regarding to minimization and preparation of sdf files for docking.
hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,
Hi Prasad, You would have to ask a specific question — we cannot go through all the molecules individually and perform in-depth consulting on your individual research project. We don’t have funding for that kind of support. I looked at the logs and mostly see just messages (not problems) except one message where the hydrogens weren’t added to one atom. It may be that almost all molecules are processed just fine, and that the structure of that one molecule is strange somehow. I don’t know. If you have a specific molecule that has a specific problem, you could use menu: Help… Report a Bug and attach the structure and describe all the steps needed to reproduce the problem. 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 2, 2019, at 1:20 AM, prasad ssv <prasad.ssva@gmail.com> wrote:
hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,
Dear all, I want to select residues/atoms only those within my cryo-EM map region so that I can highlight/color them. As I googled ("select atoms only within a map chimera"), I could find only how to select residues/atoms within certain radius from specific position/atoms. I may use phenix.map_model_cc to see which residues have higher cc to my cryo-EM map and manually select those using a script. However, I'm just curious whether there is already a good automatic chimera function that I can use to select residues/atoms only those within my cryo-EM map region. best, Doonam
Dear all, I want to select residues/atoms only those within my cryo-EM map region so that I can highlight/color them. As I googled ("select atoms only within a map chimera"), I could find only how to select residues/atoms within certain radius from specific position/atoms. I may use phenix.map_model_cc to see which residues have higher cc to my cryo-EM map and manually select those using a script. However, I'm just curious whether there is already a good automatic chimera function that I can use to select residues/atoms only those within my cryo-EM map region. best, Doonam
Hi Doonam, You can assign the local density values to atoms and then select only those atoms with values greater than some threshold. (1) Assign density values as atom attributes. menu: Tools…Volume Data… Values at Atom Positions. In that dialog choose atomic model and map model, then click Histogram. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht...> (2) … which will show the Render/Select by Attribute tool with a histogram of the values assigned to the atoms. It is showing the Render tab, in which you could color the atoms by the density values if you wanted to. To select only a subset of atoms by those values, first look at the attribute name in the Render tab, then change to the Select tab, choose that same attribute, and then move the vertical bars on the histogram to select the atoms you want (presumably the higher-value range), click Apply. You can do this all with commands. Part (1) above can be done with command “measure mapValues” in which you can also specify a name for the new attribute. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValue...> Part (2) can be done directly with the “select” command. For example, if I’d named the new attribute “mapd” then you could use a command something like: select @/mapd>0.085 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri...> 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 4, 2019, at 10:20 PM, Kim, Doo Nam <doonam@lanl.gov> wrote:
Dear all, I want to select residues/atoms only those within my cryo-EM map region so that I can highlight/color them.
As I googled ("select atoms only within a map chimera"), I could find only how to select residues/atoms within certain radius from specific position/atoms.
I may use phenix.map_model_cc to see which residues have higher cc to my cryo-EM map and manually select those using a script.
However, I'm just curious whether there is already a good automatic chimera function that I can use to select residues/atoms only those within my cryo-EM map region. best, Doonam
participants (3)
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Elaine Meng -
Kim, Doo Nam -
prasad ssv