Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however). ChimeraX also allows changing hinge spacing. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users@cgl.ucsf.edu or chimerax-users@cgl.ucsf.edu (depending on which program you’re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul@baylor.edu> wrote:
Hi,
I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up.
Thanks Debamita
hi
good evening i have sdf files,i converted all those sdf files into single mol2 files..there is a option - a single file [individual @MOLECULE sections] - multiple files [file name must contain $name or $number] - a single file [combined @MOLECULE section] may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that.
Hi Prasad, I don’t know what other words to use — it is exactly as the description says. First decide if you want one file or multiple files. If you want one file, choose whether you want all in one molecule or individual molecule sections, then choose location and enter the filename. (Most people want individual molecules, but we are giving you the choice.) If you want multiple files, choose location, but there is only one place to enter name (even though the result will have multiple names) so you have to enter something that literally includes “$name” or “$number”. Example: If you have two files that are models #1 and #2 in Chimera and you choose to save multiple files and enter file name: blahblah$number.mol2 … then you will get two files, blahblah1.mol2 and blahblah2.mol2 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 28, 2019, at 5:41 AM, prasad ssv <prasad.ssva@gmail.com> wrote:
hi good evening i have sdf files,i converted all those sdf files into single mol2 files..there is a option • a single file [individual @MOLECULE sections] • multiple files [file name must contain $name or $number] • a single file [combined @MOLECULE section] may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that.
okay, thank you for your approach towards my problem.its been solved. i have individual mol2 files in single file.please check my combined file is that file okay for docking by using dock6 suite.file is attched below thanking you, On Thu, Feb 28, 2019 at 10:43 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prasad, I don’t know what other words to use — it is exactly as the description says. First decide if you want one file or multiple files. If you want one file, choose whether you want all in one molecule or individual molecule sections, then choose location and enter the filename. (Most people want individual molecules, but we are giving you the choice.) If you want multiple files, choose location, but there is only one place to enter name (even though the result will have multiple names) so you have to enter something that literally includes “$name” or “$number”.
Example: If you have two files that are models #1 and #2 in Chimera and you choose to save multiple files and enter file name: blahblah$number.mol2 … then you will get two files, blahblah1.mol2 and blahblah2.mol2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 28, 2019, at 5:41 AM, prasad ssv <prasad.ssva@gmail.com> wrote:
hi good evening i have sdf files,i converted all those sdf files into single mol2 files..there is a option • a single file [individual @MOLECULE sections] • multiple files [file name must contain $name or $number] • a single file [combined @MOLECULE section] may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that.
Hi Prasad, You would have to look at the file format descriptions in the DOCK6 manual and try the file yourself. There is also a DOCK mailing list for DOCK questions. <http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#TriposMOL2Format> <http://dock.compbio.ucsf.edu/Contact_Info/index.htm> Best, Elaine
On Feb 28, 2019, at 8:49 PM, prasad ssv <prasad.ssva@gmail.com> wrote:
okay, thank you for your approach towards my problem.its been solved. i have individual mol2 files in single file.please check my combined file is that file okay for docking by using dock6 suite.file is attched below thanking you,
On Thu, Feb 28, 2019 at 10:43 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prasad, I don’t know what other words to use — it is exactly as the description says. First decide if you want one file or multiple files. If you want one file, choose whether you want all in one molecule or individual molecule sections, then choose location and enter the filename. (Most people want individual molecules, but we are giving you the choice.) If you want multiple files, choose location, but there is only one place to enter name (even though the result will have multiple names) so you have to enter something that literally includes “$name” or “$number”.
Example: If you have two files that are models #1 and #2 in Chimera and you choose to save multiple files and enter file name: blahblah$number.mol2 … then you will get two files, blahblah1.mol2 and blahblah2.mol2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 28, 2019, at 5:41 AM, prasad ssv <prasad.ssva@gmail.com> wrote:
hi good evening i have sdf files,i converted all those sdf files into single mol2 files..there is a option • a single file [individual @MOLECULE sections] • multiple files [file name must contain $name or $number] • a single file [combined @MOLECULE section] may i know meaning of these option and i would like to know file name must contain $name or $number may i know how to write that.
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