[PyMOL] Plea to developer and mesh_width changed

Hi I just started to look into 1.2 since there seem to be so many new features I would like to try out. I compare the precompiled PyMOL 1.0r0 and 1.2r2 on linux (and 1.1r1 on windows). When introducing new features please have them "off" by default, even tough it can mean that many users never f

[PyMOL] pseudoatoms and alignment

Hi I use the pseudoatom command to put labels at specific coordinates in space. How can I remove the pseudoatom object show up in the sequence alignment? I can not see any reason pseudoatoms should be in the alignment or? Björn ***

[PyMOL] center at x,y,z

Hi all, How do I center at a specific coordinate? Can not find any obvious way, by searching the web and manuals. --Björn *** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the

[PyMOL] secondary structure to different states

Hi all, If I read in a two pdb-files in different states, only the first one read in got assigned secondary structures. Example: load p1.pdb ,state=1 load p2.pdb ,state=2 hide all show cartoon only p1 has arrows and helixes the p2 has fat tubes. I also tried define it explicitly

[PyMOL] Ray_trace_mode,1

Hi Warren et al. I play with the ray_trace_modes and like the effects of outlines (mode 1 or 3). But why is also maps outlined. Map colour disappear and maps become black! Notice also that no outline is produced on cgo-objects (spheres). Also sticks visible behind a transparent cgo or surface l

[PyMOL] GUI output font size too small

0.99beta33 on Linux and windows. Thanks, Björn Kauppi *** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or

[PyMOL] non-round helix bug

Warren, et al, I discovered a funny bug in 0.98. If one turn off round helices and turn on cartoon highlight color: like; set cartoon_round_helices, off set cartoon_highlight_color,grey50 the highlight color and helix colors are mixed up!! Björn ***

[PyMOL] all objects on feature

Hi pymol-developers, I find it some what annoying to have all objects turned on (not every time!!?) if I click on the empty space below the objects names. What is the meaning with this feature? It is enough to have the (all) object button toggle. -- Björn **

[PyMOL] wildcards

Hi, How difficult is it to implement wildcards in selections? Example: My protein objects have long names but with A, B ,C etc extension my objects: protein_1_with_long_name_A protein_1_with_long_name_B protein_1_with_long_name_C protein_2_with_long_name_A protein_2_with_long_name_B protein_2_w

[PyMOL] object name length

Hi, all Two short questions. 1. Is it possible to have pymol display more then 16 characters in the object name bars on the right hand side on the GUI? 2. Which ascii characters is allowed in a name? Seems to be only alpha numrerics and "_" and ".". Is there away round this? I tried hyphens but

[PyMOL] Header records in pdb files

something like "PyMOL was here!" If it is difficult to implement, at a minimum I would like to see in the PyMOL-log the HEADER and TITLE cards, after reading a pdb-file, (to be I sure typed in the correct pdb-code in that nice pdb-loader plug-in, for example...) Just a thought... Bj

[PyMOL] Labels not stored in scenes

Hi, I noticed today that labels (other than distances) is not stored in scenes. Could be very handy in a "live" presentation to have pre-labeled residues. Is this hard to implement, or just an oversight? Bj

[PyMOL] plane2colour

Hi, Is it an equivalent in PyMOL to the plane2colour command in Molscript? i.e. controlling the colour of the "inside" of an cartoon-drawn helix? Or can I get a similar effect with PyMOL somehow? Björn *** This e-mail may

[PyMOL] Mono performance drop

Dear all, Sorry, not strictly PyMOL. But it relates to my usage of the program. I have a severe performance problem running the Open-GL based rendering in mono mode. The graphics are very "jumpy". If I switch to quad buffered stereo it works smooth and beautifully. I use windows 2000, PIII 73

[PyMOL] CA trace

I know something similar has been answered earlier, but I can not find it. How do I display CA trace of a molecule, if I only have CA-coordinates? -- Bjorn