[COOT] New ligand 3-letter code
Hi, What is the proper way of generating 3-letter code for a new ligand? As of now, I insert my ligand in Coot using smiles string and for the 3-letter code I picked a non-existent code by trial and error (not very efficient). A cif file with corresponding name which I generated using Phenix was imported into Coot. I am sure there is a proper way of doing this. Appreciate your feedback. Regards, Sze Yi
Re: [COOT] PyMOL v. Coot map 'level'
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Emilio, for publication purposes you can get something similar to carving by setting the map radius in Coot, creating a Raster3D output file and adjusting front and back clip. Not perfect and difficult for fine tuning, but it's a step in the right direction, I think. Best, Tim On 06/05/2015 07:34 AM, Emilia C. Arturo (Emily) wrote: Thanks Paul. To help with others' future Googling efforts on the topic of PyMOL versus Coot map levels, I'll leave here the link to the discussion that began from my initial post, on the ccp4bb: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg39219.html Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? Is there a way in Coot to display a selection of the map about a set of residues - something akin to PyMOL's 'carve' option? In Coot, we use all the grid points in the asymmetric unit - other programs make a selection of grid points around the protein (and therefore have less solvent). More solvent means lower rmsd. If one then contours in n-rmsd levels, then absolute level used in Coot will be lower - and thus seem to be noisier (perhaps). This makes sense to me - thanks for the clear response :-) It appeared to me--and it turns out to be pointless, IMO, to supply an image to prove my point, because the image is too crowded--that the Coot map was much tidier/less 'noisy' around my selection of residues. In fact, I wondered if Coot was sampling the map more/at higher frequency (?) than is PyMOL. I'll have to Google more about that; there are probably settings I need to adjust. Anyway, it definitely didn't seem noisier than PyMOL's display of the same map, which is why I am asking if Coot has something like a 'carve' feature. I suppose that if you want comparable levels from the same map/mtz file then you should use absolute levels, not rmsd. What does PyMOL's 1.0 mean in electrons/A^3? I don't know how PyMOL's map level relates to electron density, but in case Thomas Holder knows, I'll ask the question at the related ccp4bb thread where he's participating. I guess you're asking about how the maps are scaled in PyMOL? ...how are they scaled in Coot? The idea of an absolute scale, frankly, confuses me, so I am fine to take the last two questions back to my crystallography notes :-) Thanks, Emily. Regards, Paul. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFVcUfHUxlJ7aRr7hoRAsdHAKDWwbxfJyXWnxPgqXBMBAh/NhY7PACgnKdZ CWwWVhFNjjzv2NPagny5+Z8= =iRG5 -END PGP SIGNATURE-
Re: [COOT] New ligand 3-letter code
I use your method - trial error.. It would be nice if at least there was a list somewhere of unassigned codes! On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) lau_sze...@immunol.a-star.edu.sg wrote: Hi, What is the proper way of generating 3-letter code for a new ligand? As of now, I insert my ligand in Coot using smiles string and for the 3-letter code I picked a non-existent code by trial and error (not very efficient). A cif file with corresponding name which I generated using Phenix was imported into Coot. I am sure there is a proper way of doing this. Appreciate your feedback. Regards, Sze Yi
Re: [COOT] PyMOL v. Coot map 'level'
Emilia: It appears to me that based on discussion on the CCP4BB by Thomas Holder and James Holton that you should do the following: · Run MAPMASK twice, first on an asymmetric unit to normalize, and a second time to extend the map over your molecule · Issue the command “unset normalize_ccp4_maps” either in your PyMol script or the GUI · Contour the map at your choice of r.m.s.d. level · This should lead to a map that should look identical to a COOT map Alternatively, PyMol now reads MTZ files and according to an off-line discussion with Thomas Holder, “PyMOL converts MTZ files to ccp4 maps internally before loading, this means that normalize_ccp4_maps also applies to MTZ files.” What isn’t clear to me from this and I’ve never tried to have PyMOL read an MTZ file and I neglected to ask Thomas in our offline discussion is whether PyMOL is then capable of extending the electron density over regions of the molecule that were not in the asymmetric. Steven -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 05, 2015 2:55 AM To: COOT@JISCMAIL.AC.UK Subject: Re: PyMOL v. Coot map 'level' -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Emilio, for publication purposes you can get something similar to carving by setting the map radius in Coot, creating a Raster3D output file and adjusting front and back clip. Not perfect and difficult for fine tuning, but it's a step in the right direction, I think. Best, Tim On 06/05/2015 07:34 AM, Emilia C. Arturo (Emily) wrote: Thanks Paul. To help with others' future Googling efforts on the topic of PyMOL versus Coot map levels, I'll leave here the link to the discussion that began from my initial post, on the ccp4bb: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg39219.html Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? Is there a way in Coot to display a selection of the map about a set of residues - something akin to PyMOL's 'carve' option? In Coot, we use all the grid points in the asymmetric unit - other programs make a selection of grid points around the protein (and therefore have less solvent). More solvent means lower rmsd. If one then contours in n-rmsd levels, then absolute level used in Coot will be lower - and thus seem to be noisier (perhaps). This makes sense to me - thanks for the clear response :-) It appeared to me--and it turns out to be pointless, IMO, to supply an image to prove my point, because the image is too crowded--that the Coot map was much tidier/less 'noisy' around my selection of residues. In fact, I wondered if Coot was sampling the map more/at higher frequency (?) than is PyMOL. I'll have to Google more about that; there are probably settings I need to adjust. Anyway, it definitely didn't seem noisier than PyMOL's display of the same map, which is why I am asking if Coot has something like a 'carve' feature. I suppose that if you want comparable levels from the same map/mtz file then you should use absolute levels, not rmsd. What does PyMOL's 1.0 mean in electrons/A^3? I don't know how PyMOL's map level relates to electron density, but in case Thomas Holder knows, I'll ask the question at the related ccp4bb thread where he's participating. I guess you're asking about how the maps are scaled in PyMOL? ...how are they scaled in Coot? The idea of an absolute scale, frankly, confuses me, so I am fine to take the last two questions back to my crystallography notes :-) Thanks, Emily. Regards, Paul. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFVcUfHUxlJ7aRr7hoRAsdHAKDWwbxfJyXWnxPgqXBMBAh/NhY7PACgnKdZ CWwWVhFNjjzv2NPagny5+Z8= =iRG5 -END PGP SIGNATURE- This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
Re: [COOT] New ligand 3-letter code
All: Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let you assign a three-letter code, it will choose its own code. At BMS (a pharmaceutical company), we do many hundreds of structures a year with ligands and we assign the same, already assigned, three-letter code for all of our ligands (unless we have two or more different ligands in a single structure, in which case we use two or more different already assigned three-letter codes). COOT can mostly handle this. However, I believe that if you want an unassigned code, the wwPDB has set aside UNK[nown] for this purpose. Steven From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 05, 2015 6:28 AM To: COOT@JISCMAIL.AC.UK Subject: Re: New ligand 3-letter code I use your method - trial error.. It would be nice if at least there was a list somewhere of unassigned codes! On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) lau_sze...@immunol.a-star.edu.sgmailto:lau_sze...@immunol.a-star.edu.sg wrote: Hi, What is the proper way of generating 3-letter code for a new ligand? As of now, I insert my ligand in Coot using smiles string and for the 3-letter code I picked a non-existent code by trial and error (not very efficient). A cif file with corresponding name which I generated using Phenix was imported into Coot. I am sure there is a proper way of doing this. Appreciate your feedback. Regards, Sze Yi This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
