, but as you say, the overall match didn't look that great. Great to learn how to do this though! Best wishes, Maja From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, 6 May 2020 12:31 PM To: Divjak Maja <Maja.Divjak@petermac.org> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Matching a small ligand to another ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org<mailto:CyberReport@petermac.org> Hi Maja, 3eyv chain H has multiple residues that each contain C1,C2,C3. So to specify three atoms named C1,C2,C3 in 3eyv, you also have to specify in which residue (GUC 223 or GAL 224 or NDG 225 or FUC 226). Here is an image of these 4 residues in 3eyv with residue labels in green and atom labels on their carbons in tan, and another image of the pubchem molecule (hydrogens hidden for simplicity) with atom labels on its carbons in light blue. I don't know which atoms you want to match with which atoms, but for example if 3eyv was #0 and the pubchem molecule #1, then to match pubchem molecule atoms C1,C2,C3 with 3eyv chain H residue 225 atoms C3,C2,C1 (in that order) you would use command: match #1@c1,c2,c3 #0:225.h@c3,c2,c1 I am pretty sure those are not the right atoms to match, however. You would need to substitute the model numbers that you have (check in the Model Panel, opened from Favorites menu), as well as the residue number in 3eyv and the atom names that you actually want to match in the order in which you want them to be matched. If the oligosaccharides are not in a similar conformation, however, the overall match probably won't look that good. Match command and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> How to specify atoms in the command line: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:image001.png@01D623C3.08F5F520] [cid:image002.png@01D623C3.08F5F520] On May 5, 2020, at 6:53 PM, Divjak Maja <Maja.Divjak@petermac.org<mailto:Maja.Divjak@petermac.org>> wrote: Hi Elaine, Hope you're well! I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research Phone +61 3 8559 5961 Email maja.divjak@petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
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Elaine Meng