Re: [PyMOL] [EXTERNAL] How to set spectrum color by default in Pymol

I second G.V.'s question. It touches upon a problem that I have been having. The cartoon representation is shown when the structure is loaded from disk or fetched from the PDB. The default cartoon representation overrides the settings in my pymolrc file. I have the following in my .pymolrc file.

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Hi Xiang-Jun Lu, Thanks for proving me wrong. Congratulations on your duplicated model! Please share the commands that you used with DSSR to generate the duplicated helix. PyMOL does not generate the cartoon representation for the backbones of your duplicate helix. Do you know why? Best regar

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Dear Blaine, On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Xiang-Jun Lu, > > Thanks for proving me wrong. Congratulations on your duplicated model! > Please share the commands that you used with DSSR to generate the > duplicated helix. > The du

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Hello Dr. Xiang-Jun Lu, Thanks a lot for your help. The model you have duplicated is exactly what I am looking for (checked it with VMD). Unfortunately I do not have access to DSSR-Pro. Is there any way that I can reproduce your procedure with x3dna-dssr? I need to create different numbers of dupl

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Hi Amir, Please have a look at the announcement "No more grant funding for 3DNA/DSSR" ( http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/) on the 3DNA Forum. DSSR results are reproduced, period. Best wishes, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Hi Xiang-Jun, Sorry to bother. I meant if I can do the same thing you have done with DSSR pro with free version of x3dna-dssr, as I am getting some error messages: x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb Processing file 'model.pdb' total number of nucleotides: 26 [e] no m

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi < taghavi.amirhoss...@gmail.com> wrote: > Hi Xiang-Jun, > > Sorry to bother. I meant if I can do the same thing you have done with > DSSR pro with free version of x3dna-dssr, as I am getting some error > messages: > No, as made clear in my prev