[PyMOL] regarding pymol plugin windows

Hello everyone The number of plugins has become long and hence can not see the one listed at the end. Is there a way to reorganise the list of plugins in the plugin window of pymol or have a scroll bar to browse downwards. Thank you Best Regards Priyan --

Re: [PyMOL] regarding show_bumps

t; generate your movie using some python loops to enable/disable the bumps for > each frame, if you want to automate it. > > > > -Spencer > > > > On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol > wrote: > > Dear Spencer > > > > Thank you for the suggest

Re: [PyMOL] regarding show_bumps

ymolwiki.org/index.php/Split_states> > command to divide it into multiple objects, then run the script on each > state individually. > > -Spencer > > On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol wrote: > >> Hi >> >> I have a multi-state object loaded in PyM

[PyMOL] regarding show_bumps

Hi I have a multi-state object loaded in PyMOL which represents transition of a domain from one orientation to the other. I tried using "show_bumps.py" to bring up clashes during the transition but the cgo that is written out shows clashes only for the first state. Am I doing something wrong or sh

[PyMOL] regarding theseus wrapper

Dear pymol-users There is some trouble I end up with while using theseus from psico in pymol. I am not sure what is causing this. Can anyone help me fix this one. The log I get when executing theseus is given below. thank you in advance, Best Regards Priyan BEGIN THESEUS 3.0.0 > I===-===-===-

Re: [PyMOL] rendering missing segments

Hi Thank you Seth and Adam for vouching for the missing residue option. Thank you Thomas for considering the request for implememntation. Best Regards Priyan On Mon, Sep 29, 2014 at 7:04 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Seth and Adam, > > thanks a lot for the feat

Re: [PyMOL] representing missing residues in pymol

ature allows you to manually > fill in missing sequences. I have used it many times to make a specific > point, noting that the missing AAs were manually added to the figure. > > On Sep 25, 2014, at 8:38 AM, ccp4 pymol wrote: > > Thank you Thomas. > > Best Regards > Pri

Re: [PyMOL] representing missing residues in pymol

Thank you Thomas. Best Regards Priyan On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Priyan, > > unfortunately PyMOL doesn't have such functionality to include missing > atoms in the sequence viewer, neither does it read SEQRES records. > > Cheers, >

[PyMOL] representing missing residues in pymol

Hello everyone Many a times we have structures solved with residues missing as no electron density was seen. The complete sequence information is given in the SEQRES section of PDB. Is there a way in which we can identify the missing residues readily when we turn on the sequence feature by may be

[PyMOL] regarding pymol-script-repo

Hi I have successfully installed pymol on linux using instructions from this link on pymolwiki page and customized it to install to a path of my choice. Later I started to add pymol-script-repo to the same folder, after slightly twea

[PyMOL] segmentation fault with pymol 1.6 (r4050)

Hi to everyone Recently moved to latest pymol (from subversion r4050) on linux (ubuntu 12.10). Installation was fine and could launch pymol successfully. Using builder crashes with a segmentation fault. Has anyone encountered this? Please give suggestions to overcome this issue. Thanks Best Rega

Re: [PyMOL] puckering of ribose

pt-pucker.mov > > Hope that helps. > > Cheers, > Thomas > > On 01 Nov 2013, at 10:29, ccp4 pymol wrote: > > Hi to everyone, > > > > My apologies if the question is to naive. I was wondering if there was > an easier way to flip the puckering of ri

[PyMOL] puckering of ribose

Hi to everyone, My apologies if the question is to naive. I was wondering if there was an easier way to flip the puckering of ribose from endo to exo conformations at 2' and 3' positions in pymol. Thank you Best wishes Priyadarshan ---

Re: [PyMOL] regarding slerpy

Hi Can we calcule isoelectric point using structure, I mean just taking into account the residues exposed to surface/solvent accessible. Firstly is such a thing possible rather than just a sequence dependent pI. I tried some googling but in vain and so it will be really nice if someone has already

[PyMOL] regarding slerpy

Hi This is my first post to pymol-users lists. I have a problem regarding usage of slerpy. Firstly i must admit that i have no clue of how to go about using it in the first place. I know the pymol wiki has the list of commands but do not know how to exploit them in a real case. If someone can sugg