VMD-L Mailing List

From: Sampo Karkola (sampo.karkola_at_helsinki.fi)
Date: Mon Oct 01 2007 - 01:51:11 CDT

Hi John and thanks for the info.

Eventually, this turned out to be my mistake, since I did not fully
study the vmd-format. I think I'll get it to work with your instructions.

Thanks again,

Sampo

John Stone wrote:
> Hi,
> It appears that the reason you're not able to load those saved
> states is because VMD is not able to find the files in the same
> fully-qualified directory path on the Windows machine. Since the
> molecule files fail to load, you get numerous subsequent errors
> in the other parts of the process. I suggest editing the text of
> the saved state file, trimming off all the leading directories so
> that you're just left with relative pathnames in the current working
> directory. Then, to load the saved state, you'll just have to use
> the "cd" command in the VMD text console so that VMD's current working
> directory is that of the saved state file.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 28, 2007 at 09:54:58AM +0300, Sampo Karkola wrote:
>> Hi John and thanks for a quick reply!
>>
>> It's not a permission problem, vmd tries to read it and I can open the
>> files with a text editor. I tested a file again and found out that if I
>> save the coordinates, say in pdb format, everything works fine as it
>> should, because they are just coordinates. The earlier message saying
>> "ERROR> Could not read file XXX.vmd" was my mistake and did not describe
>> the actual problem.
>>
>> Now, If I save state in Ubuntu and try to open it in Windows, I see
>> ERROR in console window (see the attached jpg file, I could not copy the
>> text from the console window). I also tried to log the action but no
>> errors were logged (see the attached vmd.log)
>>
>> The vmd file I created was a protein represented as a New Ribbon and
>> coloured by structure and the ligand and heme group in the active site
>> were represented as licorice and coloured by atom name.
>>
>> Again, any help is appreciated!
>>
>> Sampo
>>
>>
>> Check out these cool words by John Stone:
>>> Hi,
>>> I've never encountered that kind of problem, and I frequently
>>> use the same state files on many platforms. Does your Windows
>>> machine have permission to access the file(s) you saved in Ubuntu?
>>> It's quite possible this is merely a permissions problem of some sort.
>>> Can you open the saved state file in a text editor?
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Thu, Sep 27, 2007 at 03:52:16PM +0300, Sampo Karkola wrote:
>>>> Dear list,
>>>>
>>>> I'm running VMD1.8.6 both on Ubuntu Linux and WinXP and found the
>>>> following problem:
>>>>
>>>> If I save molecules in Ubuntu (File/Save State with vmd extension) and
>>>> try to read them in Windows, I get an error message saying
>>>>
>>>> ERROR> Could not read file XXX.vmd
>>>>
>>>> Maybe this has been discussed on the list already, but I just joined the
>>>> list and could not find any post by a quick search.
>>>>
>>>> Any help is appreciated,
>>>>
>>>> Regards,
>>>>
>>>> Sampo
>>>>
>>>> ________________________
>>>> Sampo Karkola
>>>> Doctoral student
>>>>
>>>> Laboratory of Organic Chemistry
>>>> Department of Chemistry
>>>> POBox 55, FIN-00014
>>>> University of Helsinki
>>>> Finland
>>>>
>>>> tel. +358 9 191 50369
>>>> fax. +358 9 191 50366
>>>> sampo.karkola_at_helsinki.fi
>
>
>> # VMD for WIN32, version 1.8.6 (April 7, 2007)
>> # Log file 'vmd.log', created by user skarkola
>> material change ambient Opaque 0.000000
>> material change specular Opaque 0.500000
>> material change diffuse Opaque 0.650000
>> material change shininess Opaque 0.534020
>> material change opacity Opaque 1.000000
>> material change ambient Transparent 0.000000
>> material change specular Transparent 0.500000
>> material change diffuse Transparent 0.650000
>> material change shininess Transparent 0.534020
>> material change opacity Transparent 0.300000
>> material change ambient BrushedMetal 0.080000
>> material change specular BrushedMetal 0.340000
>> material change diffuse BrushedMetal 0.390000
>> material change shininess BrushedMetal 0.150000
>> material change opacity BrushedMetal 1.000000
>> material change ambient Diffuse 0.000000
>> material change specular Diffuse 0.000000
>> material change diffuse Diffuse 0.700000
>> material change shininess Diffuse 0.530000
>> material change opacity Diffuse 1.000000
>> material change ambient Ghost 0.000000
>> material change specular Ghost 1.000000
>> material change diffuse Ghost 0.000000
>> material change shininess Ghost 0.230000
>> material change opacity Ghost 0.100000
>> material change ambient Glass1 0.000000
>> material change specular Glass1 0.650000
>> material change diffuse Glass1 0.500000
>> material change shininess Glass1 0.530000
>> material change opacity Glass1 0.150000
>> material change ambient Glass2 0.520000
>> material change specular Glass2 0.220000
>> material change diffuse Glass2 0.760000
>> material change shininess Glass2 0.590000
>> material change opacity Glass2 0.680000
>> material change ambient Glossy 0.000000
>> material change specular Glossy 1.000000
>> material change diffuse Glossy 0.650000
>> material change shininess Glossy 0.880000
>> material change opacity Glossy 1.000000
>> material change ambient HardPlastic 0.000000
>> material change specular HardPlastic 0.280000
>> material change diffuse HardPlastic 0.560000
>> material change shininess HardPlastic 0.690000
>> material change opacity HardPlastic 1.000000
>> material change ambient MetallicPastel 0.000000
>> material change specular MetallicPastel 0.550000
>> material change diffuse MetallicPastel 0.260000
>> material change shininess MetallicPastel 0.190000
>> material change opacity MetallicPastel 1.000000
>> material change ambient Steel 0.250000
>> material change specular Steel 0.380000
>> material change diffuse Steel 0.000000
>> material change shininess Steel 0.320000
>> material change opacity Steel 1.000000
>> material change ambient Translucent 0.000000
>> material change specular Translucent 0.600000
>> material change diffuse Translucent 0.700000
>> material change shininess Translucent 0.300000
>> material change opacity Translucent 0.800000
>> display eyesep 0.065000
>> display focallength 2.000000
>> display height 6.000000
>> display distance -2.000000
>> display projection Orthographic
>> display nearclip set 0.500000
>> display farclip set 10.000000
>> display depthcue off
>> display cuestart 0.500000
>> display cueend 10.000000
>> display cuedensity 0.400000
>> display cuemode Exp2
>> mol representation NewCartoon 0.300000 6.000000 4.100000 0
>> mol color Structure
>> mol selection all
>> mol material Opaque
>> mol representation Licorice 0.300000 10.000000 10.000000
>> mol color Name
>> mol selection resname HEM ANF
>> mol material Opaque
>> color scale colors RWB{1.000000 1.000000 1.000000} {1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000}
>> color scale colors BWR{1.000000 1.000000 1.000000} {0.000000 0.000000 1.000000} {1.000000 0.000000 0.000000}
>> color scale colors RGryB{0.500000 0.500000 0.500000} {1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000}
>> color scale colors BGryR{0.500000 0.500000 0.500000} {0.000000 0.000000 1.000000} {1.000000 0.000000 0.000000}
>> color scale colors RGB{0.000000 1.000000 0.000000} {1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000}
>> color scale colors BGR{0.000000 1.000000 0.000000} {0.000000 0.000000 1.000000} {1.000000 0.000000 0.000000}
>> color scale colors RWG{1.000000 1.000000 1.000000} {1.000000 0.000000 0.000000} {0.000000 1.000000 0.000000}
>> color scale colors GWR{1.000000 1.000000 1.000000} {0.000000 1.000000 0.000000} {1.000000 0.000000 0.000000}
>> color scale colors GWB{1.000000 1.000000 1.000000} {0.000000 1.000000 0.000000} {0.000000 0.000000 1.000000}
>> color scale colors BWG{1.000000 1.000000 1.000000} {0.000000 0.000000 1.000000} {0.000000 1.000000 0.000000}
>> color scale colors BlkW{0.500000 0.500000 0.500000} {0.000000 0.000000 0.000000} {1.000000 1.000000 1.000000}
>> color scale colors WBlk{0.500000 0.500000 0.500000} {1.000000 1.000000 1.000000} {0.000000 0.000000 0.000000}
>> color scale method RWB
>> color Display BackgroundTop black
>> color Display BackgroundBot blue2
>> color Display FPS white
>> color Name F green
>> color Type F green
>> color Element X cyan
>> color Element Ac ochre
>> color Element Ag ochre
>> color Element Al ochre
>> color Element Am ochre
>> color Element Ar ochre
>> color Element As ochre
>> color Element At ochre
>> color Element Au ochre
>> color Element B ochre
>> color Element Ba ochre
>> color Element Be ochre
>> color Element Bh ochre
>> color Element Bi ochre
>> color Element Bk ochre
>> color Element Br ochre
>> color Element Ca ochre
>> color Element Cd ochre
>> color Element Ce ochre
>> color Element Cf ochre
>> color Element Cl ochre
>> color Element Cm ochre
>> color Element Co ochre
>> color Element Cr ochre
>> color Element Cs ochre
>> color Element Cu ochre
>> color Element Db ochre
>> color Element Ds ochre
>> color Element Dy ochre
>> color Element Er ochre
>> color Element Es ochre
>> color Element Eu ochre
>> color Element F ochre
>> color Element Fe ochre
>> color Element Fm ochre
>> color Element Fr ochre
>> color Element Ga ochre
>> color Element Gd ochre
>> color Element Ge ochre
>> color Element He ochre
>> color Element Hf ochre
>> color Element Hg ochre
>> color Element Ho ochre
>> color Element Hs ochre
>> color Element I ochre
>> color Element In ochre
>> color Element Ir ochre
>> color Element K ochre
>> color Element Kr ochre
>> color Element La ochre
>> color Element Li ochre
>> color Element Lr ochre
>> color Element Lu ochre
>> color Element Md ochre
>> color Element Mg ochre
>> color Element Mn ochre
>> color Element Mo ochre
>> color Element Mt ochre
>> color Element Na ochre
>> color Element Nb ochre
>> color Element Nd ochre
>> color Element Ne ochre
>> color Element Ni ochre
>> color Element No ochre
>> color Element Np ochre
>> color Element Os ochre
>> color Element Pa ochre
>> color Element Pb ochre
>> color Element Pd ochre
>> color Element Pm ochre
>> color Element Po ochre
>> color Element Pr ochre
>> color Element Pt ochre
>> color Element Pu ochre
>> color Element Ra ochre
>> color Element Rb ochre
>> color Element Re ochre
>> color Element Rf ochre
>> color Element Rg ochre
>> color Element Rh ochre
>> color Element Rn ochre
>> color Element Ru ochre
>> color Element Sb ochre
>> color Element Sc ochre
>> color Element Se ochre
>> color Element Sg ochre
>> color Element Si ochre
>> color Element Sm ochre
>> color Element Sn ochre
>> color Element Sr ochre
>> color Element Ta ochre
>> color Element Tb ochre
>> color Element Tc ochre
>> color Element Te ochre
>> color Element Th ochre
>> color Element Ti ochre
>> color Element Tl ochre
>> color Element Tm ochre
>> color Element U ochre
>> color Element V ochre
>> color Element W ochre
>> color Element Xe ochre
>> color Element Y ochre
>> color Element Yb ochre
>> color Element Zr ochre
>> color Resname ANF silver
>> color Resname HEM green
>> color Chain X blue
>> color Segname blue
>> color Conformation all blue
>> color Molecule 0 blue
>> color Structure 3_10_Helix blue
>> color Surface Grasp gray
>> color Labels Springs orange
>> color Stage Even gray
>> color Stage Odd silver
>> color change rgb 0 0.000000 0.000000 1.000000
>> color change rgb 2 0.350000 0.350000 0.350000
>> color change rgb 3 1.000000 0.500000 0.000000
>> color change rgb 4 1.000000 1.000000 0.000000
>> color change rgb 5 0.500000 0.500000 0.200000
>> color change rgb 6 0.600000 0.600000 0.600000
>> color change rgb 7 0.000000 1.000000 0.000000
>> color change rgb 9 1.000000 0.600000 0.600000
>> color change rgb 11 0.650000 0.000000 0.650000
>> color change rgb 12 0.500000 0.900000 0.400000
>> color change rgb 13 0.900000 0.400000 0.700000
>> color change rgb 14 0.500000 0.300000 0.000000
>> color change rgb 15 0.500000 0.500000 0.750000
>> color change rgb 17 0.880000 0.970000 0.020000
>> color change rgb 18 0.550000 0.900000 0.020000
>> color change rgb 19 0.000000 0.900000 0.040000
>> color change rgb 20 0.000000 0.900000 0.500000
>> color change rgb 21 0.000000 0.880000 1.000000
>> color change rgb 22 0.000000 0.760000 1.000000
>> color change rgb 23 0.020000 0.380000 0.670000
>> color change rgb 24 0.010000 0.040000 0.930000
>> color change rgb 25 0.270000 0.000000 0.980000
>> color change rgb 26 0.450000 0.000000 0.900000
>> color change rgb 27 0.900000 0.000000 0.900000
>> color change rgb 28 1.000000 0.000000 0.660000
>> color change rgb 29 0.980000 0.000000 0.230000
>> color change rgb 30 0.810000 0.000000 0.000000
>> color change rgb 31 0.890000 0.350000 0.000000
>> color change rgb 32 0.960000 0.720000 0.000000
>> label textsize 1.000000
>> # VMD for WIN32, version 1.8.6 (April 7, 2007)
>> # end of log file.
>
>