[PyMOL] How to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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[PyMOL] how to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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[PyMOL] why does coordinates not overlap with map
Dear pymol users, I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of the map. Please see the image at the following link: https://drive.google.com/file/d/1TmH-mFCnsCNghcq4RQJ9mNOBlTfCRsHW/view?usp=sharing Could anyone tell me how to map them overlap? Thank you in advance. Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label atom at proper positions?
Hello professor,
Now I have a new question: how to label the selected CA atoms with strings
representing mutations, like "T123D", "K339R", etc?
I tried to use these commands:
select CAs, resi 123+339
mut = ["T123D", "K139R", "G223S", "M321S"]
label CAs, mut.pop
but I found that the labels are put in the wrong positions. So what is the
correct way the show the labels for mutations?
Best regards
--
From:Halil İbrahim Özdemir
Send Time:2022年1月19日(星期三) 14:05
To:孙业平
Subject:Re: [PyMOL] How to label atom at proper positions?
You can modify the previous script like this,
# ONE LETTER CODES
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "%s%s" % (one_letter[resn],resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping , 19 Oca 2022 Çar, 06:43 tarihinde şunu yazdı:
Dear Professor Halil İbrahim Özdemir,
Thank you for your help. The labels shown now are fomatted as "(THR339)",
"(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the
parentheses, like "T339", "S308".
Thank you again.
Best,
--------------
From:Halil İbrahim Özdemir
Send Time:2022年1月18日(星期二) 18:50
To:孙业平
Subject:Re: [PyMOL] How to label atom at proper positions?
Hi Sunyeping,
You can easily apply the following script from PyMOL terminal. Have a nice days.
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping via PyMOL-users , 18 Oca 2022 Sal,
13:14 tarihinde şunu yazdı:
Dear pymol users,
I select a series of CA atoms in a structure in pymol and show them as sphere
in pymol and want to label them. If using the label menu at the up-right conner
of pymol, the labels shown overlaps with spheres and can not be seen. So I wish
to show the labels at a bit distance from the seleccted atoms. Is there a
method to do that? I will appreciate to any help!
Best regards
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Re: [PyMOL] How to label atom at proper positions?
Dear Professor Halil İbrahim Özdemir, Thank you for your help. The labels shown now are fomatted as "(THR339)", "(SER308)", etc. I wonder how to show them as single-letter codes plus the numbers without the parentheses, like "T339", "S308". Thank you again. Best, -- From:Halil İbrahim Özdemir Send Time:2022年1月18日(星期二) 18:50 To:孙业平 Subject:Re: [PyMOL] How to label atom at proper positions? Hi Sunyeping, You can easily apply the following script from PyMOL terminal. Have a nice days. # Select all C-Alpha atoms and set the object name as "CAs" select CAs, n. CA # Give Label Them as (Residue Name+Residue Number) label CAs, "(%s%s)" % (resn, resi) # Set Label Positions for object "CAs" set label_position, (3,2,1), CAs Regards, sunyeping via PyMOL-users , 18 Oca 2022 Sal, 13:14 tarihinde şunu yazdı: Dear pymol users, I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label atom at proper positions?
Dear pymol users, I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label on surface
Dear Pymol users, I wish to label the one-letter residue names for a bunch of selected resides on surface representation of a protein, but I found the labels cannot be seen on the image. It seems that these labels can been seen on cartoon representation when the surface is hide. Could you tell to how to show the labels on the surface? I will appreciate any help! Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to import anaconda packages in Pymol?
Dear all, I installed Pymol in CentOS from source following the guide in "https://pymolwiki.org/index.php/Linux_Install";. I compiled Pymol with the Python from anaconda, but I found that I cannot import anaconda packages (such as pandas, numpy, etc.) in Pymol. The "import pandas" command will return "no such module named pandas" error. Could yuo tell me how to let pymol use the anaconda packages? I will appreciate any help. Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] pymol installation error
Dear Mr. Jarrett, Yes, with the glm of version 0.0.9, pymol can be installed successful. Thank you very much:) -- From:Jarrett Johnson Send Time:2021年9月13日(星期一) 01:30 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] pymol installation error Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users wrote: Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: e
Re: [PyMOL] pymol installation error
Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much
[PyMOL] pymol installation error
Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much of any help. Best regards.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label residue name on top of sphere representation
Dear all, I wish to label residue name on top of sphere representation, but I find it is difficult. I tried the following command select sele, c. A & resi 47 & name CB show sphere, c. A & resi 47 lable sele, "Y47" I and the "Y47" label is hidden inside the sphere and cannot be seen. Even if I set the sphere to be 80 % transparency, the label cannot be seen yet. So what the the correct way to make such a labelling? Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Dose the thickness of residues reflect b-factor in cartoon putty representation?
Dear all, When you use "cartoon putty[, selection]" command in pymol, you will get the cartoon putty representation of your selection. And the backbond of the selection show different thickness. So dose the thickness of residues reflect b-factor in cartoon putty representation? Best regards Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi, Blaine,
Thank you, that's helpful. But a problem with creating a new object is that the
conformation of the newly created object for the selection is sightly different
from its counterpart in the original object. If the original object is shown as
cartoon, then both the putty presentation of new object and the cartoon
presentation of its counterpart in the original object at site of the
conformational difference will appear in the image produced in this way, and
that's ugly. Is there a way the avoid this shortcoming?
Best,
--
From:Mooers, Blaine H.M. (HSC)
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.
create test, resi 100:150
preset.b_factor_putty("test")
The above worked with pdb file 4dgr.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Mooers, Blaine H.M. (HSC) [blaine-moo...@ouhsc.edu]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
____________
From: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selection and still use the A>Present>b
factor putty operation?
Thank you,
Best regards
___
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[PyMOL] present b factor putty on select
Dear all, I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation? Thank you, Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to select s series of residues that contain the selected atom
Dear pymol user, I select a series of atoms with the follow command in pymol: select atoms, chian A within 4 of chain B I wonder how to select the resides containing the selected "atoms", and how to return the names and indexes of these residues. Thank you in advance! Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Effect of different align method
Hello Julien Cappèle, Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely. Best, Yeping Sun -- From:Julien CAPPELE Sent At:2020 Jun. 17 (Wed.) 17:05 To:孙业平 Subject:Re: [PyMOL] Effect of different align method Hello Sunyeping, I would suggest you to try TM-align, and a very good way to use it for multi-protein alignment is to use their server mTM-align. TM-align is a very robust alignment tool that will in most of the case, give you a better structural based alignment with low to zero input from the sequence. https://yanglab.nankai.edu.cn/mTM-align/ Also, if you are not working on secret stuff, you can give me access so I can rework the output files from mTM-align server to give you a RMSD-colored alignment in PyMOL. On PyMOL only, I didn't try to implement TM-align because I use Windows, but the developers said that a linux implementation could be possible if you are a bit familiar with compiling softwares. - Julien Cappèle Doctorant - 2ème année - ED C2MP Université de Lorraine CRM² - UMR CNRS 7036 julien.capp...@univ-lorraine.fr Tel: (+33)6 99 18 59 03 - Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users a écrit : Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Effect of different align method
Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Fw: How to compile pymol with --glut?
Using yum of centos or apt of Ubuntu cannot install the latest version. -- From:Robi Gus Sent At:2020 Feb. 14 (Fri.) 22:00 To:孙业平 Subject:Re: [PyMOL] How to compile pymol with --glut? much easier to use apt to install open source pymol binaries Sent: Friday, February 14, 2020 at 7:47 AM From: "sunyeping via PyMOL-users" To: "Thomas Holder" Cc: pymol-users Subject: Re: [PyMOL] How to compile pymol with --glut? Hi Thomas, Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem. After run the two commands: rm -rf build python2 setup.py --glut install --prefix=~/pymol-install-py2 The same error still comes out. -- From:Thomas Holder Sent At:2020 Feb. 11 (Tue.) 17:34 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to compile pymol with --glut? Hi Yeping, This has been asked before (by you :-)), see here: https://sourceforge.net/p/pymol/mailman/message/36766620/ Cheers, Thomas > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users > wrote: > > Dear pymol users, > > I compiled pymol following the guide at > https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system. > When I tried to launch pymol by the "./pymol" command, I got the following > error: > > Qt not available, using GLUT/Tk interface > Traceback (most recent call last): > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 65, in > pymol.launch(args) > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 441, in launch > _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) > NotImplementedError: compile with --glut > > I then removed the "bin" and the "lib64" directories in the > "pymol-open-source-build" directory and recompiled pymol with the following > command: >python3 setup --glut install > --prefix=~/software/Pymol/pymol-open-source-build > > However, the newly generated pymol binary file does not work either. Launch > pymol give the same "Qt not available, using GLUT/Tk interface" error. > > Could you help me with this?Thank you in advance. > > Best regards. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to compile pymol with --glut?
Hi Thomas, Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem. After run the two commands: rm -rf build python2 setup.py --glut install --prefix=~/pymol-install-py2 The same error still comes out. -- From:Thomas Holder Sent At:2020 Feb. 11 (Tue.) 17:34 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to compile pymol with --glut? Hi Yeping, This has been asked before (by you :-)), see here: https://sourceforge.net/p/pymol/mailman/message/36766620/ Cheers, Thomas > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users > wrote: > > Dear pymol users, > > I compiled pymol following the guide at > https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system. > When I tried to launch pymol by the "./pymol" command, I got the following > error: > > Qt not available, using GLUT/Tk interface > Traceback (most recent call last): > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 65, in > pymol.launch(args) > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 441, in launch > _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) > NotImplementedError: compile with --glut > > I then removed the "bin" and the "lib64" directories in the > "pymol-open-source-build" directory and recompiled pymol with the following > command: >python3 setup --glut install > --prefix=~/software/Pymol/pymol-open-source-build > > However, the newly generated pymol binary file does not work either. Launch > pymol give the same "Qt not available, using GLUT/Tk interface" error. > > Could you help me with this?Thank you in advance. > > Best regards. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?
Dear All, I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns simulation time, so each frame represents 80 ps. I wish to print time stample on each stample. For example, on the first frame, " 0 ns" is printed; on the second frame, "80 ps" is printed; on the third frame, "160 ps" is printed. How I cannot find any clue how to do this. Could you have any clue how to finish this task? Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to display electronic density for nucleic acid pymol
Dear Pymol users, I wish to prepare a image which looks like the picture at the follow link: https://drive.google.com/file/d/1HPwTCNqD7hlTPX9QDHif00YW5ZIv8PCa/view?usp=sharing I have ckecked the pymolwiki for different mode for drawing nucleic acid ladder and ring, but cannot find any thing that can produce an image like what I want. I don't know how to change the phosphoric acid backbond to stick from what looks like putty. Could you help me what this? I will be very grateful if you can help. Best regards. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] "Qt not available" error from compilation with python2 but not python3
dear all, I am trying to compile pymol from source (https://github.com/schrodinger/pymol-open-source.git). Python 3 and python 2 both have been installed in my system. I first tried compile pymol with python 3 python3 setup.py install --prefix=~/pymol-install-py3 It can work. python3 setup.py install --prefix=~/pymol-install-py2 However, when I try to compile pymol with python2: python2 setup.py install --prefix=~/pymol-install-py2 lauching pymol gives the following error: Qt not available, using GLUT/Tk interface Traceback (most recent call last): File "__init__.py", line 65, in pymol.launch(args) File "/home/sunyp/pymol-install-py2/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) NotImplementedError: compile with --glut Even if I re-compile with --glut: python2 setup.py install --prefix=~/pymol-install-py2 the same error occurs. PyQt4 has been install in my system with yum install. I am very confused and wish to know why qt cannot be fould by pymol comoled with python2. Could you help me with that? Thank you in advacne. Yeping Sun ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] APBS TOOLS 2.1 does not work
Dear all,
I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of
proteins. After I finish "set grid", I press the "set grid" button, I get the
following error,
(, ImportError('No module named pdb2pqr',),
)
In show error 2
Could you tell what is the cause of the error and how to fix it?
Best regards.___
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Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
Hello, Marko, Think you for your reply. I can use the bar object "Action" > "Levels" to set the levels/scales to -100~100, but could you tell me what are the units for the values? Best regards -- From:Marko Hyvonen Sent At:2019 Sep. 12 (Thu.) 15:58 To:pymol-users Subject:Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics? Hi Yeping, Click on the bar object "Action" > "Levels" for a few preset levels/scales. hth, Marko On 12/09/2019 08:03, sunyeping via PyMOL-users wrote: Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Hello Mat,
Thank you for your reply.
I followed your codes in the second line and get a series of output, which look
like:
(9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
I guess the first and the fourth float numbers are the rmsd, but what are other
numbers in the line?
Best regards.
Yeping
--
From:Istvan Kolossvary
Sent At:2019 Aug. 20 (Tue.) 00:29
To:Mateusz Bieniek
Cc:孙业平 ; pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Superpose all states of an object to one of the states.
print cmd.intra_fit("my-trajCA", 1)Do the same, but this time the
target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
mobile_state=s + 1, target_state=1, cycles=0, transform=0))
On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek wrote:
There is also intra_rms and instra_fit commands:
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit
For example:
intra_fit name CA and resid 1326-1350, 0
Maybe they will be useful.
Best, Mat
On Mon, 19 Aug 2019 at 13:54, sunyeping wrote:
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
cmd.align(ref, A,target_state=i)
I ran it in pymol command line, but it doesn't work. I am new to pymol
scripting. Could you write a correct one for me? Thank you very much.
Best regards,
Yeping
--
From:Mateusz Bieniek
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider the
experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith,
https://pymol.org/fellowship/). The extension relies on the MDAnalysis package
and so far includes RMSD as an example. Here is the link to the right github
branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align command as: "align A, B", but this only
gives one rmsd value. Could you tell me how to get the rmsd value between each
state of the MD simulation trajectory and the reference
structure?___
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Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
cmd.align(ref, A,target_state=i)
I ran it in pymol command line, but it doesn't work. I am new to pymol
scripting. Could you write a correct one for me? Thank you very much.
Best regards,
Yeping
--
From:Mateusz Bieniek
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider the
experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith,
https://pymol.org/fellowship/). The extension relies on the MDAnalysis package
and so far includes RMSD as an example. Here is the link to the right github
branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align command as: "align A, B", but this only
gives one rmsd value. Could you tell me how to get the rmsd value between each
state of the MD simulation trajectory and the reference
structure?___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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[PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Dear everyall, I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] APBS "%x format: an integer is required, not float" error in pymol installed with python 3.7 and "Qt not available, using GLUT/Tk interface" error
Dear everyone, I am trying to use the APBS plugin in pymol to calculate protein electrostatic potentials. My system is centos 7. The pymol was installed with python 3.7 (~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1 from the plugin menu of pymol, a window jumps out which reads: "%x format: an integer is required, not float". I've googled it and learned that this error may related to python version. So I try to swith to pymol installed with python2.7 (/usr/bin/python) I install pymol following the guide at https://pymolwiki.org/index.php/Linux_Install, with the command: /usr/bin/python setup.py install --prefix=~/software/pymol/pymol-python2.7-install After the installation finished, I tried to lauch pymol, but meet the error: Qt not available, using GLUT/Tk interface Traceback (most recent call last): File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 65, in pymol.launch(args) File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) NotImplementedError: compile with --glut Acturally the PyQt4 have been install in my system, I don't understand why it is not available by pymol. And why pymol installed with python3.7 doesn't have such a problem. Even if I reinstall pymol with --glut option: /usr/bin/python setup.py --glut build install --prefix=~/software/pymol/pymol-python2.7-install the same error still comes out. Could you help me with this problem? Thank you in advance. Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] how to delete frames from a trajectory loaded by the "load_traj" command?
Dear all, I loaded a gromacs trajetory containing about 1000 frames by the following command in pymol: load protein.gro load_traj protein.xtc I want to use these frames to make a movie. However, I find that the position of the protein in first frame is very different from the other frames some I want to delete the first frame so the protein stays in the same position in all frame. Could you tell me the command of removing the first frame? Thank you. Best regards. Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] about cealign and align
Dear all, I am now trying to compare two structures by alignment in pymol. The two proteins are similar structures from the same family with about 500 residues. I find that the "cealign" command gives much better result that the "align" command. With the "cealign" command, the two structures aligned well, but with "align" command two structure don't aligned well. The rmsd value given with the "cealign" is much smaller than that given with the "align". However, when I try the align a small region of the two structures, I get the reverse result. I create new objects corresponding to the small region I am interested in from the two whole proteins, respectively and align the two new objects with "align" and "cealign". I find the rmsd value given with "align" is much smaller that than given with "cealign". I wish know the work principle behind "align" and "celign", the calculation formula of them and what cause the difference between aligning the whole proteins and small regions. Could you help me with these? Best regards.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] The 'select' command for complex residue selection
Hi, Ali, Your command format works well. Thank you. -- From:Ali Kusay Sent At:2019 Jul. 9 (Tue.) 11:11 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] The 'select' command for complex residue selection Hi Sunyeping, I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this: select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95) c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au From: sunyeping via PyMOL-users Reply-To: sunyeping Date: Tuesday, 9 July 2019 at 12:41 pm To: pymol-users Subject: [PyMOL] The 'select' command for complex residue selection Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] The 'select' command for complex residue selection
Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to calculate RMSD among multiple proteins
Dear all, It is easy to evaluate the simularity of two proteins in pymol. We just need to align them and a RMSD will be given in pymol. However, I want to compare the strutural similiarity of multiple proteins. I can align two of them once and by doing alignment many times, I can finally get pair-wise RMSD of these proteins. Is there any simple method to do? Is there a scriipt that can automatically calculate the pair-wise RMSD among many proteins in pymol? Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label secondary structures in pymol
Thank you, Jared. -- From:Jared Sampson Sent At:2019 Jul. 8 (Mon.) 12:08 To:pymol-users ; 孙业平 Subject:Re: [PyMOL] How to label secondary structures in pymol Hi sunyeping - Yes, it is possible. You can pick one atom to label in each SS element. See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/. You can also adjust the label position/size/style using the various label settings as well. I would normally direct you to the label wiki page, but that appears (at least to me) to be broken at the moment. So here, instead, is a link to a few-years-old archive of that page. Hope that helps. Cheers, Jared On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users (pymol-users@lists.sourceforge.net) wrote: Dear all, Is it possible to label secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1", "α2", "β2", etc.. Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label secondary structures in pymol
Dear all, Is it possible to label secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1", "α2", "β2", etc.. Thank you in advance.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to color stick and surface representation separately
Hi, Thank you. I think a third method is to create a new object of the protein and display the stick in this new object, and display surface of the original object, so I can color them separately. Best regards -- From:Saurabh Gayali Sent At:2019 Jul. 6 (Sat.) 18:20 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to color stick and surface representation separately there are two ways to achieve this (might not be correct ways, but it will give you results) 1. Open the molucule and choose show as Surface [image.png] This will show complete molecule as a surface. Remember choosing show as surface after choosing line or cartoon will remove former from viewport. - Now choose parts you want to keep and color them before moving on to next part Next select the same molecule and enable line [image.png] remember to not choose line in show as menu but directly from show menu This will keep the old object and add the new line visualization. This way you can show both custom color surface and default color of line/cartoon this way has limitation that you cannot color the second scheme but have to use the default coloring way. 2. Copy the molecule you want to load and create a copy in the folder Load both moleculaes [You won't even need to align them] now You can choose any visualization for both moleculaes as they are separate files. Regards,Saurabh Gayali - I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users wrote: Dear all, I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue? Thank you in advance Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe image.png Description: Binary data image.png Description: Binary data ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to color stick and surface representation separately
Dear all, I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue? Thank you in advance Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] "Qt not available, using GLUT/Tk interface" error
Dear all, I installed pymol according to guide at https://pymolwiki.org/index.php/Linux_Install. When I launched pymol, and get the "Qt not available, using GLUT/Tk interface" error and no pymol GUI appeared. How could I deal with this problem? Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
Thank you for the reply. Do alter and rebuild commands really change the secondary structure of the specific residues or they just change the display? I saved the structure altered bt the alter and rebuild commands, but when I open the structure agian in pymol, the residues I changes are still displayed as in the original structure file. Best regards -- From:h. adam steinberg Sent At:2019 Jun. 5 (Wed.) 20:43 To:孙业平 ; pymol-users Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol? It’s the same command but just change the “S” to an “H”. Or you can use a “L” if you want a loop (unstructured). alter 3-10/, ss=‘H’ You also need to enter the command: rebuild, to redraw the structure on your screen. Use rebuild after you enter the alter command. On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users wrote: Dear pymol user, I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command: alter 61-63/, ss='S' can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix? Thank you in advance. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to assign secondary structure as 3-10 helix in pymol?
Dear pymol user, I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command: alter 61-63/, ss='S' can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix? Thank you in advance. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to show the boundary of each selected residues in surface presentation with pymol
Dear everyone, It there a way to show the boundary of each selected residues in surface presentation with pymol? Best regards Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to make protein blur but keep ligand clear?
Dear all, I have a protein-ligand complex and I wish to make the protein looks blur but keep the ligand clear and sharp with pymol. I find a "focalblur" script (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this. However I can get the fancy effect illustrated in the examples of the wiki for this script. With the follow command: FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000 I just make the ligand rather the the protein become blur (Please see the image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, and the pse file used to make this image is availabe at https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7). Could anyone help with this？ What does the argument "aperture" do? How to control which part become blur? Is there better way to make the ligand blur? Thank you very much! Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to make selected residues blurry?
Hi Jared,
Your solution is very clever and helpful, but I don't know how to use the
set_view command. I think it is vey important here because after this setting
the scene becomes very close to the original figure in the paper. Could you
explain how do you set the 18 float numbers?
Thank you very much and best regards.
Yeping
--
From:Jared Sampson
Send Time:2018 Dec 6 (Thu) 12:09
To:孙业平
Cc:pymol-users ; "Smith, Paul"
Subject:Re: [PyMOL] how to make selected residues blurry?
Hi Yeping -
I had replied to your first email (on 11/30) with a similar suggestion to
Paul's of using the `cartoon_transparency` setting, but now after looking at
the original figure you're trying to replicate more closely, I realize that
there isn't actually any transparency in that figure at all!
The authors achieved this effect simply by using lighter and darker shades of
("palecyan" and "deepteal") for the hemagglutinin chain. The following script
reproduces the original figure you shared almost exactly.
bg_color white
fetch 4gms, async=0
# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220
# antibody selection
select h2, chain H and resi 51-59
deselect
# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube
# colors
color orange, h2
color palecyan, ha
color deepteal, loops
set_view (\
-0.718157351,0.514449000, -0.468602538,\
-0.667115033, -0.317360103,0.673974276,\
0.198008969,0.796632588,0.57977,\
0.45628, -0.60942, -75.169761658,\
20.388980865, -23.567779541, 38.543788910,\
52.026283264, 98.326217651, -20.0 )
set ray_opaque_background, 1
ray 800, 800
I've uploaded the resulting image (with the script in the description) to
PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png
Hope that helps.
Cheers,
Jared
On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users
(pymol-users@lists.sourceforge.net) wrote:
Hi Paul,
Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the
structure, a small part of the structure which I don't mean to set transparent
become blur. Please see the image in the red circle in fig-3
(https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing).
How does that happen and how to fix it?
Thank you again and best regards.
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] how to make selected residues blurry?
Hi Yeping,
To avoid this ‘breaking’ of your protein you will first need to create a copy
of the entire molecule, set the transparency of the copy to your desired value,
then hide the residues you want to make transparent on your original object.
So, you will do something like this:
# create a copy of your original object:
create new_obj,
# set all residues on the copy to be transparent:
set cartoon_transparency, , new_obj
# hide the residues you wish to be transparent on your original object:
select hide,
cartoon_skip, hide and
This should prevent the your molecule from appearing to be broken.
Cheers,
Paul
From: sunyeping
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
Hi, Paul,
Thank you for your reply. I think the ‘set transparency’ command is on the
correct direction, but there is another problem. In order to apply the ‘set
transparency’, we should use "create" or "extract" command to make a new
objective for the selected atoms. However, after I select the atoms that I want
to make transparent, and use the command "extract":
extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I
use the commend:
set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part
become more obvious. Please see the figure at the line
(https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
Could you help me with the "breaking" problem?
Best regards,
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] how to make selected residues blurry?
Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the
interface between a protein and the surrounding water). I think the command
you’re after is ‘set cartoon_transparency’
(https://pymolwiki.org/index.php/Cartoon#Various_T
Re: [PyMOL] how to make selected residues blurry?
Hi Paul, Now I get closer to the final anwer! After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing). How does that happen and how to fix it? Thank you again and best regards. Yeping -- From:Smith, Paul Send Time:2018 Dec 4 (Tue) 21:00 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi Yeping, To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object. So, you will do something like this: # create a copy of your original object: create new_obj, # set all residues on the copy to be transparent: set cartoon_transparency, , new_obj # hide the residues you wish to be transparent on your original object: select hide, cartoon_skip, hide and This should prevent the your molecule from appearing to be broken. Cheers, Paul From: sunyeping Sent: Tuesday, December 4, 2018 3:23:00 AM To: pymol-users; Smith, Paul Subject: Re: [PyMOL] how to make selected residues blurry? Hi, Paul, Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract": extract new_obj, sele I find the new object is broken from the rest part of the structure. And then I use the commend: set cartoon_transparency, 0.7, new_obj The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing). Could you help me with the "breaking" problem? Best regards, Yeping -- From:Smith, Paul Send Time:2018 Dec 3 (Mon) 20:38 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi, The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’. Cheers, Paul From: sunyeping via PyMOL-users Sent: 03 December 2018 03:02 To: pymol-users Subject: [PyMOL] how to make selected residues blurry? Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to make selected residues blurry?
Hi, Paul, Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract": extract new_obj, sele I find the new object is broken from the rest part of the structure. And then I use the commend: set cartoon_transparency, 0.7, new_obj The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing). Could you help me with the "breaking" problem? Best regards, Yeping -- From:Smith, Paul Send Time:2018 Dec 3 (Mon) 20:38 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi, The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’. Cheers, Paul From: sunyeping via PyMOL-users Sent: 03 December 2018 03:02 To: pymol-users Subject: [PyMOL] how to make selected residues blurry? Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] how to make selected residues blurry?
Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] how to make selected residues blurry?
Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Error aroused when install pymol from source
Dear pymol users, I am trying to intall pymol on my centos 7 system from source using the mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install)Everything was ok until I run install script: #!/bin/bash -e prefix=/opt/pymol-svn modules=$prefix/modules # If you want to install as root, then split this line up in "build" # and "install" and run the "install" with "sudo" python2.7 setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix I got a error message and the installation process was terminated: In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0: contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such file or directory #include ^ compilation terminated. I then installed msgpack by yum command and tried to run the pymol install script again, but the same error still occurred. I googled this problem but cannot find a answer. Could anyone help me here? Best regards. Yeping Sun-- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
